DNA-based population density estimation of black bear at northern ...

African Journals Online (AJOL)

The analysis of deoxyribonucleic acid (DNA) microsatellites from hair samples obtained by the non-invasive method of traps was used to estimate the population density of black bears (Ursus americanus eremicus) in a mountain located at the county of Lampazos, Nuevo Leon, Mexico. The genotyping of bears was ...

Coupling amplified DNA from flow-sorted chromosomes to high-density SNP mapping in barley

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Bartoš Jan

2008-06-01

Full Text Available Abstract Background Flow cytometry facilitates sorting of single chromosomes and chromosome arms which can be used for targeted genome analysis. However, the recovery of microgram amounts of DNA needed for some assays requires sorting of millions of chromosomes which is laborious and time consuming. Yet, many genomic applications such as development of genetic maps or physical mapping do not require large DNA fragments. In such cases time-consuming de novo sorting can be minimized by utilizing whole-genome amplification. Results Here we report a protocol optimized in barley including amplification of DNA from only ten thousand chromosomes, which can be isolated in less than one hour. Flow-sorted chromosomes were treated with proteinase K and amplified using Phi29 multiple displacement amplification (MDA. Overnight amplification in a 20-microlitre reaction produced 3.7 – 5.7 micrograms DNA with a majority of products between 5 and 30 kb. To determine the purity of sorted fractions and potential amplification bias we used quantitative PCR for specific genes on each chromosome. To extend the analysis to a whole genome level we performed an oligonucleotide pool assay (OPA for interrogation of 1524 loci, of which 1153 loci had known genetic map positions. Analysis of unamplified genomic DNA of barley cv. Akcent using this OPA resulted in 1426 markers with present calls. Comparison with three replicates of amplified genomic DNA revealed >99% concordance. DNA samples from amplified chromosome 1H and a fraction containing chromosomes 2H – 7H were examined. In addition to loci with known map positions, 349 loci with unknown map positions were included. Based on this analysis 40 new loci were mapped to 1H. Conclusion The results indicate a significant potential of using this approach for physical mapping. Moreover, the study showed that multiple displacement amplification of flow-sorted chromosomes is highly efficient and representative which

Performance of various density functionals for the hydrogen bonds in DNA base pairs

NARCIS (Netherlands)

van der Wijst, T.; Fonseca Guerra, C.; Swart, M.; Bickelhaupt, F.M.

2006-01-01

We have investigated the performance of seven popular density functionals (B3LYP, BLYP, BP86, mPW, OPBE, PBE, PW91) for describing the geometry and stability of the hydrogen bonds in DNA base pairs. For the gas-phase situation, the hydrogen-bond lengths and strengths in the DNA pairs have been

Controlling the surface density of DNA on gold by electrically induced desorption.

Science.gov (United States)

Arinaga, Kenji; Rant, Ulrich; Knezević, Jelena; Pringsheim, Erika; Tornow, Marc; Fujita, Shozo; Abstreiter, Gerhard; Yokoyama, Naoki

2007-10-31

We report on a method to control the packing density of sulfur-bound oligonucleotide layers on metal electrodes by electrical means. In a first step, a dense nucleic acid layer is deposited by self-assembly from solution; in a second step, defined fractions of DNA molecules are released from the surface by applying a series of negative voltage cycles. Systematic investigations of the influence of the applied electrode potentials and oligonucleotide length allow us to identify a sharp desorption onset at -0.65 V versus Ag/AgCl, which is independent of the DNA length. Moreover, our results clearly show the pronounced influence of competitive adsorbents in solution on the desorption behavior, which can prevent the re-adsorption of released DNA molecules, thereby enhancing the desorption efficiency. The method is fully bio-compatible and can be employed to improve the functionality of DNA layers. This is demonstrated in hybridization experiments revealing almost perfect yields for electrically "diluted" DNA layers. The proposed control method is extremely beneficial to the field of DNA-based sensors.

High-Power-Density, High-Energy-Density Fluorinated Graphene for Primary Lithium Batteries

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Guiming Zhong

2018-03-01

Full Text Available Li/CFx is one of the highest-energy-density primary batteries; however, poor rate capability hinders its practical applications in high-power devices. Here we report a preparation of fluorinated graphene (GFx with superior performance through a direct gas fluorination method. We find that the so-called “semi-ionic” C-F bond content in all C-F bonds presents a more critical impact on rate performance of the GFx in comparison with sp2 C content in the GFx, morphology, structure, and specific surface area of the materials. The rate capability remains excellent before the semi-ionic C-F bond proportion in the GFx decreases. Thus, by optimizing semi-ionic C-F content in our GFx, we obtain the optimal x of 0.8, with which the GF0.8 exhibits a very high energy density of 1,073 Wh kg−1 and an excellent power density of 21,460 W kg−1 at a high current density of 10 A g−1. More importantly, our approach opens a new avenue to obtain fluorinated carbon with high energy densities without compromising high power densities.

Human islet viability and function is maintained during high density shipment in silicone rubber membrane vessels

Science.gov (United States)

Kitzmann, Jennifer P; Pepper, Andrew R; Lopez, Boris G; Pawlick, Rena; Kin, Tatsuya; O’Gorman, Doug; Mueller, Kathryn R; Gruessner, Angelika C; Avgoustiniatos, Efstathios S; Karatzas, Theodore; Szot, Greg L; Posselt, Andrew M; Stock, Peter G; Wilson, John R; Shapiro, AM; Papas, Klearchos K

2014-01-01

The shipment of human islets from processing centers to distant laboratories is beneficial for both research and clinical applications. The maintenance of islet viability and function in transit is critically important. Gas-permeable silicone rubber membrane (SRM) vessels reduce the risk of hypoxia-induced death or dysfunction during high-density islet culture or shipment. SRM vessels may offer additional advantages: they are cost-effective (fewer flasks, less labor needed), safer (lower contamination risk), and simpler (culture vessel can also be used for shipment). Human islets(IE) were isolated from two manufacturing centers and shipped in 10cm2 surface area SRM vessels in temperature and pressure controlled containers to a distant center following at least two days of culture (n = 6). Three conditions were examined: low density (LD), high density (HD), and a micro centrifuge tube negative control (NC). LD was designed to mimic the standard culture density for human islet preparations (200 IE/cm2), while HD was designed to have a 20-fold higher tissue density, which would enable the culture of an entire human isolation in 1–3 vessels. Upon receipt, islets were assessed for viability, measured by oxygen consumption rate normalized to DNA content (OCR/DNA), and quantity, measured by DNA, and, when possible, potency and function with dynamic glucose-stimulated insulin secretion (GSIS) measurements and transplants in immunodeficient B6 rag mice. Post-shipment OCR/DNA was not reduced in HD versus LD, and was substantially reduced in the NC condition. HD islets exhibited normal function post-shipment. Based on the data we conclude that entire islet isolations (up to 400,000 IE) may be shipped using a single, larger SRM vessel with no negative effect on viability and ex vivo and in vivo function. PMID:25131090

Utility of the pooling approach as applied to whole genome association scans with high-density Affymetrix microarrays

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Gray Joanna

2010-11-01

Full Text Available Abstract Background We report an attempt to extend the previously successful approach of combining SNP (single nucleotide polymorphism microarrays and DNA pooling (SNP-MaP employing high-density microarrays. Whereas earlier studies employed a range of Affymetrix SNP microarrays comprising from 10 K to 500 K SNPs, this most recent investigation used the 6.0 chip which displays 906,600 SNP probes and 946,000 probes for the interrogation of CNVs (copy number variations. The genotyping assay using the Affymetrix SNP 6.0 array is highly demanding on sample quality due to the small feature size, low redundancy, and lack of mismatch probes. Findings In the first study published so far using this microarray on pooled DNA, we found that pooled cheek swab DNA could not accurately predict real allele frequencies of the samples that comprised the pools. In contrast, the allele frequency estimates using blood DNA pools were reasonable, although inferior compared to those obtained with previously employed Affymetrix microarrays. However, it might be possible to improve performance by developing improved analysis methods. Conclusions Despite the decreasing costs of genome-wide individual genotyping, the pooling approach may have applications in very large-scale case-control association studies. In such cases, our study suggests that high-quality DNA preparations and lower density platforms should be preferred.

Colloidal silica films for high-capacity DNA arrays

Science.gov (United States)

Glazer, Marc Irving

The human genome project has greatly expanded the amount of genetic information available to researchers, but before this vast new source of data can be fully utilized, techniques for rapid, large-scale analysis of DNA and RNA must continue to develop. DNA arrays have emerged as a powerful new technology for analyzing genomic samples in a highly parallel format. The detection sensitivity of these arrays is dependent on the quantity and density of immobilized probe molecules. We have investigated substrates with a porous, "three-dimensional" surface layer as a means of increasing the surface area available for the synthesis of oligonucleotide probes, thereby increasing the number of available probes and the amount of detectable bound target. Porous colloidal silica films were created by two techniques. In the first approach, films were deposited by spin-coating silica colloid suspensions onto flat glass substrates, with the pores being formed by the natural voids between the solid particles (typically 23nm pores, 35% porosity). In the second approach, latex particles were co-deposited with the silica and then pyrolyzed, creating films with larger pores (36 nm), higher porosity (65%), and higher surface area. For 0.3 mum films, enhancements of eight to ten-fold and 12- to 14-fold were achieved with the pure silica films and the films "templated" with polymer latex, respectively. In gene expression assays for up to 7,000 genes using complex biological samples, the high-capacity films provided enhanced signals and performed equivalently or better than planar glass on all other functional measures, confirming that colloidal silica films are a promising platform for high-capacity DNA arrays. We have also investigated the kinetics of hybridization on planar glass and high-capacity substrates. Adsorption on planar arrays is similar to ideal Langmuir-type adsorption, although with an "overshoot" at high solution concentration. Hybridization on high-capacity films is

Interspersion of highly repetitive DNA with single copy DNA in the genome of the red crab, Geryon quinquedens

Energy Technology Data Exchange (ETDEWEB)

Christie, N.T. (Univ. of Tennessee, Oak Ridge); Skinner, D.M.

1979-02-01

Kinetic analysis of the reassociation of 420 nucleotide (NT) long fragments has shown that essentially all of the repetitive sequences of the DNA of the red crab Geryon quinquedens are highly repetitive. There are negligible amounts of low and intermediate repetitive DNAs. Though atypical of most eukaryotes, this pattern has been observed in al other brachyurans (true crabs) studied. The major repetitive component is subdivided into short runs of 300 NT and longer runs of greater than 1200 NT while the minor component has an average sequence length of 400 NT. Both components reassociate at rates commonly observed for satellite DNAs. Unique among eukaryotes the organization of the genome includes single copy DNA contiguous to short runs (300 NT) of both repetitive components. Although patent satellites are not present, subsets of the repetitive DNA have been isolated by either restriction endonuclease digestion or by centrifugation in Ag/sup +/ or Hg/sup 2 +//Cs/sub 2/SO/sub 4/ density gradients.

A high throughput DNA extraction method with high yield and quality

Directory of Open Access Journals (Sweden)

Xin Zhanguo

2012-07-01

Full Text Available Abstract Background Preparation of large quantity and high quality genomic DNA from a large number of plant samples is a major bottleneck for most genetic and genomic analyses, such as, genetic mapping, TILLING (Targeting Induced Local Lesion IN Genome, and next-generation sequencing directly from sheared genomic DNA. A variety of DNA preparation methods and commercial kits are available. However, they are either low throughput, low yield, or costly. Here, we describe a method for high throughput genomic DNA isolation from sorghum [Sorghum bicolor (L. Moench] leaves and dry seeds with high yield, high quality, and affordable cost. Results We developed a high throughput DNA isolation method by combining a high yield CTAB extraction method with an improved cleanup procedure based on MagAttract kit. The method yielded large quantity and high quality DNA from both lyophilized sorghum leaves and dry seeds. The DNA yield was improved by nearly 30 fold with 4 times less consumption of MagAttract beads. The method can also be used in other plant species, including cotton leaves and pine needles. Conclusion A high throughput system for DNA extraction from sorghum leaves and seeds was developed and validated. The main advantages of the method are low cost, high yield, high quality, and high throughput. One person can process two 96-well plates in a working day at a cost of $0.10 per sample of magnetic beads plus other consumables that other methods will also need.

Use of Low-Density DNA Microarrays and Photopolymerization for Genotyping Foodborne-Associated Noroviruses

Science.gov (United States)

Human noroviruses cause up to 21 million cases of foodborne disease in the United States annually and are the most common cause of acute gastroenteritis in industrialized countries. To reduce the burden of foodborne disease associated with viruses, the use of low density DNA microarrays in conjunct...

Computational Analysis of G-Quadruplex Forming Sequences across Chromosomes Reveals High Density Patterns Near the Terminal Ends.

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Julia H Chariker

Full Text Available G-quadruplex structures (G4 are found throughout the human genome and are known to play a regulatory role in a variety of molecular processes. Structurally, they have many configurations and can form from one or more DNA strands. At the gene level, they regulate gene expression and protein synthesis. In this paper, chromosomal-level patterns of distribution are analyzed on the human genome to identify high-level distribution patterns potentially related to global functional processes. Here we show unique high density banding patterns on individual chromosomes that are highly correlated, appearing in a mirror pattern, across forward and reverse DNA strands. The highest density of G4 sequences occurs within four megabases of one end of most chromosomes and contains G4 motifs that bind with zinc finger proteins. These findings suggest that G4 may play a role in global chromosomal processes such as those found in meiosis.

Biomimetic High Density Lipoprotein Nanoparticles For Nucleic Acid Delivery

Science.gov (United States)

McMahon, Kaylin M.; Mutharasan, R. Kannan; Tripathy, Sushant; Veliceasa, Dorina; Bobeica, Mariana; Shumaker, Dale K.; Luthi, Andrea J.; Helfand, Brian T.; Ardehali, Hossein; Mirkin, Chad A.; Volpert, Olga; Thaxton, C. Shad

2014-01-01

We report a gold nanoparticle-templated high density lipoprotein (HDL AuNP) platform for gene therapy which combines lipid-based nucleic acid transfection strategies with HDL biomimicry. For proof-of-concept, HDL AuNPs are shown to adsorb antisense cholesterylated DNA. The conjugates are internalized by human cells, can be tracked within cells using transmission electron microscopy (TEM), and regulate target gene expression. Overall, the ability to directly image the AuNP core within cells, the chemical tailorability of the HDL AuNP platform, and the potential for cell-specific targeting afforded by HDL biomimicry make this platform appealing for nucleic acid delivery. PMID:21319839

Non-Gaussian Distribution of DNA Barcode Extension In Nanochannels Using High-throughput Imaging

Science.gov (United States)

Sheats, Julian; Reinhart, Wesley; Reifenberger, Jeff; Gupta, Damini; Muralidhar, Abhiram; Cao, Han; Dorfman, Kevin

2015-03-01

We present experimental data for the extension of internal segments of highly confined DNA using a high-­throughput experimental setup. Barcode­-labeled E. coli genomic DNA molecules were imaged at a high areal density in square nanochannels with sizes ranging from 40 nm to 51 nm in width. Over 25,000 molecules were used to obtain more than 1,000,000 measurements for genomic distances between 2,500 bp and 100,000 bp. The distribution of extensions has positive excess kurtosis and is skew­ left due to weak backfolding in the channel. As a result, the two Odijk theories for the chain extension and variance bracket the experimental data. We compared to predictions of a harmonic approximation for the confinement free energy and show that it produces a substantial error in the variance. These results suggest an inherent error associated with any statistical analysis of barcoded DNA that relies on harmonic models for chain extension. Present address: Department of Chemical and Biological Engineering, Princeton University.

Crystal structure of Pfu, the high fidelity DNA polymerase from Pyrococcus furiosus.

Science.gov (United States)

Kim, Suhng Wook; Kim, Dong-Uk; Kim, Jin Kwang; Kang, Lin-Woo; Cho, Hyun-Soo

2008-05-01

We have determined a 2.6A resolution crystal structure of Pfu DNA polymerase, the most commonly used high fidelity PCR enzyme, from Pyrococcus furiosus. Although the structures of Pfu and KOD1 are highly similar, the structure of Pfu elucidates the electron density of the interface between the exonuclease and thumb domains, which has not been previously observed in the KOD1 structure. The interaction of these two domains is known to coordinate the proofreading and polymerization activity of DNA polymerases, especially via H147 that is present within the loop (residues 144-158) of the exonuclease domain. In our structure of Pfu, however, E148 rather than H147 is located at better position to interact with the thumb domain. In addition, the structural analysis of Pfu and KOD1 shows that both the Y-GG/A and beta-hairpin motifs of Pfu are found to differ with that of KOD1, and may explain differences in processivity. This information enables us to better understand the mechanisms of polymerization and proofreading of DNA polymerases.

An Ultra-High-Density, Transcript-Based, Genetic Map of Lettuce

Science.gov (United States)

Truco, Maria José; Ashrafi, Hamid; Kozik, Alexander; van Leeuwen, Hans; Bowers, John; Wo, Sebastian Reyes Chin; Stoffel, Kevin; Xu, Huaqin; Hill, Theresa; Van Deynze, Allen; Michelmore, Richard W.

2013-01-01

We have generated an ultra-high-density genetic map for lettuce, an economically important member of the Compositae, consisting of 12,842 unigenes (13,943 markers) mapped in 3696 genetic bins distributed over nine chromosomal linkage groups. Genomic DNA was hybridized to a custom Affymetrix oligonucleotide array containing 6.4 million features representing 35,628 unigenes of Lactuca spp. Segregation of single-position polymorphisms was analyzed using 213 F7:8 recombinant inbred lines that had been generated by crossing cultivated Lactuca sativa cv. Salinas and L. serriola acc. US96UC23, the wild progenitor species of L. sativa. The high level of replication of each allele in the recombinant inbred lines was exploited to identify single-position polymorphisms that were assigned to parental haplotypes. Marker information has been made available using GBrowse to facilitate access to the map. This map has been anchored to the previously published integrated map of lettuce providing candidate genes for multiple phenotypes. The high density of markers achieved in this ultradense map allowed syntenic studies between lettuce and Vitis vinifera as well as other plant species. PMID:23550116

An Ultra-High-Density, Transcript-Based, Genetic Map of Lettuce.

Science.gov (United States)

Truco, Maria José; Ashrafi, Hamid; Kozik, Alexander; van Leeuwen, Hans; Bowers, John; Wo, Sebastian Reyes Chin; Stoffel, Kevin; Xu, Huaqin; Hill, Theresa; Van Deynze, Allen; Michelmore, Richard W

2013-04-09

We have generated an ultra-high-density genetic map for lettuce, an economically important member of the Compositae, consisting of 12,842 unigenes (13,943 markers) mapped in 3696 genetic bins distributed over nine chromosomal linkage groups. Genomic DNA was hybridized to a custom Affymetrix oligonucleotide array containing 6.4 million features representing 35,628 unigenes of Lactuca spp. Segregation of single-position polymorphisms was analyzed using 213 F 7:8 recombinant inbred lines that had been generated by crossing cultivated Lactuca sativa cv. Salinas and L. serriola acc. US96UC23, the wild progenitor species of L. sativa The high level of replication of each allele in the recombinant inbred lines was exploited to identify single-position polymorphisms that were assigned to parental haplotypes. Marker information has been made available using GBrowse to facilitate access to the map. This map has been anchored to the previously published integrated map of lettuce providing candidate genes for multiple phenotypes. The high density of markers achieved in this ultradense map allowed syntenic studies between lettuce and Vitis vinifera as well as other plant species. Copyright © 2013 Truco et al.

Resistance to DNA denaturation in irradiated Chinese hamster V79 fibroblasts is linked to cell shape

International Nuclear Information System (INIS)

Olive, P.L.; Vanderbyl, S.; MacPhail, S.H.

1991-01-01

Exponentially growing Chinese hamster V79-171b lung fibroblasts seeded at high density on plastic (approximately 7 x 10(3) cells/cm2) flatten, elongate, and produce significant amounts of extracellular fibronectin. When lysed in weak alkali/high salt, the rate of DNA denaturation following exposure to ionizing radiation is exponential. Conversely, cells plated at low density (approximately 7 x 10(2) cells/cm2) on plastic are more rounded 24 h later, produce little extracellular fibronectin, and display unusual DNA denaturation kinetics after X-irradiation. DNA in these cells resists denaturation, as though constraints to DNA unwinding have developed. Cell doubling time and distribution of cells in the growth cycle are identical for both high and low density cultures as is cell survival in response to radiation damage. The connection between DNA conformation and cell shape was examined further in low density cultures grown in conditioned medium. Under these conditions, cells at low density were able to elongate, and DNA denaturation of low density cultures was identical to that of high density cultures. Conversely, cytochalasin D, which interferes with actin polymerization causing cells to round up and release fibronectin, allowed development of constraints in high density cultures. These results suggest that DNA conformation is sensitive to changes in cell shape which result when cells are grown in different environments. However, these changes in DNA conformation detected by the DNA unwinding assay do not appear to play a direct role in radiation-induced cell killing

DNA stable-isotope probing (DNA-SIP).

Science.gov (United States)

Dunford, Eric A; Neufeld, Josh D

2010-08-02

DNA stable-isotope probing (DNA-SIP) is a powerful technique for identifying active microorganisms that assimilate particular carbon substrates and nutrients into cellular biomass. As such, this cultivation-independent technique has been an important methodology for assigning metabolic function to the diverse communities inhabiting a wide range of terrestrial and aquatic environments. Following the incubation of an environmental sample with stable-isotope labelled compounds, extracted nucleic acid is subjected to density gradient ultracentrifugation and subsequent gradient fractionation to separate nucleic acids of differing densities. Purification of DNA from cesium chloride retrieves labelled and unlabelled DNA for subsequent molecular characterization (e.g. fingerprinting, microarrays, clone libraries, metagenomics). This JoVE video protocol provides visual step-by-step explanations of the protocol for density gradient ultracentrifugation, gradient fractionation and recovery of labelled DNA. The protocol also includes sample SIP data and highlights important tips and cautions that must be considered to ensure a successful DNA-SIP analysis.

The effect of volume exclusion on the formation of DNA minicircle networks: implications to kinetoplast DNA

International Nuclear Information System (INIS)

Diao, Y; Hinson, K; Sun, Y; Arsuaga, J

2015-01-01

Kinetoplast DNA (kDNA) is the mitochondrial of DNA of disease causing organisms such as Trypanosoma Brucei (T. Brucei) and Trypanosoma Cruzi (T. Cruzi). In most organisms, KDNA is made of thousands of small circular DNA molecules that are highly condensed and topologically linked forming a gigantic planar network. In our previous work we have developed mathematical and computational models to test the confinement hypothesis, that is that the formation of kDNA minicircle networks is a product of the high DNA condensation achieved in the mitochondrion of these organisms. In these studies we studied three parameters that characterize the growth of the network topology upon confinement: the critical percolation density, the mean saturation density and the mean valence (i.e. the number of mini circles topologically linked to any chosen minicircle). Experimental results on insect-infecting organisms showed that the mean valence is equal to three, forming a structure similar to those found in medieval chain-mails. These same studies hypothesized that this value of the mean valence was driven by the DNA excluded volume. Here we extend our previous work on kDNA by characterizing the effects of DNA excluded volume on the three descriptive parameters. Using computer simulations of polymer swelling we found that (1) in agreement with previous studies the linking probability of two minicircles does not decrease linearly with the distance between the two minicircles, (2) the mean valence grows linearly with the density of minicircles and decreases with the thickness of the excluded volume, (3) the critical percolation and mean saturation densities grow linearly with the thickness of the excluded volume. Our results therefore suggest that the swelling of the DNA molecule, due to electrostatic interactions, has relatively mild implications on the overall topology of the network. Our results also validate our topological descriptors since they appear to reflect the changes in the

The effect of volume exclusion on the formation of DNA minicircle networks: implications to kinetoplast DNA

Science.gov (United States)

Diao, Y.; Hinson, K.; Sun, Y.; Arsuaga, J.

2015-10-01

Kinetoplast DNA (kDNA) is the mitochondrial of DNA of disease causing organisms such as Trypanosoma Brucei (T. Brucei) and Trypanosoma Cruzi (T. Cruzi). In most organisms, KDNA is made of thousands of small circular DNA molecules that are highly condensed and topologically linked forming a gigantic planar network. In our previous work we have developed mathematical and computational models to test the confinement hypothesis, that is that the formation of kDNA minicircle networks is a product of the high DNA condensation achieved in the mitochondrion of these organisms. In these studies we studied three parameters that characterize the growth of the network topology upon confinement: the critical percolation density, the mean saturation density and the mean valence (i.e. the number of mini circles topologically linked to any chosen minicircle). Experimental results on insect-infecting organisms showed that the mean valence is equal to three, forming a structure similar to those found in medieval chain-mails. These same studies hypothesized that this value of the mean valence was driven by the DNA excluded volume. Here we extend our previous work on kDNA by characterizing the effects of DNA excluded volume on the three descriptive parameters. Using computer simulations of polymer swelling we found that (1) in agreement with previous studies the linking probability of two minicircles does not decrease linearly with the distance between the two minicircles, (2) the mean valence grows linearly with the density of minicircles and decreases with the thickness of the excluded volume, (3) the critical percolation and mean saturation densities grow linearly with the thickness of the excluded volume. Our results therefore suggest that the swelling of the DNA molecule, due to electrostatic interactions, has relatively mild implications on the overall topology of the network. Our results also validate our topological descriptors since they appear to reflect the changes in the

Importing low-density ideas to high-density revitalisation

DEFF Research Database (Denmark)

Arnholtz, Jens; Ibsen, Christian Lyhne; Ibsen, Flemming

2016-01-01

Why did union officials from a high-union-density country like Denmark choose to import an organising strategy from low-density countries such as the US and the UK? Drawing on in-depth interviews with key union officials and internal documents, the authors of this article argue two key points. Fi...

To DNA, all information is equal

DEFF Research Database (Denmark)

Sennels, Lau; Bentin, Thomas

2012-01-01

Information storage capabilities are key in most aspects of society and the requirement for storage space is rapidly expanding. In principle, DNA could be a high-density medium for information storage. Church and coworkers recently demonstrated how binary data can be encoded, stored in, and retri......Information storage capabilities are key in most aspects of society and the requirement for storage space is rapidly expanding. In principle, DNA could be a high-density medium for information storage. Church and coworkers recently demonstrated how binary data can be encoded, stored in...

Assessing environmental DNA detection in controlled lentic systems.

Science.gov (United States)

Moyer, Gregory R; Díaz-Ferguson, Edgardo; Hill, Jeffrey E; Shea, Colin

2014-01-01

Little consideration has been given to environmental DNA (eDNA) sampling strategies for rare species. The certainty of species detection relies on understanding false positive and false negative error rates. We used artificial ponds together with logistic regression models to assess the detection of African jewelfish eDNA at varying fish densities (0, 0.32, 1.75, and 5.25 fish/m3). Our objectives were to determine the most effective water stratum for eDNA detection, estimate true and false positive eDNA detection rates, and assess the number of water samples necessary to minimize the risk of false negatives. There were 28 eDNA detections in 324, 1-L, water samples collected from four experimental ponds. The best-approximating model indicated that the per-L-sample probability of eDNA detection was 4.86 times more likely for every 2.53 fish/m3 (1 SD) increase in fish density and 1.67 times less likely for every 1.02 C (1 SD) increase in water temperature. The best section of the water column to detect eDNA was the surface and to a lesser extent the bottom. Although no false positives were detected, the estimated likely number of false positives in samples from ponds that contained fish averaged 3.62. At high densities of African jewelfish, 3-5 L of water provided a >95% probability for the presence/absence of its eDNA. Conversely, at moderate and low densities, the number of water samples necessary to achieve a >95% probability of eDNA detection approximated 42-73 and >100 L, respectively. Potential biases associated with incomplete detection of eDNA could be alleviated via formal estimation of eDNA detection probabilities under an occupancy modeling framework; alternatively, the filtration of hundreds of liters of water may be required to achieve a high (e.g., 95%) level of certainty that African jewelfish eDNA will be detected at low densities (i.e., <0.32 fish/m3 or 1.75 g/m3).

High Energy Density Laboratory Astrophysics

CERN Document Server

Lebedev, Sergey V

2007-01-01

During the past decade, research teams around the world have developed astrophysics-relevant research utilizing high energy-density facilities such as intense lasers and z-pinches. Every two years, at the International conference on High Energy Density Laboratory Astrophysics, scientists interested in this emerging field discuss the progress in topics covering: - Stellar evolution, stellar envelopes, opacities, radiation transport - Planetary Interiors, high-pressure EOS, dense plasma atomic physics - Supernovae, gamma-ray bursts, exploding systems, strong shocks, turbulent mixing - Supernova remnants, shock processing, radiative shocks - Astrophysical jets, high-Mach-number flows, magnetized radiative jets, magnetic reconnection - Compact object accretion disks, x-ray photoionized plasmas - Ultrastrong fields, particle acceleration, collisionless shocks. These proceedings cover many of the invited and contributed papers presented at the 6th International Conference on High Energy Density Laboratory Astrophys...

Photolysis of phosphodiester bonds in plasmid DNA by high intensity UV laser irradiation

International Nuclear Information System (INIS)

Croke, D.T.; Blau, Werner; OhUigin, Colm; Kelly, J.M.; McConnell, D.J.

1988-01-01

The cleavage of phosphodiester bonds in DNA exposed to high intensity UV laser pulses in aerated aqueous solution has been investigated using a krypton fluoride excimer laser (248 nm) and bacterial plasmid DNA. The dependence of strand breakage on fluence and intensity has been studied in detail and shows that the process is non-linear with respect to intensity. The relationship between the quantum yield for strand breakage and intensity shows that the strand breakage reaction involves two-photon excitation of DNA bases. The quantum yield rises with intensity from a lower value of 7 x 10 -5 until a maximum value of 4.5 x 10 -4 is attained at intensities of 10 11 W m -2 and above. This value is approximately fifty-fold higher than the quantum yield for strand breakage induced by exposure to low density UV irradiation (254 nm, 12 W m -2 ). DNA sequencing experiments have shown that strand breakage occurs by the specific cleavage of the phosphodiester bond which lies immediately 3' to guanine residues in the DNA, leaving some alkali-labile remnant attached to the terminal phosphate. A mechanism for DNA strand breakage which involves the generation of guanine radical cations is proposed. (author)

Large-scale preparation of plasmid DNA.

Science.gov (United States)

Heilig, J S; Elbing, K L; Brent, R

2001-05-01

Although the need for large quantities of plasmid DNA has diminished as techniques for manipulating small quantities of DNA have improved, occasionally large amounts of high-quality plasmid DNA are desired. This unit describes the preparation of milligram quantities of highly purified plasmid DNA. The first part of the unit describes three methods for preparing crude lysates enriched in plasmid DNA from bacterial cells grown in liquid culture: alkaline lysis, boiling, and Triton lysis. The second part describes four methods for purifying plasmid DNA in such lysates away from contaminating RNA and protein: CsCl/ethidium bromide density gradient centrifugation, polyethylene glycol (PEG) precipitation, anion-exchange chromatography, and size-exclusion chromatography.

High-density multicore fibers

DEFF Research Database (Denmark)

Takenaga, K.; Matsuo, S.; Saitoh, K.

2016-01-01

High-density single-mode multicore fibers were designed and fabricated. A heterogeneous 30-core fiber realized a low crosstalk of −55 dB. A quasi-single-mode homogeneous 31-core fiber attained the highest core count as a single-mode multicore fiber.......High-density single-mode multicore fibers were designed and fabricated. A heterogeneous 30-core fiber realized a low crosstalk of −55 dB. A quasi-single-mode homogeneous 31-core fiber attained the highest core count as a single-mode multicore fiber....

High-field, high-density tokamak power reactor

International Nuclear Information System (INIS)

Cohn, D.R.; Cook, D.L.; Hay, R.D.; Kaplan, D.; Kreischer, K.; Lidskii, L.M.; Stephany, W.; Williams, J.E.C.; Jassby, D.L.; Okabayashi, M.

1977-11-01

A conceptual design of a compact (R 0 = 6.0 m) high power density (average P/sub f/ = 7.7 MW/m 3 ) tokamak demonstration power reactor has been developed. High magnetic field (B/sub t/ = 7.4 T) and moderate elongation (b/a = 1.6) permit operation at the high density (n(0) approximately 5 x 10 14 cm -3 ) needed for ignition in a relatively small plasma, with a spatially-averaged toroidal beta of only 4%. A unique design for the Nb 3 Sn toroidal-field magnet system reduces the stress in the high-field trunk region, and allows modularization for simpler disassembly. The modest value of toroidal beta permits a simple, modularized plasma-shaping coil system, located inside the TF coil trunk. Heating of the dense central plasma is attained by the use of ripple-assisted injection of 120-keV D 0 beams. The ripple-coil system also affords dynamic control of the plasma temperature during the burn period. A FLIBE-lithium blanket is designed especially for high-power-density operation in a high-field environment, and gives an overall tritium breeding ratio of 1.05 in the slowly pumped lithium

High density harp for SSCL linac

International Nuclear Information System (INIS)

Fritsche, C.T.; Krogh, M.L.; Crist, C.E.

1993-01-01

AlliedSignal Inc., Kansas City Division, and the Superconducting Super Collider Laboratory (SSCL) are collaboratively developing a high density harp for the SSCL linac. This harp is designed using hybrid microcircuit (HMC) technology to obtain a higher wire density than previously available. The developed harp contains one hundred twenty-eight 33-micron-diameter carbon wires on 0.38-mm centers. The harp features an onboard broken wire detection circuit. Carbon wire preparation and attachment processes were developed. High density surface mount connectors were located. The status of high density harp development will be presented along with planned future activities

High density harp for SSCL linac

International Nuclear Information System (INIS)

Fritsche, C.T.; Krogh, M.L.

1993-05-01

AlliedSignal Inc., Kansas City Division, and the Superconducting Super Collider Laboratory (SSCL) are collaboratively developing a high density harp for the SSCL linac. This harp is designed using hybrid microcircuit (HMC) technology to obtain a higher wire density than previously available. The developed harp contains one hundred twenty-eight 33-micron-diameter carbon wires on 0.38-mm centers. The harp features an onboard broken wire detection circuit. Carbon wire preparation and attachment processes were developed. High density surface mount connectors were located. The status of high density harp development will be presented along with planned future activities

High density dispersion fuel

International Nuclear Information System (INIS)

Hofman, G.L.

1996-01-01

A fuel development campaign that results in an aluminum plate-type fuel of unlimited LEU burnup capability with an uranium loading of 9 grams per cm 3 of meat should be considered an unqualified success. The current worldwide approved and accepted highest loading is 4.8 g cm -3 with U 3 Si 2 as fuel. High-density uranium compounds offer no real density advantage over U 3 Si 2 and have less desirable fabrication and performance characteristics as well. Of the higher-density compounds, U 3 Si has approximately a 30% higher uranium density but the density of the U 6 X compounds would yield the factor 1.5 needed to achieve 9 g cm -3 uranium loading. Unfortunately, irradiation tests proved these peritectic compounds have poor swelling behavior. It is for this reason that the authors are turning to uranium alloys. The reason pure uranium was not seriously considered as a dispersion fuel is mainly due to its high rate of growth and swelling at low temperatures. This problem was solved at least for relatively low burnup application in non-dispersion fuel elements with small additions of Si, Fe, and Al. This so called adjusted uranium has nearly the same density as pure α-uranium and it seems prudent to reconsider this alloy as a dispersant. Further modifications of uranium metal to achieve higher burnup swelling stability involve stabilization of the cubic γ phase at low temperatures where normally α phase exists. Several low neutron capture cross section elements such as Zr, Nb, Ti and Mo accomplish this in various degrees. The challenge is to produce a suitable form of fuel powder and develop a plate fabrication procedure, as well as obtain high burnup capability through irradiation testing

High regression rate, high density hybrid fuels, Phase I

Data.gov (United States)

National Aeronautics and Space Administration — This SBIR program will investigate high energy density novel nanofuels combined with high density binders for use with an N2O oxidizer. Terves has developed...

Isolation and analysis of high quality nuclear DNA with reduced organellar DNA for plant genome sequencing and resequencing

Directory of Open Access Journals (Sweden)

Zdepski Anna

2011-05-01

Full Text Available Abstract Background High throughput sequencing (HTS technologies have revolutionized the field of genomics by drastically reducing the cost of sequencing, making it feasible for individual labs to sequence or resequence plant genomes. Obtaining high quality, high molecular weight DNA from plants poses significant challenges due to the high copy number of chloroplast and mitochondrial DNA, as well as high levels of phenolic compounds and polysaccharides. Multiple methods have been used to isolate DNA from plants; the CTAB method is commonly used to isolate total cellular DNA from plants that contain nuclear DNA, as well as chloroplast and mitochondrial DNA. Alternatively, DNA can be isolated from nuclei to minimize chloroplast and mitochondrial DNA contamination. Results We describe optimized protocols for isolation of nuclear DNA from eight different plant species encompassing both monocot and eudicot species. These protocols use nuclei isolation to minimize chloroplast and mitochondrial DNA contamination. We also developed a protocol to determine the number of chloroplast and mitochondrial DNA copies relative to the nuclear DNA using quantitative real time PCR (qPCR. We compared DNA isolated from nuclei to total cellular DNA isolated with the CTAB method. As expected, DNA isolated from nuclei consistently yielded nuclear DNA with fewer chloroplast and mitochondrial DNA copies, as compared to the total cellular DNA prepared with the CTAB method. This protocol will allow for analysis of the quality and quantity of nuclear DNA before starting a plant whole genome sequencing or resequencing experiment. Conclusions Extracting high quality, high molecular weight nuclear DNA in plants has the potential to be a bottleneck in the era of whole genome sequencing and resequencing. The methods that are described here provide a framework for researchers to extract and quantify nuclear DNA in multiple types of plants.

Magnetization of High Density Hadronic Fluid

DEFF Research Database (Denmark)

Bohr, Henrik; Providencia, Constanca; da Providencia, João

2012-01-01

In the present paper the magnetization of a high density relativistic fluid of elementary particles is studied. At very high densities, such as may be found in the interior of a neutron star, when the external magnetic field is gradually increased, the energy of the normal phase of the fluid...... in the particle fluid. For nuclear densities above 2 to 3 rho(0), where rho(0) is the equilibrium nuclear density, the resulting magnetic field turns out to be rather huge, of the order of 10(17) Gauss....

High-Throughput Block Optical DNA Sequence Identification.

Science.gov (United States)

Sagar, Dodderi Manjunatha; Korshoj, Lee Erik; Hanson, Katrina Bethany; Chowdhury, Partha Pratim; Otoupal, Peter Britton; Chatterjee, Anushree; Nagpal, Prashant

2018-01-01

Optical techniques for molecular diagnostics or DNA sequencing generally rely on small molecule fluorescent labels, which utilize light with a wavelength of several hundred nanometers for detection. Developing a label-free optical DNA sequencing technique will require nanoscale focusing of light, a high-throughput and multiplexed identification method, and a data compression technique to rapidly identify sequences and analyze genomic heterogeneity for big datasets. Such a method should identify characteristic molecular vibrations using optical spectroscopy, especially in the "fingerprinting region" from ≈400-1400 cm -1 . Here, surface-enhanced Raman spectroscopy is used to demonstrate label-free identification of DNA nucleobases with multiplexed 3D plasmonic nanofocusing. While nanometer-scale mode volumes prevent identification of single nucleobases within a DNA sequence, the block optical technique can identify A, T, G, and C content in DNA k-mers. The content of each nucleotide in a DNA block can be a unique and high-throughput method for identifying sequences, genes, and other biomarkers as an alternative to single-letter sequencing. Additionally, coupling two complementary vibrational spectroscopy techniques (infrared and Raman) can improve block characterization. These results pave the way for developing a novel, high-throughput block optical sequencing method with lossy genomic data compression using k-mer identification from multiplexed optical data acquisition. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Role of the Coulomb interaction in the low-frequency density of states of DNA double helices

International Nuclear Information System (INIS)

Garcia, A.E.; Krumhansl, J.A.

1988-01-01

The complete vibrational frequency spectrum of several DNA double-helical oligomers is calculated using established pair potentials. Various cutoff values are used for the range of the Coulomb interactions. At very low frequency the integrated density of states shows a noninteger exponent with values ranging from 0.75 to 1.55, depending on the cutoff value for the Coulomb interactions. We conclude that the cumulative densities of states in those molecules depend more on competing interactions than on various proposed universal laws

Construction of Halomonas bluephagenesis capable of high cell density growth for efficient PHA production.

Science.gov (United States)

Ren, Yilin; Ling, Chen; Hajnal, Ivan; Wu, Qiong; Chen, Guo-Qiang

2018-05-01

High-cell-density cultivation is an effective way to improve the productivity of microbial fermentations and in turn reduce the cost of the final products, especially in the case of intracellular products. Halomonas bluephagenesis TD01 is a halophilic platform bacterium for the next generation of industrial biotechnology with a native PHA synthetic pathway, able to grow under non-sterile continuous fermentation conditions. A selection strategy for mutant strains that can grow to a high cell density was developed. Based on an error-prone DNA polymerase III ε subunit, a genome-wide random mutagenesis system was established and used in conjunction with an artificial high cell density culture environment during the selection process. A high-cell-density H. bluephagenesis TDHCD-R3 obtained after 3 rounds of selection showed an obvious enhancement of resistance to toxic metabolites including acetate, formate, lactate and ethanol compared to wild-type. H. bluephagenesis TDHCD-R3-8-3 constructed from H. bluephagenesis TDHCD-R3 by overexpressing an optimized phaCAB operon was able to grow to 15 g/L cell dry weight (CDW) containing 94% PHA in shake flask studies. H. bluephagenesis TDHCD-R3-8-3 was grown to more than 90 g/L CDW containing 79% PHA compared with only 81 g/L with 70% PHA by the wild type when incubated in a 7-L fermentor under the same conditions.

Use of spatial capture-recapture modeling and DNA data to estimate densities of elusive animals

Science.gov (United States)

Kery, Marc; Gardner, Beth; Stoeckle, Tabea; Weber, Darius; Royle, J. Andrew

2011-01-01

Assessment of abundance, survival, recruitment rates, and density (i.e., population assessment) is especially challenging for elusive species most in need of protection (e.g., rare carnivores). Individual identification methods, such as DNA sampling, provide ways of studying such species efficiently and noninvasively. Additionally, statistical methods that correct for undetected animals and account for locations where animals are captured are available to efficiently estimate density and other demographic parameters. We collected hair samples of European wildcat (Felis silvestris) from cheek-rub lure sticks, extracted DNA from the samples, and identified each animals' genotype. To estimate the density of wildcats, we used Bayesian inference in a spatial capture-recapture model. We used WinBUGS to fit a model that accounted for differences in detection probability among individuals and seasons and between two lure arrays. We detected 21 individual wildcats (including possible hybrids) 47 times. Wildcat density was estimated at 0.29/km2 (SE 0.06), and 95% of the activity of wildcats was estimated to occur within 1.83 km from their home-range center. Lures located systematically were associated with a greater number of detections than lures placed in a cell on the basis of expert opinion. Detection probability of individual cats was greatest in late March. Our model is a generalized linear mixed model; hence, it can be easily extended, for instance, to incorporate trap- and individual-level covariates. We believe that the combined use of noninvasive sampling techniques and spatial capture-recapture models will improve population assessments, especially for rare and elusive animals.

extraction of high quality dna from polysaccharides-secreting ...

African Journals Online (AJOL)

cistvr

A DNA extraction method using CTAB was used for the isolation of genomic DNA from ten. Xanthomonas campestris pathovars, ten isolates of Xanthomonas albilineans and one isolate of. Pseudomonas rubrisubalbicans. High quality DNA was obtained that was ideal for molecular analy- ses. Extracellular polysaccharides ...

High resolution optical DNA mapping

Science.gov (United States)

Baday, Murat

Many types of diseases including cancer and autism are associated with copy-number variations in the genome. Most of these variations could not be identified with existing sequencing and optical DNA mapping methods. We have developed Multi-color Super-resolution technique, with potential for high throughput and low cost, which can allow us to recognize more of these variations. Our technique has made 10--fold improvement in the resolution of optical DNA mapping. Using a 180 kb BAC clone as a model system, we resolved dense patterns from 108 fluorescent labels of two different colors representing two different sequence-motifs. Overall, a detailed DNA map with 100 bp resolution was achieved, which has the potential to reveal detailed information about genetic variance and to facilitate medical diagnosis of genetic disease.

Recent Advancements in DNA Damage-Transcription Crosstalk and High-Resolution Mapping of DNA Breaks.

Science.gov (United States)

Vitelli, Valerio; Galbiati, Alessandro; Iannelli, Fabio; Pessina, Fabio; Sharma, Sheetal; d'Adda di Fagagna, Fabrizio

2017-08-31

Until recently, DNA damage arising from physiological DNA metabolism was considered a detrimental by-product for cells. However, an increasing amount of evidence has shown that DNA damage could have a positive role in transcription activation. In particular, DNA damage has been detected in transcriptional elements following different stimuli. These physiological DNA breaks are thought to be instrumental for the correct expression of genomic loci through different mechanisms. In this regard, although a plethora of methods are available to precisely map transcribed regions and transcription start sites, commonly used techniques for mapping DNA breaks lack sufficient resolution and sensitivity to draw a robust correlation between DNA damage generation and transcription. Recently, however, several methods have been developed to map DNA damage at single-nucleotide resolution, thus providing a new set of tools to correlate DNA damage and transcription. Here, we review how DNA damage can positively regulate transcription initiation, the current techniques for mapping DNA breaks at high resolution, and how these techniques can benefit future studies of DNA damage and transcription.

Highly efficient DNA extraction method from skeletal remains

Directory of Open Access Journals (Sweden)

Irena Zupanič Pajnič

2011-03-01

Full Text Available Background: This paper precisely describes the method of DNA extraction developed to acquire high quality DNA from the Second World War skeletal remains. The same method is also used for molecular genetic identification of unknown decomposed bodies in routine forensic casework where only bones and teeth are suitable for DNA typing. We analysed 109 bones and two teeth from WWII mass graves in Slovenia. Methods: We cleaned the bones and teeth, removed surface contaminants and ground the bones into powder, using liquid nitrogen . Prior to isolating the DNA in parallel using the BioRobot EZ1 (Qiagen, the powder was decalcified for three days. The nuclear DNA of the samples were quantified by real-time PCR method. We acquired autosomal genetic profiles and Y-chromosome haplotypes of the bones and teeth with PCR amplification of microsatellites, and mtDNA haplotypes 99. For the purpose of traceability in the event of contamination, we prepared elimination data bases including genetic profiles of the nuclear and mtDNA of all persons who have been in touch with the skeletal remains in any way. Results: We extracted up to 55 ng DNA/g of the teeth, up to 100 ng DNA/g of the femurs, up to 30 ng DNA/g of the tibias and up to 0.5 ng DNA/g of the humerus. The typing of autosomal and YSTR loci was successful in all of the teeth, in 98 % dekalof the femurs, and in 75 % to 81 % of the tibias and humerus. The typing of mtDNA was successful in all of the teeth, and in 96 % to 98 % of the bones. Conclusions: We managed to obtain nuclear DNA for successful STR typing from skeletal remains that were over 60 years old . The method of DNA extraction described here has proved to be highly efficient. We obtained 0.8 to 100 ng DNA/g of teeth or bones and complete genetic profiles of autosomal DNA, Y-STR haplotypes, and mtDNA haplotypes from only 0.5g bone and teeth samples.

Density measurements of small amounts of high-density solids by a floatation method

International Nuclear Information System (INIS)

Akabori, Mitsuo; Shiba, Koreyuki

1984-09-01

A floatation method for determining the density of small amounts of high-density solids is described. The use of a float combined with an appropriate floatation liquid allows us to measure the density of high-density substances in small amounts. Using the sample of 0.1 g in weight, the floatation liquid of 3.0 g cm -3 in density and the float of 1.5 g cm -3 in apparent density, the sample densities of 5, 10 and 20 g cm -3 are determined to an accuracy better than +-0.002, +-0.01 and +-0.05 g cm -3 , respectively that correspond to about +-1 x 10 -5 cm 3 in volume. By means of appropriate degassing treatments, the densities of (Th,U)O 2 pellets of --0.1 g in weight and --9.55 g cm -3 in density were determined with an accuracy better than +-0.05 %. (author)

Research on high energy density plasmas and applications

International Nuclear Information System (INIS)

1999-01-01

Recently, technologies on lasers, accelerators, and pulse power machines have been significantly advanced and input power density covers the intensity range from 10 10 W/cm 2 to higher than 10 20 W/cm 2 . As the results, high pressure gas and solid targets can be heated up to very high temperature to create hot dense plasmas which have never appeared on the earth. The high energy density plasmas opened up new research fields such as inertial confinement fusion, high brightness X-ray radiation sources, interiors of galactic nucleus,supernova, stars and planets, ultra high pressure condensed matter physics, plasma particle accelerator, X-ray laser, and so on. Furthermore, since these fields are intimately connected with various industrial sciences and technologies, the high energy density plasma is now studied in industries, government institutions, and so on. This special issue of the Journal of Plasma Physics and Nuclear Fusion Research reviews the high energy density plasma science for the comprehensive understanding of such new fields. In May, 1998, the review committee for investigating the present status and the future prospects of high energy density plasma science was established in the Japan Society of Plasma Science and Nuclear Fusion Research. We held three committee meetings to discuss present status and critical issues of research items related to high energy density plasmas. This special issue summarizes the understandings of the committee. This special issue consists of four chapters: They are Chapter 1: Physics important in the high energy density plasmas, Chapter 2: Technologies related to the plasma generation; drivers such as lasers, pulse power machines, particle beams and fabrication of various targets, Chapter 3: Plasma diagnostics important in high energy density plasma experiments, Chapter 4: A variety of applications of high energy density plasmas; X-ray radiation, particle acceleration, inertial confinement fusion, laboratory astrophysics

Surveys of environmental DNA (eDNA): a new approach to estimate occurrence in Vulnerable manatee populations

Science.gov (United States)

Hunter, Margaret; Meigs-Friend, Gaia; Ferrante, Jason; Takoukam Kamla, Aristide; Dorazio, Robert; Keith Diagne, Lucy; Luna, Fabia; Lanyon, Janet M.; Reid, James P.

2018-01-01

Environmental DNA (eDNA) detection is a technique used to non-invasively detect cryptic, low density, or logistically difficult-to-study species, such as imperiled manatees. For eDNA measurement, genetic material shed into the environment is concentrated from water samples and analyzed for the presence of target species. Cytochrome bquantitative PCR and droplet digital PCR eDNA assays were developed for the 3 Vulnerable manatee species: African, Amazonian, and both subspecies of the West Indian (Florida and Antillean) manatee. Environmental DNA assays can help to delineate manatee habitat ranges, high use areas, and seasonal population changes. To validate the assay, water was analyzed from Florida’s east coast containing a high-density manatee population and produced 31564 DNA molecules l-1on average and high occurrence (ψ) and detection (p) estimates (ψ = 0.84 [0.40-0.99]; p = 0.99 [0.95-1.00]; limit of detection 3 copies µl-1). Similar occupancy estimates were produced in the Florida Panhandle (ψ = 0.79 [0.54-0.97]) and Cuba (ψ = 0.89 [0.54-1.00]), while occupancy estimates in Cameroon were lower (ψ = 0.49 [0.09-0.95]). The eDNA-derived detection estimates were higher than those generated using aerial survey data on the west coast of Florida and may be effective for population monitoring. Subsequent eDNA studies could be particularly useful in locations where manatees are (1) difficult to identify visually (e.g. the Amazon River and Africa), (2) are present in patchy distributions or are on the verge of extinction (e.g. Jamaica, Haiti), and (3) where repatriation efforts are proposed (e.g. Brazil, Guadeloupe). Extension of these eDNA techniques could be applied to other imperiled marine mammal populations such as African and Asian dugongs.

The Influence of Spatial Variation in Chromatin Density Determined by X-Ray Tomograms on the Time to Find DNA Binding Sites

Science.gov (United States)

Larabell, Carolyn A.; Le Gros, Mark A.; McQueen, David M.; Peskin, Charles S.

2014-01-01

In this work, we examine how volume exclusion caused by regions of high chromatin density might influence the time required for proteins to find specific DNA binding sites. The spatial variation of chromatin density within mouse olfactory sensory neurons is determined from soft X-ray tomography reconstructions of five nuclei. We show that there is a division of the nuclear space into regions of low-density euchromatin and high-density heterochromatin. Volume exclusion experienced by a diffusing protein caused by this varying density of chromatin is modeled by a repulsive potential. The value of the potential at a given point in space is chosen to be proportional to the density of chromatin at that location. The constant of proportionality, called the volume exclusivity, provides a model parameter that determines the strength of volume exclusion. Numerical simulations demonstrate that the mean time for a protein to locate a binding site localized in euchromatin is minimized for a finite, nonzero volume exclusivity. For binding sites in heterochromatin, the mean time is minimized when the volume exclusivity is zero (the protein experiences no volume exclusion). An analytical theory is developed to explain these results. The theory suggests that for binding sites in euchromatin there is an optimal level of volume exclusivity that balances a reduction in the volume searched in finding the binding site, with the height of effective potential barriers the protein must cross during the search process. PMID:23955281

Mark-recapture using tetracycline and genetics reveal record-high bear density

Science.gov (United States)

Peacock, E.; Titus, K.; Garshelis, D.L.; Peacock, M.M.; Kuc, M.

2011-01-01

We used tetracycline biomarking, augmented with genetic methods to estimate the size of an American black bear (Ursus americanus) population on an island in Southeast Alaska. We marked 132 and 189 bears that consumed remote, tetracycline-laced baits in 2 different years, respectively, and observed 39 marks in 692 bone samples subsequently collected from hunters. We genetically analyzed hair samples from bait sites to determine the sex of marked bears, facilitating derivation of sex-specific population estimates. We obtained harvest samples from beyond the study area to correct for emigration. We estimated a density of 155 independent bears/100 km2, which is equivalent to the highest recorded for this species. This high density appears to be maintained by abundant, accessible natural food. Our population estimate (approx. 1,000 bears) could be used as a baseline and to set hunting quotas. The refined biomarking method for abundance estimation is a useful alternative where physical captures or DNA-based estimates are precluded by cost or logistics. Copyright ?? 2011 The Wildlife Society.

Toward Low-Cost, High-Energy Density, and High-Power Density Lithium-Ion Batteries

Science.gov (United States)

Li, Jianlin; Du, Zhijia; Ruther, Rose E.; AN, Seong Jin; David, Lamuel Abraham; Hays, Kevin; Wood, Marissa; Phillip, Nathan D.; Sheng, Yangping; Mao, Chengyu; Kalnaus, Sergiy; Daniel, Claus; Wood, David L.

2017-09-01

Reducing cost and increasing energy density are two barriers for widespread application of lithium-ion batteries in electric vehicles. Although the cost of electric vehicle batteries has been reduced by 70% from 2008 to 2015, the current battery pack cost (268/kWh in 2015) is still >2 times what the USABC targets (125/kWh). Even though many advancements in cell chemistry have been realized since the lithium-ion battery was first commercialized in 1991, few major breakthroughs have occurred in the past decade. Therefore, future cost reduction will rely on cell manufacturing and broader market acceptance. This article discusses three major aspects for cost reduction: (1) quality control to minimize scrap rate in cell manufacturing; (2) novel electrode processing and engineering to reduce processing cost and increase energy density and throughputs; and (3) material development and optimization for lithium-ion batteries with high-energy density. Insights on increasing energy and power densities of lithium-ion batteries are also addressed.

Links between DNA methylation and nucleosome occupancy in the human genome.

Science.gov (United States)

Collings, Clayton K; Anderson, John N

2017-01-01

DNA methylation is an epigenetic modification that is enriched in heterochromatin but depleted at active promoters and enhancers. However, the debate on whether or not DNA methylation is a reliable indicator of high nucleosome occupancy has not been settled. For example, the methylation levels of DNA flanking CTCF sites are higher in linker DNA than in nucleosomal DNA, while other studies have shown that the nucleosome core is the preferred site of methylation. In this study, we make progress toward understanding these conflicting phenomena by implementing a bioinformatics approach that combines MNase-seq and NOMe-seq data and by comprehensively profiling DNA methylation and nucleosome occupancy throughout the human genome. The results demonstrated that increasing methylated CpG density is correlated with nucleosome occupancy in the total genome and within nearly all subgenomic regions. Features with elevated methylated CpG density such as exons, SINE-Alu sequences, H3K36-trimethylated peaks, and methylated CpG islands are among the highest nucleosome occupied elements in the genome, while some of the lowest occupancies are displayed by unmethylated CpG islands and unmethylated transcription factor binding sites. Additionally, outside of CpG islands, the density of CpGs within nucleosomes was shown to be important for the nucleosomal location of DNA methylation with low CpG frequencies favoring linker methylation and high CpG frequencies favoring core particle methylation. Prominent exceptions to the correlations between methylated CpG density and nucleosome occupancy include CpG islands marked by H3K27me3 and CpG-poor heterochromatin marked by H3K9me3, and these modifications, along with DNA methylation, distinguish the major silencing mechanisms of the human epigenome. Thus, the relationship between DNA methylation and nucleosome occupancy is influenced by the density of methylated CpG dinucleotides and by other epigenomic components in chromatin.

Properties of matter at ultra-high densities

International Nuclear Information System (INIS)

Banerjee, B.; Chitre, S.M.

1975-01-01

The recent discovery of pulsars and their subsequent identification with neutron stars has given a great impetus to the study of the behaviour of matter at ultra high densities. The object of these studies is to calculate the equation of state as a function of density. In this paper, the properties of electrically neutral, cold (T=0) matter at unusually high densities has been reviewed. The physics of the equation of state of such matter divides quite naturally in four density ranges. (i) At the very lowest densities the state of minimum energy is a lattice of 56 Fe atoms. This state persists upto 10 7 g/cm 3 . (ii) In the next density region the nuclei at the lattice sites become neutron rich because the high electron Fermi energy makes inverse beta decay possible. (iii) At a density 4.3 x 10 11 the nuclei become so neutron rich that the neutrons start 'dripping' out of the nuclei and form a gas. This density range is characterised by large, neutron-rich nuclei immersed in a neutron gas. (iv) At a density 2.4 x 10 14 g/cm 3 , the nuclei disappear and a fluid of uniform neutron matter with a small percentage of protons and electrons results. The above four density ranges have been discussed in detail as the equation of state is now well established upto the nuclear density 3 x 10 14 g/cm 3 . The problems of extending the equation of state beyond this density are also touched upon. (author)

Transcriptional effect of an Aframomum angustifolium seed extract on human cutaneous cells using low-density DNA chips.

Science.gov (United States)

Bonnet-Duquennoy, Mathilde; Dumas, Marc; Debacker, Adeline; Lazou, Kristell; Talbourdet, Sylvie; Franchi, Jocelyne; Heusèle, Catherine; André, Patrice; Schnebert, Sylvianne; Bonté, Frédéric; Kurfürst, Robin

2007-06-01

Studying photoexposed and photoprotected skin biopsies from young and aged women, it has been found that a specific zone, composed of the basal layers of the epidermis, the dermal epidermal junction, and the superficial dermis, is major target of aging and reactive oxygen species. We showed that this zone is characterized by significant variations at a transcriptional and/or protein levels. Using low-density DNA chip technology, we evaluated the effect of a natural mixture of Aframomum angustifolium seed extract containing labdane diterpenoids on these aging markers. Expression profiles of normal human fibroblasts (NHF) were studied using a customized cDNA macroarray system containing genes covering dermal structure, inflammatory responses, and oxidative stress defense mechanisms. For normal human keratinocyte (NHK) investigations, we chose OLISA technique, a sensitive and quantitative method developed by BioMérieux specifically designed to investigate cell death, proliferation, epidermal structure, differentiation, and oxidative stress defense response. We observed that this extract strongly modified gene expression profiles of treated NHK, but weakly for NHF. This extract regulated antioxidant defenses, dermal-epidermal junction components, and epidermal renewal-related genes. Using low-density DNA chip technology, we identified new potential actions of A. angustifolium seed extract on skin aging.

A Novel Low Temperature PCR Assured High-Fidelity DNA Amplification

Directory of Open Access Journals (Sweden)

Shaoxia Zhou

2013-06-01

Full Text Available As previously reported, a novel low temperature (LoTemp polymerase chain reaction (PCR catalyzed by a moderately heat-resistant (MHR DNA polymerase with a chemical-assisted denaturation temperature set at 85 °C instead of the conventional 94–96 °C can achieve high-fidelity DNA amplification of a target DNA, even after up to 120 PCR thermal cycles. Furthermore, such accurate amplification is not achievable with conventional PCR. Now, using a well-recognized L1 gene segment of the human papillomavirus (HPV type 52 (HPV-52 as the template for experiments, we demonstrate that the LoTemp high-fidelity DNA amplification is attributed to an unusually high processivity and stability of the MHR DNA polymerase whose high fidelity in template-directed DNA synthesis is independent of non-existent 3'–5' exonuclease activity. Further studies and understanding of the characteristics of the LoTemp PCR technology may facilitate implementation of DNA sequencing-based diagnostics at the point of care in community hospital laboratories.

High-density carbon ablator ignition path with low-density gas-filled rugby hohlraum

International Nuclear Information System (INIS)

Amendt, Peter; Ho, Darwin D.; Jones, Ogden S.

2015-01-01

A recent low gas-fill density (0.6 mg/cc 4 He) cylindrical hohlraum experiment on the National Ignition Facility has shown high laser-coupling efficiency (>96%), reduced phenomenological laser drive corrections, and improved high-density carbon capsule implosion symmetry [Jones et al., Bull. Am. Phys. Soc. 59(15), 66 (2014)]. In this Letter, an ignition design using a large rugby-shaped hohlraum [Amendt et al., Phys. Plasmas 21, 112703 (2014)] for high energetics efficiency and symmetry control with the same low gas-fill density (0.6 mg/cc 4 He) is developed as a potentially robust platform for demonstrating thermonuclear burn. The companion high-density carbon capsule for this hohlraum design is driven by an adiabat-shaped [Betti et al., Phys. Plasmas 9, 2277 (2002)] 4-shock drive profile for robust high gain (>10) 1-D ignition performance and large margin to 2-D perturbation growth

High-density carbon ablator ignition path with low-density gas-filled rugby hohlraum

Science.gov (United States)

Amendt, Peter; Ho, Darwin D.; Jones, Ogden S.

2015-04-01

A recent low gas-fill density (0.6 mg/cc 4He) cylindrical hohlraum experiment on the National Ignition Facility has shown high laser-coupling efficiency (>96%), reduced phenomenological laser drive corrections, and improved high-density carbon capsule implosion symmetry [Jones et al., Bull. Am. Phys. Soc. 59(15), 66 (2014)]. In this Letter, an ignition design using a large rugby-shaped hohlraum [Amendt et al., Phys. Plasmas 21, 112703 (2014)] for high energetics efficiency and symmetry control with the same low gas-fill density (0.6 mg/cc 4He) is developed as a potentially robust platform for demonstrating thermonuclear burn. The companion high-density carbon capsule for this hohlraum design is driven by an adiabat-shaped [Betti et al., Phys. Plasmas 9, 2277 (2002)] 4-shock drive profile for robust high gain (>10) 1-D ignition performance and large margin to 2-D perturbation growth.

High-density carbon ablator ignition path with low-density gas-filled rugby hohlraum

Energy Technology Data Exchange (ETDEWEB)

Amendt, Peter; Ho, Darwin D.; Jones, Ogden S. [Lawrence Livermore National Laboratory, Livermore, California 94551 (United States)

2015-04-15

A recent low gas-fill density (0.6 mg/cc {sup 4}He) cylindrical hohlraum experiment on the National Ignition Facility has shown high laser-coupling efficiency (>96%), reduced phenomenological laser drive corrections, and improved high-density carbon capsule implosion symmetry [Jones et al., Bull. Am. Phys. Soc. 59(15), 66 (2014)]. In this Letter, an ignition design using a large rugby-shaped hohlraum [Amendt et al., Phys. Plasmas 21, 112703 (2014)] for high energetics efficiency and symmetry control with the same low gas-fill density (0.6 mg/cc {sup 4}He) is developed as a potentially robust platform for demonstrating thermonuclear burn. The companion high-density carbon capsule for this hohlraum design is driven by an adiabat-shaped [Betti et al., Phys. Plasmas 9, 2277 (2002)] 4-shock drive profile for robust high gain (>10) 1-D ignition performance and large margin to 2-D perturbation growth.

Theory of high-force DNA stretching and overstretching.

Science.gov (United States)

Storm, C; Nelson, P C

2003-05-01

Single-molecule experiments on single- and double-stranded DNA have sparked a renewed interest in the force versus extension of polymers. The extensible freely jointed chain (FJC) model is frequently invoked to explain the observed behavior of single-stranded DNA, but this model does not satisfactorily describe recent high-force stretching data. We instead propose a model (the discrete persistent chain) that borrows features from both the FJC and the wormlike chain, and show that it resembles the data more closely. We find that most of the high-force behavior previously attributed to stretch elasticity is really a feature of the corrected entropic elasticity; the true stretch compliance of single-stranded DNA is several times smaller than that found by previous authors. Next we elaborate our model to allow coexistence of two conformational states of DNA, each with its own stretch and bend elastic constants. Our model is computationally simple and gives an excellent fit through the entire overstretching transition of nicked, double-stranded DNA. The fit gives the first value for the bend stiffness of the overstretched state. In particular, we find the effective bend stiffness for DNA in this state to be about 12 nm k(B)T, a value quite different from either the B-form or single-stranded DNA.

Photoionization and High Density Gas

Science.gov (United States)

Kallman, T.; Bautista, M.; White, Nicholas E. (Technical Monitor)

2002-01-01

We present results of calculations using the XSTAR version 2 computer code. This code is loosely based on the XSTAR v.1 code which has been available for public use for some time. However it represents an improvement and update in several major respects, including atomic data, code structure, user interface, and improved physical description of ionization/excitation. In particular, it now is applicable to high density situations in which significant excited atomic level populations are likely to occur. We describe the computational techniques and assumptions, and present sample runs with particular emphasis on high density situations.

Super-resolution optical DNA Mapping via DNA methyltransferase-directed click chemistry

DEFF Research Database (Denmark)

Vranken, Charlotte; Deen, Jochem; Dirix, Lieve

2014-01-01

We demonstrate an approach to optical DNA mapping, which enables near single-molecule characterization of whole bacteriophage genomes. Our approach uses a DNA methyltransferase enzyme to target labelling to specific sites and copper-catalysed azide-alkyne cycloaddition to couple a fluorophore...... to the DNA. We achieve a labelling efficiency of ∼70% with an average labelling density approaching one site every 500 bp. Such labelling density bridges the gap between the output of a typical DNA sequencing experiment and the long-range information derived from traditional optical DNA mapping. We lay...... the foundations for a wider-scale adoption of DNA mapping by screening 11 methyltransferases for their ability to direct sequence-specific DNA transalkylation; the first step of the DNA labelling process and by optimizing reaction conditions for fluorophore coupling via a click reaction. Three of 11 enzymes...

Estimating black bear density using DNA data from hair snares

Science.gov (United States)

Gardner, B.; Royle, J. Andrew; Wegan, M.T.; Rainbolt, R.E.; Curtis, P.D.

2010-01-01

DNA-based mark-recapture has become a methodological cornerstone of research focused on bear species. The objective of such studies is often to estimate population size; however, doing so is frequently complicated by movement of individual bears. Movement affects the probability of detection and the assumption of closure of the population required in most models. To mitigate the bias caused by movement of individuals, population size and density estimates are often adjusted using ad hoc methods, including buffering the minimum polygon of the trapping array. We used a hierarchical, spatial capturerecapture model that contains explicit components for the spatial-point process that governs the distribution of individuals and their exposure to (via movement), and detection by, traps. We modeled detection probability as a function of each individual's distance to the trap and an indicator variable for previous capture to account for possible behavioral responses. We applied our model to a 2006 hair-snare study of a black bear (Ursus americanus) population in northern New York, USA. Based on the microsatellite marker analysis of collected hair samples, 47 individuals were identified. We estimated mean density at 0.20 bears/km2. A positive estimate of the indicator variable suggests that bears are attracted to baited sites; therefore, including a trap-dependence covariate is important when using bait to attract individuals. Bayesian analysis of the model was implemented in WinBUGS, and we provide the model specification. The model can be applied to any spatially organized trapping array (hair snares, camera traps, mist nests, etc.) to estimate density and can also account for heterogeneity and covariate information at the trap or individual level. ?? The Wildlife Society.

Electronic DC transformer with high power density

NARCIS (Netherlands)

Pavlovský, M.

2006-01-01

This thesis is concerned with the possibilities of increasing the power density of high-power dc-dc converters with galvanic isolation. Three cornerstones for reaching high power densities are identified as: size reduction of passive components, reduction of losses particularly in active components

Functional DNA-containing nanomaterials: cellular applications in biosensing, imaging, and targeted therapy.

Science.gov (United States)

Liang, Hao; Zhang, Xiao-Bing; Lv, Yifan; Gong, Liang; Wang, Ruowen; Zhu, Xiaoyan; Yang, Ronghua; Tan, Weihong

2014-06-17

CONSPECTUS: DNA performs a vital function as a carrier of genetic code, but in the field of nanotechnology, DNA molecules can catalyze chemical reactions in the cell, that is, DNAzymes, or bind with target-specific ligands, that is, aptamers. These functional DNAs with different modifications have been developed for sensing, imaging, and therapeutic systems. Thus, functional DNAs hold great promise for future applications in nanotechnology and bioanalysis. However, these functional DNAs face challenges, especially in the field of biomedicine. For example, functional DNAs typically require the use of cationic transfection reagents to realize cellular uptake. Such reagents enter the cells, increasing the difficulty of performing bioassays in vivo and potentially damaging the cell's nucleus. To address this obstacle, nanomaterials, such as metallic, carbon, silica, or magnetic materials, have been utilized as DNA carriers or assistants. In this Account, we describe selected examples of functional DNA-containing nanomaterials and their applications from our recent research and those of others. As models, we have chosen to highlight DNA/nanomaterial complexes consisting of gold nanoparticles, graphene oxides, and aptamer-micelles, and we illustrate the potential of such complexes in biosensing, imaging, and medical diagnostics. Under proper conditions, multiple ligand-receptor interactions, decreased steric hindrance, and increased surface roughness can be achieved from a high density of DNA that is bound to the surface of nanomaterials, resulting in a higher affinity for complementary DNA and other targets. In addition, this high density of DNA causes a high local salt concentration and negative charge density, which can prevent DNA degradation. For example, DNAzymes assembled on gold nanoparticles can effectively catalyze chemical reactions even in living cells. And it has been confirmed that DNA-nanomaterial complexes can enter cells more easily than free single

Lipofection: a highly efficient, lipid-mediated DNA-transfection procedure.

OpenAIRE

Felgner, P L; Gadek, T R; Holm, M; Roman, R; Chan, H W; Wenz, M; Northrop, J P; Ringold, G M; Danielsen, M

1987-01-01

A DNA-transfection protocol has been developed that makes use of a synthetic cationic lipid, N-[1-(2,3-dioleyloxy)propyl]-N,N,N-trimethylammonium chloride (DOTMA). Small unilamellar liposomes containing DOTMA interact spontaneously with DNA to form lipid-DNA complexes with 100% entrapment of the DNA, DOTMA facilitates fusion of the complex with the plasma membrane of tissue culture cells, resulting in both uptake and expression of the DNA. The technique is simple, highly reproducible, and eff...

DNA condensation by partially acetylated poly(amido amine) dendrimers: effects of dendrimer charge density on complex formation.

Science.gov (United States)

Yu, Shi; Li, Ming-Hsin; Choi, Seok Ki; Baker, James R; Larson, Ronald G

2013-09-03

The ability of poly(amido amine) (or PAMAM) dendrimers to condense semiflexible dsDNA and penetrate cell membranes gives them great potential in gene therapy and drug delivery but their high positive surface charge makes them cytotoxic. Here, we describe the effects of partial neutralization by acetylation on DNA condensation using light scattering, circular dichroism, and single molecule imaging of dendrimer-DNA complexes combed onto surfaces and tethered to those surfaces under flow. We find that DNA can be condensed by generation-five (G5) dendrimers even when the surface charges are more than 65% neutralized, but that such dendrimers bind negligibly when an end-tethered DNA is stretched in flow. We also find that when fully charged dendrimers are introduced by flow to end-tethered DNA, all DNA molecules become equally highly coated with dendrimers at a rate that becomes very fast at high dendrimer concentration, and that dendrimers remain bound during subsequent flow of dendrimer-free buffer. These results suggest that the presence of dendrimer-free DNA coexisting with dendrimer-bound DNA after bulk mixing of the two in solution may result from diffusion-limited irreversible dendrimer-DNA binding, rather than, or in addition to, the previously proposed cooperative binding mechanism of dendrimers to DNA.

DNA Condensation by Partially Acetylated Poly(amido amine Dendrimers: Effects of Dendrimer Charge Density on Complex Formation

Directory of Open Access Journals (Sweden)

Ronald G. Larson

2013-09-01

Full Text Available The ability of poly(amido amine (or PAMAM dendrimers to condense semiflexible dsDNA and penetrate cell membranes gives them great potential in gene therapy and drug delivery but their high positive surface charge makes them cytotoxic. Here, we describe the effects of partial neutralization by acetylation on DNA condensation using light scattering, circular dichroism, and single molecule imaging of dendrimer-DNA complexes combed onto surfaces and tethered to those surfaces under flow. We find that DNA can be condensed by generation-five (G5 dendrimers even when the surface charges are more than 65% neutralized, but that such dendrimers bind negligibly when an end-tethered DNA is stretched in flow. We also find that when fully charged dendrimers are introduced by flow to end-tethered DNA, all DNA molecules become equally highly coated with dendrimers at a rate that becomes very fast at high dendrimer concentration, and that dendrimers remain bound during subsequent flow of dendrimer-free buffer. These results suggest that the presence of dendrimer-free DNA coexisting with dendrimer-bound DNA after bulk mixing of the two in solution may result from diffusion-limited irreversible dendrimer-DNA binding, rather than, or in addition to, the previously proposed cooperative binding mechanism of dendrimers to DNA.

High-speed detection of DNA translocation in nanopipettes

Science.gov (United States)

Fraccari, Raquel L.; Ciccarella, Pietro; Bahrami, Azadeh; Carminati, Marco; Ferrari, Giorgio; Albrecht, Tim

2016-03-01

We present a high-speed electrical detection scheme based on a custom-designed CMOS amplifier which allows the analysis of DNA translocation in glass nanopipettes on a microsecond timescale. Translocation of different DNA lengths in KCl electrolyte provides a scaling factor of the DNA translocation time equal to p = 1.22, which is different from values observed previously with nanopipettes in LiCl electrolyte or with nanopores. Based on a theoretical model involving electrophoresis, hydrodynamics and surface friction, we show that the experimentally observed range of p-values may be the result of, or at least be affected by DNA adsorption and friction between the DNA and the substrate surface.We present a high-speed electrical detection scheme based on a custom-designed CMOS amplifier which allows the analysis of DNA translocation in glass nanopipettes on a microsecond timescale. Translocation of different DNA lengths in KCl electrolyte provides a scaling factor of the DNA translocation time equal to p = 1.22, which is different from values observed previously with nanopipettes in LiCl electrolyte or with nanopores. Based on a theoretical model involving electrophoresis, hydrodynamics and surface friction, we show that the experimentally observed range of p-values may be the result of, or at least be affected by DNA adsorption and friction between the DNA and the substrate surface. Electronic supplementary information (ESI) available: Gel electrophoresis confirming lengths and purity of DNA samples, comparison between Axopatch 200B and custom-built setup, comprehensive low-noise amplifier characterization, representative I-V curves of nanopipettes used, typical scatter plots of τ vs. peak amplitude for the four LDNA's used, table of most probable τ values, a comparison between different fitting models for the DNA translocation time distribution, further details on the stochastic numerical simulation of the scaling statistics and the derivation of the extended

Spontaneous magnetization in high-density quark matter

DEFF Research Database (Denmark)

Tsue, Yasuhiko; da Providência, João; Providência, Constanca

2015-01-01

It is shown that spontaneous magnetization occurs due to the anomalous magnetic moments of quarks in high-density quark matter under the tensor-type four-point interaction. The spin polarized condensate for each flavor of quark appears at high baryon density, which leads to the spontaneous magnet...

High Energy Density Sciences with High Power Lasers at SACLA

Science.gov (United States)

Kodama, Ryosuke

2013-10-01

One of the interesting topics on high energy density sciences with high power lasers is creation of extremely high pressures in material. The pressures of more than 0.1 TPa are the energy density corresponding to the chemical bonding energy, resulting in expectation of dramatic changes in the chemical reactions. At pressures of more than TPa, most of material would be melted on the shock Hugoniot curve. However, if the temperature is less than 1eV or lower than a melting point at pressures of more than TPa, novel solid states of matter must be created through a pressured phase transition. One of the interesting materials must be carbon. At pressures of more than TPa, the diamond structure changes to BC and cubic at more than 3TPa. To create such novel states of matter, several kinds of isentropic-like compression techniques are being developed with high power lasers. To explore the ``Tera-Pascal Science,'' now we have a new tool which is an x-ray free electron laser as well as high power lasers. The XFEL will clear the details of the HED states and also efficiently create hot dense matter. We have started a new project on high energy density sciences using an XFEL (SACLA) in Japan, which is a HERMES (High Energy density Revolution of Matter in Extreme States) project.

The high density and high βpol disruption mechanism on TFTR

International Nuclear Information System (INIS)

Fredrickson, E.D.; Manickam, J.; McGuire, K.M.; Monticello, D.; Nagayama, Y.; Park, W.; Taylor, G.

1992-01-01

Studies of disruptions on TFTR have been extended to include high density disruptions as well as the high β pol disruptions. The data strongly suggests that the (m,n)=(1,1) mode plays an important role in both types of disruptions. Further, for the first time, it is unambiguously shown, using a fast electron cyclotron emission (ECE) instrument for the electron temperature profile measurements, that the (m,n)=(1,1) precursor to the high density disruptions has a 'cold bubble' structure. The precursor to the major disruption at high density resembles the 'vacuum bubble' model of disruptions first proposed by Kadomtsev and Pogutse. (author) 2 refs., 2 figs

Electrode/Dielectric Strip For High-Energy-Density Capacitor

Science.gov (United States)

Yen, Shiao-Ping S.

1994-01-01

Improved unitary electrode/dielectric strip serves as winding in high-energy-density capacitor in pulsed power supply. Offers combination of qualities essential for high energy density: high permittivity of dielectric layers, thinness, and high resistance to breakdown of dielectric at high electric fields. Capacitors with strip material not impregnated with liquid.

New expanded bed adsorbents for the recovery of DNA

DEFF Research Database (Denmark)

Theodossiou, Irini; Olander, M. A.; Sondergaard, M.

2000-01-01

A 20-40 mum pellicular high density (similar to3.7 g cm(-3)) expanded bed material has been designed for the capture of DNA and other large macromolecules. Anion exchangers fashioned out of these supports exhibited dramatically enhanced DNA binding capacities over commercial anion exchange...

DNA Nucleotides Detection via capacitance properties of Graphene

Science.gov (United States)

Khadempar, Nahid; Berahman, Masoud; Yazdanpanah, Arash

2016-05-01

In the present paper a new method is suggested to detect the DNA nucleotides on a first-principles calculation of the electronic features of DNA bases which chemisorbed to a graphene sheet placed between two gold electrodes in a contact-channel-contact system. The capacitance properties of graphene in the channel are surveyed using non-equilibrium Green's function coupled with the Density Functional Theory. Thus, the capacitance properties of graphene are theoretically investigated in a biological environment, and, using a novel method, the effect of the chemisorbed DNA nucleotides on electrical charges on the surface of graphene is deciphered. Several parameters in this method are also extracted including Electrostatic energy, Induced density, induced electrostatic potential, Electron difference potential and Electron difference density. The qualitative and quantitative differences among these parameters can be used to identify DNA nucleotides. Some of the advantages of this approach include its ease and high accuracy. What distinguishes the current research is that it is the first experiment to investigate the capacitance properties of gaphene changes in the biological environment and the effect of chemisorbed DNA nucleotides on the surface of graphene on the charge.

Laser fusion and high energy density science

International Nuclear Information System (INIS)

Kodama, Ryosuke

2005-01-01

High-power laser technology is now opening a variety of new fields of science and technology using laser-produced plasmas. The laser plasma is now recognized as one of the important tools for the investigation and application of matter under extreme conditions, which is called high energy density science. This chapter shows a variety of applications of laser-produced plasmas as high energy density science. One of the more attractive industrial and science applications is the generation of intense pulse-radiation sources, such as the generation of electro-magnetic waves in the ranges of EUV (Extreme Ultra Violet) to gamma rays and laser acceleration of charged particles. The laser plasma is used as an energy converter in this regime. The fundamental science applications of high energy density physics are shown by introducing laboratory astrophysics, the equation of state of high pressure matter, including warm dense matter and nuclear science. Other applications are also presented, such as femto-second laser propulsion and light guiding. Finally, a new systematization is proposed to explore the possibility of the high energy density plasma application, which is called high energy plasma photonics''. This is also exploration of the boundary regions between laser technology and beam optics based on plasma physics. (author)

Operation and control of high density tokamak reactors

International Nuclear Information System (INIS)

Attenberger, S.E.; McAlees, D.G.

1976-01-01

The incentive for high density operation of a tokamak reactor was discussed. It is found that high density permits ignition in a relatively small, moderately elongated plasma with a moderate magnetic field strength. Under these conditions, neutron wall loadings approximately 4 MW/m 2 must be tolerated. The sensitivity analysis with respect to impurity effects shows that impurity control will most likely be necessary to achieve the desired plasma conditions. The charge exchange sputtered impurities are found to have an important effect so that maintaining a low neutral density in the plasma is critical. If it is assumed that neutral beams will be used to heat the plasma to ignition, high energy injection is required (approximately 250 keV) when heating is accompished at full density. A scenario is outlined where the ignition temperature is established at low density and then the fueling rate is increased to attain ignition. This approach may permit beams with energies being developed for use in TFTR to be successfully used to heat a high density device of the type described here to ignition

High density high-TC ceramic superconductors by hot pressing

International Nuclear Information System (INIS)

Mak, S.; Chaklader, A.C.D.

1989-01-01

High density and high T C superconductor specimens, YBa 2 Cu 3 O x , have been produced by hot-pressing. The factors studied are the effect of hot pressing on the density, the oxygen stoichiometry, the crystal structure, and the critical temperature. Hot pressing followed by heat treatment increased the density of the specimen to 93%. The hot pressing itself did not significantly affect the oxygen content in the specimen, and although the crystal structure appeared to be orthorhombic, the specimens were not superconducting above liquid nitrogen temperature. The superconductivity was restored after head treatment in oxygen. The highest critical temperature (T C ) of the hot pressed pellets was 82K, which was slightly lower than the T C that could be obtained with the cold pressed/sintered pellets. (6 refs., 5 figs., tab.)

Feedback controlled, reactor relevant, high-density, high-confinement scenarios at ASDEX Upgrade

Science.gov (United States)

Lang, P. T.; Blanken, T. C.; Dunne, M.; McDermott, R. M.; Wolfrum, E.; Bobkov, V.; Felici, F.; Fischer, R.; Janky, F.; Kallenbach, A.; Kardaun, O.; Kudlacek, O.; Mertens, V.; Mlynek, A.; Ploeckl, B.; Stober, J. K.; Treutterer, W.; Zohm, H.; ASDEX Upgrade Team

2018-03-01

One main programme topic at the ASDEX Upgrade all-metal-wall tokamak is development of a high-density regime with central densities at reactor grade level while retaining high-confinement properties. This required development of appropriate control techniques capable of coping with the pellet tool, a powerful means of fuelling but one which presented challenges to the control system for handling of related perturbations. Real-time density profile control was demonstrated, raising the core density well above the Greenwald density while retaining the edge density in order to avoid confinement losses. Recently, a new model-based approach was implemented that allows direct control of the central density. Investigations focussed first on the N-seeding scenario owing to its proven potential to yield confinement enhancements. Combining pellets and N seeding was found to improve the divertor buffering further and enhance the operational range accessible. For core densities up to about the Greenwald density, a clear improvement with respect to the non-seeding reference was achieved; however, at higher densities this benefit is reduced. This behaviour is attributed to recurrence of an outward shift of the edge density profile, resulting in a reduced peeling-ballooning stability. This is similar to the shift seen during strong gas puffing, which is required to prevent impurity influx in ASDEX Upgrade. First tests indicate that highly-shaped plasma configurations like the ITER base-line scenario, respond very well to pellet injection, showing efficient fuelling with no measurable impact on the edge density profile.

High Density Digital Data Storage System

Science.gov (United States)

Wright, Kenneth D., II; Gray, David L.; Rowland, Wayne D.

1991-01-01

The High Density Digital Data Storage System was designed to provide a cost effective means for storing real-time data from the field-deployable digital acoustic measurement system. However, the high density data storage system is a standalone system that could provide a storage solution for many other real time data acquisition applications. The storage system has inputs for up to 20 channels of 16-bit digital data. The high density tape recorders presently being used in the storage system are capable of storing over 5 gigabytes of data at overall transfer rates of 500 kilobytes per second. However, through the use of data compression techniques the system storage capacity and transfer rate can be doubled. Two tape recorders have been incorporated into the storage system to produce a backup tape of data in real-time. An analog output is provided for each data channel as a means of monitoring the data as it is being recorded.

Environmental DNA as a new method for early detection of New Zealand mudsnails (Potamopyrgus antipodarum)

Science.gov (United States)

Goldberg, Caren S.; Sepulveda, Adam; Ray, Andrew; Baumgardt, Jeremy A.; Waits, Lisette P.

2013-01-01

Early detection of aquatic invasive species is a critical task for management of aquatic ecosystems. This task is hindered by the difficulty and cost of surveying aquatic systems thoroughly. The New Zealand mudsnail (Potamopyrgus antipodarum) is a small, invasive parthenogenic mollusk that can reach very high population densities and severely affects ecosystem functioning. To assist in the early detection of this invasive species, we developed and validated a highly sensitive environmental deoxyribonucleic acid (eDNA) assay. We used a dose–response laboratory experiment to investigate the relationship between New Zealand mudsnail density and eDNA detected through time. We documented that as few as 1 individual in 1.5 L of water for 2 d could be detected with this method, and that eDNA from this species may remain detectable for 21 to 44 d after mudsnail removal. We used the eDNA method to confirm the presence of New Zealand mudsnail eDNA at densities as low as 11 to 144 snails/m2 in a eutrophic 5th-order river. Combined, these results demonstrate the high potential for eDNA surveys to assist with early detection of a widely distributed invasive aquatic invertebrate.

Effects of charge density and hydrophobicity of poly(amido amine)s for non-viral gene delivery

NARCIS (Netherlands)

Piest, Martin; Engbersen, Johannes F.J.

2010-01-01

High cationic charge densities in polymeric vectors result in tight DNA condensation, leading to small highly positively charged polyplexes which show generally high cellular uptake in vitro. However, high cationic charge densities also introduce membrane-disruptive properties to the polymers,

High-density-plasma diagnostics in magnetic-confinement fusion

International Nuclear Information System (INIS)

Jahoda, F.C.

1982-01-01

The lectures will begin by defining high density in the context of magnetic confinement fusion research and listing some alternative reactor concepts, ranging from n/sub e/ approx. 2 x 10 14 cm -3 to several orders of magnitude greater, that offer potential advantages over the main-line, n/sub e/ approx. 1 x 10 14 cm -3 , Tokamak reactor designs. The high density scalings of several major diagnostic techniques, some favorable and some disadvantageous, will be discussed. Special emphasis will be given to interferometric methods, both electronic and photographic, for which integral n/sub e/dl measurements and associated techniques are accessible with low wavelength lasers. Reactor relevant experience from higher density, smaller dimension devices exists. High density implies high β, which implies economies of scale. The specialized features of high β diagnostics will be discussed

Probing topological relations between high-density and low-density regions of 2MASS with hexagon cells

Energy Technology Data Exchange (ETDEWEB)

Wu, Yongfeng [American Physical Society, San Diego, CA (United States); Xiao, Weike, E-mail: yongfeng.wu@maine.edu [Department of Astronautics Engineering, Harbin Institute of Technology, P.O. Box 345, Heilongjiang Province 150001 (China)

2014-02-01

We introduced a new two-dimensional (2D) hexagon technique for probing the topological structure of the universe in which we mapped regions of the sky with high and low galaxy densities onto a 2D lattice of hexagonal unit cells. We defined filled cells as corresponding to high-density regions and empty cells as corresponding to low-density regions. The numbers of filled cells and empty cells were kept the same by controlling the size of the cells. By analyzing the six sides of each hexagon, we could obtain and compare the statistical topological properties of high-density and low-density regions of the universe in order to have a better understanding of the evolution of the universe. We applied this hexagonal method to Two Micron All Sky Survey data and discovered significant topological differences between the high-density and low-density regions. Both regions had significant (>5σ) topological shifts from both the binomial distribution and the random distribution.

Lipofection: A Highly Efficient, Lipid-Mediated DNA-Transfection Procedure

Science.gov (United States)

Felgner, Philip L.; Gadek, Thomas R.; Holm, Marilyn; Roman, Richard; Chan, Hardy W.; Wenz, Michael; Northrop, Jeffrey P.; Ringold, Gordon M.; Danielsen, Mark

1987-11-01

A DNA-transfection protocol has been developed that makes use of a synthetic cationic lipid, N-[1-(2,3-dioleyloxy)propyl]-N,N,N-trimethylammonium chloride (DOTMA). Small unilamellar liposomes containing DOTMA interact spontaneously with DNA to form lipid-DNA complexes with 100% entrapment of the DNA. DOTMA facilitates fusion of the complex with the plasma membrane of tissue culture cells, resulting in both uptake and expression of the DNA. The technique is simple, highly reproducible, and effective for both transient and stable expression of transfected DNA. Depending upon the cell line, lipofection is from 5- to >100-fold more effective than either the calcium phosphate or the DEAE-dextran transfection technique.

High-Throughput DNA sequencing of ancient wood.

Science.gov (United States)

Wagner, Stefanie; Lagane, Frédéric; Seguin-Orlando, Andaine; Schubert, Mikkel; Leroy, Thibault; Guichoux, Erwan; Chancerel, Emilie; Bech-Hebelstrup, Inger; Bernard, Vincent; Billard, Cyrille; Billaud, Yves; Bolliger, Matthias; Croutsch, Christophe; Čufar, Katarina; Eynaud, Frédérique; Heussner, Karl Uwe; Köninger, Joachim; Langenegger, Fabien; Leroy, Frédéric; Lima, Christine; Martinelli, Nicoletta; Momber, Garry; Billamboz, André; Nelle, Oliver; Palomo, Antoni; Piqué, Raquel; Ramstein, Marianne; Schweichel, Roswitha; Stäuble, Harald; Tegel, Willy; Terradas, Xavier; Verdin, Florence; Plomion, Christophe; Kremer, Antoine; Orlando, Ludovic

2018-03-01

Reconstructing the colonization and demographic dynamics that gave rise to extant forests is essential to forecasts of forest responses to environmental changes. Classical approaches to map how population of trees changed through space and time largely rely on pollen distribution patterns, with only a limited number of studies exploiting DNA molecules preserved in wooden tree archaeological and subfossil remains. Here, we advance such analyses by applying high-throughput (HTS) DNA sequencing to wood archaeological and subfossil material for the first time, using a comprehensive sample of 167 European white oak waterlogged remains spanning a large temporal (from 550 to 9,800 years) and geographical range across Europe. The successful characterization of the endogenous DNA and exogenous microbial DNA of 140 (~83%) samples helped the identification of environmental conditions favouring long-term DNA preservation in wood remains, and started to unveil the first trends in the DNA decay process in wood material. Additionally, the maternally inherited chloroplast haplotypes of 21 samples from three periods of forest human-induced use (Neolithic, Bronze Age and Middle Ages) were found to be consistent with those of modern populations growing in the same geographic areas. Our work paves the way for further studies aiming at using ancient DNA preserved in wood to reconstruct the micro-evolutionary response of trees to climate change and human forest management. © 2018 John Wiley & Sons Ltd.

Towards high-density matter with relativistic heavy-ion collisions

International Nuclear Information System (INIS)

Nagamiya, Shoji.

1990-04-01

Recent progress in nucleus-nucleus collisions at BNL and CERN suggests a hint that the formation of high-density nuclear matter could be possible with relativistic heavy-ion beams. What is the maximum density that can be achieved by heavy-ion collisions? Are there data which show evidence or hints on the formation of high density matter? Why is the research of high-density interesting? How about the future possibilities on this subject? These points are discussed. (author)

New aspects of high energy density plasma

International Nuclear Information System (INIS)

Hotta, Eiki

2005-10-01

The papers presented at the symposium on 'New aspects of high energy density plasma' held at National Institute for Fusion Science are collected in this proceedings. The papers reflect the present status and recent progress in the experiments and theoretical works on high energy density plasma produced by pulsed power technology. The 13 of the presented papers are indexed individually. (J.P.N.)

High current density ion source

International Nuclear Information System (INIS)

King, H.J.

1977-01-01

A high-current-density ion source with high total current is achieved by individually directing the beamlets from an electron bombardment ion source through screen and accelerator electrodes. The openings in these screen and accelerator electrodes are oriented and positioned to direct the individual beamlets substantially toward a focus point. 3 figures, 1 table

Coupling amplified DNA from flow-sorted chromosomes to high-density SNP mapping in barley

Czech Academy of Sciences Publication Activity Database

Šimková, Hana; Svensson, J.T.; Condamine, P.; Hřibová, Eva; Suchánková, Pavla; Bhat, P.R.; Bartoš, Jan; Šafář, Jan; Close, T.J.; Doležel, Jaroslav

2008-01-01

Roč. 9, č. 294 (2008), s. 1-9 ISSN 1471-2164 R&D Projects: GA ČR GD521/05/H013; GA MŠk ME 884; GA MŠk(CZ) LC06004 Institutional research plan: CEZ:AV0Z50380511 Keywords : Flow cytometry * DNA amplification * Hordeum vulgare L. Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.926, year: 2008

Plasma Photonic Devices for High Energy Density Science

International Nuclear Information System (INIS)

Kodama, R.

2005-01-01

High power laser technologies are opening a variety of attractive fields of science and technology using high energy density plasmas such as plasma physics, laboratory astrophysics, material science, nuclear science including medical applications and laser fusion. The critical issues in the applications are attributed to the control of intense light and enormous density of charged particles including efficient generation of the particles such as MeV electrons and protons with a current density of TA/cm2. Now these application possibilities are limited only by the laser technology. These applications have been limited in the control of the high power laser technologies and their optics. However, if we have another device consisted of the 4th material, i.e. plasma, we will obtain a higher energy density condition and explore the application possibilities, which could be called high energy plasma device. One of the most attractive devices has been demonstrated in the fast ignition scheme of the laser fusion, which is cone-guiding of ultra-intense laser light in to high density regions1. This is one of the applications of the plasma device to control the ultra-intense laser light. The other role of the devices consisted of transient plasmas is control of enormous energy-density particles in a fashion analogous to light control with a conventional optical device. A plasma fibre (5?m/1mm), as one example of the devices, has guided and deflected the high-density MeV electrons generated by ultra-intense laser light 2. The electrons have been well collimated with either a lens-like plasma device or a fibre-like plasma, resulting in isochoric heating and creation of ultra-high pressures such as Giga bar with an order of 100J. Plasmas would be uniquely a device to easily control the higher energy density particles like a conventional optical device as well as the ultra-intense laser light, which could be called plasma photonic device. (Author)

Models for Experimental High Density Housing

Science.gov (United States)

Bradecki, Tomasz; Swoboda, Julia; Nowak, Katarzyna; Dziechciarz, Klaudia

2017-10-01

The article presents the effects of research on models of high density housing. The authors present urban projects for experimental high density housing estates. The design was based on research performed on 38 examples of similar housing in Poland that have been built after 2003. Some of the case studies show extreme density and that inspired the researchers to test individual virtual solutions that would answer the question: How far can we push the limits? The experimental housing projects show strengths and weaknesses of design driven only by such indexes as FAR (floor attenuation ratio - housing density) and DPH (dwellings per hectare). Although such projects are implemented, the authors believe that there are reasons for limits since high index values may be in contradiction to the optimum character of housing environment. Virtual models on virtual plots presented by the authors were oriented toward maximising the DPH index and DAI (dwellings area index) which is very often the main driver for developers. The authors also raise the question of sustainability of such solutions. The research was carried out in the URBAN model research group (Gliwice, Poland) that consists of academic researchers and architecture students. The models reflect architectural and urban regulations that are valid in Poland. Conclusions might be helpful for urban planners, urban designers, developers, architects and architecture students.

Fibre autoradiography of repair and replication in DNA from single cells: the effect of DNA synthesis inhibitors

Energy Technology Data Exchange (ETDEWEB)

Ockey, C.H.

1982-04-01

DNA fibre autoradiography, after incorporation of high specific activity /sup 3/H-thymidine and /sup 3/H-deoxycytidine, has been used to investigate repair in DNA fibres from single cells following UV, or methyl-methane sulphonate (MMS) treatment. Asynchronously growing human fibroblasts, leucocytes, and HeLa cells at different phases of the cell cycle have been investigated. Isotope incorporation in repair could be differentiated from that involved in replication by the distribution and density of silver grains along the DNA fibres. Grain distribution due to repair was continuous over long stretches of the fibres and was at a low density, occasionally interspersed with short slightly denser segments. Replication labelling on the other hand, was dense and usually in short tandem segments. Repair labelling was of a similar overall density in fibres from a single cell, but differed in intensity from cell to cell. In mutagen treated Go (leucocytes) of G/sub 1/ (HeLa cells), repair labelling was not increased by the presence of the DNA inhibitors, hydroxyurea (HU) or 5-fluorodeoxyuridine (FUdR). Repair was not detectable in S cells however without the use of these inhibitors to reduce endogenous nucleoside production. FUdR enhanced the repair labelling in S cells only slightly, while HU increased it beyond that observed in UV irradiated, HU treated, G/sub 1/ cells. The intensity of repair labelling in fibres from mutagen treated S cells appears to be proportional to the degree of reduction of DNA chain elongation in replicons.

High density operation in pulsator

International Nuclear Information System (INIS)

Klueber, O.; Cannici, B.; Engelhardt, W.; Gernhardt, J.; Glock, E.; Karger, F.; Lisitano, G.; Mayer, H.M.; Meisel, D.; Morandi, P.

1976-03-01

This report summarizes the results of experiments at high electron densities (>10 14 cm -3 ) which have been achieved by pulsed gas inflow during the discharge. At these densities a regime is established which is characterized by βsub(p) > 1, nsub(i) approximately nsub(e), Tsub(i) approximately Tsub(e) and tausub(E) proportional to nsub(e). Thus the toroidal magnetic field contributes considerably to the plasma confinement and the ions constitute almost half of the plasma pressure. Furthermore, the confinement is appreciably improved and the plasma becomes impermeable to hot neutrals. (orig.) [de

Flexible asymmetric supercapacitors with high energy and high power density in aqueous electrolytes

Science.gov (United States)

Cheng, Yingwen; Zhang, Hongbo; Lu, Songtao; Varanasi, Chakrapani V.; Liu, Jie

2013-01-01

Supercapacitors with both high energy and high power densities are critical for many practical applications. In this paper, we discuss the design and demonstrate the fabrication of flexible asymmetric supercapacitors based on nanocomposite electrodes of MnO2, activated carbon, carbon nanotubes and graphene. The combined unique properties of each of these components enable highly flexible and mechanically strong films that can serve as electrodes directly without using any current collectors or binders. Using these flexible electrodes and a roll-up approach, asymmetric supercapacitors with 2 V working voltage were successfully fabricated. The fabricated device showed excellent rate capability, with 78% of the original capacitance retained when the scan rate was increased from 2 mV s-1 to 500 mV s-1. Owing to the unique composite structure, these supercapacitors were able to deliver high energy density (24 W h kg-1) under high power density (7.8 kW kg-1) conditions. These features could enable supercapacitor based energy storage systems to be very attractive for a variety of critical applications, such as the power sources in hybrid electric vehicles and the back-up powers for wind and solar energy, where both high energy density and high power density are required.Supercapacitors with both high energy and high power densities are critical for many practical applications. In this paper, we discuss the design and demonstrate the fabrication of flexible asymmetric supercapacitors based on nanocomposite electrodes of MnO2, activated carbon, carbon nanotubes and graphene. The combined unique properties of each of these components enable highly flexible and mechanically strong films that can serve as electrodes directly without using any current collectors or binders. Using these flexible electrodes and a roll-up approach, asymmetric supercapacitors with 2 V working voltage were successfully fabricated. The fabricated device showed excellent rate capability, with 78% of

Curcumin chemosensitizes 5-fluorouracil resistant MMR-deficient human colon cancer cells in high density cultures.

Directory of Open Access Journals (Sweden)

Mehdi Shakibaei

Full Text Available OBJECTIVE: Treatment of colorectal cancer (CRC remains a clinical challenge, as more than 15% of patients are resistant to 5-Fluorouracil (5-FU-based chemotherapeutic regimens, and tumor recurrence rates can be as high as 50-60%. Cancer stem cells (CSC are capable of surviving conventional chemotherapies that permits regeneration of original tumors. Therefore, we investigated the effectiveness of 5-FU and plant polyphenol (curcumin in context of DNA mismatch repair (MMR status and CSC activity in 3D cultures of CRC cells. METHODS: High density 3D cultures of CRC cell lines HCT116, HCT116+ch3 (complemented with chromosome 3 and their corresponding isogenic 5-FU-chemo-resistant derivative clones (HCT116R, HCT116+ch3R were treated with 5-FU either without or with curcumin in time- and dose-dependent assays. RESULTS: Pre-treatment with curcumin significantly enhanced the effect of 5-FU on HCT116R and HCR116+ch3R cells, in contrast to 5-FU alone as evidenced by increased disintegration of colonospheres, enhanced apoptosis and by inhibiting their growth. Curcumin and/or 5-FU strongly affected MMR-deficient CRC cells in high density cultures, however MMR-proficient CRC cells were more sensitive. These effects of curcumin in enhancing chemosensitivity to 5-FU were further supported by its ability to effectively suppress CSC pools as evidenced by decreased number of CSC marker positive cells, highlighting the suitability of this 3D culture model for evaluating CSC marker expression in a close to vivo setting. CONCLUSION: Our results illustrate novel and previously unrecognized effects of curcumin in enhancing chemosensitization to 5-FU-based chemotherapy on DNA MMR-deficient and their chemo-resistant counterparts by targeting the CSC sub-population. (246 words in abstract.

Curcumin chemosensitizes 5-fluorouracil resistant MMR-deficient human colon cancer cells in high density cultures.

Science.gov (United States)

Shakibaei, Mehdi; Buhrmann, Constanze; Kraehe, Patricia; Shayan, Parviz; Lueders, Cora; Goel, Ajay

2014-01-01

Treatment of colorectal cancer (CRC) remains a clinical challenge, as more than 15% of patients are resistant to 5-Fluorouracil (5-FU)-based chemotherapeutic regimens, and tumor recurrence rates can be as high as 50-60%. Cancer stem cells (CSC) are capable of surviving conventional chemotherapies that permits regeneration of original tumors. Therefore, we investigated the effectiveness of 5-FU and plant polyphenol (curcumin) in context of DNA mismatch repair (MMR) status and CSC activity in 3D cultures of CRC cells. High density 3D cultures of CRC cell lines HCT116, HCT116+ch3 (complemented with chromosome 3) and their corresponding isogenic 5-FU-chemo-resistant derivative clones (HCT116R, HCT116+ch3R) were treated with 5-FU either without or with curcumin in time- and dose-dependent assays. Pre-treatment with curcumin significantly enhanced the effect of 5-FU on HCT116R and HCR116+ch3R cells, in contrast to 5-FU alone as evidenced by increased disintegration of colonospheres, enhanced apoptosis and by inhibiting their growth. Curcumin and/or 5-FU strongly affected MMR-deficient CRC cells in high density cultures, however MMR-proficient CRC cells were more sensitive. These effects of curcumin in enhancing chemosensitivity to 5-FU were further supported by its ability to effectively suppress CSC pools as evidenced by decreased number of CSC marker positive cells, highlighting the suitability of this 3D culture model for evaluating CSC marker expression in a close to vivo setting. Our results illustrate novel and previously unrecognized effects of curcumin in enhancing chemosensitization to 5-FU-based chemotherapy on DNA MMR-deficient and their chemo-resistant counterparts by targeting the CSC sub-population. (246 words in abstract).

Some recent efforts toward high density implosions

International Nuclear Information System (INIS)

McClellan, G.E.

1980-01-01

Some recent Livermore efforts towards achieving high-density implosions are presented. The implosion dynamics necessary to compress DT fuel to 10 to 100 times liquid density are discussed. Methods of diagnosing the maximum DT density for a specific design are presented along with results to date. The dynamics of the double-shelled target with an exploding outer shell are described, and some preliminary experimental results are presented

Improved GAMMA 10 tandem mirror confinement in high density plasma

International Nuclear Information System (INIS)

Yatsu, K.; Cho, T.; Higaki, H.; Hirata, M.; Hojo, H.; Ichimura, M.; Ishii, K.; Ishimoto, Y.; Itakura, A.; Katanuma, I.; Kohagura, J.; Minami, R.; Nakashima, Y.; Numakura, T.; Saito, T.; Saosaki, S.; Takemura, Y.; Tatematsu, Y.; Yoshida, M.; Yoshikawa, M.

2003-01-01

GAMMA 10 experiments have advanced in high density experiments after the last IAEA fusion energy conference in 2000 where we reported the production of the high density plasma through use of ion cyclotron range of frequency heating at a high harmonic frequency and neutral beam injection in the anchor cells. However, the diamagnetic signal of the plasma decreased when electron cyclotron resonance heating was applied for the potential formation. Recently a high density plasma has been obtained without degradation of the diamagnetic signal and with much improved reproducibility than before. The high density plasma was attained through adjustment of the spacing of the conducting plates installed in the anchor transition regions. The potential confinement of the plasma has been extensively studied. Dependences of the ion confinement time, ion-energy confinement time and plasma confining potential on plasma density were obtained for the first time in the high density region up to a density of 4x10 18 m -3 . (author)

Genomotyping of Pseudomonas putida strains using P. putida KT2440-based high-density DNA microarrays: Implications for transcriptomics studies

NARCIS (Netherlands)

Ballerstedt, H.; Volkers, R.J.M.; Mars, A.E.; Hallsworth, J.E.; Santos, V.A.M.D.; Puchalka, J.; Duuren, J. van; Eggink, G.; Timmis, K.N.; Bont, J.A.M. de; Wery, J.

2007-01-01

Pseudomonas putida KT2440 is the only fully sequenced P. putida strain. Thus, for transcriptomics and proteomics studies with other P. putida strains, the P. putida KT2440 genomic database serves as standard reference. The utility of KT2440 whole-genome, high-density oligonucleotide microarrays for

High-density limit of quantum chromodynamics

International Nuclear Information System (INIS)

Alvarez, E.

1983-01-01

By means of a formal expansion of the partition function presumably valid at large baryon densities, the propagator of the quarks is expressed in terms of the gluon propagator. This result is interpreted as implying that correlations between quarks and gluons are unimportant at high enough density, so that a kind of mean-field approximation gives a very accurate description of the physical system

Fueling with edge recycling to high-density in DIII-D

Energy Technology Data Exchange (ETDEWEB)

Leonard, A.W., E-mail: leonard@fusion.gat.com [General Atomics, P.O. Box 85608, San Diego, CA 92186-5608 (United States); Elder, J.D. [University of Toronto Institute of Aerospace Studies, Toronto, Canada M3H 5T6 (Canada); Canik, J.M. [Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN 37831 (United States); Groebner, R.J.; Osborne, T.H. [General Atomics, P.O. Box 85608, San Diego, CA 92186-5608 (United States)

2013-07-15

Pedestal fueling through edge recycling is examined with the interpretive OEDGE code for high-density discharges in DIII-D. A high current, high-density discharge is found to have a similar radial ion flux profile through the pedestal to a lower current, lower density discharge. The higher density discharge, however, has a greater density gradient indicating a pedestal particle diffusion coefficient that scales near linear with 1/I{sub p}. The time dependence of density profile is taken into account in the analysis of a discharge with low frequency ELMs. The time-dependent analysis indicates that the inferred neutral ionization source is inadequate to account for the increase in the density profile between ELMs, implying an inward density convection, or density pinch, near the top of the pedestal.

High efficiency hydrodynamic DNA fragmentation in a bubbling system

NARCIS (Netherlands)

Li, Lanhui; Jin, Mingliang; Sun, Chenglong; Wang, Xiaoxue; Xie, Shuting; Zhou, Guofu; Van Den Berg, Albert; Eijkel, Jan C.T.; Shui, Lingling

2017-01-01

DNA fragmentation down to a precise fragment size is important for biomedical applications, disease determination, gene therapy and shotgun sequencing. In this work, a cheap, easy to operate and high efficiency DNA fragmentation method is demonstrated based on hydrodynamic shearing in a bubbling

Low density, variation in sintered density and high nitrogen in uranium dioxide

International Nuclear Information System (INIS)

Balakrishna, Palanki; Murty, B.N.; Anuradha, M.; Nageshwara Rao, P.; Jayaraj, R.N.; Ganguly, C.

2000-01-01

Low sintered density and density variation in sintered UO 2 were found to have been caused by non uniformity in the granule feed characteristics to the compacting press. The nitrogen impurity content of sintered UO 2 was found to be sintering furnace related and associated with low sintered density pellets. The problems of low density, variation in sintered density and high nitrogen could be solved by the replacement of the prevailing four punch precompaction by a single punch process; by the introduction of a vibro-sieve for the separation of fine particles from the press feed granules; by innovation in the powder feed shoe design for simultaneous and uniform dispensing of powder in all the die holes; by increasing the final compaction pressure and by modifying the gas flows and preheat temperature in the sintering furnace. (author)

High molecular weight DNA assembly in vivo for synthetic biology applications.

Science.gov (United States)

Juhas, Mario; Ajioka, James W

2017-05-01

DNA assembly is the key technology of the emerging interdisciplinary field of synthetic biology. While the assembly of smaller DNA fragments is usually performed in vitro, high molecular weight DNA molecules are assembled in vivo via homologous recombination in the host cell. Escherichia coli, Bacillus subtilis and Saccharomyces cerevisiae are the main hosts used for DNA assembly in vivo. Progress in DNA assembly over the last few years has paved the way for the construction of whole genomes. This review provides an update on recent synthetic biology advances with particular emphasis on high molecular weight DNA assembly in vivo in E. coli, B. subtilis and S. cerevisiae. Special attention is paid to the assembly of whole genomes, such as those of the first synthetic cell, synthetic yeast and minimal genomes.

High throughput nonparametric probability density estimation.

Science.gov (United States)

Farmer, Jenny; Jacobs, Donald

2018-01-01

In high throughput applications, such as those found in bioinformatics and finance, it is important to determine accurate probability distribution functions despite only minimal information about data characteristics, and without using human subjectivity. Such an automated process for univariate data is implemented to achieve this goal by merging the maximum entropy method with single order statistics and maximum likelihood. The only required properties of the random variables are that they are continuous and that they are, or can be approximated as, independent and identically distributed. A quasi-log-likelihood function based on single order statistics for sampled uniform random data is used to empirically construct a sample size invariant universal scoring function. Then a probability density estimate is determined by iteratively improving trial cumulative distribution functions, where better estimates are quantified by the scoring function that identifies atypical fluctuations. This criterion resists under and over fitting data as an alternative to employing the Bayesian or Akaike information criterion. Multiple estimates for the probability density reflect uncertainties due to statistical fluctuations in random samples. Scaled quantile residual plots are also introduced as an effective diagnostic to visualize the quality of the estimated probability densities. Benchmark tests show that estimates for the probability density function (PDF) converge to the true PDF as sample size increases on particularly difficult test probability densities that include cases with discontinuities, multi-resolution scales, heavy tails, and singularities. These results indicate the method has general applicability for high throughput statistical inference.

High-Throughput Analysis of T-DNA Location and Structure Using Sequence Capture.

Science.gov (United States)

Inagaki, Soichi; Henry, Isabelle M; Lieberman, Meric C; Comai, Luca

2015-01-01

Agrobacterium-mediated transformation of plants with T-DNA is used both to introduce transgenes and for mutagenesis. Conventional approaches used to identify the genomic location and the structure of the inserted T-DNA are laborious and high-throughput methods using next-generation sequencing are being developed to address these problems. Here, we present a cost-effective approach that uses sequence capture targeted to the T-DNA borders to select genomic DNA fragments containing T-DNA-genome junctions, followed by Illumina sequencing to determine the location and junction structure of T-DNA insertions. Multiple probes can be mixed so that transgenic lines transformed with different T-DNA types can be processed simultaneously, using a simple, index-based pooling approach. We also developed a simple bioinformatic tool to find sequence read pairs that span the junction between the genome and T-DNA or any foreign DNA. We analyzed 29 transgenic lines of Arabidopsis thaliana, each containing inserts from 4 different T-DNA vectors. We determined the location of T-DNA insertions in 22 lines, 4 of which carried multiple insertion sites. Additionally, our analysis uncovered a high frequency of unconventional and complex T-DNA insertions, highlighting the needs for high-throughput methods for T-DNA localization and structural characterization. Transgene insertion events have to be fully characterized prior to use as commercial products. Our method greatly facilitates the first step of this characterization of transgenic plants by providing an efficient screen for the selection of promising lines.

Highly efficient red electrophosphorescent devices at high current densities

International Nuclear Information System (INIS)

Wu Youzhi; Zhu Wenqing; Zheng Xinyou; Sun, Runguang; Jiang Xueyin; Zhang Zhilin; Xu Shaohong

2007-01-01

Efficiency decrease at high current densities in red electrophosphorescent devices is drastically restrained compared with that from conventional electrophosphorescent devices by using bis(2-methyl-8-quinolinato)4-phenylphenolate aluminum (BAlq) as a hole and exciton blocker. Ir complex, bis(2-(2'-benzo[4,5-α]thienyl) pyridinato-N,C 3' ) iridium (acetyl-acetonate) is used as an emitter, maximum external quantum efficiency (QE) of 7.0% and luminance of 10000cd/m 2 are obtained. The QE is still as high as 4.1% at higher current density J=100mA/cm 2 . CIE-1931 co-ordinates are 0.672, 0.321. A carrier trapping mechanism is revealed to dominate in the process of electroluminescence

Fundamental properties of high-quality carbon nanofoam: from low to high density

Directory of Open Access Journals (Sweden)

Natalie Frese

2016-12-01

Full Text Available Highly uniform samples of carbon nanofoam from hydrothermal sucrose carbonization were studied by helium ion microscopy (HIM, X-ray photoelectron spectroscopy (XPS, and Raman spectroscopy. Foams with different densities were produced by changing the process temperature in the autoclave reactor. This work illustrates how the geometrical structure, electron core levels, and the vibrational signatures change when the density of the foams is varied. We find that the low-density foams have very uniform structure consisting of micropearls with ≈2–3 μm average diameter. Higher density foams contain larger-sized micropearls (≈6–9 μm diameter which often coalesced to form nonspherical μm-sized units. Both, low- and high-density foams are comprised of predominantly sp2-type carbon. The higher density foams, however, show an advanced graphitization degree and a stronger sp3-type electronic contribution, related to the inclusion of sp3 connections in their surface network.

Sputtered thin films for high density tape recording

NARCIS (Netherlands)

Nguyen, L.T.

This thesis describes the investigation of sputtered thin film media for high density tape recording. As discussed in Chapter 1, to meet the tremendous demand of data storage, the density of recording tape has to be increased continuously. For further increasing the bit density the key factors are:

Enzyme controlled glucose auto-delivery for high cell density cultivations in microplates and shake flasks

Directory of Open Access Journals (Sweden)

Casteleijn Marco G

2008-11-01

Full Text Available Abstract Background Here we describe a novel cultivation method, called EnBase™, or enzyme-based-substrate-delivery, for the growth of microorganisms in millilitre and sub-millilitre scale which yields 5 to 20 times higher cell densities compared to standard methods. The novel method can be directly applied in microwell plates and shake flasks without any requirements for additional sensors or liquid supply systems. EnBase is therefore readily applicable for many high throughput applications, such as DNA production for genome sequencing, optimisation of protein expression, production of proteins for structural genomics, bioprocess development, and screening of enzyme and metagenomic libraries. Results High cell densities with EnBase are obtained by applying the concept of glucose-limited fed-batch cultivation which is commonly used in industrial processes. The major difference of the novel method is that no external glucose feed is required, but glucose is released into the growth medium by enzymatic degradation of starch. To cope with the high levels of starch necessary for high cell density cultivation, starch is supplied to the growing culture suspension by continuous diffusion from a storage gel. Our results show that the controlled enzyme-based supply of glucose allows a glucose-limited growth to high cell densities of OD600 = 20 to 30 (corresponding to 6 to 9 g l-1 cell dry weight without the external feed of additional compounds in shake flasks and 96-well plates. The final cell density can be further increased by addition of extra nitrogen during the cultivation. Production of a heterologous triosphosphate isomerase in E. coli BL21(DE3 resulted in 10 times higher volumetric product yield and a higher ratio of soluble to insoluble product when compared to the conventional production method. Conclusion The novel EnBase method is robust and simple-to-apply for high cell density cultivation in shake flasks and microwell plates. The

High-density housing that works for all

Energy Technology Data Exchange (ETDEWEB)

Hasan, Arif

2010-03-15

In an urbanising world, the way people fit into cities is vastly important - socially, economically, environmentally, even psychologically. So density, or the number of people living in a given area, is central to urban design and planning. Both governments and markets tend to get density wrong, leading to overcrowding, urban sprawl or often both. A case in point are the high-rise buildings springing up throughtout urban Asia - perceived as key features of that widely touted concept, the 'world-class city'. While some may offer a viable solution to land pressures and density requirements, many built to house evicted or resettled 'slum' dwellers are a social and economic nightmare - inconveniently sited, overcrowded and costly. New evidence from Karachi, Pakistan, reveals a real alternative. Poor people can create liveable high-density settlements as long as community control, the right technical assistance and flexible designs are in place. A city is surely 'world-class' only when it is cosmopolitan – built to serve all, including the poorest.

High density high performance plasma with internal diffusion barrier in Large Helical Device

International Nuclear Information System (INIS)

Sakamoto, R.; Kobayashi, M.; Miyazawa, J.

2008-10-01

A attractive high density plasma operational regime, namely an internal diffusion barrier (IDB), has been discovered in the intrinsic helical divertor configuration on the Large Helical Device (LHD). The IDB which enables core plasma to access a high density/high pressure regime has been developed. It is revealed that the IDB is reproducibly formed by pellet fueling in the magnetic configurations shifted outward in major radius. Attainable central plasma density exceeds 1x10 21 m -3 . Central pressure reaches 1.5 times atmospheric pressure and the central β value becomes fairly high even at high magnetic field, i.e. β(0)=5.5% at B t =2.57 T. (author)

High density data recording for SSCL linac

International Nuclear Information System (INIS)

VanDeusen, A.L.; Crist, C.

1993-01-01

The Superconducting Super Collider Laboratory and AlliedSignal Aerospace have collaboratively developed a high density data monitoring system for beam diagnostic activities. The 128 channel data system is based on a custom multi-channel high speed digitizer card for the VXI bus. The card is referred to as a Modular Input VXI (MIX) digitizer. Multiple MIX cards are used in the complete system to achieve the necessary high channel density requirements. Each MIX digitizer card also contains programmable signal conditioning, and enough local memory to complete an entire beam scan without assistance from the host processor

Characterization of the high density plasma etching process of CCTO thin films for the fabrication of very high density capacitors

International Nuclear Information System (INIS)

Altamore, C; Tringali, C; Sparta', N; Marco, S Di; Grasso, A; Ravesi, S

2010-01-01

In this work the feasibility of CCTO (Calcium Copper Titanate) patterning by etching process is demonstrated and fully characterized in a hard to etch materials etcher. CCTO sintered in powder shows a giant relative dielectric constant (10 5 ) measured at 1 MHz at room temperature. This feature is furthermore coupled with stability from 10 1 Hz to 10 6 Hz in a wide temperature range (100K - 600K). In principle, this property can allow to fabricate very high capacitance density condenser. Due to its perovskite multi-component structure, CCTO can be considered a hard to etch material. For high density capacitor fabrication, CCTO anisotropic etching is requested by using high density plasma. The behavior of etched CCTO was studied in a HRe- (High Density Reflected electron) plasma etcher using Cl 2 /Ar chemistry. The relationship between the etch rate and the Cl 2 /Ar ratio was also studied. The effects of RF MHz, KHz Power and pressure variation, the impact of HBr addiction to the Cl 2 /Ar chemistry on the CCTO etch rate and on its selectivity to Pt and photo resist was investigated.

Characterization of the high density plasma etching process of CCTO thin films for the fabrication of very high density capacitors

Energy Technology Data Exchange (ETDEWEB)

Altamore, C; Tringali, C; Sparta' , N; Marco, S Di; Grasso, A; Ravesi, S [STMicroelectronics, Industial and Multi-segment Sector R and D, Catania (Italy)

2010-02-15

In this work the feasibility of CCTO (Calcium Copper Titanate) patterning by etching process is demonstrated and fully characterized in a hard to etch materials etcher. CCTO sintered in powder shows a giant relative dielectric constant (10{sup 5}) measured at 1 MHz at room temperature. This feature is furthermore coupled with stability from 10{sup 1} Hz to 10{sup 6} Hz in a wide temperature range (100K - 600K). In principle, this property can allow to fabricate very high capacitance density condenser. Due to its perovskite multi-component structure, CCTO can be considered a hard to etch material. For high density capacitor fabrication, CCTO anisotropic etching is requested by using high density plasma. The behavior of etched CCTO was studied in a HRe- (High Density Reflected electron) plasma etcher using Cl{sub 2}/Ar chemistry. The relationship between the etch rate and the Cl{sub 2}/Ar ratio was also studied. The effects of RF MHz, KHz Power and pressure variation, the impact of HBr addiction to the Cl{sub 2}/Ar chemistry on the CCTO etch rate and on its selectivity to Pt and photo resist was investigated.

Production of enzymatically active recombinant full-length barley high pI alpha-glucosidase of glycoside family 31 by high cell-density fermentation of Pichia pastoris and affinity purification

DEFF Research Database (Denmark)

Næsted, Henrik; Kramhøft, Birte; Lok, F.

2006-01-01

Recombinant barley high pI alpha-glucosidase was produced by high cell-density fermentation of Pichia pastoris expressing the cloned full-length gene. The gene was amplified from a genomic clone and exons (coding regions) were assembled by overlap PCR. The resulting cDNA was expressed under contr...... nM x s(-1), and 85 s(-1) using maltose as substrate. This work presents the first production of fully active recombinant alpha-glucosidase of glycoside hydrolase family 31 from higher plants. (c) 2005 Elsevier Inc. All rights reserved....

Compensated readout for high-density MOS-gated memristor crossbar array

KAUST Repository

Zidan, Mohammed A.

2015-01-01

Leakage current is one of the main challenges facing high-density MOS-gated memristor arrays. In this study, we show that leakage current ruins the memory readout process for high-density arrays, and analyze the tradeoff between the array density and its power consumption. We propose a novel readout technique and its underlying circuitry, which is able to compensate for the transistor leakage-current effect in the high-density gated memristor array.

Action of some drugs on enzymes involved in DNA-repair and semiconservative DNA-synthesis

International Nuclear Information System (INIS)

Wawra, E.; Klein, W.; Kocsis, F.; Weniger, P.

1975-07-01

Different antirheumatic and cytostatic drugs had been tested by measurement of the thymidine incorporation into DNA of spleen cells under conditions, under which either DNA-synthesis or repair after gamma- or UV-irradiation takes place. There are substances, which inhibit either only the semiconservative DNA-synthesis (vinblastine, isonicotinic acid hydracide) or only DNA-repair after gamma-irradiation (mixture of penicillin-G and procaine-penicillin-G) or both (cyclophosphamide, phenylbutazone, procarbazine, nalidixic acid). Vincristine shows no effect on the thymidine incorporation in DNA, but by density gradient centrifugation it has been found that it influences the ligase reaction. Two DNA polymerases had been isolated from spleen cells, one of the low molecular and one of the high molecular weight type. The influences of the described drugs on these enzymes and on a deoxyribonuclease I from beef pancreas have been tested in ''in vitro'' systems. In all cases, it has been found that there is no effect or only a very small one, compared with the action of well known inhibitors as e.g. ethidium bromide and p-chloromercuribenzoate, and this cannot be responsible for the suppressions found in DNA-repair and semiconservative DNA-synthesis. (author)

High-Throughput Analysis of T-DNA Location and Structure Using Sequence Capture.

Directory of Open Access Journals (Sweden)

Soichi Inagaki

Full Text Available Agrobacterium-mediated transformation of plants with T-DNA is used both to introduce transgenes and for mutagenesis. Conventional approaches used to identify the genomic location and the structure of the inserted T-DNA are laborious and high-throughput methods using next-generation sequencing are being developed to address these problems. Here, we present a cost-effective approach that uses sequence capture targeted to the T-DNA borders to select genomic DNA fragments containing T-DNA-genome junctions, followed by Illumina sequencing to determine the location and junction structure of T-DNA insertions. Multiple probes can be mixed so that transgenic lines transformed with different T-DNA types can be processed simultaneously, using a simple, index-based pooling approach. We also developed a simple bioinformatic tool to find sequence read pairs that span the junction between the genome and T-DNA or any foreign DNA. We analyzed 29 transgenic lines of Arabidopsis thaliana, each containing inserts from 4 different T-DNA vectors. We determined the location of T-DNA insertions in 22 lines, 4 of which carried multiple insertion sites. Additionally, our analysis uncovered a high frequency of unconventional and complex T-DNA insertions, highlighting the needs for high-throughput methods for T-DNA localization and structural characterization. Transgene insertion events have to be fully characterized prior to use as commercial products. Our method greatly facilitates the first step of this characterization of transgenic plants by providing an efficient screen for the selection of promising lines.

Quantification of damage in DNA recovered from highly degraded samples – a case study on DNA in faeces

Directory of Open Access Journals (Sweden)

Eveson J Paige

2006-08-01

Full Text Available Abstract Background Poorly preserved biological tissues have become an important source of DNA for a wide range of zoological studies. Measuring the quality of DNA obtained from these samples is often desired; however, there are no widely used techniques available for quantifying damage in highly degraded DNA samples. We present a general method that can be used to determine the frequency of polymerase blocking DNA damage in specific gene-regions in such samples. The approach uses quantitative PCR to measure the amount of DNA present at several fragment sizes within a sample. According to a model of random degradation the amount of available template will decline exponentially with increasing fragment size in damaged samples, and the frequency of DNA damage (λ can be estimated by determining the rate of decline. Results The method is illustrated through the analysis of DNA extracted from sea lion faecal samples. Faeces contain a complex mixture of DNA from several sources and different components are expected to be differentially degraded. We estimated the frequency of DNA damage in both predator and prey DNA within individual faecal samples. The distribution of fragment lengths for each target fit well with the assumption of a random degradation process and, in keeping with our expectations, the estimated frequency of damage was always less in predator DNA than in prey DNA within the same sample (mean λpredator = 0.0106 per nucleotide; mean λprey = 0.0176 per nucleotide. This study is the first to explicitly define the amount of template damage in any DNA extracted from faeces and the first to quantify the amount of predator and prey DNA present within individual faecal samples. Conclusion We present an approach for characterizing mixed, highly degraded PCR templates such as those often encountered in ecological studies using non-invasive samples as a source of DNA, wildlife forensics investigations and ancient DNA research. This method will

Understanding environmental DNA detection probabilities: A case study using a stream-dwelling char Salvelinus fontinalis

Science.gov (United States)

Wilcox, Taylor M; Mckelvey, Kevin S.; Young, Michael K.; Sepulveda, Adam; Shepard, Bradley B.; Jane, Stephen F; Whiteley, Andrew R.; Lowe, Winsor H.; Schwartz, Michael K.

2016-01-01

Environmental DNA sampling (eDNA) has emerged as a powerful tool for detecting aquatic animals. Previous research suggests that eDNA methods are substantially more sensitive than traditional sampling. However, the factors influencing eDNA detection and the resulting sampling costs are still not well understood. Here we use multiple experiments to derive independent estimates of eDNA production rates and downstream persistence from brook trout (Salvelinus fontinalis) in streams. We use these estimates to parameterize models comparing the false negative detection rates of eDNA sampling and traditional backpack electrofishing. We find that using the protocols in this study eDNA had reasonable detection probabilities at extremely low animal densities (e.g., probability of detection 0.18 at densities of one fish per stream kilometer) and very high detection probabilities at population-level densities (e.g., probability of detection > 0.99 at densities of ≥ 3 fish per 100 m). This is substantially more sensitive than traditional electrofishing for determining the presence of brook trout and may translate into important cost savings when animals are rare. Our findings are consistent with a growing body of literature showing that eDNA sampling is a powerful tool for the detection of aquatic species, particularly those that are rare and difficult to sample using traditional methods.

Numerical analysis of energy density and particle density in high energy heavy-ion collisions

International Nuclear Information System (INIS)

Fu Yuanyong; Lu Zhongdao

2004-01-01

Energy density and particle density in high energy heavy-ion collisions are calculated with infinite series expansion method and Gauss-Laguerre formulas in numerical integration separately, and the results of these two methods are compared, the higher terms and linear terms in series expansion are also compared. The results show that Gauss-Laguerre formulas is a good method in calculations of high energy heavy-ion collisions. (author)

Synthesis of CdS nanoparticles based on DNA network templates

International Nuclear Information System (INIS)

Yao Yong; Song Yonghai; Wang Li

2008-01-01

CdS nanoparticles have been successfully synthesized by using DNA networks as templates. The synthesis was carried out by first dropping a mixture of cadmium acetate and DNA on a mica surface for the formation of the DNA network template and then transferring the sample into a heated thiourea solution. The Cd 2+ reacted with thiourea at high temperature and formed CdS nanoparticles on the DNA network template. UV-vis spectroscopy, photoluminescence, x-ray diffraction and atomic force microscopy (AFM) were used to characterize the CdS nanoparticles in detail. AFM results showed that the resulted CdS nanoparticles were directly aligned on the DNA network templates and that the synthesis and assembly of CdS nanoparticles was realized in one step. CdS nanoparticles fabricated with this method were smaller than those directly synthesized in a thiourea solution and were uniformly aligned on the DNA networks. By adjusting the density of the DNA networks and the concentration of Cd 2+ , the size and density of the CdS nanoparticles could be effectively controlled and CdS nanoparticles could grow along the DNA chains into nanowires. The possible growth mechanism has also been discussed in detail

High density regimes and beta limits in JET

International Nuclear Information System (INIS)

Smeulders, P.

1990-01-01

Results are first presented on the density limit in JET discharges with graphite (C), Be gettered graphite and Be limiters. There is a clear improvement in the case of Be limiters. The Be gettered phase showed no increase in the gas fueled density limit, except with Ion Cyclotron Resonance Heating (ICRH), but, the limit changed character. During MARFE-formation, any further increase in density was prevented, leading to a soft density limit. The soft density limit was a function of input power and impurity content with a week dependence on q. Helium and pellet fuelled discharges exceeded the gas-fuelled global density limits, but essentially had the same edge limit. In the second part, results are presented of high β operation in low-B Double-Null (DN) X-point configurations with Be-gettered carbon target plates. The Troyon limit was reached during H-mode discharges and toroidal β values of 5.5% were obtained. At high beta, the sawteeth were modified and characterised by very rapid heat-waves and fishbone-like pre- and post-cursors with strongly ballooning character. 17 refs., 5 figs

The use of low density high accuracy (LDHA) data for correction of high density low accuracy (HDLA) point cloud

Science.gov (United States)

Rak, Michal Bartosz; Wozniak, Adam; Mayer, J. R. R.

2016-06-01

Coordinate measuring techniques rely on computer processing of coordinate values of points gathered from physical surfaces using contact or non-contact methods. Contact measurements are characterized by low density and high accuracy. On the other hand optical methods gather high density data of the whole object in a short time but with accuracy at least one order of magnitude lower than for contact measurements. Thus the drawback of contact methods is low density of data, while for non-contact methods it is low accuracy. In this paper a method for fusion of data from two measurements of fundamentally different nature: high density low accuracy (HDLA) and low density high accuracy (LDHA) is presented to overcome the limitations of both measuring methods. In the proposed method the concept of virtual markers is used to find a representation of pairs of corresponding characteristic points in both sets of data. In each pair the coordinates of the point from contact measurements is treated as a reference for the corresponding point from non-contact measurement. Transformation enabling displacement of characteristic points from optical measurement to their match from contact measurements is determined and applied to the whole point cloud. The efficiency of the proposed algorithm was evaluated by comparison with data from a coordinate measuring machine (CMM). Three surfaces were used for this evaluation: plane, turbine blade and engine cover. For the planar surface the achieved improvement was of around 200 μm. Similar results were obtained for the turbine blade but for the engine cover the improvement was smaller. For both freeform surfaces the improvement was higher for raw data than for data after creation of mesh of triangles.

High energy density capacitors fabricated by thin film technology

International Nuclear Information System (INIS)

Barbee, T W; Johnson, G W; Wagner, A V.

1999-01-01

Low energy density in conventional capacitors severely limits efforts to miniaturize power electronics and imposes design limitations on electronics in general. We have successfully applied physical vapor deposition technology to greatly increase capacitor energy density. The high dielectric breakdown strength we have achieved in alumina thin films allows high energy density to be achieved with this moderately low dielectric constant material. The small temperature dependence of the dielectric constant, and the high reliability, high resistivity, and low dielectric loss of Al 2 O 3 , make it even more appealing. We have constructed single dielectric layer thin film capacitors and shown that they can be stacked to form multilayered structures with no loss in yield for a given capacitance. Control of film growth morphology is critical for achieving the smooth, high quality interfaces between metal and dielectric necessary for device operation at high electric fields. Most importantly, high rate deposition with extremely low particle generation is essential for achieving high energy storage at a reasonable cost. This has been achieved by reactive magnetron sputtering in which the reaction to form the dielectric oxide has been confined to the deposition surface. By this technique we have achieved a yield of over 50% for 1 cm 2 devices with an energy density of 14 J per cubic centimeter of Al 2 O 3 dielectric material in 1.2 kV, 4 nF devices. By further reducing defect density and increasing the dielectric constant of the material, we will be able to increase capacitance and construct high energy density devices to meet the requirements of applications in power electronics

HIGH DENSITY QCD WITH HEAVY-IONS

CERN Multimedia

The Addendum 1 to Volume 2 of the CMS Physics TDR has been published The Heavy-Ion analysis group completed the writing of a TDR summarizing the CMS plans in using heavy ion collisions to study high density QCD. The document was submitted to the LHCC in March and presented in the Open Session of the LHCC on May 9th. The study of heavy-ion physics at the LHC is promising to be very exciting. LHC will open a new energy frontier in ultra-relativistic heavy-ion physics. The collision energy of heavy nuclei at sNN = 5.5 TeV will be thirty times larger than what is presently available at RHIC. We will certainly probe quark and gluon matter at unprecedented values of energy density. The prime goal of this research programme is to study the fundamental theory of the strong interaction - Quantum Chromodynamics (QCD) - in extreme conditions of temperature, density and parton momentum fraction (low-x). Such studies, with impressive experimental and theoretical advances in recent years thanks to the wealth of high-qua...

Excitonic AND Logic Gates on DNA Brick Nanobreadboards

Science.gov (United States)

2015-01-01

A promising application of DNA self-assembly is the fabrication of chromophore-based excitonic devices. DNA brick assembly is a compelling method for creating programmable nanobreadboards on which chromophores may be rapidly and easily repositioned to prototype new excitonic devices, optimize device operation, and induce reversible switching. Using DNA nanobreadboards, we have demonstrated each of these functions through the construction and operation of two different excitonic AND logic gates. The modularity and high chromophore density achievable via this brick-based approach provide a viable path toward developing information processing and storage systems. PMID:25839049

An x-ray backlit Talbot-Lau deflectometer for high-energy-density electron density diagnostics

Science.gov (United States)

Valdivia, M. P.; Stutman, D.; Stoeckl, C.; Theobald, W.; Mileham, C.; Begishev, I. A.; Bromage, J.; Regan, S. P.

2016-02-01

X-ray phase-contrast techniques can measure electron density gradients in high-energy-density plasmas through refraction induced phase shifts. An 8 keV Talbot-Lau interferometer consisting of free standing ultrathin gratings was deployed at an ultra-short, high-intensity laser system using K-shell emission from a 1-30 J, 8 ps laser pulse focused on thin Cu foil targets. Grating survival was demonstrated for 30 J, 8 ps laser pulses. The first x-ray deflectometry images obtained under laser backlighting showed up to 25% image contrast and thus enabled detection of electron areal density gradients with a maximum value of 8.1 ± 0.5 × 1023 cm-3 in a low-Z millimeter sized sample. An electron density profile was obtained from refraction measurements with an error of x-ray source-size, similar to conventional radiography.

Highly multiplexed targeted DNA sequencing from single nuclei.

Science.gov (United States)

Leung, Marco L; Wang, Yong; Kim, Charissa; Gao, Ruli; Jiang, Jerry; Sei, Emi; Navin, Nicholas E

2016-02-01

Single-cell DNA sequencing methods are challenged by poor physical coverage, high technical error rates and low throughput. To address these issues, we developed a single-cell DNA sequencing protocol that combines flow-sorting of single nuclei, time-limited multiple-displacement amplification (MDA), low-input library preparation, DNA barcoding, targeted capture and next-generation sequencing (NGS). This approach represents a major improvement over our previous single nucleus sequencing (SNS) Nature Protocols paper in terms of generating higher-coverage data (>90%), thereby enabling the detection of genome-wide variants in single mammalian cells at base-pair resolution. Furthermore, by pooling 48-96 single-cell libraries together for targeted capture, this approach can be used to sequence many single-cell libraries in parallel in a single reaction. This protocol greatly reduces the cost of single-cell DNA sequencing, and it can be completed in 5-6 d by advanced users. This single-cell DNA sequencing protocol has broad applications for studying rare cells and complex populations in diverse fields of biological research and medicine.

Extraction of high quality DNA from seized Moroccan cannabis resin (Hashish.

Directory of Open Access Journals (Sweden)

Moulay Abdelaziz El Alaoui

Full Text Available The extraction and purification of nucleic acids is the first step in most molecular biology analysis techniques. The objective of this work is to obtain highly purified nucleic acids derived from Cannabis sativa resin seizure in order to conduct a DNA typing method for the individualization of cannabis resin samples. To obtain highly purified nucleic acids from cannabis resin (Hashish free from contaminants that cause inhibition of PCR reaction, we have tested two protocols: the CTAB protocol of Wagner and a CTAB protocol described by Somma (2004 adapted for difficult matrix. We obtained high quality genomic DNA from 8 cannabis resin seizures using the adapted protocol. DNA extracted by the Wagner CTAB protocol failed to give polymerase chain reaction (PCR amplification of tetrahydrocannabinolic acid (THCA synthase coding gene. However, the extracted DNA by the second protocol permits amplification of THCA synthase coding gene using different sets of primers as assessed by PCR. We describe here for the first time the possibility of DNA extraction from (Hashish resin derived from Cannabis sativa. This allows the use of DNA molecular tests under special forensic circumstances.

Ultra-high Density SNParray in Neuroblastoma Molecular Diagnostics

Directory of Open Access Journals (Sweden)

Inge M. Ambros

2014-08-01

Full Text Available Neuroblastoma serves as a paradigm for applying tumor genomic data for determining patient prognosis and thus for treatment allocation. MYCN status, i.e. amplified vs. non-amplified, was one of the very first biomarkers in oncology to discriminate aggressive from less aggressive or even favorable clinical courses of neuroblastoma. However, MYCN amplification is by far not the only genetic change associated with unfavorable clinical courses: so called segmental chromosomal aberrations, i.e. gains or losses of chromosomal fragments, can also indicate tumor aggressiveness. The clinical use of these genomic aberrations has, however, been hampered for many years by methodical and interpretational problems. Only after reaching worldwide consensus on markers, methodology, and data interpretation, information on SCAs has recently been implemented in clinical studies. Now, a number of collaborative studies within COG, GPOH and SIOPEN use genomic information to stratify therapy for patients with localized and metastatic disease. Recently, new types of DNA based aberrations influencing the clinical behavior of neuroblastomas have been described. Deletions or mutations of genes like ATRX and a phenomenon referred to as chromothripsis are all assumed to correlate with an unfavorable clinical behavior. However, these genomic aberrations need to be scrutinized in larger studies applying the most appropriate techniques. Single nucleotide polymorphism (SNP arrays have proven successful in deciphering genomic aberrations of cancer cells; these techniques, however, are usually not applied in the daily routine. Here, we present an ultra-high density (UHD SNParray technique which is, because of its high specificity and sensitivity and the combined copy number and allele information, highly appropriate for the genomic diagnosis of neuroblastoma and other malignancies.

Chapter 7: High-Density H-Mode Operation in ASDEX Upgrade

International Nuclear Information System (INIS)

Stober, Joerg Karl; Lang, Peter Thomas; Mertens, Vitus

2003-01-01

Recent results are reported on the maximum achievable H-mode density and the behavior of pedestal density and central density peaking as this limit is approached. The maximum achievable H-mode density roughly scales as the Greenwald density, though a dependence on B t is clearly observed. In contrast to the stiff temperature profiles, the density profiles seem to allow more shape variation and especially with high-field-side pellet-injection, strongly peaked profiles with good confinement have been achieved. Also, spontaneous density peaking at high densities is observed in ASDEX Upgrade, which is related to the generally observed large time constants for the density profile equilibration. The equilibrated density profile shapes depend strongly on the heat-flux profile in the sense that central heating leads to significantly flatter profiles

Experimental study of high density foods for the Space Operations Center

Science.gov (United States)

Ahmed, S. M.

1981-01-01

The experimental study of high density foods for the Space Operations Center is described. A sensory evaluation of the high density foods was conducted first to test the acceptability of the products. A shelf-life study of the high density foods was also conducted for three different time lengths at three different temperatures. The nutritional analysis of the high density foods is at present incomplete.

Fluorescent Fe K Emission from High Density Accretion Disks

Science.gov (United States)

Bautista, Manuel; Mendoza, Claudio; Garcia, Javier; Kallman, Timothy R.; Palmeri, Patrick; Deprince, Jerome; Quinet, Pascal

2018-06-01

Iron K-shell lines emitted by gas closely orbiting black holes are observed to be grossly broadened and skewed by Doppler effects and gravitational redshift. Accordingly, models for line profiles are widely used to measure the spin (i.e., the angular momentum) of astrophysical black holes. The accuracy of these spin estimates is called into question because fitting the data requires very high iron abundances, several times the solar value. Meanwhile, no plausible physical explanation has been proffered for why these black hole systems should be so iron rich. The most likely explanation for the super-solar iron abundances is a deficiency in the models, and the leading candidate cause is that current models are inapplicable at densities above 1018 cm-3. We study the effects of high densities on the atomic parameters and on the spectral models for iron ions. At high densities, Debye plasma can affect the effective atomic potential of the ions, leading to observable changes in energy levels and atomic rates with respect to the low density case. High densities also have the effec of lowering energy the atomic continuum and reducing the recombination rate coefficients. On the spectral modeling side, high densities drive level populations toward a Boltzman distribution and very large numbers of excited atomic levels, typically accounted for in theoretical spectral models, may contribute to the K-shell spectrum.

Phenomenology of high density disruptions in the TFTR tokamak

International Nuclear Information System (INIS)

Fredrickson, E.D.; McGuire, K.M.; Bell, M.G.

1993-01-01

Studies of high density disruptions on TFTR, including a comparison of minor and major disruptions at high density, provide important new information regarding the nature of the disruption mechanism. Further, for the first time, an (m,n)=(1,1) 'cold bubble' precursor to high density disruptions has been experimentally observed in the electron temperature profile. The precursor to major disruptions resembles the 'vacuum bubble' model of disruptions first proposed by B.B. Kadomtsev and O.P. Pogutse (Sov. Phys. - JETP 38 (1974) 283). (author). Letter-to-the-editor. 25 refs, 3 figs

High Energy Density Polymer Film Capacitors

National Research Council Canada - National Science Library

Boufelfel, Ali

2006-01-01

High-energy-density capacitors that are compact and light-weight are extremely valuable in a number of critical DoD systems that include portable field equipment, pulsed lasers, detection equipment...

Two high-mobility group box domains act together to underwind and kink DNA

Energy Technology Data Exchange (ETDEWEB)

Sánchez-Giraldo, R.; Acosta-Reyes, F. J. [Universitat Politecnica de Catalunya, 08028 Barcelona (Spain); Malarkey, C. S. [University of Colorado School of Medicine, Aurora, CO 80045 (United States); Saperas, N. [Universitat Politecnica de Catalunya, 08028 Barcelona (Spain); Churchill, M. E. A., E-mail: mair.churchill@ucdenver.edu [University of Colorado School of Medicine, Aurora, CO 80045 (United States); Campos, J. L., E-mail: mair.churchill@ucdenver.edu [Universitat Politecnica de Catalunya, 08028 Barcelona (Spain)

2015-06-30

The crystal structure of HMGB1 box A bound to an unmodified AT-rich DNA fragment is reported at a resolution of 2 Å. A new mode of DNA recognition for HMG box proteins is found in which two box A domains bind in an unusual configuration generating a highly kinked DNA structure. High-mobility group protein 1 (HMGB1) is an essential and ubiquitous DNA architectural factor that influences a myriad of cellular processes. HMGB1 contains two DNA-binding domains, box A and box B, which have little sequence specificity but have remarkable abilities to underwind and bend DNA. Although HMGB1 box A is thought to be responsible for the majority of HMGB1–DNA interactions with pre-bent or kinked DNA, little is known about how it recognizes unmodified DNA. Here, the crystal structure of HMGB1 box A bound to an AT-rich DNA fragment is reported at a resolution of 2 Å. Two box A domains of HMGB1 collaborate in an unusual configuration in which the Phe37 residues of both domains stack together and intercalate the same CG base pair, generating highly kinked DNA. This represents a novel mode of DNA recognition for HMGB proteins and reveals a mechanism by which structure-specific HMG boxes kink linear DNA.

Two high-mobility group box domains act together to underwind and kink DNA

International Nuclear Information System (INIS)

Sánchez-Giraldo, R.; Acosta-Reyes, F. J.; Malarkey, C. S.; Saperas, N.; Churchill, M. E. A.; Campos, J. L.

2015-01-01

The crystal structure of HMGB1 box A bound to an unmodified AT-rich DNA fragment is reported at a resolution of 2 Å. A new mode of DNA recognition for HMG box proteins is found in which two box A domains bind in an unusual configuration generating a highly kinked DNA structure. High-mobility group protein 1 (HMGB1) is an essential and ubiquitous DNA architectural factor that influences a myriad of cellular processes. HMGB1 contains two DNA-binding domains, box A and box B, which have little sequence specificity but have remarkable abilities to underwind and bend DNA. Although HMGB1 box A is thought to be responsible for the majority of HMGB1–DNA interactions with pre-bent or kinked DNA, little is known about how it recognizes unmodified DNA. Here, the crystal structure of HMGB1 box A bound to an AT-rich DNA fragment is reported at a resolution of 2 Å. Two box A domains of HMGB1 collaborate in an unusual configuration in which the Phe37 residues of both domains stack together and intercalate the same CG base pair, generating highly kinked DNA. This represents a novel mode of DNA recognition for HMGB proteins and reveals a mechanism by which structure-specific HMG boxes kink linear DNA

High density matter at RHIC

Indian Academy of Sciences (India)

QCD predicts a phase transition between hadronic matter and a quark-gluon plasma at high energy density. The relativistic heavy ion collider (RHIC) at Brookhaven National Laboratory is a new facility dedicated to the experimental study of matter under extreme conditions. Already the first round of experimental results at ...

Edge operational space for high density/high confinement ELMY H-modes in JET

International Nuclear Information System (INIS)

Sartori, R.; Saibene, G.; Loarte, A.

2002-01-01

This paper discusses how the proximity to the L-H threshold affects the confinement of ELMy H-modes at high density. The largest reduction in confinement at high density is observed at the transition from the Type I to the Type III ELMy regime. At medium plasma triangularity, δ≅0.3 (where δ is the average triangularity at the separatrix), JET experiments show that by increasing the margin above the L-H threshold power and maintaining the edge temperature above the critical temperature for the transition to Type III ELMs, it is possible to avoid the degradation of the pedestal pressure with density, normally observed at lower power. As a result, the range of achievable densities (both in the core and in the pedestal) is increased. At high power above the L-H threshold power the core density was equal to the Greenwald limit with H97≅0.9. There is evidence that a mixed regime of Type I and Type II ELMs has been obtained at this intermediate triangularity, possibly as a result of this increase in density. At higher triangularity, δ≅0.5, the power required to achieve similar results is lower. (author)

Irish study of high-density Schizophrenia families: Field methods and power to detect linkage

Energy Technology Data Exchange (ETDEWEB)

Kendler, K.S.; Straub, R.E.; MacLean, C.J. [Virginia Commonwealth Univ., Richmond, VA (United States)] [and others

1996-04-09

Large samples of multiplex pedigrees will probably be needed to detect susceptibility loci for schizophrenia by linkage analysis. Standardized ascertainment of such pedigrees from culturally and ethnically homogeneous populations may improve the probability of detection and replication of linkage. The Irish Study of High-Density Schizophrenia Families (ISHDSF) was formed from standardized ascertainment of multiplex schizophrenia families in 39 psychiatric facilities covering over 90% of the population in Ireland and Northern Ireland. We here describe a phenotypic sample and a subset thereof, the linkage sample. Individuals were included in the phenotypic sample if adequate diagnostic information, based on personal interview and/or hospital record, was available. Only individuals with available DNA were included in the linkage sample. Inclusion of a pedigree into the phenotypic sample required at least two first, second, or third degree relatives with non-affective psychosis (NAP), one of whom had schizophrenia (S) or poor-outcome schizoaffective disorder (PO-SAD). Entry into the linkage sample required DNA samples on at least two individuals with NAP, of whom at least one had S or PO-SAD. Affection was defined by narrow, intermediate, and broad criteria. 75 refs., 6 tabs.

Directed PCR-free engineering of highly repetitive DNA sequences

Directory of Open Access Journals (Sweden)

Preissler Steffen

2011-09-01

Full Text Available Abstract Background Highly repetitive nucleotide sequences are commonly found in nature e.g. in telomeres, microsatellite DNA, polyadenine (poly(A tails of eukaryotic messenger RNA as well as in several inherited human disorders linked to trinucleotide repeat expansions in the genome. Therefore, studying repetitive sequences is of biological, biotechnological and medical relevance. However, cloning of such repetitive DNA sequences is challenging because specific PCR-based amplification is hampered by the lack of unique primer binding sites resulting in unspecific products. Results For the PCR-free generation of repetitive DNA sequences we used antiparallel oligonucleotides flanked by restriction sites of Type IIS endonucleases. The arrangement of recognition sites allowed for stepwise and seamless elongation of repetitive sequences. This facilitated the assembly of repetitive DNA segments and open reading frames encoding polypeptides with periodic amino acid sequences of any desired length. By this strategy we cloned a series of polyglutamine encoding sequences as well as highly repetitive polyadenine tracts. Such repetitive sequences can be used for diverse biotechnological applications. As an example, the polyglutamine sequences were expressed as His6-SUMO fusion proteins in Escherichia coli cells to study their aggregation behavior in vitro. The His6-SUMO moiety enabled affinity purification of the polyglutamine proteins, increased their solubility, and allowed controlled induction of the aggregation process. We successfully purified the fusions proteins and provide an example for their applicability in filter retardation assays. Conclusion Our seamless cloning strategy is PCR-free and allows the directed and efficient generation of highly repetitive DNA sequences of defined lengths by simple standard cloning procedures.

Growth limitation of Lemna minor due to high plant density

NARCIS (Netherlands)

Driever, S.M.; Nes, van E.H.; Roijackers, R.M.M.

2005-01-01

The effect of high population densities on the growth rate of Lemna minor (L.) was studied under laboratory conditions at 23°C in a medium with sufficient nutrients. At high population densities, we found a non-linear decreasing growth rate with increasing L. minor density. Above a L. minor biomass

Density-dependent phonoriton states in highly excited semiconductors

International Nuclear Information System (INIS)

Nguyen Hong Quang; Nguyen Minh Khue; Nguyen Que Huong

1995-09-01

The dynamical aspects of the phonoriton state in highly-photoexcited semiconductors is studied theoretically. The effect of the exciton-exciton interaction and nonbosonic character of high-density excitons are taken into account. Using Green's function method and within the Random Phase Approximation it is shown that the phonoriton dispersion and damping are very sensitive to the exciton density, characterizing the excitation degree of semiconductors. (author). 18 refs, 3 figs

Charge transfer through DNA/DNA duplexes and DNA/RNA hybrids: complex theoretical and experimental studies.

Science.gov (United States)

Kratochvílová, Irena; Vala, Martin; Weiter, Martin; Špérová, Miroslava; Schneider, Bohdan; Páv, Ondřej; Šebera, Jakub; Rosenberg, Ivan; Sychrovský, Vladimír

2013-01-01

Oligonucleotides conduct electric charge via various mechanisms and their characterization and understanding is a very important and complicated task. In this work, experimental (temperature dependent steady state fluorescence spectroscopy, time-resolved fluorescence spectroscopy) and theoretical (Density Functional Theory) approaches were combined to study charge transfer processes in short DNA/DNA and RNA/DNA duplexes with virtually equivalent sequences. The experimental results were consistent with the theoretical model - the delocalized nature of HOMO orbitals and holes, base stacking, electronic coupling and conformational flexibility formed the conditions for more effective short distance charge transfer processes in RNA/DNA hybrids. RNA/DNA and DNA/DNA charge transfer properties were strongly connected with temperature affected structural changes of molecular systems - charge transfer could be used as a probe of even tiny changes of molecular structures and settings. © 2013. Published by Elsevier B.V. All rights reserved.

Production of highly knotted DNA by means of cosmid circularization inside phage capsids

Directory of Open Access Journals (Sweden)

Trigueros Sonia

2007-12-01

Full Text Available Abstract Background The formation of DNA knots is common during biological transactions. Yet, functional implications of knotted DNA are not fully understood. Moreover, potential applications of DNA molecules condensed by means of knotting remain to be explored. A convenient method to produce abundant highly knotted DNA would be highly valuable for these studies. Results We had previously shown that circularization of the 11.2 kb linear DNA of phage P4 inside its viral capsid generates complex knots by the effect of confinement. We demonstrate here that this mechanism is not restricted to the viral genome. We constructed DNA cosmids as small as 5 kb and introduced them inside P4 capsids. Such cosmids were then recovered as a complex mixture of highly knotted DNA circles. Over 250 μg of knotted cosmid were typically obtained from 1 liter of bacterial culture. Conclusion With this biological system, DNA molecules of varying length and sequence can be shaped into very complex and heterogeneous knotted forms. These molecules can be produced in preparative amounts suitable for systematic studies and applications.

Multiplexed, high density electrophysiology with nanofabricated neural probes.

Directory of Open Access Journals (Sweden)

Jiangang Du

Full Text Available Extracellular electrode arrays can reveal the neuronal network correlates of behavior with single-cell, single-spike, and sub-millisecond resolution. However, implantable electrodes are inherently invasive, and efforts to scale up the number and density of recording sites must compromise on device size in order to connect the electrodes. Here, we report on silicon-based neural probes employing nanofabricated, high-density electrical leads. Furthermore, we address the challenge of reading out multichannel data with an application-specific integrated circuit (ASIC performing signal amplification, band-pass filtering, and multiplexing functions. We demonstrate high spatial resolution extracellular measurements with a fully integrated, low noise 64-channel system weighing just 330 mg. The on-chip multiplexers make possible recordings with substantially fewer external wires than the number of input channels. By combining nanofabricated probes with ASICs we have implemented a system for performing large-scale, high-density electrophysiology in small, freely behaving animals that is both minimally invasive and highly scalable.

Double trouble at high density:

DEFF Research Database (Denmark)

Gergs, André; Palmqvist, Annemette; Preuss, Thomas G

2014-01-01

Population size is often regulated by negative feedback between population density and individual fitness. At high population densities, animals run into double trouble: they might concurrently suffer from overexploitation of resources and also from negative interference among individuals...... regardless of resource availability, referred to as crowding. Animals are able to adapt to resource shortages by exhibiting a repertoire of life history and physiological plasticities. In addition to resource-related plasticity, crowding might lead to reduced fitness, with consequences for individual life...... history. We explored how different mechanisms behind resource-related plasticity and crowding-related fitness act independently or together, using the water flea Daphnia magna as a case study. For testing hypotheses related to mechanisms of plasticity and crowding stress across different biological levels...

High density data storage principle, technology, and materials

CERN Document Server

Zhu, Daoben

2009-01-01

The explosive increase in information and the miniaturization of electronic devices demand new recording technologies and materials that combine high density, fast response, long retention time and rewriting capability. As predicted, the current silicon-based computer circuits are reaching their physical limits. Further miniaturization of the electronic components and increase in data storage density are vital for the next generation of IT equipment such as ultra high-speed mobile computing, communication devices and sophisticated sensors. This original book presents a comprehensive introduction to the significant research achievements on high-density data storage from the aspects of recording mechanisms, materials and fabrication technologies, which are promising for overcoming the physical limits of current data storage systems. The book serves as an useful guide for the development of optimized materials, technologies and device structures for future information storage, and will lead readers to the fascin...

Alignment of Gold Nanoparticle-Decorated DNA Origami Nanotubes: Substrate Prepatterning versus Molecular Combing.

Science.gov (United States)

Teschome, Bezu; Facsko, Stefan; Gothelf, Kurt V; Keller, Adrian

2015-11-24

DNA origami has become an established technique for designing well-defined nanostructures with any desired shape and for the controlled arrangement of functional nanostructures with few nanometer resolution. These unique features make DNA origami nanostructures promising candidates for use as scaffolds in nanoelectronics and nanophotonics device fabrication. Consequently, a number of studies have shown the precise organization of metallic nanoparticles on various DNA origami shapes. In this work, we fabricated large arrays of aligned DNA origami decorated with a high density of gold nanoparticles (AuNPs). To this end, we first demonstrate the high-yield assembly of high-density AuNP arrangements on DNA origami adsorbed to Si surfaces with few unbound background nanoparticles by carefully controlling the concentrations of MgCl2 and AuNPs in the hybridization buffer and the hybridization time. Then, we evaluate two methods, i.e., hybridization to prealigned DNA origami and molecular combing in a receding meniscus, with respect to their potential to yield large arrays of aligned AuNP-decorated DNA origami nanotubes. Because of the comparatively low MgCl2 concentration required for the efficient immobilization of the AuNPs, the prealigned DNA origami become mobile and displaced from their original positions, thereby decreasing the alignment yield. This increased mobility, on the other hand, makes the adsorbed origami susceptible to molecular combing, and a total alignment yield of 86% is obtained in this way.

Fifth International Conference on High Energy Density Physics

Energy Technology Data Exchange (ETDEWEB)

Beg, Farhat

2017-07-05

The Fifth International Conference on High Energy Density Physics (ICHED 2015) was held in the Catamaran Hotel in San Diego from August 23-27, 2015. This meeting was the fifth in a series which began in 2008 in conjunction with the April meeting of the American Physical Society (APS). The main goal of this conference has been to bring together researchers from all fields of High Energy Density Science (HEDS) into one, unified meeting.

Use of electroporation for high-molecular-weight DNA-mediated gene transfer.

Science.gov (United States)

Jastreboff, M M; Ito, E; Bertino, J R; Narayanan, R

1987-08-01

Electroporation was used to introduce high-molecular-weight DNA into murine hematopoietic cells and NIH3T3 cells. CCRF-CEM cells were stably transfected with SV2NEO plasmid and the genomic DNA from G-418-resistant clones (greater than 65 kb) was introduced into mouse bone marrow and NIH3T3 cells by electroporation. NEO sequences and expression were detected in the hematopoietic tissues of lethally irradiated mice, with 24% of individual spleen colonies expressing NEO. The frequency of genomic DNA transfer into NIH3T3 cells was 0.25 X 10(-3). Electroporation thus offers a powerful mode of gene transfer not only of cloned genes but also of high-molecular-weight DNA into cells.

Intramolecularly Protein-Crosslinked DNA Gels: New Biohybrid Nanomaterials with Controllable Size and Catalytic Activity.

Science.gov (United States)

Zhou, Li; Morel, Mathieu; Rudiuk, Sergii; Baigl, Damien

2017-07-01

DNA micro- and nanogels-small-sized hydrogels made of a crosslinked DNA backbone-constitute new promising materials, but their functions have mainly been limited to those brought by DNA. Here a new way is described to prepare sub-micrometer-sized DNA gels of controllable crosslinking density that are able to embed novel functions, such as an enzymatic activity. It consists of using proteins, instead of traditional base-pairing assembly or covalent approaches, to form crosslinks inside individual DNA molecules, resulting in structures referred to as intramolecularly protein-crosslinked DNA gels (IPDGs). It is first shown that the addition of streptavidin to biotinylated T4DNA results in the successful formation of thermally stable IPDGs with a controllable crosslinking density, forming structures ranging from elongated to raspberry-shaped and pearl-necklace-like morphologies. Using reversible DNA condensation strategies, this paper shows that the gels can be reversibly actuated at a low crosslinking density, or further stabilized when they are highly crosslinked. Finally, by using streptavidin-protein conjugates, IPDGs with various enzymes are successfully functionalized. It is demonstrated that the enzymes keep their catalytic activity upon their incorporation into the gels, opening perspectives ranging from biotechnologies (e.g., enzyme manipulation) to nanomedicine (e.g., vectorization). © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

High performance H-mode plasmas at densities above the Greenwald limit

International Nuclear Information System (INIS)

Mahdavi, M.A.; Osborne, T.H.; Leonard, A.W.

2001-01-01

Densities up to 40 percent above the Greenwald limit are reproducibly achieved in high confinement (H ITER89p =2) ELMing H-mode discharges. Simultaneous gas fueling and divertor pumping were used to obtain these results. Confinement of these discharges, similar to moderate density H-mode, is characterized by a stiff temperature profile, and therefore sensitive to the density profile. A particle transport model is presented that explains the roles of divertor pumping and geometry for access to high densities. Energy loss per ELM at high density is a factor of five lower than predictions of an earlier scaling, based on data from lower density discharges. (author)

Novel nanostructured materials for high energy density supercapacitors

Energy Technology Data Exchange (ETDEWEB)

Yuan, C.Z.; Zhang, X.G. [Nanjing Univ. of Aeronautics and Astronautics (China). College of Material Science and Engineering

2010-07-01

Researchers are currently examining methods of improving energy density while not sacrificing the high power density of supercapacitors. In this study, nanostructured materials assembled from nanometer-sized building blocks with mesoporosity were synthesized in order investigate diffusion time, kinetics, and capacitances. Petal-like cobalt hydroxide Co(OH){sub 2} mesocrystals, urchin-like Co(OH){sub 2} and dicobalt tetroxide (Co{sub 2}O{sub 4}) ordered arrays as well as N{sub i}O microspheres were assembled from 0-D nanoparticles, 1-D mesoporous nanowires and nanobelts, and 2-D mesoporous nanopetals. The study showed that all the synthesized nanostructured materials delivered larger energy densities while showing electrochemical stability at high rates.

ON THE ORIGIN OF THE HIGH COLUMN DENSITY TURNOVER IN THE H I COLUMN DENSITY DISTRIBUTION

International Nuclear Information System (INIS)

Erkal, Denis; Gnedin, Nickolay Y.; Kravtsov, Andrey V.

2012-01-01

We study the high column density regime of the H I column density distribution function and argue that there are two distinct features: a turnover at N H I ≈ 10 21 cm –2 , which is present at both z = 0 and z ≈ 3, and a lack of systems above N H I ≈ 10 22 cm –2 at z = 0. Using observations of the column density distribution, we argue that the H I-H 2 transition does not cause the turnover at N H I ≈ 10 21 cm –2 but can plausibly explain the turnover at N H I ∼> 10 22 cm –2 . We compute the H I column density distribution of individual galaxies in the THINGS sample and show that the turnover column density depends only weakly on metallicity. Furthermore, we show that the column density distribution of galaxies, corrected for inclination, is insensitive to the resolution of the H I map or to averaging in radial shells. Our results indicate that the similarity of H I column density distributions at z = 3 and 0 is due to the similarity of the maximum H I surface densities of high-z and low-z disks, set presumably by universal processes that shape properties of the gaseous disks of galaxies. Using fully cosmological simulations, we explore other candidate physical mechanisms that could produce a turnover in the column density distribution. We show that while turbulence within giant molecular clouds cannot affect the damped Lyα column density distribution, stellar feedback can affect it significantly if the feedback is sufficiently effective in removing gas from the central 2-3 kpc of high-redshift galaxies. Finally, we argue that it is meaningful to compare column densities averaged over ∼ kpc scales with those estimated from quasar spectra that probe sub-pc scales due to the steep power spectrum of H I column density fluctuations observed in nearby galaxies.

Structure-function relationships of new lipids designed for DNA transfection.

Science.gov (United States)

Dittrich, Matthias; Heinze, Martin; Wölk, Christian; Funari, Sergio S; Dobner, Bodo; Möhwald, Helmuth; Brezesinski, Gerald

2011-08-22

Cationic liposome/DNA complexes can be used as nonviral vectors for direct delivery of DNA-based biopharmaceuticals to damaged cells and tissues. To obtain more effective and safer liposome-based gene transfection systems, two cationic lipids with identical head groups but different chain structures are investigated with respect to their in vitro gene-transfer activity, their cell-damaging characteristics, and their physicochemical properties. The gene-transfer activities of the two lipids are very different. Differential scanning calorimetry and synchrotron small- and wide-angle X-ray scattering give valuable structural insight. A subgel-like structure with high packing density and high phase-transition temperature from gel to liquid-crystalline state are found for lipid 7 (N'-2-[(2,6-diamino-1-oxohexyl)amino]ethyl-2,N-bis(hexadecyl)propanediamide) containing two saturated chains. Additionally, an ordered head-group lattice based on formation of a hydrogen-bond network is present. In contrast, lipid 8 (N'-2-[(2,6-diamino-1-oxohexyl)amino]ethyl-2-hexadecyl-N-[(9Z)-octadec-9-enyl]propanediamide) with one unsaturated and one saturated chain shows a lower phase-transition temperature and a reduced packing density. These properties enhance incorporation of the helper lipid cholesterol needed for gene transfection. Both lipids, either pure or in mixtures with cholesterol, form lamellar phases, which are preserved after addition of DNA. However, the system separates into phases containing DNA and phases without DNA. On increasing the temperature, DNA is released and only a lipid phase without intercalated DNA strands is observed. The conversion temperatures are very different in the two systems studied. The important parameter seems to be the charge density of the lipid membranes, which is a result of different solubility of cholesterol in the two lipid membranes. Therefore, different binding affinities of the DNA to the lipid mixtures are achieved. Copyright © 2011

Image-Based Modeling Reveals Dynamic Redistribution of DNA Damageinto Nuclear Sub-Domains

Energy Technology Data Exchange (ETDEWEB)

Costes Sylvain V., Ponomarev Artem, Chen James L.; Nguyen, David; Cucinotta, Francis A.; Barcellos-Hoff, Mary Helen

2007-08-03

Several proteins involved in the response to DNA doublestrand breaks (DSB) f orm microscopically visible nuclear domains, orfoci, after exposure to ionizing radiation. Radiation-induced foci (RIF)are believed to be located where DNA damage occurs. To test thisassumption, we analyzed the spatial distribution of 53BP1, phosphorylatedATM, and gammaH2AX RIF in cells irradiated with high linear energytransfer (LET) radiation and low LET. Since energy is randomly depositedalong high-LET particle paths, RIF along these paths should also berandomly distributed. The probability to induce DSB can be derived fromDNA fragment data measured experimentally by pulsed-field gelelectrophoresis. We used this probability in Monte Carlo simulations topredict DSB locations in synthetic nuclei geometrically described by acomplete set of human chromosomes, taking into account microscope opticsfrom real experiments. As expected, simulations produced DNA-weightedrandom (Poisson) distributions. In contrast, the distributions of RIFobtained as early as 5 min after exposure to high LET (1 GeV/amu Fe) werenon-random. This deviation from the expected DNA-weighted random patterncan be further characterized by "relative DNA image measurements." Thisnovel imaging approach shows that RIF were located preferentially at theinterface between high and low DNA density regions, and were morefrequent than predicted in regions with lower DNA density. The samepreferential nuclear location was also measured for RIF induced by 1 Gyof low-LET radiation. This deviation from random behavior was evidentonly 5 min after irradiation for phosphorylated ATM RIF, while gammaH2AXand 53BP1 RIF showed pronounced deviations up to 30 min after exposure.These data suggest that DNA damage induced foci are restricted to certainregions of the nucleus of human epithelial cells. It is possible that DNAlesions are collected in these nuclear sub-domains for more efficientrepair.

Effect of mix proportion of high density concrete on compressive strength, density and radiation absorption

International Nuclear Information System (INIS)

Noor Azreen Masenwat; Mohamad Pauzi Ismail; Suhairy Sani; Ismail Mustapha; Nasharuddin Isa; Mohamad Haniza Mahmud; Mohammad Shahrizan Samsu

2014-01-01

To prevent radiation leaks at nuclear reactors, high-density concrete is used as an absorbent material for radiation from spreading into the environment. High-density concrete is a mixture of cement, sand, aggregate (usually high-density minerals) and water. In this research, hematite stone is used because of its mineral density higher than the granite used in conventional concrete mixing. Mix concrete in this study were divided into part 1 and part 2. In part 1, the concrete mixture is designed with the same ratio of 1: 2: 4 but differentiated in terms of water-cement ratio (0.60, 0.65, 0.70, 0.75, 0.80 ). Whereas, in part 2, the concrete mixture is designed to vary the ratio of 1: 1: 2, 1: 1.5: 3, 1: 2: 3, 1: 3: 6, 1: 2: 6 with water-cement ratio (0.7, 0.8, 0.85, 0.9). In each section, the division has also performed in a mixture of sand and fine sand hematite. Then, the physical characteristics of the density and the compressive strength of the mixture of part 1 and part 2 is measured. Comparisons were also made in terms of absorption of radiation by Cs-137 and Co-60 source for each mix. This paper describes and discusses the relationship between the concrete mixture ratio, the relationship with the water-cement ratio, compressive strength, density, different mixture of sand and fine sand hematite. (author)

Label-Free Potentiometry for Detecting DNA Hybridization Using Peptide Nucleic Acid and DNA Probes

Science.gov (United States)

Goda, Tatsuro; Singi, Ankit Balram; Maeda, Yasuhiro; Matsumoto, Akira; Torimura, Masaki; Aoki, Hiroshi; Miyahara, Yuji

2013-01-01

Peptide nucleic acid (PNA) has outstanding affinity over DNA for complementary nucleic acid sequences by forming a PNA-DNA heterodimer upon hybridization via Watson-Crick base-pairing. To verify whether PNA probes on an electrode surface enhance sensitivity for potentiometric DNA detection or not, we conducted a comparative study on the hybridization of PNA and DNA probes on the surface of a 10-channel gold electrodes microarray. Changes in the charge density as a result of hybridization at the solution/electrode interface on the self-assembled monolayer (SAM)-formed microelectrodes were directly transformed into potentiometric signals using a high input impedance electrometer. The charge readout allows label-free, reagent-less, and multi-parallel detection of target oligonucleotides without any optical assistance. The differences in the probe lengths between 15- to 22-mer dramatically influenced on the sensitivity of the PNA and DNA sensors. Molecular type of the capturing probe did not affect the degree of potential shift. Theoretical model for charged rod-like duplex using the Gouy-Chapman equation indicates the dominant effect of electrostatic attractive forces between anionic DNA and underlying electrode at the electrolyte/electrode interface in the potentiometry. PMID:23435052

Label-Free Potentiometry for Detecting DNA Hybridization Using Peptide Nucleic Acid and DNA Probes

Directory of Open Access Journals (Sweden)

Yuji Miyahara

2013-02-01

Full Text Available Peptide nucleic acid (PNA has outstanding affinity over DNA for complementary nucleic acid sequences by forming a PNA-DNA heterodimer upon hybridization via Watson-Crick base-pairing. To verify whether PNA probes on an electrode surface enhance sensitivity for potentiometric DNA detection or not, we conducted a comparative study on the hybridization of PNA and DNA probes on the surface of a 10-channel gold electrodes microarray. Changes in the charge density as a result of hybridization at the solution/electrode interface on the self-assembled monolayer (SAM-formed microelectrodes were directly transformed into potentiometric signals using a high input impedance electrometer. The charge readout allows label-free, reagent-less, and multi-parallel detection of target oligonucleotides without any optical assistance. The differences in the probe lengths between 15- to 22-mer dramatically influenced on the sensitivity of the PNA and DNA sensors. Molecular type of the capturing probe did not affect the degree of potential shift. Theoretical model for charged rod-like duplex using the Gouy-Chapman equation indicates the dominant effect of electrostatic attractive forces between anionic DNA and underlying electrode at the electrolyte/electrode interface in the potentiometry.

Switchable DNA interfaces for the highly sensitive detection of label-free DNA targets.

Science.gov (United States)

Rant, Ulrich; Arinaga, Kenji; Scherer, Simon; Pringsheim, Erika; Fujita, Shozo; Yokoyama, Naoki; Tornow, Marc; Abstreiter, Gerhard

2007-10-30

We report a method to detect label-free oligonucleotide targets. The conformation of surface-tethered probe nucleic acids is modulated by alternating electric fields, which cause the molecules to extend away from or fold onto the biased surface. Binding (hybridization) of targets to the single-stranded probes results in a pronounced enhancement of the layer-height modulation amplitude, monitored optically in real time. The method features an exceptional detection limit of <3 x 10(8) bound targets per cm(2) sensor area. Single base-pair mismatches in the sequences of DNA complements may readily be identified; moreover, binding kinetics and binding affinities can be determined with high accuracy. When driving the DNA to oscillate at frequencies in the kHz regime, distinct switching kinetics are revealed for single- and double-stranded DNA. Molecular dynamics are used to identify the binding state of molecules according to their characteristic kinetic fingerprints by using a chip-compatible detection format.

High density fuel storage rack

International Nuclear Information System (INIS)

Zezza, L.J.

1980-01-01

High storage density for spent nuclear fuel assemblies in a pool achieved by positioning fuel storage cells of high thermal neutron absorption materials in an upright configuration in a rack. The rack holds the cells at required pitch. Each cell carries an internal fuel assembly support, and most cells are vertically movable in the rack so that they rest on the pool bottom. Pool water circulation through the cells and around the fuel assemblies is permitted by circulation openings at the top and bottom of the cells above and below the fuel assemblies

Persistence of environmental DNA in freshwater ecosystems.

Directory of Open Access Journals (Sweden)

Tony Dejean

Full Text Available The precise knowledge of species distribution is a key step in conservation biology. However, species detection can be extremely difficult in many environments, specific life stages and in populations at very low density. The aim of this study was to improve the knowledge on DNA persistence in water in order to confirm the presence of the focus species in freshwater ecosystems. Aquatic vertebrates (fish: Siberian sturgeon and amphibian: Bullfrog tadpoles were used as target species. In control conditions (tanks and in the field (ponds, the DNA detectability decreases with time after the removal of the species source of DNA. DNA was detectable for less than one month in both conditions. The density of individuals also influences the dynamics of DNA detectability in water samples. The dynamics of detectability reflects the persistence of DNA fragments in freshwater ecosystems. The short time persistence of detectable amounts of DNA opens perspectives in conservation biology, by allowing access to the presence or absence of species e.g. rare, secretive, potentially invasive, or at low density. This knowledge of DNA persistence will greatly influence planning of biodiversity inventories and biosecurity surveys.

Supercoiled circular DNA of an insect granulosis virus.

Science.gov (United States)

Tweeten, K A; Bulla, L A; Consigli, R A

1977-08-01

The DNA of the granulosis virus of the Indian meal moth, Plodia interpunctella, was characterized by physical chemical and electron microscopic techniques. Twenty-five percent of the DNA extracted from purified virus was isolated as supercoiled circular molecules. The remaining 75% consisted of relaxed circular molecules. These molecular forms were indicated by the production of two radioactive bands during sedimentation of (3)H-labeled granulosis virus DNA in alkaline sucrose gradients or in equilibrium density gradients of neutral cesium chloride/propidium iodide. Electron microscopic visualization of the DNA that banded at the higher density in the latter gradients revealed supercoiled structures whereas that of DNA that banded at the lower density demonstrated relaxed circular molecules. The superhelical molecules were converted to relaxed circles by treatment with pancreatic DNase. The molecular weight of the viral DNA was calculated to be 81 x 10(6) by sedimentation in neutral sucrose and 78 x 10(6) by sedimentation in alkaline sucrose. The molecular weight estimated from length measurements in electron micrographs was 76 x 10(6). The buoyant density of the granulosis virus DNA was 1.703 g/cm(3) and that of its insect host DNA was 1.697 g/cm(3). Equilibrium sedimentation in cesium chloride and thermal denaturation indicated G + C contents of 44% and 39% for the viral and host DNA, respectively.

Large-scale DNA Barcode Library Generation for Biomolecule Identification in High-throughput Screens.

Science.gov (United States)

Lyons, Eli; Sheridan, Paul; Tremmel, Georg; Miyano, Satoru; Sugano, Sumio

2017-10-24

High-throughput screens allow for the identification of specific biomolecules with characteristics of interest. In barcoded screens, DNA barcodes are linked to target biomolecules in a manner allowing for the target molecules making up a library to be identified by sequencing the DNA barcodes using Next Generation Sequencing. To be useful in experimental settings, the DNA barcodes in a library must satisfy certain constraints related to GC content, homopolymer length, Hamming distance, and blacklisted subsequences. Here we report a novel framework to quickly generate large-scale libraries of DNA barcodes for use in high-throughput screens. We show that our framework dramatically reduces the computation time required to generate large-scale DNA barcode libraries, compared with a naїve approach to DNA barcode library generation. As a proof of concept, we demonstrate that our framework is able to generate a library consisting of one million DNA barcodes for use in a fragment antibody phage display screening experiment. We also report generating a general purpose one billion DNA barcode library, the largest such library yet reported in literature. Our results demonstrate the value of our novel large-scale DNA barcode library generation framework for use in high-throughput screening applications.

Quality Analysis of DNA from Cord Blood Buffy Coat: The Best Neonatal DNA Source for Epidemiological Studies?

Science.gov (United States)

Zhou, Guangdi; Li, Qin; Huang, Lisu; Wu, Yuhang; Wu, Meiqin; Wang, Weiye C

2016-04-01

Umbilical cord blood is an economical and easy to obtain source of high-quality neonatal genomic DNA. However, although large numbers of cord blood samples have been collected, information on the yield and quality of the DNA extracted from cord blood is scarce. Moreover, considerable doubt still exists on the utility of the buffy coat instead of whole blood as a DNA source. We compared the sample storage and DNA extraction costs for whole blood, buffy coat, and all-cell pellet. We evaluated three different DNA purification kits and selected the most suitable one to purify 1011 buffy coat samples. We determined the DNA yield and optical density (OD) ratios and analyzed 48 single-nucleotide polymorphisms using time-of-flight mass spectrometry (TOF MS). We also analyzed eight possible preanalytical variables that may correlate with DNA yield or quality. Buffy coat was the most economical and least labor-intensive source for sample storage and DNA extraction. The average yield of genomic DNA from 200 μL of buffy coat sample was 16.01 ± 8.00 μg, which is sufficient for analytic experiments. The mean A260/A280 ratio and the mean A260/A230 ratio were 1.89 ± 0.09 and 1.95 ± 0.66, respectively. More than 99.5% of DNA samples passed the TOF MS test. Only hemolysis showed a strong correlation with OD ratios of DNA, but not with yield. Our findings show that cord blood buffy coat yields high-quality DNA in sufficient quantities to meet the requirements of experiments. Buffy coat was also found to be the most economic, efficient, and stable source of genomic DNA.

High Density GEOSAT/GM Altimeter Data

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — The high density Geosat/GM altimeter data south of 30 S have finally arrived. In addition, ERS-1 has completed more than 6 cycles of its 35-day repeat track. These...

LET-effects in DNA

International Nuclear Information System (INIS)

Kraft, G.; Taucher-Scholz, G.; Heilmann, J.

1995-01-01

The use of heavy particles in radiobiological experiments provides a fundamental tool to study the influence of different ionization densities and to prove the physical basis of models and theories. The knowledge of the interaction of high LET radiation (LET: linear energy transfer [keV/microm]) with biological matter is of great importance for the application of neutrons, protons and heavier ions in radiotherapy. It is also essential in radioprotection to estimate the risk in case of exposure to high LET radiation. In this contribution, an introductory view on the physical properties of ions is given and the cellular response to high LET radiation is summarized. Then the measurements of strand break induction of DNA in solution and in intracellular DNA are reported and compared to cell survival. The possibility of changes in the quality of the lesions is discussed and finally the present status of model calculations in comparison to the experiments is given

High-Current-Density Vertical-Tunneling Transistors from Graphene/Highly Doped Silicon Heterostructures.

Science.gov (United States)

Liu, Yuan; Sheng, Jiming; Wu, Hao; He, Qiyuan; Cheng, Hung-Chieh; Shakir, Muhammad Imran; Huang, Yu; Duan, Xiangfeng

2016-06-01

Scalable fabrication of vertical-tunneling transistors is presented based on heterostructures formed between graphene, highly doped silicon, and its native oxide. Benefiting from the large density of states of highly doped silicon, the tunneling transistors can deliver a current density over 20 A cm(-2) . This study demonstrates that the interfacial native oxide plays a crucial role in governing the carrier transport in graphene-silicon heterostructures. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Radiation-induced DNA double strand breaks in Ehrlich ascites tumour cells and their possible effects on cell survival

International Nuclear Information System (INIS)

Bloecher, D.

1981-01-01

A method to prepare high-molecular, pure DNA with the aid of enzymes, detergents, and heat treatment is presented. A sedimentation technique with neutral density gradients has been introduced which permits mass separation and molecular mass analysis of high-molecular DNA (msub(r) 10 ). Using this method, the induction of DNA double strand breaks (DSB) in the dose range between 10 Gy [de

The creation of high energy densities with antimatter beams

International Nuclear Information System (INIS)

Gibbs, W.R.; Kruk, J.W.; Rice Univ., Houston, TX

1989-01-01

The use of antiprotons (and antideuterons) for the study of the behavior of nuclear matter at high energy density is considered. It is shown that high temperatures and high energy densities can be achieved for small volumes. Also investigated is the strangeness production in antimatter annihilation. It is found that the high rate of Lambda production seen in a recent experiment is easily understood. The Lambda and K-short rapidity distributions are also reproduced by the model considered. 11 refs., 6 figs

High baryon density from relativistic heavy ion collisions

Energy Technology Data Exchange (ETDEWEB)

Pang, Y.; Kahana, S.H. [Brookhaven National Lab., Upton, NY (United States); Schlagel, T.J. [Brookhaven National Lab., Upton, NY (United States)]|[State Univ. of New York, Stony Brook, NY (United States)

1993-10-01

A quantitative model, based on hadronic physics, is developed and applied to heavy ion collisions at BNL-AGS energies. This model is in excellent agreement with observed particle spectra in heavy ion collisions using Si beams, where baryon densities of three and four times the normal nuclear matter density ({rho}{sub 0}) are reached. For Au on Au collisions, the authors predict the formation of matter at very high densities (up to 10 {rho}{sub 0}).

Serum osteoprotegerin levels and mammographic density among high-risk women.

Science.gov (United States)

Moran, Olivia; Zaman, Tasnim; Eisen, Andrea; Demsky, Rochelle; Blackmore, Kristina; Knight, Julia A; Elser, Christine; Ginsburg, Ophira; Zbuk, Kevin; Yaffe, Martin; Narod, Steven A; Salmena, Leonardo; Kotsopoulos, Joanne

2018-06-01

Mammographic density is a risk factor for breast cancer but the mechanism behind this association is unclear. The receptor activator of nuclear factor κB (RANK)/RANK ligand (RANKL) pathway has been implicated in the development of breast cancer. Given the role of RANK signaling in mammary epithelial cell proliferation, we hypothesized this pathway may also be associated with mammographic density. Osteoprotegerin (OPG), a decoy receptor for RANKL, is known to inhibit RANK signaling. Thus, it is of interest to evaluate whether OPG levels modify breast cancer risk through mammographic density. We quantified serum OPG levels in 57 premenopausal and 43 postmenopausal women using an enzyme-linked immunosorbent assay (ELISA). Cumulus was used to measure percent density, dense area, and non-dense area for each mammographic image. Subjects were classified into high versus low OPG levels based on the median serum OPG level in the entire cohort (115.1 pg/mL). Multivariate models were used to assess the relationship between serum OPG levels and the measures of mammographic density. Serum OPG levels were not associated with mammographic density among premenopausal women (P ≥ 0.42). Among postmenopausal women, those with low serum OPG levels had higher mean percent mammographic density (20.9% vs. 13.7%; P = 0.04) and mean dense area (23.4 cm 2 vs. 15.2 cm 2 ; P = 0.02) compared to those with high serum OPG levels after covariate adjustment. These findings suggest that low OPG levels may be associated with high mammographic density, particularly in postmenopausal women. Targeting RANK signaling may represent a plausible, non-surgical prevention option for high-risk women with high mammographic density, especially those with low circulating OPG levels.

An optimized rapid bisulfite conversion method with high recovery of cell-free DNA.

Science.gov (United States)

Yi, Shaohua; Long, Fei; Cheng, Juanbo; Huang, Daixin

2017-12-19

Methylation analysis of cell-free DNA is a encouraging tool for tumor diagnosis, monitoring and prognosis. Sensitivity of methylation analysis is a very important matter due to the tiny amounts of cell-free DNA available in plasma. Most current methods of DNA methylation analysis are based on the difference of bisulfite-mediated deamination of cytosine between cytosine and 5-methylcytosine. However, the recovery of bisulfite-converted DNA based on current methods is very poor for the methylation analysis of cell-free DNA. We optimized a rapid method for the crucial steps of bisulfite conversion with high recovery of cell-free DNA. A rapid deamination step and alkaline desulfonation was combined with the purification of DNA on a silica column. The conversion efficiency and recovery of bisulfite-treated DNA was investigated by the droplet digital PCR. The optimization of the reaction results in complete cytosine conversion in 30 min at 70 °C and about 65% of recovery of bisulfite-treated cell-free DNA, which is higher than current methods. The method allows high recovery from low levels of bisulfite-treated cell-free DNA, enhancing the analysis sensitivity of methylation detection from cell-free DNA.

Density Functional Methods for Shock Physics and High Energy Density Science

Science.gov (United States)

Desjarlais, Michael

2017-06-01

Molecular dynamics with density functional theory has emerged over the last two decades as a powerful and accurate framework for calculating thermodynamic and transport properties with broad application to dynamic compression, high energy density science, and warm dense matter. These calculations have been extensively validated against shock and ramp wave experiments, are a principal component of high-fidelity equation of state generation, and are having wide-ranging impacts on inertial confinement fusion, planetary science, and shock physics research. In addition to thermodynamic properties, phase boundaries, and the equation of state, one also has access to electrical conductivity, thermal conductivity, and lower energy optical properties. Importantly, all these properties are obtained within the same theoretical framework and are manifestly consistent. In this talk I will give a brief history and overview of molecular dynamics with density functional theory and its use in calculating a wide variety of thermodynamic and transport properties for materials ranging from ambient to extreme conditions and with comparisons to experimental data. I will also discuss some of the limitations and difficulties, as well as active research areas. Sandia is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

Morphodynamics of supercritical high-density turbidity currents

NARCIS (Netherlands)

Cartigny, M.

2012-01-01

Seafloor and outcrop observations combined with numerical and physical experiments show that turbidity currents are likely 1) to be in a supercritical flow state and 2) to carry high sediment concentrations (being of high-density). The thesis starts with an experimental study of bedforms

Foldable, High Energy Density Lithium Ion Batteries

Science.gov (United States)

Suresh, Shravan

Lithium Ion Batteries (LIBs) have become ubiquitous owing to its low cost, high energy density and, power density. Due to these advantages, LIBs have garnered a lot of attention as the primary energy storage devices in consumer electronics and electric vehicles. Recent advances in the consumer electronics research and, the drive to reduce greenhouse gases have created a demand for a shape conformable, high energy density batteries. This thesis focuses on the aforementioned two aspects of LIBs: (a) shape conformability (b) energy density and provides potential solutions to enhance them. This thesis is divided into two parts viz. (i) achieving foldability in batteries and, (ii) improving its energy density. Conventional LIBs are not shape conformable due to two limitations viz. inelasticity of metallic foils, and delamination of the active materials while bending. In the first part of the thesis (in Chapter 3), this problem is solved by replacing metallic current collector with Carbon Nanotube Macrofilms (CNMs). CNMs are superelastic films comprising of porous interconnected nanotube network. Using Molecular Dynamics (MD) simulation, we found that in the presence of an interconnected nanotube network CNMs can be fully folded. This is because the resultant stress due to bending and, the effective bending angle at the interface is reduced due to the network of nanotubes. Hence, unlike an isolated nanotube (which ruptures beyond 120 degrees of bending), a network of nanotubes can be completely folded. Thus, by replacing metallic current collector foils with CNMs, the flexibility limitation of a conventional LIB can be transcended. The second part of this thesis focusses on enhancing the energy density of LIBs. Two strategies adopted to achieve this goal are (a) removing the dead weight of the batteries, and (b) incorporating high energy density electrode materials. By incorporating CNMs, the weight of the batteries was reduced by 5-10 times due to low mass loading of

Structure determination of uracil-DNA N-glycosylase from Deinococcus radiodurans in complex with DNA.

Science.gov (United States)

Pedersen, Hege Lynum; Johnson, Kenneth A; McVey, Colin E; Leiros, Ingar; Moe, Elin

2015-10-01

Uracil-DNA N-glycosylase (UNG) is a DNA-repair enzyme in the base-excision repair (BER) pathway which removes uracil from DNA. Here, the crystal structure of UNG from the extremophilic bacterium Deinococcus radiodurans (DrUNG) in complex with DNA is reported at a resolution of 1.35 Å. Prior to the crystallization experiments, the affinity between DrUNG and different DNA oligonucleotides was tested by electrophoretic mobility shift assays (EMSAs). As a result of this analysis, two 16 nt double-stranded DNAs were chosen for the co-crystallization experiments, one of which (16 nt AU) resulted in well diffracting crystals. The DNA in the co-crystal structure contained an abasic site (substrate product) flipped into the active site of the enzyme, with no uracil in the active-site pocket. Despite the high resolution, it was not possible to fit all of the terminal nucleotides of the DNA complex into electron density owing to disorder caused by a lack of stabilizing interactions. However, the DNA which was in contact with the enzyme, close to the active site, was well ordered and allowed detailed analysis of the enzyme-DNA interaction. The complex revealed that the interaction between DrUNG and DNA is similar to that in the previously determined crystal structure of human UNG (hUNG) in complex with DNA [Slupphaug et al. (1996). Nature (London), 384, 87-92]. Substitutions in a (here defined) variable part of the leucine loop result in a shorter loop (eight residues instead of nine) in DrUNG compared with hUNG; regardless of this, it seems to fulfil its role and generate a stabilizing force with the minor groove upon flipping out of the damaged base into the active site. The structure also provides a rationale for the previously observed high catalytic efficiency of DrUNG caused by high substrate affinity by demonstrating an increased number of long-range electrostatic interactions between the enzyme and the DNA. Interestingly, specific interactions between residues

Biopolymer-nanocarbon composite electrodes for use as high-energy high-power density electrodes

Science.gov (United States)

Karakaya, Mehmet; Roberts, Mark; Arcilla-Velez, Margarita; Zhu, Jingyi; Podila, Ramakrishna; Rao, Apparao

2014-03-01

Supercapacitors (SCs) address our current energy storage and delivery needs by combining the high power, rapid switching, and exceptional cycle life of a capacitor with the high energy density of a battery. Although activated carbon is extensively used as a supercapacitor electrode due to its inexpensive nature, its low specific capacitance (100-120 F/g) fundamentally limits the energy density of SCs. We demonstrate that a nano-carbon based mechanically robust, electrically conducting, free-standing buckypaper electrode modified with an inexpensive biorenewable polymer, viz., lignin increases the electrode's specific capacitance (~ 600-700 F/g) while maintaining rapid discharge rates. In these systems, the carbon nanomaterials provide the high surface area, electrical conductivity and porosity, while the redox polymers provide a mechanism for charge storage through Faradaic charge transfer. The design of redox polymers and their incorporation into nanomaterial electrodes will be discussed with a focus on enabling high power and high energy density electrodes. Research supported by US NSF CMMI Grant 1246800.

Breast density estimation from high spectral and spatial resolution MRI

Science.gov (United States)

Li, Hui; Weiss, William A.; Medved, Milica; Abe, Hiroyuki; Newstead, Gillian M.; Karczmar, Gregory S.; Giger, Maryellen L.

2016-01-01

Abstract. A three-dimensional breast density estimation method is presented for high spectral and spatial resolution (HiSS) MR imaging. Twenty-two patients were recruited (under an Institutional Review Board--approved Health Insurance Portability and Accountability Act-compliant protocol) for high-risk breast cancer screening. Each patient received standard-of-care clinical digital x-ray mammograms and MR scans, as well as HiSS scans. The algorithm for breast density estimation includes breast mask generating, breast skin removal, and breast percentage density calculation. The inter- and intra-user variabilities of the HiSS-based density estimation were determined using correlation analysis and limits of agreement. Correlation analysis was also performed between the HiSS-based density estimation and radiologists’ breast imaging-reporting and data system (BI-RADS) density ratings. A correlation coefficient of 0.91 (pdensity estimations. An interclass correlation coefficient of 0.99 (pdensity estimations. A moderate correlation coefficient of 0.55 (p=0.0076) was observed between HiSS-based breast density estimations and radiologists’ BI-RADS. In summary, an objective density estimation method using HiSS spectral data from breast MRI was developed. The high reproducibility with low inter- and low intra-user variabilities shown in this preliminary study suggest that such a HiSS-based density metric may be potentially beneficial in programs requiring breast density such as in breast cancer risk assessment and monitoring effects of therapy. PMID:28042590

High dislocation density of tin induced by electric current

International Nuclear Information System (INIS)

Liao, Yi-Han; Liang, Chien-Lung; Lin, Kwang-Lung; Wu, Albert T.

2015-01-01

A dislocation density of as high as 10 17 /m 2 in a tin strip, as revealed by high resolution transmission electron microscope, was induced by current stressing at 6.5 x 10 3 A/ cm 2 . The dislocations exist in terms of dislocation line, dislocation loop, and dislocation aggregates. Electron Backscattered Diffraction images reflect that the high dislocation density induced the formation of low deflection angle subgrains, high deflection angle Widmanstätten grains, and recrystallization. The recrystallization gave rise to grain refining

Preparation and characterization of high-Tc superconducting thin films with high critical current densities

International Nuclear Information System (INIS)

Vase, P.

1991-08-01

The project was carried out in relation to possible cable and electronics applications of high-T c materials. Laser ablation was used as the deposition technique because of its stoichiometry conservation. Films were made in the YBa 2 Cu 3 O 7 compound due to its relatively simple stoichiometry compared to other High-T c compounds. Much attention was paid to the critical current density. A very high critical current density was reached. By using texture analysis by X-ray diffraction, it was found that films with high critical current densities were epitaxial, while films with low critical current densities contained several crystalline orientations. Four techniques for patterning the films were used - photo lithography and wet etch, laser ablation lithography, laser writing and electron beam lithography and ion milling. Sub-micron patterning has been demonstrated without degradation of the superconducting properties. The achieved patterning resolution is sufficient for preparation of many superconducting components. (AB)

Changing perceptions of hunger on a high nutrient density diet

Directory of Open Access Journals (Sweden)

Glaser Dale

2010-11-01

Full Text Available Abstract Background People overeat because their hunger directs them to consume more calories than they require. The purpose of this study was to analyze the changes in experience and perception of hunger before and after participants shifted from their previous usual diet to a high nutrient density diet. Methods This was a descriptive study conducted with 768 participants primarily living in the United States who had changed their dietary habits from a low micronutrient to a high micronutrient diet. Participants completed a survey rating various dimensions of hunger (physical symptoms, emotional symptoms, and location when on their previous usual diet versus the high micronutrient density diet. Statistical analysis was conducted using non-parametric tests. Results Highly significant differences were found between the two diets in relation to all physical and emotional symptoms as well as the location of hunger. Hunger was not an unpleasant experience while on the high nutrient density diet, was well tolerated and occurred with less frequency even when meals were skipped. Nearly 80% of respondents reported that their experience of hunger had changed since starting the high nutrient density diet, with 51% reporting a dramatic or complete change in their experience of hunger. Conclusions A high micronutrient density diet mitigates the unpleasant aspects of the experience of hunger even though it is lower in calories. Hunger is one of the major impediments to successful weight loss. Our findings suggest that it is not simply the caloric content, but more importantly, the micronutrient density of a diet that influences the experience of hunger. It appears that a high nutrient density diet, after an initial phase of adjustment during which a person experiences "toxic hunger" due to withdrawal from pro-inflammatory foods, can result in a sustainable eating pattern that leads to weight loss and improved health. A high nutrient density diet provides

High Efficiency Hydrodynamic DNA Fragmentation in a Bubbling System.

Science.gov (United States)

Li, Lanhui; Jin, Mingliang; Sun, Chenglong; Wang, Xiaoxue; Xie, Shuting; Zhou, Guofu; van den Berg, Albert; Eijkel, Jan C T; Shui, Lingling

2017-01-18

DNA fragmentation down to a precise fragment size is important for biomedical applications, disease determination, gene therapy and shotgun sequencing. In this work, a cheap, easy to operate and high efficiency DNA fragmentation method is demonstrated based on hydrodynamic shearing in a bubbling system. We expect that hydrodynamic forces generated during the bubbling process shear the DNA molecules, extending and breaking them at the points where shearing forces are larger than the strength of the phosphate backbone. Factors of applied pressure, bubbling time and temperature have been investigated. Genomic DNA could be fragmented down to controllable 1-10 Kbp fragment lengths with a yield of 75.30-91.60%. We demonstrate that the ends of the genomic DNAs generated from hydrodynamic shearing can be ligated by T4 ligase and the fragmented DNAs can be used as templates for polymerase chain reaction. Therefore, in the bubbling system, DNAs could be hydrodynamically sheared to achieve smaller pieces in dsDNAs available for further processes. It could potentially serve as a DNA sample pretreatment technique in the future.

High power density yeast catalyzed microbial fuel cells

Science.gov (United States)

Ganguli, Rahul

Microbial fuel cells leverage whole cell biocatalysis to convert the energy stored in energy-rich renewable biomolecules such as sugar, directly to electrical energy at high efficiencies. Advantages of the process include ambient temperature operation, operation in natural streams such as wastewater without the need to clean electrodes, minimal balance-of-plant requirements compared to conventional fuel cells, and environmentally friendly operation. These make the technology very attractive as portable power sources and waste-to-energy converters. The principal problem facing the technology is the low power densities compared to other conventional portable power sources such as batteries and traditional fuel cells. In this work we examined the yeast catalyzed microbial fuel cell and developed methods to increase the power density from such fuel cells. A combination of cyclic voltammetry and optical absorption measurements were used to establish significant adsorption of electron mediators by the microbes. Mediator adsorption was demonstrated to be an important limitation in achieving high power densities in yeast-catalyzed microbial fuel cells. Specifically, the power densities are low for the length of time mediator adsorption continues to occur. Once the mediator adsorption stops, the power densities increase. Rotating disk chronoamperometry was used to extract reaction rate information, and a simple kinetic expression was developed for the current observed in the anodic half-cell. Since the rate expression showed that the current was directly related to microbe concentration close to the electrode, methods to increase cell mass attached to the anode was investigated. Electrically biased electrodes were demonstrated to develop biofilm-like layers of the Baker's yeast with a high concentration of cells directly connected to the electrode. The increased cell mass did increase the power density 2 times compared to a non biofilm fuel cell, but the power density

The Influence of Decreased Levels of High Density Lipoprotein ...

African Journals Online (AJOL)

very low density lipoprotein cholesterol, and triglyceride were assayed. ... Abiodun and Gwarzo: Association of high density lipoprotein cholesterol with haemolysis in sickle cell disease ... analyses were carried out to determine the correlation.

High Power Density Power Electronic Converters for Large Wind Turbines

DEFF Research Database (Denmark)

Senturk, Osman Selcuk

. For these VSCs, high power density is required due to limited turbine nacelle space. Also, high reliability is required since maintenance cost of these remotely located wind turbines is quite high and these turbines operate under harsh operating conditions. In order to select a high power density and reliability......In large wind turbines (in MW and multi-MW ranges), which are extensively utilized in wind power plants, full-scale medium voltage (MV) multi-level (ML) voltage source converters (VSCs) are being more preferably employed nowadays for interfacing these wind turbines with electricity grids...... VSC solution for wind turbines, first, the VSC topology and the switch technology to be employed should be specified such that the highest possible power density and reliability are to be attained. Then, this qualitative approach should be complemented with the power density and reliability...

High density implosion experiments at Nova

International Nuclear Information System (INIS)

Cable, M.D.; Hatchett, S.P.; Nelson, M.B.; Lerche, R.A.; Murphy, T.J.; Ress, D.B.

1994-01-01

Deuterium filled glass microballoons are used as indirectly driven targets for implosion experiments at the Nova Laser Fusion Facility. High levels of laser precision were required to achieve fuel densities and convergences to an ignition scale hot spot. (AIP) copyright 1994 American Institute of Physics

Quantitative characterization of conformational-specific protein-DNA binding using a dual-spectral interferometric imaging biosensor

Science.gov (United States)

Zhang, Xirui; Daaboul, George G.; Spuhler, Philipp S.; Dröge, Peter; Ünlü, M. Selim

2016-03-01

DNA-binding proteins play crucial roles in the maintenance and functions of the genome and yet, their specific binding mechanisms are not fully understood. Recently, it was discovered that DNA-binding proteins recognize specific binding sites to carry out their functions through an indirect readout mechanism by recognizing and capturing DNA conformational flexibility and deformation. High-throughput DNA microarray-based methods that provide large-scale protein-DNA binding information have shown effective and comprehensive analysis of protein-DNA binding affinities, but do not provide information of DNA conformational changes in specific protein-DNA complexes. Building on the high-throughput capability of DNA microarrays, we demonstrate a quantitative approach that simultaneously measures the amount of protein binding to DNA and nanometer-scale DNA conformational change induced by protein binding in a microarray format. Both measurements rely on spectral interferometry on a layered substrate using a single optical instrument in two distinct modalities. In the first modality, we quantitate the amount of binding of protein to surface-immobilized DNA in each DNA spot using a label-free spectral reflectivity technique that accurately measures the surface densities of protein and DNA accumulated on the substrate. In the second modality, for each DNA spot, we simultaneously measure DNA conformational change using a fluorescence vertical sectioning technique that determines average axial height of fluorophores tagged to specific nucleotides of the surface-immobilized DNA. The approach presented in this paper, when combined with current high-throughput DNA microarray-based technologies, has the potential to serve as a rapid and simple method for quantitative and large-scale characterization of conformational specific protein-DNA interactions.DNA-binding proteins play crucial roles in the maintenance and functions of the genome and yet, their specific binding mechanisms are

Evaluating differential nuclear DNA yield rates and osteocyte numbers among human bone tissue types: A synchrotron radiation micro-CT approach.

Science.gov (United States)

Andronowski, Janna M; Mundorff, Amy Z; Pratt, Isaac V; Davoren, Jon M; Cooper, David M L

2017-05-01

Molecular human identification has conventionally focused on DNA sampling from dense, weight-bearing cortical bone tissue, typically from femora or tibiae. A comparison of skeletal elements from three contemporary individuals demonstrated that elements with high quantities of cancellous bone yielded nuclear DNA at the highest rates, suggesting that preferentially sampling cortical bone may be suboptimal (Mundorff & Davoren, 2014). Despite these findings, the reason for the differential DNA yields between cortical and cancellous bone tissues remains unknown. The primary goal of this work is to ascertain whether differences in bone microstructure can be used to explain differential nuclear DNA yield among bone tissue types observed by Mundorff and Davoren (2014), with a focus on osteocytes and the three-dimensional (3D) quantification of their associated lacunae. Osteocytes and other bone cells are recognized to house DNA in bone tissue, thus examining the density of their lacunae may explain why nuclear DNA yield rates differ among bone tissue types. Lacunae were visualized and quantified using synchrotron radiation-based micro-Computed Tomographic imaging (SR micro-CT). Volumes of interest (VOIs) from cortical and cancellous bone tissues (n=129) were comparatively analyzed from the three skeletons sampled for Mundorff and Davoren's (2014) study. Analyses tested the primary hypothesis that the abundance and density of osteocytes (inferred from their lacunar spaces) vary between cortical and cancellous bone tissue types. Results demonstrated that osteocyte lacunar abundance and density vary between cortical and cancellous bone tissue types, with cortical bone VOIs containing a higher lacunar abundance and density. We found that the osteocyte lacunar density values are independent of nuclear DNA yield, suggesting an alternative explanation for the higher nuclear DNA yields from bones with greater quantities of cancellous bone tissue. The use of SR micro-CT allowed for

DNA-dispersed graphene/NiO hybrid materials for highly sensitive non-enzymatic glucose sensor

International Nuclear Information System (INIS)

Lv Wei; Jin Fengmin; Guo Quangui; Yang Quanhong; Kang Feiyu

2012-01-01

Highlights: ► We investigated the potential of GNS/NiO/DNA hybrid used as a nonenzymatic sensor. ► DNA is a highly efficient disperse agent for GNS/NiO hybrid than ionic surfactants. ► GNS/NiO/DNA hybrid shows fast electron transfer in the electrochemical reaction. ► GNS/NiO/DNA hybrid shows good detection performance towards glucose. - Abstract: We demonstrate graphene nanosheet/NiO hybrids (GNS/NiO) as the active material for high-performance non-enzymatic glucose sensors. Such sensors are fabricated by DNA-dispersed GNS/NiO suspension deposited on glassy carbon electrodes. ss-DNA shows strong dispersing ability for the GNS/NiO hybrid materials resulting in stable water-dispersible GNS/NiO/DNA hybrids with fully separated layers. The GNS/NiO/DNA hybrids show enhanced electron transfer in the electrocatalytic reaction process, and accordingly, such hybrids modified electrodes show good sensing performance towards glucose and are characterized by large detection ranges, short response periods, low detection limit and high sensitivity and stability.

High-energy density physics at Los Alamos

International Nuclear Information System (INIS)

Byrnes, P.; Younger, S.M.

1993-03-01

This brochure describes the facilities of the Above Ground Experiments II (AGEX II) and the Inertial Confinement Fusion (ICF) programs at Los Alamo. Combined, these programs represent, an unparalleled capability to address important issues in high-energy density physics that are critical to the future defense, energy, and research needs of th e United States. The mission of the AGEX II program at Los Alamos is to provide additional experimental opportunities for the nuclear weapons program. For this purpose we have assembled at Los Alamos the broadest array of high-energy density physics facilities of any laboratory in the world. Inertial confinement fusion seeks to achieve thermonuclear burn on a laboratory scale through the implosion of a small quantity of deuterium and tritium fuel to very high Pressure and temperature.The Los Alamos ICF program is focused on target physics. With the largest scientific computing center in the world, We can perform calculations of unprecedented sophistication and precision. We field experiments at facilities worldwide-including our own Trident and Mercury lasers-to confirm our understanding and to provide the necessary data base to proceed toward the historic goal of controlled fusion in the laboratory. In addition to direct programmatic high-energy density physics is a nc scientific endeavor in itself. The ultrahigh magnetic fields produced in our high explosive pulsed-power generators can be used in awide variety of solid state physics and temperature superconductor studies. The structure and dynamics of planetary atmospheres can be simulated through the compression of gas mixtures

Workshop on High Power ICH Antenna Designs for High Density Tokamaks

Science.gov (United States)

Aamodt, R. E.

1990-02-01

A workshop in high power ICH antenna designs for high density tokamaks was held to: (1) review the data base relevant to the high power heating of high density tokamaks; (2) identify the important issues which need to be addressed in order to ensure the success of the ICRF programs on CIT and Alcator C-MOD; and (3) recommend approaches for resolving the issues in a timely realistic manner. Some specific performance goals for the antenna system define a successful design effort. Simply stated these goals are: couple the specified power per antenna into the desired ion species; produce no more than an acceptable level of RF auxiliary power induced impurities; and have a mechanical structure which safely survives the thermal, mechanical and radiation stresses in the relevant environment. These goals are intimately coupled and difficult tradeoffs between scientific and engineering constraints have to be made.

Plasma Diagnostics in High Density Reactors

International Nuclear Information System (INIS)

Daltrini, A. M.; Moshkalyov, S.; Monteiro, M. J. R.; Machida, M.; Kostryukov, A.; Besseler, E.; Biasotto, C.; Diniz, J. A.

2006-01-01

Langmuir electric probes and optical emission spectroscopy diagnostics were developed for applications in high density plasmas. These diagnostics were employed in two plasma sources: an electron cyclotron resonance (ECR) plasma and an RF driven inductively coupled plasma (ICP) plasma. Langmuir probes were tested using a number of probing dimensions, probe tip materials, circuits for probe bias and filters. Then, the results were compared with the optical spectroscopy measurements. With these diagnostics, analyses of various plasma processes were performed in both reactors. For example, it has been shown that species like NH radicals generated in gas phase can have critical impact on films deposited by ECR plasmas. In the ICP source, plasmas in atomic and molecular gases were shown to have different spatial distributions, likely due to nonlocal electron heating. The low-to-high density transitions in the ICP plasma were also studied. The role of metastables is shown to be significant in Ar plasmas, in contrast to plasmas with additions of molecular gases

Possible new form of matter at high density

International Nuclear Information System (INIS)

Lee, T.D.

1974-01-01

As a preliminary to discussion of the possibility of new forms of matter at high density, questions relating to the vacuum and vacuum excitation are considered. A quasi-classical approach to the development of abnormal nuclear states is undertaken using a Fermi gas of nucleons of uniform density. Discontinuous transitions are considered in the sigma model (tree approximation) followed by brief consideration of higher order loop diagrams. Production and detection of abnormal nuclear states are discussed in the context of high energy heavy ion collisions. Remarks are made on motivation for such research. 8 figures

The high density effects in the Drell-Yan process

International Nuclear Information System (INIS)

Betemps, M.A.; Gay Ducati, M.B.; Ayala Filho, A.L.

2003-01-01

The high density effects in the Drell-Yan process (q q-bar → γ * →l + l - ) are investigated for pA collisions at RHIC and LHC energies. In particular, we use a set of nuclear parton distributions that describes the present nuclear eA and pA data in the DGLAP approach including the high density effects introduced in the perturbative Glauber-Mueller approach. (author)

Efficient self-assembly of DNA-functionalized fluorophores and gold nanoparticles with DNA functionalized silicon surfaces: the effect of oligomer spacers

Science.gov (United States)

Milton, James A.; Patole, Samson; Yin, Huabing; Xiao, Qiang; Brown, Tom; Melvin, Tracy

2013-01-01

Although strategies for the immobilization of DNA oligonucleotides onto surfaces for bioanalytical and top-down bio-inspired nanobiofabrication approaches are well developed, the effect of introducing spacer molecules between the surface and the DNA oligonucleotide for the hybridization of nanoparticle–DNA conjugates has not been previously assessed in a quantitative manner. The hybridization efficiency of DNA oligonucleotides end-labelled with gold nanoparticles (1.4 or 10 nm diameter) with DNA sequences conjugated to silicon surfaces via hexaethylene glycol phosphate diester oligomer spacers (0, 1, 2, 6 oligomers) was found to be independent of spacer length. To quantify both the density of DNA strands attached to the surfaces and hybridization with the surface-attached DNA, new methodologies have been developed. Firstly, a simple approach based on fluorescence has been developed for determination of the immobilization density of DNA oligonucleotides. Secondly, an approach using mass spectrometry has been created to establish (i) the mean number of DNA oligonucleotides attached to the gold nanoparticles and (ii) the hybridization density of nanoparticle–oligonucleotide conjugates with the silicon surface–attached complementary sequence. These methods and results will be useful for application with nanosensors, the self-assembly of nanoelectronic devices and the attachment of nanoparticles to biomolecules for single-molecule biophysical studies. PMID:23361467

BCS Theory of Hadronic Matter at High Densities

DEFF Research Database (Denmark)

Bohr, Henrik; Panda, Prafulla K.; Providencia, Constanca

2012-01-01

The equilibrium between the so-called 2SC and CFL phases of strange quark matter at high densities is investigated in the framework of a simple schematic model of the NJL type. Equal densities are assumed for quarks u, d and s. The 2SC phase is here described by a color-flavor symmetric state, in...

Sr-doped Lanthanum Nickelate Nanofibers for High Energy Density Supercapacitors

International Nuclear Information System (INIS)

Cao, Yi; Lin, Baoping; Sun, Ying; Yang, Hong; Zhang, Xueqin

2015-01-01

Highlights: • The electrode made by LNF-0.7 possessed excellent performance (719 F g −1 ) at Na 2 SO 4 electrolyte • LNF-0.7//LNF-0.7 symmetric supercapacitor device were firstly prepared • The maximum energy density of 81.4 Wh·kg −1 are achieved at a power density of 500W·kg −1 • This symmetric supercapacitor also shows an excellent cycling life - Abstract: The series La x Sr 1−x NiO 3−δ (0.3≤x≤1) nanofibers (LNF-x) samples are prepared by using electrospun method. We investigate the structure and the electrochemical properties of LNF-x in detail. As a result, LNF-x nanofibers present a perovskite structure, and the LNF-0.7 sample with high specific surface area display remarkable performance as an electrode material for supercapacitors. The maximum specific capacitance value of 719 F·g −1 at a current density of 2 A·g −1 , which retains 505 F·g −1 at a high current density of 20 A·g −1 , is obtained for LNF-0.7 electrode in 1 M Na 2 SO 4 aqueous electrolyte. Moreover, the LNF-0.7//LNF-0.7 symmetric supercapacitor device using 1 M Na 2 SO 4 aqueous solution is successfully demonstrated. The capacitor device can operate at a cell voltage as high as 2 V, and it exhibits an energy density of 30.5 Wh·kg −1 at a high power density of 10 kW·kg −1 and a high energy density of 81.4 Wh·kg −1 at a low power density of 500 W·kg −1 . More importantly, this symmetric supercapacitor also shows an excellent cycling performance with 90% specific capacitance retention after 2000 charging and discharging cycles. Those results offer a suitable design of electrode materials for high-performance supercapacitors

High-Stacking-Density, Superior-Roughness LDH Bridged with Vertically Aligned Graphene for High-Performance Asymmetric Supercapacitors.

Science.gov (United States)

Guo, Wei; Yu, Chang; Li, Shaofeng; Yang, Juan; Liu, Zhibin; Zhao, Changtai; Huang, Huawei; Zhang, Mengdi; Han, Xiaotong; Niu, Yingying; Qiu, Jieshan

2017-10-01

The high-performance electrode materials with tuned surface and interface structure and functionalities are highly demanded for advanced supercapacitors. A novel strategy is presented to conFigure high-stacking-density, superior-roughness nickel manganese layered double hydroxide (LDH) bridged by vertically aligned graphene (VG) with nickel foam (NF) as the conductive collector, yielding the LDH-NF@VG hybrids for asymmetric supercapacitors. The VG nanosheets provide numerous electron transfer channels for quick redox reactions, and well-developed open structure for fast mass transport. Moreover, the high-stacking-density LDH grown and assembled on VG nanosheets result in a superior hydrophilicity derived from the tuned nano/microstructures, especially microroughness. Such a high stacking density with abundant active sites and superior wettability can be easily accessed by aqueous electrolytes. Benefitting from the above features, the LDH-NF@VG can deliver a high capacitance of 2920 F g -1 at a current density of 2 A g -1 , and the asymmetric supercapacitor with the LDH-NF@VG as positive electrode and activated carbon as negative electrode can deliver a high energy density of 56.8 Wh kg -1 at a power density of 260 W kg -1 , with a high specific capacitance retention rate of 87% even after 10 000 cycles. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

High-throughput STR analysis for DNA database using direct PCR.

Science.gov (United States)

Sim, Jeong Eun; Park, Su Jeong; Lee, Han Chul; Kim, Se-Yong; Kim, Jong Yeol; Lee, Seung Hwan

2013-07-01

Since the Korean criminal DNA database was launched in 2010, we have focused on establishing an automated DNA database profiling system that analyzes short tandem repeat loci in a high-throughput and cost-effective manner. We established a DNA database profiling system without DNA purification using a direct PCR buffer system. The quality of direct PCR procedures was compared with that of conventional PCR system under their respective optimized conditions. The results revealed not only perfect concordance but also an excellent PCR success rate, good electropherogram quality, and an optimal intra/inter-loci peak height ratio. In particular, the proportion of DNA extraction required due to direct PCR failure could be minimized to <3%. In conclusion, the newly developed direct PCR system can be adopted for automated DNA database profiling systems to replace or supplement conventional PCR system in a time- and cost-saving manner. © 2013 American Academy of Forensic Sciences Published 2013. This article is a U.S. Government work and is in the public domain in the U.S.A.

High-fidelity DNA replication in Mycobacterium tuberculosis relies on a trinuclear zinc center.

Science.gov (United States)

Baños-Mateos, Soledad; van Roon, Anne-Marie M; Lang, Ulla F; Maslen, Sarah L; Skehel, J Mark; Lamers, Meindert H

2017-10-11

High-fidelity DNA replication depends on a proofreading 3'-5' exonuclease that is associated with the replicative DNA polymerase. The replicative DNA polymerase DnaE1 from the major pathogen Mycobacterium tuberculosis (Mtb) uses its intrinsic PHP-exonuclease that is distinct from the canonical DEDD exonucleases found in the Escherichia coli and eukaryotic replisomes. The mechanism of the PHP-exonuclease is not known. Here, we present the crystal structure of the Mtb DnaE1 polymerase. The PHP-exonuclease has a trinuclear zinc center, coordinated by nine conserved residues. Cryo-EM analysis reveals the entry path of the primer strand in the PHP-exonuclease active site. Furthermore, the PHP-exonuclease shows a striking similarity to E. coli endonuclease IV, which provides clues regarding the mechanism of action. Altogether, this work provides important insights into the PHP-exonuclease and reveals unique properties that make it an attractive target for novel anti-mycobacterial drugs.The polymerase and histidinol phosphatase (PHP) domain in the DNA polymerase DnaE1 is essential for mycobacterial high-fidelity DNA replication. Here, the authors determine the DnaE1 crystal structure, which reveals the PHP-exonuclease mechanism that can be exploited for antibiotic development.

Edge density profiles in high-performance JET plasmas

International Nuclear Information System (INIS)

Summers, D.D.R.; Viaccoz, B.; Vince, J.

1997-01-01

Detailed electron density profiles of the scrape-off layer in high-performance JET plasmas (plasma current, I p nbi ∝17 MW) have been measured by means of a lithium beam diagnostic system featuring high spatial resolution [Kadota (1978)[. Measurements were taken over a period of several seconds, allowing examination of the evolution of the edge profile at a location upstream from the divertor target. The data clearly show the effects of the H-mode transition - an increase in density near the plasma separatrix and a reduction in density scrape-off length. The profiles obtained under various plasma conditions are compared firstly with data from other diagnostics, located elsewhere in the vessel, and also with the predictions of an 'onion-skin' model (DIVIMP), which used, as initial parameters, data from an array of probes located in the divertor target. (orig.)

DNA-modified electrodes fabricated using copper-free click chemistry for enhanced protein detection.

Science.gov (United States)

Furst, Ariel L; Hill, Michael G; Barton, Jacqueline K

2013-12-31

A method of DNA monolayer formation has been developed using copper-free click chemistry that yields enhanced surface homogeneity and enables variation in the amount of DNA assembled; extremely low-density DNA monolayers, with as little as 5% of the monolayer being DNA, have been formed. These DNA-modified electrodes (DMEs) were characterized visually, with AFM, and electrochemically, and were found to facilitate DNA-mediated reduction of a distally bound redox probe. These low-density monolayers were found to be more homogeneous than traditional thiol-modified DNA monolayers, with greater helix accessibility through an increased surface area-to-volume ratio. Protein binding efficiency of the transcriptional activator TATA-binding protein (TBP) was also investigated on these surfaces and compared to that on DNA monolayers formed with standard thiol-modified DNA. Our low-density monolayers were found to be extremely sensitive to TBP binding, with a signal decrease in excess of 75% for 150 nM protein. This protein was detectable at 4 nM, on the order of its dissociation constant, with our low-density monolayers. The improved DNA helix accessibility and sensitivity of our low-density DNA monolayers to TBP binding reflects the general utility of this method of DNA monolayer formation for DNA-based electrochemical sensor development.

High Density Lipoprotein and it's Dysfunction.

Science.gov (United States)

Eren, Esin; Yilmaz, Necat; Aydin, Ozgur

2012-01-01

Plasma high-density lipoprotein cholesterol(HDL-C) levels do not predict functionality and composition of high-density lipoprotein(HDL). Traditionally, keeping levels of low-density lipoprotein cholesterol(LDL-C) down and HDL-C up have been the goal of patients to prevent atherosclerosis that can lead to coronary vascular disease(CVD). People think about the HDL present in their cholesterol test, but not about its functional capability. Up to 65% of cardiovascular death cannot be prevented by putative LDL-C lowering agents. It well explains the strong interest in HDL increasing strategies. However, recent studies have questioned the good in using drugs to increase level of HDL. While raising HDL is a theoretically attractive target, the optimal approach remains uncertain. The attention has turned to the quality, rather than the quantity, of HDL-C. An alternative to elevations in HDL involves strategies to enhance HDL functionality. The situation poses an opportunity for clinical chemists to take the lead in the development and validation of such biomarkers. The best known function of HDL is the capacity to promote cellular cholesterol efflux from peripheral cells and deliver cholesterol to the liver for excretion, thereby playing a key role in reverse cholesterol transport (RCT). The functions of HDL that have recently attracted attention include anti-inflammatory and anti-oxidant activities. High antioxidant and anti-inflammatory activities of HDL are associated with protection from CVD.This review addresses the current state of knowledge regarding assays of HDL functions and their relationship to CVD. HDL as a therapeutic target is the new frontier with huge potential for positive public health implications.

Analysis of JC virus DNA replication using a quantitative and high-throughput assay

International Nuclear Information System (INIS)

Shin, Jong; Phelan, Paul J.; Chhum, Panharith; Bashkenova, Nazym; Yim, Sung; Parker, Robert; Gagnon, David; Gjoerup, Ole; Archambault, Jacques; Bullock, Peter A.

2014-01-01

Progressive Multifocal Leukoencephalopathy (PML) is caused by lytic replication of JC virus (JCV) in specific cells of the central nervous system. Like other polyomaviruses, JCV encodes a large T-antigen helicase needed for replication of the viral DNA. Here, we report the development of a luciferase-based, quantitative and high-throughput assay of JCV DNA replication in C33A cells, which, unlike the glial cell lines Hs 683 and U87, accumulate high levels of nuclear T-ag needed for robust replication. Using this assay, we investigated the requirement for different domains of T-ag, and for specific sequences within and flanking the viral origin, in JCV DNA replication. Beyond providing validation of the assay, these studies revealed an important stimulatory role of the transcription factor NF1 in JCV DNA replication. Finally, we show that the assay can be used for inhibitor testing, highlighting its value for the identification of antiviral drugs targeting JCV DNA replication. - Highlights: • Development of a high-throughput screening assay for JCV DNA replication using C33A cells. • Evidence that T-ag fails to accumulate in the nuclei of established glioma cell lines. • Evidence that NF-1 directly promotes JCV DNA replication in C33A cells. • Proof-of-concept that the HTS assay can be used to identify pharmacological inhibitor of JCV DNA replication

Analysis of JC virus DNA replication using a quantitative and high-throughput assay

Energy Technology Data Exchange (ETDEWEB)

Shin, Jong; Phelan, Paul J.; Chhum, Panharith; Bashkenova, Nazym; Yim, Sung; Parker, Robert [Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA 02111 (United States); Gagnon, David [Institut de Recherches Cliniques de Montreal (IRCM), 110 Pine Avenue West, Montreal, Quebec, Canada H2W 1R7 (Canada); Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Quebec (Canada); Gjoerup, Ole [Molecular Oncology Research Institute, Tufts Medical Center, Boston, MA 02111 (United States); Archambault, Jacques [Institut de Recherches Cliniques de Montreal (IRCM), 110 Pine Avenue West, Montreal, Quebec, Canada H2W 1R7 (Canada); Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Quebec (Canada); Bullock, Peter A., E-mail: Peter.Bullock@tufts.edu [Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA 02111 (United States)

2014-11-15

Progressive Multifocal Leukoencephalopathy (PML) is caused by lytic replication of JC virus (JCV) in specific cells of the central nervous system. Like other polyomaviruses, JCV encodes a large T-antigen helicase needed for replication of the viral DNA. Here, we report the development of a luciferase-based, quantitative and high-throughput assay of JCV DNA replication in C33A cells, which, unlike the glial cell lines Hs 683 and U87, accumulate high levels of nuclear T-ag needed for robust replication. Using this assay, we investigated the requirement for different domains of T-ag, and for specific sequences within and flanking the viral origin, in JCV DNA replication. Beyond providing validation of the assay, these studies revealed an important stimulatory role of the transcription factor NF1 in JCV DNA replication. Finally, we show that the assay can be used for inhibitor testing, highlighting its value for the identification of antiviral drugs targeting JCV DNA replication. - Highlights: • Development of a high-throughput screening assay for JCV DNA replication using C33A cells. • Evidence that T-ag fails to accumulate in the nuclei of established glioma cell lines. • Evidence that NF-1 directly promotes JCV DNA replication in C33A cells. • Proof-of-concept that the HTS assay can be used to identify pharmacological inhibitor of JCV DNA replication.

Workshop on high power ICH antenna designs for high density tokamaks

International Nuclear Information System (INIS)

Aamodt, R.E.

1990-01-01

A workshop in high power ICH antenna designs for high density tokamaks was held in Boulder, Colorado on January 31 through February 2, 1990. The purposes of the workshop were to: (1) review the data base relevant to the high power heating of high density tokamaks; (2) identify the important issues which need to be addressed in order to ensure the success of the ICRF programs on CIT and Alcator C-MOD; and (3) recommend approaches for resolving the issues in a timely realistic manner. Some specific performance goals for the antenna system define a successful design effort. Simply stated these goals are: couple the specified power per antenna into the desired ion species; produce no more than an acceptable level of rf auxiliary power induced impurities; and have a mechanical structure which safely survives the thermal, mechanical and radiation stresses in the relevant environment. These goals are intimately coupled and difficult tradeoffs between scientific and engineering constraints have to be made

Relativistic many-body theory of high density matter

International Nuclear Information System (INIS)

Chin, S.A.

1977-01-01

A fully relativistic quantum many-body theory is applied to the study of high-density matter. The latter is identified with the zero-temperature ground state of a system of interacting baryons. In accordance with the observed short-range repulsive and long-range attractive character of the nucleon--nucleon force, baryons are described as interacting with each other via a massive scalar and a massive vector meson exchange. In the Hartree approximation, the theory yields the same result as the mean-field theory, but with additional vacuum fluctuation corrections. The resultant equation of state for neutron matter is used to determine properties of neutron stars. The relativistic exchange energy, its corresponding single-particle excitation spectrum, and its effect on the neutron matter equation of state, are calculated. The correlation energy from summing the set of ring diagrams is derived directly from the energy-momentum tensor, with renormalization carried out by adding counterterms to the original Lagrangian and subtracting purely vacuum expectation values. Terms of order g 4 lng 2 are explicitly given. Effects of scalar-vector mixing are discussed. Collective modes corresponding to macroscopic density fluctuation are investigated. Two basic modes are found, a plasma-like mode and zero sound, with the latter dominant at high density. The stability and damping of these modes are studied. Last, the effect of vacuum polarization in high-density matter is examined

High Efficiency Acetylcholinesterase Immobilization on DNA Aptamer Modified Surfaces

Directory of Open Access Journals (Sweden)

Orada Chumphukam

2014-04-01

Full Text Available We report here the in vitro selection of DNA aptamers for electric eel acetylcholinesterase (AChE. One selected aptamer sequence (R15/19 has a high affinity towards the enzyme (Kd = 157 ± 42 pM. Characterization of the aptamer showed its binding is not affected by low ionic strength (~20 mM, however significant reduction in affinity occurred at high ionic strength (~1.2 M. In addition, this aptamer does not inhibit the catalytic activity of AChE that we exploit through immobilization of the DNA on a streptavidin-coated surface. Subsequent immobilization of AChE by the aptamer results in a 4-fold higher catalytic activity when compared to adsorption directly on to plastic.

Selection of DNA aptamers against epidermal growth factor receptor with high affinity and specificity

Energy Technology Data Exchange (ETDEWEB)

Wang, Deng-Liang [The First Clinical Medical College of Fujian Medical University, Fuzhou (China); Department of Neurosurgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou (China); Song, Yan-Ling; Zhu, Zhi; Li, Xi-Lan; Zou, Yuan [State Key Laboratory for Physical Chemistry of Solid Surfaces, Key Laboratory for Chemical Biology of Fujian Province, Key Laboratory of Analytical Chemistry, and Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005 (China); Yang, Hai-Tao; Wang, Jiang-Jie [The First Clinical Medical College of Fujian Medical University, Fuzhou (China); Yao, Pei-Sen [Department of Neurosurgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou (China); Pan, Ru-Jun [The First Clinical Medical College of Fujian Medical University, Fuzhou (China); Yang, Chaoyong James, E-mail: cyyang@xmu.edu.cn [State Key Laboratory for Physical Chemistry of Solid Surfaces, Key Laboratory for Chemical Biology of Fujian Province, Key Laboratory of Analytical Chemistry, and Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005 (China); Kang, De-Zhi, E-mail: kdzy99988@163.com [The First Clinical Medical College of Fujian Medical University, Fuzhou (China); Department of Neurosurgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou (China)

2014-10-31

Highlights: • This is the first report of DNA aptamer against EGFR in vitro. • Aptamer can bind targets with high affinity and selectivity. • DNA aptamers are more stable, cheap and efficient than RNA aptamers. • Our selected DNA aptamer against EGFR has high affinity with K{sub d} 56 ± 7.3 nM. • Our selected DNA aptamer against EGFR has high selectivity. - Abstract: Epidermal growth factor receptor (EGFR/HER1/c-ErbB1), is overexpressed in many solid cancers, such as epidermoid carcinomas, malignant gliomas, etc. EGFR plays roles in proliferation, invasion, angiogenesis and metastasis of malignant cancer cells and is the ideal antigen for clinical applications in cancer detection, imaging and therapy. Aptamers, the output of the systematic evolution of ligands by exponential enrichment (SELEX), are DNA/RNA oligonucleotides which can bind protein and other substances with specificity. RNA aptamers are undesirable due to their instability and high cost of production. Conversely, DNA aptamers have aroused researcher’s attention because they are easily synthesized, stable, selective, have high binding affinity and are cost-effective to produce. In this study, we have successfully identified DNA aptamers with high binding affinity and selectivity to EGFR. The aptamer named TuTu22 with K{sub d} 56 ± 7.3 nM was chosen from the identified DNA aptamers for further study. Flow cytometry analysis results indicated that the TuTu22 aptamer was able to specifically recognize a variety of cancer cells expressing EGFR but did not bind to the EGFR-negative cells. With all of the aforementioned advantages, the DNA aptamers reported here against cancer biomarker EGFR will facilitate the development of novel targeted cancer detection, imaging and therapy.

Selection of DNA aptamers against epidermal growth factor receptor with high affinity and specificity

International Nuclear Information System (INIS)

Wang, Deng-Liang; Song, Yan-Ling; Zhu, Zhi; Li, Xi-Lan; Zou, Yuan; Yang, Hai-Tao; Wang, Jiang-Jie; Yao, Pei-Sen; Pan, Ru-Jun; Yang, Chaoyong James; Kang, De-Zhi

2014-01-01

Highlights: • This is the first report of DNA aptamer against EGFR in vitro. • Aptamer can bind targets with high affinity and selectivity. • DNA aptamers are more stable, cheap and efficient than RNA aptamers. • Our selected DNA aptamer against EGFR has high affinity with K d 56 ± 7.3 nM. • Our selected DNA aptamer against EGFR has high selectivity. - Abstract: Epidermal growth factor receptor (EGFR/HER1/c-ErbB1), is overexpressed in many solid cancers, such as epidermoid carcinomas, malignant gliomas, etc. EGFR plays roles in proliferation, invasion, angiogenesis and metastasis of malignant cancer cells and is the ideal antigen for clinical applications in cancer detection, imaging and therapy. Aptamers, the output of the systematic evolution of ligands by exponential enrichment (SELEX), are DNA/RNA oligonucleotides which can bind protein and other substances with specificity. RNA aptamers are undesirable due to their instability and high cost of production. Conversely, DNA aptamers have aroused researcher’s attention because they are easily synthesized, stable, selective, have high binding affinity and are cost-effective to produce. In this study, we have successfully identified DNA aptamers with high binding affinity and selectivity to EGFR. The aptamer named TuTu22 with K d 56 ± 7.3 nM was chosen from the identified DNA aptamers for further study. Flow cytometry analysis results indicated that the TuTu22 aptamer was able to specifically recognize a variety of cancer cells expressing EGFR but did not bind to the EGFR-negative cells. With all of the aforementioned advantages, the DNA aptamers reported here against cancer biomarker EGFR will facilitate the development of novel targeted cancer detection, imaging and therapy

SNP Discovery and Development of a High-Density Genotyping Array for Sunflower

Science.gov (United States)

Bachlava, Eleni; Taylor, Christopher A.; Tang, Shunxue; Bowers, John E.; Mandel, Jennifer R.; Burke, John M.; Knapp, Steven J.

2012-01-01

Recent advances in next-generation DNA sequencing technologies have made possible the development of high-throughput SNP genotyping platforms that allow for the simultaneous interrogation of thousands of single-nucleotide polymorphisms (SNPs). Such resources have the potential to facilitate the rapid development of high-density genetic maps, and to enable genome-wide association studies as well as molecular breeding approaches in a variety of taxa. Herein, we describe the development of a SNP genotyping resource for use in sunflower (Helianthus annuus L.). This work involved the development of a reference transcriptome assembly for sunflower, the discovery of thousands of high quality SNPs based on the generation and analysis of ca. 6 Gb of transcriptome re-sequencing data derived from multiple genotypes, the selection of 10,640 SNPs for inclusion in the genotyping array, and the use of the resulting array to screen a diverse panel of sunflower accessions as well as related wild species. The results of this work revealed a high frequency of polymorphic SNPs and relatively high level of cross-species transferability. Indeed, greater than 95% of successful SNP assays revealed polymorphism, and more than 90% of these assays could be successfully transferred to related wild species. Analysis of the polymorphism data revealed patterns of genetic differentiation that were largely congruent with the evolutionary history of sunflower, though the large number of markers allowed for finer resolution than has previously been possible. PMID:22238659

Variable kernel density estimation in high-dimensional feature spaces

CSIR Research Space (South Africa)

Van der Walt, Christiaan M

2017-02-01

Full Text Available Estimating the joint probability density function of a dataset is a central task in many machine learning applications. In this work we address the fundamental problem of kernel bandwidth estimation for variable kernel density estimation in high...

Highly Compressed Ion Beams for High Energy Density Science

CERN Document Server

Friedman, Alex; Briggs, Richard J; Callahan, Debra; Caporaso, George; Celata, C M; Davidson, Ronald C; Faltens, Andy; Grant-Logan, B; Grisham, Larry; Grote, D P; Henestroza, Enrique; Kaganovich, Igor D; Lee, Edward; Lee, Richard; Leitner, Matthaeus; Nelson, Scott D; Olson, Craig; Penn, Gregory; Reginato, Lou; Renk, Tim; Rose, David; Sessler, Andrew M; Staples, John W; Tabak, Max; Thoma, Carsten H; Waldron, William; Welch, Dale; Wurtele, Jonathan; Yu, Simon

2005-01-01

The Heavy Ion Fusion Virtual National Laboratory (HIF-VNL) is developing the intense ion beams needed to drive matter to the High Energy Density (HED) regimes required for Inertial Fusion Energy (IFE) and other applications. An interim goal is a facility for Warm Dense Matter (WDM) studies, wherein a target is heated volumetrically without being shocked, so that well-defined states of matter at 1 to 10 eV are generated within a diagnosable region. In the approach we are pursuing, low to medium mass ions with energies just above the Bragg peak are directed onto thin target "foils," which may in fact be foams or "steel wool" with mean densities 1% to 100% of solid. This approach complements that being pursued at GSI, wherein high-energy ion beams deposit a small fraction of their energy in a cylindrical target. We present the requirements for warm dense matter experiments, and describe suitable accelerator concepts, including novel broadband traveling wave pulse-line, drift-tube linac, RF, and single-gap approa...

A high energy density relaxor antiferroelectric pulsed capacitor dielectric

Energy Technology Data Exchange (ETDEWEB)

Jo, Hwan Ryul; Lynch, Christopher S. [Department of Mechanical and Aerospace Engineering, University of California, Los Angeles (UCLA), Los Angeles, California 90095 (United States)

2016-01-14

Pulsed capacitors require high energy density and low loss, properties that can be realized through selection of composition. Ceramic (Pb{sub 0.88}La{sub 0.08})(Zr{sub 0.91}Ti{sub 0.09})O{sub 3} was found to be an ideal candidate. La{sup 3+} doping and excess PbO were used to produce relaxor antiferroelectric behavior with slim and slanted hysteresis loops to reduce the dielectric hysteresis loss, to increase the dielectric strength, and to increase the discharge energy density. The discharge energy density of this composition was found to be 3.04 J/cm{sup 3} with applied electric field of 170 kV/cm, and the energy efficiency, defined as the ratio of the discharge energy density to the charging energy density, was 0.920. This high efficiency reduces the heat generated under cyclic loading and improves the reliability. The properties were observed to degrade some with temperature increase above 80 °C. Repeated electric field cycles up to 10 000 cycles were applied to the specimen with no observed performance degradation.

A model for the mechanism of strand passage by DNA gyrase

DEFF Research Database (Denmark)

Kampranis, S C; Bates, A D; Maxwell, A

1999-01-01

this mechanism by probing the topology of the bound DNA segment at distinct steps of the catalytic cycle. We propose a model in which gyrase captures a contiguous DNA segment with high probability, irrespective of the superhelical density of the DNA substrate, setting up an equilibrium of the transported segment......The mechanism of type II DNA topoisomerases involves the formation of an enzyme-operated gate in one double-stranded DNA segment and the passage of another segment through this gate. DNA gyrase is the only type II topoisomerase able to introduce negative supercoils into DNA, a feature that requires...... the enzyme to dictate the directionality of strand passage. Although it is known that this is a consequence of the characteristic wrapping of DNA by gyrase, the detailed mechanism by which the transported DNA segment is captured and directed through the DNA gate is largely unknown. We have addressed...

A novel method to quantify local CpG methylation density by regional methylation elongation assay on microarray

Directory of Open Access Journals (Sweden)

Qiao Yingjuan

2008-01-01

Full Text Available Abstract Background DNA methylation based techniques are important tools in both clinical diagnostics and therapeutics. But most of these methods only analyze a few CpG sites in a target region. Indeed, difference of site-specific methylation may also lead to a change of methylation density in many cases, and it has been found that the density of methylation is more important than methylation of single CpG site for gene silencing. Results We have developed a novel approach for quantitative analysis of CpG methylation density on the basis of microarray-based hybridization and incorporation of Cy5-dCTP into the Cy3 labeled target DNA by using Taq DNA Polymerase on microarray. The quantification is achieved by measuring Cy5/Cy3 signal ratio which is proportional to methylation density. This methylation-sensitive technique, termed RMEAM (regional methylation elongation assay on microarray, provides several advantages over existing methods used for methylation analysis. It can determine an exact methylation density of the given region, and has potential of high throughput. We demonstrate a use of this method in determining the methylation density of the promoter region of the tumor-related gene MLH1, TERT and MGMT in colorectal carcinoma patients. Conclusion This technique allows for quantitative analysis of regional methylation density, which is the representative of all allelic methylation patterns in the sample. The results show that this technique has the characteristics of simplicity, rapidness, specificity and high-throughput.

High density UO2 powder preparation for HWR fuel

International Nuclear Information System (INIS)

Hwang, S. T.; Chang, I. S.; Choi, Y. D.; Cho, B. R.; Kwon, S. W.; Kim, B. H.; Moon, B. H.; Kim, S. D.; Phyu, K. M.; Lee, K. A.

1992-01-01

The objective of this project is to study on the preparation of method high density UO 2 powder for HWR Fuel. Accordingly, it is necessary to character ize the AUC processed UO 2 powder and to search method for the preparation of high density UO 2 powder for HWR Fuel. Therefore, it is expected that the results of this study can effect the producing of AUC processed UO 2 powder having sinterability. (Author)

Electrical and mechanical properties of highly elongated high density polyethylene as cryogenic insulation materials

International Nuclear Information System (INIS)

Yoshino, Katsumi; Park, Dae-Hee; Miyata, Kiyomi; Yamaoka, Hitoshi; Itoh, Minoru; Ichihara, Syouji.

1989-01-01

Electrical and mechanical properties of highly elongated high density polyethylene were investigated in the temperature range between 4.2 K and 400 K from a viewpoint of electrical insulation at low temperature and the following properties have been clarified. (1) The electrical conductivity of samples decreases with increasing draw ratio, and also decreases at cryogenic temperature. (2) Breakdown strength of highly elongated sample is similar to that of non-elongated sample. It is nearby temperature independent below 300 K but at higher temperature it falls steeply. (3) Mechanical breakdown stress and elastic modulus of high density polyethylene increase with increasing draw ratio. Their values at liquid nitrogen temperature are much higher than that at room temperature. On the other hand, strains decreases at liquid nitrogen temperature. (4) Break of the sample develops in the direction of 45deg from the direction of stress both at room temperature and at cryogenic temperature. (5) The characteristic of mechanical breakdown at liquid nitrogen temperature can be explained by a brittleness fracture process. (6) Toughness of high density polyethylene increases with increasing draw ratio until draw ratio of 5, and it decreased, and increase at higher draw ratio. However at extremely high draw ratio of 10 it again increases. These findings clearly indicate that highly elongated high density polyethylene has good electrical and mechanical properties at cryogenic temperature and can be used as the insulating materials at cryogenic temperature. (author)

Self-Assembly DNA Polyplex Vaccine inside Dissolving Microneedles for High-Potency Intradermal Vaccination

Science.gov (United States)

Liao, Jing-Fong; Lee, Jin-Ching; Lin, Chun-Kuang; Wei, Kuo-Chen; Chen, Pin-Yuan; Yang, Hung-Wei

2017-01-01

The strong immunogenicity induction is the powerful weapon to prevent the virus infections. This study demonstrated that one-step synthesis of DNA polyplex vaccine in microneedle (MN) patches can induce high immunogenicity through intradermal vaccination and increase the vaccine stability for storage outside the cold chain. More negative charged DNA vaccine was entrapped into the needle region of MNs followed by DNA polyplex formation with branched polyethylenimine (bPEI) pre-coated in the cavities of polydimethylsiloxane (PDMS) molds that can deliver more DNA vaccine to immune-cell rich epidermis with high transfection efficiency. Our data in this study support the safety and immunogenicity of the MN-based vaccine; the MN patch delivery system induced an immune response 3.5-fold as strong as seen with conventional intramuscular administration; the DNA polyplex formulation provided excellent vaccine stability at high temperature (could be stored at 45ºC for at least 4 months); the DNA vaccine is expected to be manufactured at low cost and not generate sharps waste. We think this study is significant to public health because there is a pressing need for an effective vaccination in developing countries. PMID:28819449

Large-scale symmetry-adapted perturbation theory computations via density fitting and Laplace transformation techniques: investigating the fundamental forces of DNA-intercalator interactions.

Science.gov (United States)

Hohenstein, Edward G; Parrish, Robert M; Sherrill, C David; Turney, Justin M; Schaefer, Henry F

2011-11-07

Symmetry-adapted perturbation theory (SAPT) provides a means of probing the fundamental nature of intermolecular interactions. Low-orders of SAPT (here, SAPT0) are especially attractive since they provide qualitative (sometimes quantitative) results while remaining tractable for large systems. The application of density fitting and Laplace transformation techniques to SAPT0 can significantly reduce the expense associated with these computations and make even larger systems accessible. We present new factorizations of the SAPT0 equations with density-fitted two-electron integrals and the first application of Laplace transformations of energy denominators to SAPT. The improved scalability of the DF-SAPT0 implementation allows it to be applied to systems with more than 200 atoms and 2800 basis functions. The Laplace-transformed energy denominators are compared to analogous partial Cholesky decompositions of the energy denominator tensor. Application of our new DF-SAPT0 program to the intercalation of DNA by proflavine has allowed us to determine the nature of the proflavine-DNA interaction. Overall, the proflavine-DNA interaction contains important contributions from both electrostatics and dispersion. The energetics of the intercalator interaction are are dominated by the stacking interactions (two-thirds of the total), but contain important contributions from the intercalator-backbone interactions. It is hypothesized that the geometry of the complex will be determined by the interactions of the intercalator with the backbone, because by shifting toward one side of the backbone, the intercalator can form two long hydrogen-bonding type interactions. The long-range interactions between the intercalator and the next-nearest base pairs appear to be negligible, justifying the use of truncated DNA models in computational studies of intercalation interaction energies.

Extreme states of matter high energy density physics

CERN Document Server

Fortov, Vladimir E

2016-01-01

With its many beautiful colour pictures, this book gives fascinating insights into the unusual forms and behaviour of matter under extremely high pressures and temperatures. These extreme states are generated, among other things, by strong shock, detonation and electric explosion waves, dense laser beams,electron and ion beams, hypersonic entry of spacecraft into dense atmospheres of planets, and in many other situations characterized by extremely high pressures and temperatures.Written by one of the world's foremost experts on the topic, this book will inform and fascinate all scientists dealing with materials properties and physics, and also serve as an excellent introduction to plasma-, shock-wave and high-energy-density physics for students and newcomers seeking an overview. This second edition is thoroughly revised and expanded, in particular with new material on high energy-density physics, nuclear explosions and other nuclear transformation processes.

Supernovae and high density nuclear matter

Energy Technology Data Exchange (ETDEWEB)

Kahana, S.

1986-01-01

The role of the nuclear equation of state (EOS) in producing prompt supernova explosions is examined. Results of calculations of Baron, Cooperstein, and Kahana incorporating general relativity and a new high density EOS are presented, and the relevance of these calculations to laboratory experiments with heavy ions considered. 31 refs., 6 figs., 2 tabs.

Supernovae and high density nuclear matter

International Nuclear Information System (INIS)

Kahana, S.

1986-01-01

The role of the nuclear equation of state (EOS) in producing prompt supernova explosions is examined. Results of calculations of Baron, Cooperstein, and Kahana incorporating general relativity and a new high density EOS are presented, and the relevance of these calculations to laboratory experiments with heavy ions considered. 31 refs., 6 figs., 2 tabs

The validity of sedimentation data from high molecular weight DNA and the effects of additives on radiation-induced single-strand breakage

International Nuclear Information System (INIS)

Dugle, D.L.

1979-10-01

The optimization of many of the factors governing reproducible sedimentation behaviour of high molecular weight single-strand DNA in a particular alkaline sucrose density gradient system is described. A range of angular momenta is defined for which a constant strand breakage efficiency is required, despite a rotor speed effect which increases the measured molecular weights at decreasing rotor speeds for larger DNA molecules. The possibility is discussed that the bimodal control DNA profiles obtained after sedimentation at 11 500 rev/min (12 400 g) or less represent structural subunits of the chromatid. The random induction of single-strand DNA breaks by ionizing radiation is demonstrated by the computer-derived fits to the experimental profiles. The enhancement of single-strand break (SSB) yields in hypoxic cells by oxygen, para-nitroacetophenone (PNAP), or any of the three nitrofuran derivatives used was well correlated with increased cell killing. Furthermore, reductions in SSB yields for known hydroxyl radical (OH.) scavengers correlates with the reactivities of these compounds toward OH.. This supports the contention that some type of OH.-induced initial lesion, which may ultimately be expressed as an unrepaired or misrepaired double-strand break, constitutes a lethal event. (author)

ADX: a high field, high power density, Advanced Divertor test eXperiment

Science.gov (United States)

Vieira, R.; Labombard, B.; Marmar, E.; Irby, J.; Shiraiwa, S.; Terry, J.; Wallace, G.; Whyte, D. G.; Wolfe, S.; Wukitch, S.; ADX Team

2014-10-01

The MIT PSFC and collaborators are proposing an advanced divertor experiment (ADX) - a tokamak specifically designed to address critical gaps in the world fusion research program on the pathway to FNSF/DEMO. This high field (6.5 tesla, 1.5 MA), high power density (P/S ~ 1.5 MW/m2) facility would utilize Alcator magnet technology to test innovative divertor concepts for next-step DT fusion devices (FNSF, DEMO) at reactor-level boundary plasma pressures and parallel heat flux densities while producing high performance core plasma conditions. The experimental platform would also test advanced lower hybrid current drive (LHCD) and ion-cyclotron range of frequency (ICRF) actuators and wave physics at the plasma densities and magnetic field strengths of a DEMO, with the unique ability to deploy launcher structures both on the low-magnetic-field side and the high-field side - a location where energetic plasma-material interactions can be controlled and wave physics is most favorable for efficient current drive, heating and flow drive. This innovative experiment would perform plasma science and technology R&D necessary to inform the conceptual development and accelerate the readiness-for-deployment of FNSF/DEMO - in a timely manner, on a cost-effective research platform. Supported by DE-FC02-99ER54512.

High density plasmas formation in Inertial Confinement Fusion and Astrophysics

International Nuclear Information System (INIS)

Martinez-Val, J. M.; Minguez, E.; Velarde, P.; Perlado, J. M.; Velarde, G.; Bravo, E.; Eliezer, S.; Florido, R.; Garcia Rubiano, J.; Garcia-Senz, D.; Gil de la Fe, J. M.; Leon, P. T.; Martel, P.; Ogando, F.; Piera, M.; Relano, A.; Rodriguez, R.; Garcia, C.; Gonzalez, E.; Lachaise, M.; Oliva, E.

2005-01-01

In inertially confined fusion (ICF), high densities are required to obtain high gains. In Fast Ignition, a high density, low temperature plasma can be obtained during the compression. If the final temperature reached is low enough, the electrons of the plasma can be degenerate. In degenerate plasmas. Bremsstrahlung emission is strongly suppressed an ignition temperature becomes lower than in classical plasmas, which offers a new design window for ICF. The main difficulty of degenerate plasmas in the compression energy needed for high densities. Besides that, the low specific heat of degenerate electrons (as compared to classical values) is also a problem because of the rapid heating of the plasma. Fluid dynamic evolution of supernovae remnants is a very interesting problem in order to predict the thermodynamical conditions achieved in their collision regions. Those conditions have a strong influence in the emission of light and therefore the detection of such events. A laboratory scale system has been designed reproducing the fluid dynamic field in high energy experiments. The evolution of the laboratory system has been calculated with ARWEN code, 2D Radiation CFD that works with Adaptive Mesh Refinement. Results are compared with simulations on the original system obtained with a 3D SPH astrophysical code. New phenomena at the collision plane and scaling of the laboratory magnitudes will be described. Atomic physics for high density plasmas has been studied with participation in experiments to obtain laser produced high density plasmas under NLTE conditions, carried out at LULI. A code, ATOM3R, has been developed which solves rate equations for optically thin plasmas as well as for homogeneous optically thick plasmas making use of escape factors. New improvements in ATOM3R are been done to calculate level populations and opacities for non homogeneous thick plasmas in NLTE, with emphasis in He and H lines for high density plasma diagnosis. Analytical expression

High-density hybrid interconnect methodologies

International Nuclear Information System (INIS)

John, J.; Zimmermann, L.; Moor, P.De; Hoof, C.Van

2003-01-01

Full text: The presentation gives an overview of the state-of-the-art of hybrid integration and in particular the IMEC technological approaches that will be able to address future hybrid detector needs. The dense hybrid flip-chip integration of an array of detectors and its dedicated readout electronics can be achieved with a variety of solderbump techniques such as pure Indium or Indium alloys, Ph-In, Ni/PbSn, but also conducting polymers... Particularly for cooled applications or ultra-high density applications, Indium solderbump technology (electroplated or evaporated) is the method of choice. The state-of-the-art of solderbump technologies that are to a high degree independent of the underlying detector material will be presented and examples of interconnect densities between 5x1E4cm-2 and 1x1E6 cm-2 will be demonstrated. For several classes of detectors, flip-chip integration is not allowed since the detectors have to be illuminated from the top. This applies to image sensors for EUV applications such as GaN/AlGaN based detectors and to MEMS-based sensors. In such cases, the only viable interconnection method has to be through the (thinned) detector wafer followed by a solderbump-based integration. The approaches for dense and ultra-dense through-the-wafer interconnect 'vias' will be presented and wafer thinning approaches will be shown

Brickworx builds recurrent RNA and DNA structural motifs into medium- and low-resolution electron-density maps

Energy Technology Data Exchange (ETDEWEB)

Chojnowski, Grzegorz, E-mail: gchojnowski@genesilico.pl [International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw (Poland); Waleń, Tomasz [International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw (Poland); University of Warsaw, Banacha 2, 02-097 Warsaw (Poland); Piątkowski, Paweł; Potrzebowski, Wojciech [International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw (Poland); Bujnicki, Janusz M. [International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw (Poland); Adam Mickiewicz University, Umultowska 89, 61-614 Poznan (Poland)

2015-03-01

A computer program that builds crystal structure models of nucleic acid molecules is presented. Brickworx is a computer program that builds crystal structure models of nucleic acid molecules using recurrent motifs including double-stranded helices. In a first step, the program searches for electron-density peaks that may correspond to phosphate groups; it may also take into account phosphate-group positions provided by the user. Subsequently, comparing the three-dimensional patterns of the P atoms with a database of nucleic acid fragments, it finds the matching positions of the double-stranded helical motifs (A-RNA or B-DNA) in the unit cell. If the target structure is RNA, the helical fragments are further extended with recurrent RNA motifs from a fragment library that contains single-stranded segments. Finally, the matched motifs are merged and refined in real space to find the most likely conformations, including a fit of the sequence to the electron-density map. The Brickworx program is available for download and as a web server at http://iimcb.genesilico.pl/brickworx.

Brickworx builds recurrent RNA and DNA structural motifs into medium- and low-resolution electron-density maps

International Nuclear Information System (INIS)

Chojnowski, Grzegorz; Waleń, Tomasz; Piątkowski, Paweł; Potrzebowski, Wojciech; Bujnicki, Janusz M.

2015-01-01

A computer program that builds crystal structure models of nucleic acid molecules is presented. Brickworx is a computer program that builds crystal structure models of nucleic acid molecules using recurrent motifs including double-stranded helices. In a first step, the program searches for electron-density peaks that may correspond to phosphate groups; it may also take into account phosphate-group positions provided by the user. Subsequently, comparing the three-dimensional patterns of the P atoms with a database of nucleic acid fragments, it finds the matching positions of the double-stranded helical motifs (A-RNA or B-DNA) in the unit cell. If the target structure is RNA, the helical fragments are further extended with recurrent RNA motifs from a fragment library that contains single-stranded segments. Finally, the matched motifs are merged and refined in real space to find the most likely conformations, including a fit of the sequence to the electron-density map. The Brickworx program is available for download and as a web server at http://iimcb.genesilico.pl/brickworx

Anti-Ferroelectric Ceramics for High Energy Density Capacitors

Directory of Open Access Journals (Sweden)

Aditya Chauhan

2015-11-01

Full Text Available With an ever increasing dependence on electrical energy for powering modern equipment and electronics, research is focused on the development of efficient methods for the generation, storage and distribution of electrical power. In this regard, the development of suitable dielectric based solid-state capacitors will play a key role in revolutionizing modern day electronic and electrical devices. Among the popular dielectric materials, anti-ferroelectrics (AFE display evidence of being a strong contender for future ceramic capacitors. AFE materials possess low dielectric loss, low coercive field, low remnant polarization, high energy density, high material efficiency, and fast discharge rates; all of these characteristics makes AFE materials a lucrative research direction. However, despite the evident advantages, there have only been limited attempts to develop this area. This article attempts to provide a focus to this area by presenting a timely review on the topic, on the relevant scientific advancements that have been made with respect to utilization and development of anti-ferroelectric materials for electric energy storage applications. The article begins with a general introduction discussing the need for high energy density capacitors, the present solutions being used to address this problem, and a brief discussion of various advantages of anti-ferroelectric materials for high energy storage applications. This is followed by a general description of anti-ferroelectricity and important anti-ferroelectric materials. The remainder of the paper is divided into two subsections, the first of which presents various physical routes for enhancing the energy storage density while the latter section describes chemical routes for enhanced storage density. This is followed by conclusions and future prospects and challenges which need to be addressed in this particular field.

Exploring high-density baryonic matter: Maximum freeze-out density

Energy Technology Data Exchange (ETDEWEB)

Randrup, Joergen [Lawrence Berkeley National Laboratory, Nuclear Science Division, Berkeley, CA (United States); Cleymans, Jean [University of Cape Town, UCT-CERN Research Centre and Department of Physics, Rondebosch (South Africa)

2016-08-15

The hadronic freeze-out line is calculated in terms of the net baryon density and the energy density instead of the usual T and μ{sub B}. This analysis makes it apparent that the freeze-out density exhibits a maximum as the collision energy is varied. This maximum freeze-out density has μ{sub B} = 400 - 500 MeV, which is above the critical value, and it is reached for a fixed-target bombarding energy of 20-30 GeV/N well within the parameters of the proposed NICA collider facility. (orig.)

Low-enriched uranium high-density target project. Compendium report

Energy Technology Data Exchange (ETDEWEB)

Vandegrift, George; Brown, M. Alex; Jerden, James L.; Gelis, Artem V.; Stepinski, Dominique C.; Wiedmeyer, Stanley; Youker, Amanda; Hebden, Andrew; Solbrekken, G; Allen, C; Robertson., D; El-Gizawy, Sherif; Govindarajan, Srisharan; Hoyer, Annemarie; Makarewicz, Philip; Harris, Jacob; Graybill, Brian; Gunn, Andy; Berlin, James; Bryan, Chris; Sherman, Steven; Hobbs, Randy; Griffin, F. P.; Chandler, David; Hurt, C. J.; Williams, Paul; Creasy, John; Tjader, Barak; McFall, Danielle; Longmire, Hollie

2016-09-01

At present, most ⁹⁹Mo is produced in research, test, or isotope production reactors by irradiation of highly enriched uranium targets. To achieve the denser form of uranium needed for switching from high to low enriched uranium (LEU), targets in the form of a metal foil (~125-150 µm thick) are being developed. The LEU High Density Target Project successfully demonstrated several iterations of an LEU-fission-based Mo-99 technology that has the potential to provide the world’s supply of Mo-99, should major producers choose to utilize the technology. Over 50 annular high density targets have been successfully tested, and the assembly and disassembly of targets have been improved and optimized. Two target front-end processes (acidic and electrochemical) have been scaled up and demonstrated to allow for the high-density target technology to mate up to the existing producer technology for target processing. In the event that a new target processing line is started, the chemical processing of the targets is greatly simplified. Extensive modeling and safety analysis has been conducted, and the target has been qualified to be inserted into the High Flux Isotope Reactor, which is considered above and beyond the requirements for the typical use of this target due to high fluence and irradiation duration.

High Channel Count, High Density Microphone Arrays for Wind Tunnel Environments, Phase I

Data.gov (United States)

National Aeronautics and Space Administration — The Interdisciplinary Consulting Corporation (IC2) proposes the development of high channel count, high density, reduced cost per channel, directional microphone...

Highly sensitive polymerase chain reaction-free quantum dot-based quantification of forensic genomic DNA

International Nuclear Information System (INIS)

Tak, Yu Kyung; Kim, Won Young; Kim, Min Jung; Han, Eunyoung; Han, Myun Soo; Kim, Jong Jin; Kim, Wook; Lee, Jong Eun; Song, Joon Myong

2012-01-01

Highlights: ► Genomic DNA quantification were performed using a quantum dot-labeled Alu sequence. ► This probe provided PCR-free determination of human genomic DNA. ► Qdot-labeled Alu probe-hybridized genomic DNAs had a 2.5-femtogram detection limit. ► Qdot-labeled Alu sequence was used to assess DNA samples for human identification. - Abstract: Forensic DNA samples can degrade easily due to exposure to light and moisture at the crime scene. In addition, the amount of DNA acquired at a criminal site is inherently limited. This limited amount of human DNA has to be quantified accurately after the process of DNA extraction. The accurately quantified extracted genomic DNA is then used as a DNA template in polymerase chain reaction (PCR) amplification for short tandem repeat (STR) human identification. Accordingly, highly sensitive and human-specific quantification of forensic DNA samples is an essential issue in forensic study. In this work, a quantum dot (Qdot)-labeled Alu sequence was developed as a probe to simultaneously satisfy both the high sensitivity and human genome selectivity for quantification of forensic DNA samples. This probe provided PCR-free determination of human genomic DNA and had a 2.5-femtogram detection limit due to the strong emission and photostability of the Qdot. The Qdot-labeled Alu sequence has been used successfully to assess 18 different forensic DNA samples for STR human identification.

High current density magnets for INTOR and TIBER

International Nuclear Information System (INIS)

Miller, J.R.; Henning, C.D.; Kerns, J.A.; Slack, D.S.; Summers, L.T.; Zbasnik, J.P.

1986-12-01

The adoption of high current density, high field, superconducting magnets for INTOR and TIBER would prove beneficial. When combined with improved radiation tolerance of the magnets to minimize the inner leg shielding, a substantial reduction in machine dimensions and capital costs can be achieved. Fortunately, cable-in-conduit conductors (CICC) which are capable of the desired enhancements are being developed. Because conductor stability in a CICC depends more on the trapped helium enthalpy, rather than the copper resistivity, higher current densities of the order of 40 A/mm 2 at 12 T are possible. Radiation damage to the copper stabilizer is less important because the growth in resistance is a second-order effect on stability. Such CICC conductors lend themselves naturally to niobium-tin utilization, with the benefits of the high current-sharing temperature of this material being taken to advantage in absorbing radiation heating. When the helium coolant is injected at near the critical pressure, Joule-Thompson expansion in the flow path tends to stabilize the fluid temperature at under 6 K. Thus, higher fields, as well as higher current densities, can be considered for INTOR or TIBER

High volumetric power density, non-enzymatic, glucose fuel cells.

Science.gov (United States)

Oncescu, Vlad; Erickson, David

2013-01-01

The development of new implantable medical devices has been limited in the past by slow advances in lithium battery technology. Non-enzymatic glucose fuel cells are promising replacement candidates for lithium batteries because of good long-term stability and adequate power density. The devices developed to date however use an "oxygen depletion design" whereby the electrodes are stacked on top of each other leading to low volumetric power density and complicated fabrication protocols. Here we have developed a novel single-layer fuel cell with good performance (2 μW cm⁻²) and stability that can be integrated directly as a coating layer on large implantable devices, or stacked to obtain a high volumetric power density (over 16 μW cm⁻³). This represents the first demonstration of a low volume non-enzymatic fuel cell stack with high power density, greatly increasing the range of applications for non-enzymatic glucose fuel cells.

Anomalous evolution of Ar metastable density with electron density in high density Ar discharge

International Nuclear Information System (INIS)

Park, Min; Chang, Hong-Young; You, Shin-Jae; Kim, Jung-Hyung; Shin, Yong-Hyeon

2011-01-01

Recently, an anomalous evolution of argon metastable density with plasma discharge power (electron density) was reported [A. M. Daltrini, S. A. Moshkalev, T. J. Morgan, R. B. Piejak, and W. G. Graham, Appl. Phys. Lett. 92, 061504 (2008)]. Although the importance of the metastable atom and its density has been reported in a lot of literature, however, a basic physics behind the anomalous evolution of metastable density has not been clearly understood yet. In this study, we investigated a simple global model to elucidate the underlying physics of the anomalous evolution of argon metastable density with the electron density. On the basis of the proposed simple model, we reproduced the anomalous evolution of the metastable density and disclosed the detailed physics for the anomalous result. Drastic changes of dominant mechanisms for the population and depopulation processes of Ar metastable atoms with electron density, which take place even in relatively low electron density regime, is the clue to understand the result.

High-current discharge channel contraction in high density gas

International Nuclear Information System (INIS)

Rutberg, Ph. G.; Bogomaz, A. A.; Pinchuk, M. E.; Budin, A. V.; Leks, A. G.; Pozubenkov, A. A.

2011-01-01

Research results for discharges at current amplitudes of 0.5-1.6 MA and current rise rate of ∼10 10 A/s are presented. The discharge is performed in the hydrogen environment at the initial pressure of 5-35 MPa. Initiation is implemented by a wire explosion. The time length of the first half-period of the discharge current is 70-150 μs. Under such conditions, discharge channel contraction is observed; the contraction is followed by soft x-ray radiation. The phenomena are discussed, which are determined by high density of the gas surrounding the discharge channel. These phenomena are increase of the current critical value, where the channel contraction begins and growth of temperature in the axis region of the channel, where the initial density of the gas increases.

Still rethinking the value of high wood density.

Science.gov (United States)

Larjavaara, Markku; Muller-Landau, Helene C

2012-01-01

In a previous paper, we questioned the traditional interpretation of the advantages and disadvantages of high wood density (Functional Ecology 24: 701-705). Niklas and Spatz (American Journal of Botany 97: 1587-1594) challenged the biomechanical relevance of studying properties of dry wood, including dry wood density, and stated that we erred in our claims regarding scaling. We first present the full derivation of our previous claims regarding scaling. We then examine how the fresh modulus of rupture and the elastic modulus scale with dry wood density and compare these scaling relationships with those for dry mechanical properties, using almost exactly the same data set analyzed by Niklas and Spatz. The derivation shows that given our assumptions that the modulus of rupture and elastic modulus are both proportional to wood density, the resistance to bending is inversely proportional to wood density and strength is inversely proportional with the square root of wood density, exactly as we previously claimed. The analyses show that the elastic modulus of fresh wood scales proportionally with wood density (exponent 1.05, 95% CI 0.90-1.11) but that the modulus of rupture of fresh wood does not, scaling instead with the 1.25 power of wood density (CI 1.18-1.31). The deviation from proportional scaling for modulus of rupture is so small that our central conclusion remains correct: for a given construction cost, trees with lower wood density have higher strength and higher resistance to bending.

High-frequency emissions during the propagation of an electron beam in a high-density plasma

International Nuclear Information System (INIS)

Lalita and Tripathi, V.K.

1988-01-01

A relativistic annular electron beam passing through a high-density plasma excites Langmuir waves via Cerenkov interaction. The Langmuir waves are backscattered off ions via nonlinear ion Landau damping. At moderately high amplitudes these waves are parametrically up-converted by the beam into high-frequency electromagnetic radiation, as observed in some recent experiments. A nonlocal theory of this process is developed in a cylindrical geometry. It is seen that the growth rate of the Langmuir wave scales as one-third power of beam density. The growth rate of parametric instability scales as one-fourth power of beam density and the square root of beam thickness

High Energy Density Physics and Exotic Acceleration Schemes

International Nuclear Information System (INIS)

Cowan, T.; Colby, E.

2005-01-01

The High Energy Density and Exotic Acceleration working group took as our goal to reach beyond the community of plasma accelerator research with its applications to high energy physics, to promote exchange with other disciplines which are challenged by related and demanding beam physics issues. The scope of the group was to cover particle acceleration and beam transport that, unlike other groups at AAC, are not mediated by plasmas or by electromagnetic structures. At this Workshop, we saw an impressive advancement from years past in the area of Vacuum Acceleration, for example with the LEAP experiment at Stanford. And we saw an influx of exciting new beam physics topics involving particle propagation inside of solid-density plasmas or at extremely high charge density, particularly in the areas of laser acceleration of ions, and extreme beams for fusion energy research, including Heavy-ion Inertial Fusion beam physics. One example of the importance and extreme nature of beam physics in HED research is the requirement in the Fast Ignitor scheme of inertial fusion to heat a compressed DT fusion pellet to keV temperatures by injection of laser-driven electron or ion beams of giga-Amp current. Even in modest experiments presently being performed on the laser-acceleration of ions from solids, mega-amp currents of MeV electrons must be transported through solid foils, requiring almost complete return current neutralization, and giving rise to a wide variety of beam-plasma instabilities. As keynote talks our group promoted Ion Acceleration (plenary talk by A. MacKinnon), which historically has grown out of inertial fusion research, and HIF Accelerator Research (invited talk by A. Friedman), which will require impressive advancements in space-charge-limited ion beam physics and in understanding the generation and transport of neutralized ion beams. A unifying aspect of High Energy Density applications was the physics of particle beams inside of solids, which is proving to

A test of the transcription model for biased inheritance of yeast mitochondrial DNA.

Science.gov (United States)

Lorimer, H E; Brewer, B J; Fangman, W L

1995-09-01

Two strand-specific origins of replication appear to be required for mammalian mitochondrial DNA (mtDNA) replication. Structural equivalents of these origins are found in the rep sequences of Saccharomyces cerevisiae mtDNA. These striking similarities have contributed to a universal model for the initiation of mtDNA replication in which a primer is created by cleavage of an origin region transcript. Consistent with this model are the properties of deletion mutants of yeast mtDNA ([rho-]) with a high density of reps (HS [rho-]). These mutant mtDNAs are preferentially inherited by the progeny resulting from the mating of HS [rho-] cells with cells containing wild-type mtDNA ([rho+]). This bias is presumed to result from a replication advantage conferred on HS [rho-] mtDNA by the high density of rep sequences acting as origins. To test whether transcription is indeed required for the preferential inheritance of HS [rho-] mtDNA, we deleted the nuclear gene (RPO41) for the mitochondrial RNA polymerase, reducing transcripts by at least 1000-fold. Since [rho-] genomes, but not [rho+] genomes, are stable when RPO41 is deleted, we examined matings between HS [rho-] and neutral [rho-] cells. Neutral [rho-] mtDNAs lack rep sequences and are not preferentially inherited in [rho-] x [rho+] crosses. In HS [rho-] x neutral [rho-] matings, the HS [rho-] mtDNA was preferentially inherited whether both parents were wild type or both were deleted for RPO41. Thus, transcription from the rep promoter does not appear to be necessary for biased inheritance. Our results, and analysis of the literature, suggest that priming by transcription is not a universal mechanism for mtDNA replication initiation.

A robotics platform for automated batch fabrication of high density, microfluidics-based DNA microarrays, with applications to single cell, multiplex assays of secreted proteins

Science.gov (United States)

Ahmad, Habib; Sutherland, Alex; Shin, Young Shik; Hwang, Kiwook; Qin, Lidong; Krom, Russell-John; Heath, James R.

2011-09-01

Microfluidics flow-patterning has been utilized for the construction of chip-scale miniaturized DNA and protein barcode arrays. Such arrays have been used for specific clinical and fundamental investigations in which many proteins are assayed from single cells or other small sample sizes. However, flow-patterned arrays are hand-prepared, and so are impractical for broad applications. We describe an integrated robotics/microfluidics platform for the automated preparation of such arrays, and we apply it to the batch fabrication of up to eighteen chips of flow-patterned DNA barcodes. The resulting substrates are comparable in quality with hand-made arrays and exhibit excellent substrate-to-substrate consistency. We demonstrate the utility and reproducibility of robotics-patterned barcodes by utilizing two flow-patterned chips for highly parallel assays of a panel of secreted proteins from single macrophage cells.

A robotics platform for automated batch fabrication of high density, microfluidics-based DNA microarrays, with applications to single cell, multiplex assays of secreted proteins.

Science.gov (United States)

Ahmad, Habib; Sutherland, Alex; Shin, Young Shik; Hwang, Kiwook; Qin, Lidong; Krom, Russell-John; Heath, James R

2011-09-01

Microfluidics flow-patterning has been utilized for the construction of chip-scale miniaturized DNA and protein barcode arrays. Such arrays have been used for specific clinical and fundamental investigations in which many proteins are assayed from single cells or other small sample sizes. However, flow-patterned arrays are hand-prepared, and so are impractical for broad applications. We describe an integrated robotics/microfluidics platform for the automated preparation of such arrays, and we apply it to the batch fabrication of up to eighteen chips of flow-patterned DNA barcodes. The resulting substrates are comparable in quality with hand-made arrays and exhibit excellent substrate-to-substrate consistency. We demonstrate the utility and reproducibility of robotics-patterned barcodes by utilizing two flow-patterned chips for highly parallel assays of a panel of secreted proteins from single macrophage cells. © 2011 American Institute of Physics

High quality DNA from human papillomavirus (HPV for PCR/RFLPs

Directory of Open Access Journals (Sweden)

Denise Wanderlei-Silva

2005-01-01

Full Text Available The analysis of DNA in clinical samples for a secure diagnostic has become indispensable nowadays. Techniques approaching isolation of high molecular weigth DNA of HPV could lead to efficient amplification and early clinical diagnosis of the virus DNA by PCR (polymerase chain reaction. We describe a fast, non-toxical, efficient and cheap method for DNA isolation of human papilloma virus (HPV from cervical smears using guanidine (DNAzol solution. A 450 bp DNA band correponding to the late region (L1 of the virus genome was detected by PCR, showing that the DNAzol extraction soluction generated a good viral DNA yield. The electrophoretic pattern after digestion with restriction endonucleases (RFLPs/PCR revealed the predominance of HPV-16 and HPV-33 in the samples from the State of Alagoas, Brazil.A detecção de DNA em amostras clínicas visando um diagnóstico mais seguro vem se tornando uma prática comum em laboratórios de análise clínica. Metodologias que objetivem o isolamento de DNA de alto peso molecular de HPV podem levar a uma amplificação precisa e diagnose precoce do DNA do vírus por PCR (reação de polimerase em cadeia. Nós descrevemos um método para o isolamento do DNA do vírus do papiloma humano de amostras cervicais utilizando o detergente guanidina (solução DNAzol. O método foi rápido, não-tóxico e eficiente. Uma banda de DNA de 450 pb correspondente à região tardia (L1 do genoma viral foi detectada por PCR, mostrando que a extração com DNAzol gerou quantidade suficiente de DNA para análise. O padrão eletroforético, após digestão com endonucleases de restrição (RFLPs/PCR, revelou predominância de HPV 16 e HPV-33 nas amostras no Estado de Alagoas, Brasil.

Interplay of charge density wave and spin density wave in high-Tc superconductors

International Nuclear Information System (INIS)

Pradhan, B.; Raj, B.K.; Rout, G.C.

2008-01-01

We present a mean-field theory theoretical model study for the coexistence of the two strongly interacting charge density wave (CDW) and spin density wave (SDW) for high-T c cuprates in the underdoped region before the onset of the superconductivity in the system. The analytic expressions for the temperature dependence of the CDW and SDW order parameters are derived and solved self-consistently. Their interplay is studied by varying their respective coupling constants. It is observed that in the interplay region both the gap parameters exhibit very strong dependence of their gap values for the coupling constants. Further, the electronic density of states (DOS) for the conduction electrons, which represents the scanning tunneling data, show two gap parameters in the interplay region from these experimental data. Our model can help to determine separately the CDW and SDW parameters

Persistent DNA damage after high dose in vivo gamma exposure of minipig skin.

Directory of Open Access Journals (Sweden)

Emad A Ahmed

Full Text Available Exposure to high doses of ionizing radiation (IR can lead to localized radiation injury of the skin and exposed cells suffer dsDNA breaks that may elicit cell death or stochastic changes. Little is known about the DNA damage response after high-dose exposure of the skin. Here, we investigate the cellular and DNA damage response in acutely irradiated minipig skin.IR-induced DNA damage, repair and cellular survival were studied in 15 cm(2 of minipig skin exposed in vivo to ~50 Co-60 γ rays. Skin biopsies of control and 4 h up to 96 days post exposure were investigated for radiation-induced foci (RIF formation using γ-H2AX, 53BP1, and active ATM-p immunofluorescence. High-dose IR induced massive γ-H2AX phosphorylation and high 53BP1 RIF numbers 4 h, 20 h after IR. As time progressed RIF numbers dropped to a low of 3-fold elevated at all subsequent time points. Replicating basal cells (Ki67+ were reduced 3 days post IR followed by increased proliferation and recovery of epidermal cellularity after 28 days.Acute high dose irradiation of minipig epidermis impaired stem cell replication and induced elevated apoptosis from 3 days onward. DNA repair cleared the high numbers of DBSs in skin cells, while RIFs that persisted in <1% cells marked complex and potentially lethal DNA damage up to several weeks after exposure. An elevated frequency of keratinocytes with persistent RIFs may thus serve as indicator of previous acute radiation exposure, which may be useful in the follow up of nuclear or radiological accident scenarios.

A high-density linkage map and QTL mapping of fruit-related traits in pumpkin (Cucurbita moschata Duch.).

Science.gov (United States)

Zhong, Yu-Juan; Zhou, Yang-Yang; Li, Jun-Xing; Yu, Ting; Wu, Ting-Quan; Luo, Jian-Ning; Luo, Shao-Bo; Huang, He-Xun

2017-10-06

Pumpkin (Cucurbita moschata) is an economically worldwide crop. Few quantitative trait loci (QTLs) were reported previously due to the lack of genomic and genetic resources. In this study, a high-density linkage map of C. moschata was structured by double-digest restriction site-associated DNA sequencing, using 200 F2 individuals of CMO-1 × CMO-97. By filtering 74,899 SNPs, a total of 3,470 high quality SNP markers were assigned to the map spanning a total genetic distance of 3087.03 cM on 20 linkage groups (LGs) with an average genetic distance of 0.89 cM. Based on this map, both pericarp color and strip were fined mapped to a novel single locus on LG8 in the same region of 0.31 cM with phenotypic variance explained (PVE) of 93.6% and 90.2%, respectively. QTL analysis was also performed on carotenoids, sugars, tuberculate fruit, fruit diameter, thickness and chamber width with a total of 12 traits. 29 QTLs distributed in 9 LGs were detected with PVE from 9.6% to 28.6%. It was the first high-density linkage SNP map for C. moschata which was proved to be a valuable tool for gene or QTL mapping. This information will serve as significant basis for map-based gene cloning, draft genome assembling and molecular breeding.

Interaction of a non-histone chromatin protein (high-mobility group protein 2) with DNA

International Nuclear Information System (INIS)

Goodwin, G.H.; Shooter, K.V.; Johns, E.W.

1975-01-01

The interaction with DNA of the calf thymus chromatin non-histone protein termed the high-mobility group protein 2 has been studied by sedimentation analysis in the ultracentrifuge and by measuring the binding of the 125 I-labelled protein to DNA. The results have been compared with those obtained previously by us [Eur. J. Biochem. (1974) 47, 263-270] for the interaction of high-mobility group protein 1 with DNA. Although the binding parameters are similar for these two proteins, high-mobility group protein 2 differs from high-mobility group protein 1 in that the former appears to change the shape of the DNA to a more compact form. The molecular weight of high-mobility group protein 2 has been determined by equilibrium sedimentation and a mean value of 26,000 was obtained. A low level of nuclease activity detected in one preparation of high-mobility group protein 2 has been investigated. (orig.) [de

Evaluating Approaches to Rendering Braille Text on a High-Density Pin Display.

Science.gov (United States)

Morash, Valerie S; Russomanno, Alexander; Gillespie, R Brent; OModhrain, Sile

2017-10-13

Refreshable displays for tactile graphics are typically composed of pins that have smaller diameters and spacing than standard braille dots. We investigated configurations of high-density pins to form braille text on such displays using non-refreshable stimuli produced with a 3D printer. Normal dot braille (diameter 1.5 mm) was compared to high-density dot braille (diameter 0.75 mm) wherein each normal dot was rendered by high-density simulated pins alone or in a cluster of pins configured in a diamond, X, or square; and to "blobs" that could result from covering normal braille and high-density multi-pin configurations with a thin membrane. Twelve blind participants read MNREAD sentences displayed in these conditions. For high-density simulated pins, single pins were as quickly and easily read as normal braille, but diamond, X, and square multi-pin configurations were slower and/or harder to read than normal braille. We therefore conclude that as long as center-to-center dot spacing and dot placement is maintained, the dot diameter may be open to variability for rendering braille on a high density tactile display.

Quench protection and design of large high-current-density superconducting magnets

International Nuclear Information System (INIS)

Green, M.A.

1981-03-01

Although most large superconducting magnets have been designed using the concept of cryostability, there is increased need for large magnets which operate at current densities above the cryostable limit (greater than 10 8 Am -2 ). Large high current density superconducting magnets are chosen for the following reasons: reduced mass, reduced coil thickness or size, and reduced cost. The design of large high current density, adiabatically stable, superconducting magnets requires a very different set of design rules than either large cryostable superconducting magnets or small self-protected high current density magnets. The problems associated with large high current density superconducting magnets fall into three categories; (a) quench protection, (b) stress and training, and (c) cryogenic design. The three categories must be considered simultaneously. The paper discusses quench protection and its implication for magnets of large stored energies (this includes strings of smaller magnets). Training and its relationship to quench protection and magnetic strain are discussed. Examples of magnets, built at the Lawrence Berkeley Laboratory and elsewhere using the design guidelines given in this report, are presented

High-density and high-ρR fuel assembly for fast-ignition inertial confinement fusion

International Nuclear Information System (INIS)

Betti, R.; Zhou, C.

2005-01-01

Scaling relations to optimize implosion parameters for fast-ignition inertial confinement fusion are derived and used to design high-gain fast-ignition targets. A method to assemble thermonuclear fuel at high densities, high ρR, and with a small-size hot spot is presented. Massive cryogenic shells can be imploded with a low implosion velocity V I on a low adiabat α using the relaxation-pulse technique. While the low V I yields a small hot spot, the low α leads to large peak values of the density and areal density. It is shown that a 750 kJ laser can assemble fuel with V I ≅1.7x10 7 cm/s, α≅0.7, ρ≅400 g/cc, ρR≅3 g/cm 2 , and a hot-spot volume of less than 10% of the compressed core. If fully ignited, this fuel assembly can produce high gains of interest to inertial fusion energy applications

A Rewritable, Random-Access DNA-Based Storage System.

Science.gov (United States)

Yazdi, S M Hossein Tabatabaei; Yuan, Yongbo; Ma, Jian; Zhao, Huimin; Milenkovic, Olgica

2015-09-18

We describe the first DNA-based storage architecture that enables random access to data blocks and rewriting of information stored at arbitrary locations within the blocks. The newly developed architecture overcomes drawbacks of existing read-only methods that require decoding the whole file in order to read one data fragment. Our system is based on new constrained coding techniques and accompanying DNA editing methods that ensure data reliability, specificity and sensitivity of access, and at the same time provide exceptionally high data storage capacity. As a proof of concept, we encoded parts of the Wikipedia pages of six universities in the USA, and selected and edited parts of the text written in DNA corresponding to three of these schools. The results suggest that DNA is a versatile media suitable for both ultrahigh density archival and rewritable storage applications.

Surface density dependence of PCR amplicon hybridization on PNA/DNA probe layers

DEFF Research Database (Denmark)

Yao, Danfeng; Kim, Junyoung; Yu, Fang

2005-01-01

at an intermediate sodium concentration (approximately 100 mM). These effects were mainly ascribed to the electrostatic cross talk among the hybridized DNA molecules and the secondary structure of PCR amplicons. For the negatively charged DNA probes, the hybridization reaction was subjected additionally to the DNA....../DNA electrostatic barrier, particularly in lower ionic strength range (e.g., 10 approximately 150 mM Na(+)). The electrostatic cross talk was shown to be largely reduced if the PNA probe layer was sufficiently diluted by following a strategic templated immobilization method. As a consequence, a pseudo...

Numerical simulation of SU(2)c high density state

International Nuclear Information System (INIS)

Muroya, Shin; Nakamura, Atsushi; Nonaka, Chiho

2003-01-01

We report a study of the high baryon number density system with use of the two-color lattice QCD with Wilson fermions[1]. First we investigate thermodynamical quantities such as the Polyakov line, gluon energy density, and baryon number density in the (κ, μ) plane, where κ and μ are the hopping parameter and chemical potential, respectively. Then we calculate propagators of meson (q-barΓq) and baryon (qΓq) states in addition to the potential between quark lines. (author)

High follicle density does not decrease sweat gland density in Huacaya alpacas.

Science.gov (United States)

Moore, K E; Maloney, S K; Blache, D

2015-01-01

When exposed to high ambient temperatures, mammals lose heat evaporatively by either sweating from glands in the skin or by respiratory panting. Like other camelids, alpacas are thought to evaporate more water by sweating than panting, despite a thick fleece, unlike sheep which mostly pant in response to heat stress. Alpacas were brought to Australia to develop an alternative fibre industry to sheep wool. In Australia, alpacas can be exposed to ambient temperatures higher than in their native South America. As a young industry there is a great deal of variation in the quality and quantity of the fleece produced in the national flock. There is selection pressure towards animals with finer and denser fleeces. Because the fibre from secondary follicles is finer than that from primary follicles, selecting for finer fibres might alter the ratio of primary and secondary follicles. In turn the selection might alter sweat gland density because the sweat glands are associated with the primary follicle. Skin biopsy and fibre samples were obtained from the mid-section of 33 Huacaya alpacas and the skin sections were processed into horizontal sections at the sebaceous gland level. Total, primary, and secondary follicles and the number of sweat gland ducts were quantified. Fibre samples from each alpaca were further analysed for mean fibre diameter. The finer-fibred animals had a higher total follicle density (Palpacas with high follicle density should not be limited for potential sweating ability. Copyright © 2014 Elsevier Ltd. All rights reserved.

PCR cycles above routine numbers do not compromise high-throughput DNA barcoding results.

Science.gov (United States)

Vierna, J; Doña, J; Vizcaíno, A; Serrano, D; Jovani, R

2017-10-01

High-throughput DNA barcoding has become essential in ecology and evolution, but some technical questions still remain. Increasing the number of PCR cycles above the routine 20-30 cycles is a common practice when working with old-type specimens, which provide little amounts of DNA, or when facing annealing issues with the primers. However, increasing the number of cycles can raise the number of artificial mutations due to polymerase errors. In this work, we sequenced 20 COI libraries in the Illumina MiSeq platform. Libraries were prepared with 40, 45, 50, 55, and 60 PCR cycles from four individuals belonging to four species of four genera of cephalopods. We found no relationship between the number of PCR cycles and the number of mutations despite using a nonproofreading polymerase. Moreover, even when using a high number of PCR cycles, the resulting number of mutations was low enough not to be an issue in the context of high-throughput DNA barcoding (but may still remain an issue in DNA metabarcoding due to chimera formation). We conclude that the common practice of increasing the number of PCR cycles should not negatively impact the outcome of a high-throughput DNA barcoding study in terms of the occurrence of point mutations.

Potential formation and confinement in high density plasma on the GAMMA 10 tandem mirror

International Nuclear Information System (INIS)

Yatsu, K.

2002-01-01

After the attainment of doubling of the density due to the potential confinement, GAMMA 10 experiments have been directed to realization of a high density plasma and also to study dependence of the confining potential and confinement time on the plasma density. These problems are important to understand the physics of potential formation in tandem mirrors and also for the development of a tandem mirror reactor. We reported high density plasma production by using an ion cyclotron range of frequency heating at a high harmonic frequency in the last IAEA Conference. However, the diamagnetic signal of the high density plasma decreased when electron cyclotron resonance heating (ECRH) was applied due to some instabilities. Recently, the high density plasma production was much improved by adjusting the spacing of the conducting plates installed in the anchor transition regions, which enabled us to produce a high density plasma without degradation of the diamagnetic signal with ECRH and also to study the density dependence. In this paper we report production of a high density plasma and dependence of the confining potential and the confinement time on the density. (author)

High Energy Density Dielectrics for Pulsed Power Applications

National Research Council Canada - National Science Library

Wu, Richard L; Bray, Kevin R

2008-01-01

This report was developed under a SBIR contract. Aluminum oxynitride (AlON) capacitors exhibit several promising characteristics for high energy density capacitor applications in extreme environments...

Pair-density waves, charge-density waves, and vortices in high-Tc cuprates

Science.gov (United States)

Dai, Zhehao; Zhang, Ya-Hui; Senthil, T.; Lee, Patrick A.

2018-05-01

A recent scanning tunneling microscopy (STM) experiment reports the observation of a charge-density wave (CDW) with a period of approximately 8a in the halo region surrounding the vortex core, in striking contrast to the approximately 4a period CDWs that are commonly observed in the cuprates. Inspired by this work, we study a model where a bidirectional pair-density wave (PDW) with period 8 is at play. This further divides into two classes: (1) where the PDW is a competing state of the d -wave superconductor and can exist only near the vortex core where the d -wave order is suppressed and (2) where the PDW is the primary order, the so-called "mother state" that persists with strong phase fluctuations to high temperature and high magnetic field and lies behind the pseudogap phenomenology. We study the charge-density wave structures near the vortex core in these models. We emphasize the importance of the phase winding of the d -wave order parameter. The PDW can be pinned by the vortex core due to this winding and become static. Furthermore, the period-8 CDW inherits the properties of this winding, which gives rise to a special feature of the Fourier transform peak, namely, it is split in certain directions. There is also a line of zeros in the inverse Fourier transform of filtered data. We propose that these are key experimental signatures that can distinguish between the PDW-driven scenario from the more mundane option that the period-8 CDW is primary. We discuss the pro's and con's of the options considered above. Finally, we attempt to place the STM experiment in the broader context of pseudogap physics of underdoped cuprates and relate this observation to the unusual properties of x-ray scattering data on CDW carried out to very high magnetic field.

Lithium-Based High Energy Density Flow Batteries

Science.gov (United States)

Bugga, Ratnakumar V. (Inventor); West, William C. (Inventor); Kindler, Andrew (Inventor); Smart, Marshall C. (Inventor)

2014-01-01

Systems and methods in accordance with embodiments of the invention implement a lithium-based high energy density flow battery. In one embodiment, a lithium-based high energy density flow battery includes a first anodic conductive solution that includes a lithium polyaromatic hydrocarbon complex dissolved in a solvent, a second cathodic conductive solution that includes a cathodic complex dissolved in a solvent, a solid lithium ion conductor disposed so as to separate the first solution from the second solution, such that the first conductive solution, the second conductive solution, and the solid lithium ionic conductor define a circuit, where when the circuit is closed, lithium from the lithium polyaromatic hydrocarbon complex in the first conductive solution dissociates from the lithium polyaromatic hydrocarbon complex, migrates through the solid lithium ionic conductor, and associates with the cathodic complex of the second conductive solution, and a current is generated.

DNA repair and the evolution of transformation in Bacillus subtilis. 3. Sex with damaged DNA

International Nuclear Information System (INIS)

Hoelzer, M.A.; Michod, R.E.

1991-01-01

Natural genetic transformation in the bacterium Bacillus subtilis provides an experimental system for studying the evolutionary function of sexual recombination. The repair hypothesis proposes that during transformation the exogenous DNA taken up by cells is used as template for recombinational repair of damages in the recipient cell's genome. Earlier results demonstrated that the population density of transformed cells (i.e., sexual cells) increases, relative to nontransformed cells (primarily asexual cells), with increasing dosage of ultraviolet irradiation, provided that the cells are transformed with undamaged homologous DNA after they have become damaged. In nature, however, donor DNA for transformation is likely to come from cells that are as damaged as the recipient cells. In order to better simulate the effects of transformation in natural populations we conducted similar experiments as those just described using damaged donor DNA. The authors document in this report that transformants continue to increase in relative density even if they are transformed with damaged donor DNA. These results suggest that sites of transformation are often damaged sites in the recipient cell's genome

Association between high risk papillomavirus DNA and nitric oxide release in the human uterine cervix.

Science.gov (United States)

Rahkola, Paivi; Mikkola, Tomi S; Ylikorkala, Olavi; Vaisanen-Tommiska, Mervi

2009-08-01

Local cervical factors may determine the outcome of human papillomavirus (HPV) infection. Nitric oxide (NO) may be one such factor, since it is produced by uterine cervical cells and it takes part in both immunological and carcinogenic reactions. We studied the association between the presence of cervical high risk (hr) HPV DNA and NO in the cervical canal in women. High risk HPV DNA status was assessed from 328 women by using a specific DNA test and the release of cervical NO was assessed as nitrate/nitrite in cervical fluid. Cervical NO was then compared between women showing different status of hr HPV DNA and different cytological and histological findings. High risk HPV DNA was present in 175/328 (53%) women. The cervical NO release in women with hr HPV DNA was 90% higher compared to hr HPV DNA negative women (poral contraception, intrauterine devices, or signs of bacterial vaginosis or candida infection. Cytologically healthy epithelium and epithelium with mild cytological or histological changes showed elevated NO release if hr HPV DNA was present. The presence of hr HPV DNA is associated with an increased release of NO in the human uterine cervix. The clinical significance of this phenomenon remains open.

Apparatus and method for generating high density pulses of electrons

International Nuclear Information System (INIS)

Lee, C.; Oettinger, P.E.

1981-01-01

An apparatus and method are described for the production of high density pulses of electrons using a laser energized emitter. Caesium atoms from a low pressure vapour atmosphere are absorbed on and migrate from a metallic target rapidly heated by a laser to a high temperature. Due to this heating time being short compared with the residence time of the caesium atoms adsorbed on the target surface, copious electrons are emitted which form a high current density pulse. (U.K.)

Compatibility of advanced tokamak plasma with high density and high radiation loss operation in JT-60U

International Nuclear Information System (INIS)

Takenaga, H.; Asakura, N.; Kubo, H.; Higashijima, S.; Konoshima, S.; Nakano, T.; Oyama, N.; Ide, S.; Fujita, T.; Takizuka, T.; Kamada, Y.; Miura, Y.; Porter, G.D.; Rognlien, T.D.; Rensink, M.E.

2005-01-01

Compatibility of advanced tokamak plasmas with high density and high radiation loss has been investigated in both reversed shear (RS) plasmas and high β p H-mode plasmas with a weak positive shear on JT-60U. In the RS plasmas, the operation regime is extended to high density above the Greenwald density (n GW ) with high confinement (HH y2 >1) and high radiation loss fraction (f rad >0.9) by tailoring the internal transport barriers (ITBs). High confinement of HH y2 =1.2 is sustained even with 80% radiation from the main plasma enhanced by accumulated metal impurity. The divertor radiation is enhanced by Ne seeding and the ratio of the divertor radiation to the total radiation is increased from 20% without seeding to 40% with Ne seeding. In the high β p H-mode plasmas, high confinement (HH y2 =0.96) is maintained at high density (n-bar e /n GW =0.92) with high radiation loss fraction (f rad ∼1) by utilizing high-field-side pellets and Ar injections. The high n-bar e /n GW is obtained due to a formation of clear density ITB. Strong core-edge parameter linkage is observed, as well as without Ar injection. In this linkage, the pedestal β p , defined as β p ped =p ped /(B p 2 /2μ 0 ) where p ped is the plasma pressure at the pedestal top, is enhanced with the total β p . The radiation profile in the main plasma is peaked due to Ar accumulation inside the ITB and the measured central radiation is ascribed to Ar. The impurity transport analyses indicate that Ar accumulation by a factor of 2 more than the electron, as observed in the high β p H-mode plasma, is acceptable even with peaked density profile in a fusion reactor for impurity seeding. (author)

Comparison of low density and high density pedicle screw instrumentation in Lenke 1 adolescent idiopathic scoliosis.

Science.gov (United States)

Shen, Mingkui; Jiang, Honghui; Luo, Ming; Wang, Wengang; Li, Ning; Wang, Lulu; Xia, Lei

2017-08-02

The correlation between implant density and deformity correction has not yet led to a precise conclusion in adolescent idiopathic scoliosis (AIS). The aim of this study was to evaluate the effects of low density (LD) and high density (HD) pedicle screw instrumentation in terms of the clinical, radiological and Scoliosis Research Society (SRS)-22 outcomes in Lenke 1 AIS. We retrospectively reviewed 62 consecutive Lenke 1 AIS patients who underwent posterior spinal arthrodesis using all-pedicle screw instrumentation with a minimum follow-up of 24 months. The implant density was defined as the number of screws per spinal level fused. Patients were then divided into two groups according to the average implant density for the entire study. The LD group (n = 28) had fewer than 1.61 screws per level, while the HD group (n = 34) had more than 1.61 screws per level. The radiographs were analysed preoperatively, postoperatively and at final follow-up. The perioperative and SRS-22 outcomes were also assessed. Independent sample t tests were used between the two groups. Comparisons between the two groups showed no significant differences in the correction of the main thoracic curve and thoracic kyphosis, blood transfusion, hospital stay, and SRS-22 scores. Compared with the HD group, there was a decreased operating time (278.4 vs. 331.0 min, p = 0.004) and decreased blood loss (823.6 vs. 1010.9 ml, p = 0.048), pedicle screws needed (15.1 vs. 19.6, p density and high density pedicle screw instrumentation achieved satisfactory deformity correction in Lenke 1 AIS patients. However, the operating time and blood loss were reduced, and the implant costs were decreased with the use of low screw density constructs.

Two efficient methods for isolation of high-quality genomic DNA from entomopathogenic fungi.

Science.gov (United States)

Serna-Domínguez, María G; Andrade-Michel, Gilda Y; Arredondo-Bernal, Hugo C; Gallou, Adrien

2018-03-27

Conventional and commercial methods for isolation of nucleic acids are available for fungal samples including entomopathogenic fungi (EPF). However, there is not a unique optimal method for all organisms. The cell wall structure and the wide range of secondary metabolites of EPF can broadly interfere with the efficiency of the DNA extraction protocol. This study compares three commercial protocols: DNeasy® Plant Mini Kit (Qiagen), Wizard® Genomic DNA Purification Kit (Promega), and Axygen™ Multisource Genomic DNA Miniprep Kit (Axygen) and three conventional methods based on different buffers: SDS, CTAB/PVPP, and CTAB/β-mercaptoethanol versus three cell lysis procedures: liquid nitrogen homogenization and two bead-beating materials (i.e., tungsten-carbide and stainless-steel) for four representative species of EPF (i.e., Beauveria bassiana, Hirsutella citriformis, Isaria javanica, and Metarhizium anisopliae). Liquid nitrogen homogenization combined with DNeasy® Plant Mini Kit (i.e., QN) or SDS buffer (i.e., SN) significantly improved the yield with a good purity (~1.8) and high integrity (>20,000 bp) of genomic DNA in contrast with other methods, also, these results were better when compared with the two bead-beating materials. The purified DNA was evaluated by PCR-based techniques: amplification of translation elongation factor 1-α (TEF) and two highly sensitive molecular markers (i.e., ISSR and AFLP) with reliable and reproducible results. Despite a variation in yield, purity, and integrity of extracted DNA across the four species of EPF with the different DNA extraction methods, the SN and QN protocols maintained a high-quality of DNA which is required for downstream molecular applications. Copyright © 2018 Elsevier B.V. All rights reserved.

Plasmid fermentation process for DNA immunization applications.

Science.gov (United States)

Carnes, Aaron E; Williams, James A

2014-01-01

Plasmid DNA for immunization applications must be of the highest purity and quality. The ability of downstream purification to efficiently produce a pure final product is directly influenced by the performance of the upstream fermentation process. While several clinical manufacturing facilities already have validated fermentation processes in place to manufacture plasmid DNA for use in humans, a simple and inexpensive laboratory-scale fermentation process can be valuable for in-house production of plasmid DNA for use in animal efficacy studies. This chapter describes a simple fed-batch fermentation process for producing bacterial cell paste enriched with high-quality plasmid DNA. A constant feeding strategy results in a medium cell density culture with continuously increasing plasmid amplification towards the end of the process. Cell banking and seed culture preparation protocols, which can dramatically influence final product yield and quality, are also described. These protocols are suitable for production of research-grade plasmid DNA at the 100 mg-to-1.5 g scale from a typical 10 L laboratory benchtop fermentor.

Coupling DNA nano-breadboards to solid state conductors

International Nuclear Information System (INIS)

Wang, Liqian; Morales, Piero; Dalmastri, Claudia; Rapone, Bruno; Gothelf, Kurt; Krissanaprasit, Abhichart; Rettere, Scott

2015-01-01

DNA is not only a most extraordinary information storage medium: the programmable pairing of DNA single strands into precisely engineered, connecting double helices make it an extremely appealing material for assemblage of nanoscale architectures. This is the basis of DNA nanotechnology, and designing almost any structure made of DNA at the nanometer scale, decorating it with a variety of functional molecules, and accomplishing it by virtually inexpensive self-assembly, is already a reality in many research laboratories in the world. But can we extend the range of applications of this technology by coupling DNA grafted molecular electronic nano circuitry to solid state devices, and interface molecular smart functions to our senses? This challenging research is addressed by a collaborative research among ENEA, the Universities of Roma 'Tor Vergata' and 'Aarhus', and the CNMS of the Oak Ridge National Laboratory. The first results obtained by our consortium pave the way to the technological ability to interface and use completely self-assembled, DNA-based electronic nano-breadboards, endowed with ultra-high-density functional organic components [it

Winnowing DNA for rare sequences: highly specific sequence and methylation based enrichment.

Directory of Open Access Journals (Sweden)

Jason D Thompson

Full Text Available Rare mutations in cell populations are known to be hallmarks of many diseases and cancers. Similarly, differential DNA methylation patterns arise in rare cell populations with diagnostic potential such as fetal cells circulating in maternal blood. Unfortunately, the frequency of alleles with diagnostic potential, relative to wild-type background sequence, is often well below the frequency of errors in currently available methods for sequence analysis, including very high throughput DNA sequencing. We demonstrate a DNA preparation and purification method that through non-linear electrophoretic separation in media containing oligonucleotide probes, achieves 10,000 fold enrichment of target DNA with single nucleotide specificity, and 100 fold enrichment of unmodified methylated DNA differing from the background by the methylation of a single cytosine residue.

Winnowing DNA for rare sequences: highly specific sequence and methylation based enrichment.

Science.gov (United States)

Thompson, Jason D; Shibahara, Gosuke; Rajan, Sweta; Pel, Joel; Marziali, Andre

2012-01-01

Rare mutations in cell populations are known to be hallmarks of many diseases and cancers. Similarly, differential DNA methylation patterns arise in rare cell populations with diagnostic potential such as fetal cells circulating in maternal blood. Unfortunately, the frequency of alleles with diagnostic potential, relative to wild-type background sequence, is often well below the frequency of errors in currently available methods for sequence analysis, including very high throughput DNA sequencing. We demonstrate a DNA preparation and purification method that through non-linear electrophoretic separation in media containing oligonucleotide probes, achieves 10,000 fold enrichment of target DNA with single nucleotide specificity, and 100 fold enrichment of unmodified methylated DNA differing from the background by the methylation of a single cytosine residue.

High density operation on the HT-7 superconducting tokamak

International Nuclear Information System (INIS)

Xiang Gao

2000-01-01

The structure of the operation region has been studied in the HT-7 superconducting tokamak, and progress on the extension of the HT-7 ohmic discharge operation region is reported. A density corresponding to 1.2 times the Greenwald limit was achieved by RF boronization. The density limit appears to be connected to the impurity content and the edge parameters, so the best results are obtained with very clean plasmas and peaked electron density profiles. The peaking factors of electron density profiles for different current and line averaged densities were observed. The density behaviour and the fuelling efficiency for gas puffing (20-30%), pellet injection (70-80%) and molecular beam injection (40-50%) were studied. The core crash sawteeth and MHD behaviour, which were induced by an injected pellet, were observed and the events correlated with the change of current profile and reversed magnetic shear. The MARFE phenomena on HT-7 are summarized. The best correlation has been found between the total input ohmic power and the product of the edge line averaged density and Z eff . HT-7 could be easily operated in the high density region MARFE-free using RF boronization. (author)

Triglycerides, total cholesterol, high density lipoprotein cholesterol and low density lipoprotein cholesterol in rats exposed to premium motor spirit fumes.

Science.gov (United States)

Aberare, Ogbevire L; Okuonghae, Patrick; Mukoro, Nathaniel; Dirisu, John O; Osazuwa, Favour; Odigie, Elvis; Omoregie, Richard

2011-06-01

Deliberate and regular exposure to premium motor spirit fumes is common and could be a risk factor for liver disease in those who are occupationally exposed. A possible association between premium motor spirit fumes and plasma levels of triglyceride, total cholesterol, high density lipoprotein cholesterol and low density lipoprotein cholesterol using a rodent model could provide new insights in the pathology of diseases where cellular dysfunction is an established risk factor. The aim of this study was to evaluate the possible effect of premium motor spirit fumes on lipids and lipoproteins in workers occupationally exposed to premium motor spirit fumes using rodent model. Twenty-five Wister albino rats (of both sexes) were used for this study between the 4(th) of August and 7(th) of September, 2010. The rats were divided into five groups of five rats each. Group 1 rats were not exposed to premium motor spirit fumes (control group), group 2 rats were exposed for 1 hour daily, group 3 for 3 hours daily, group 4 for 5 hours daily and group 5 for 7 hours daily. The experiment lasted for a period of 4 weeks. Blood samples obtained from all the groups after 4 weeks of exposure were used for the estimation of plasma levels of triglyceride, total cholesterol, high density lipoprotein- cholesterol and low density lipoprotein- cholesterol. Results showed significant increase in means of plasma total cholesterol and low density lipoprotein levels (P<0.05). The mean triglyceride and total body weight were significantly lower (P<0.05) in the exposed group when compared with the unexposed. The plasma level of high density lipoprotein, the ratio of low density lipoprotein to high density lipoprotein and the ratio of total cholesterol to high density lipoprotein did not differ significantly in exposed subjects when compared with the control group. These results showed that frequent exposure to petrol fumes may be highly deleterious to the liver cells.

Synthetic LNA/DNA nano-scaffolds for highly efficient diagnostics of nucleic acids and autoimmune antibodies

DEFF Research Database (Denmark)

Astakhova, Irina Kira

2014-01-01

) strands and a series of fluorescent azides. The multiply labeled fluorescent LNA/DNA probes prepared herein generally display high binding affinity to complementary DNA/RNA, high quantum yields and, hence, high fluorescence brightness values. With the novel fluorescent probes, specific sensing...

High-density amorphous ice: nucleation of nanosized low-density amorphous ice

Science.gov (United States)

Tonauer, Christina M.; Seidl-Nigsch, Markus; Loerting, Thomas

2018-01-01

The pressure dependence of the crystallization temperature of different forms of expanded high-density amorphous ice (eHDA) was scrutinized. Crystallization at pressures 0.05-0.30 GPa was followed using volumetry and powder x-ray diffraction. eHDA samples were prepared via isothermal decompression of very high-density amorphous ice at 140 K to different end pressures between 0.07-0.30 GPa (eHDA0.07-0.3). At 0.05-0.17 GPa the crystallization line T x (p) of all eHDA variants is the same. At pressures  >0.17 GPa, all eHDA samples decompressed to pressures  <0.20 GPa exhibit significantly lower T x values than eHDA0.2 and eHDA0.3. We rationalize our findings with the presence of nanoscaled low-density amorphous ice (LDA) seeds that nucleate in eHDA when it is decompressed to pressures  <0.20 GPa at 140 K. Below ~0.17 GPa, these nanosized LDA domains are latent within the HDA matrix, exhibiting no effect on T x of eHDA<0.2. Upon heating at pressures  ⩾0.17 GPa, these nanosized LDA nuclei transform to ice IX nuclei. They are favored sites for crystallization and, hence, lower T x . By comparing crystallization experiments of bulk LDA with the ones involving nanosized LDA we are able to estimate the Laplace pressure and radius of ~0.3-0.8 nm for the nanodomains of LDA. The nucleation of LDA in eHDA revealed here is evidence for the first-order-like nature of the HDA  →  LDA transition, supporting water’s liquid-liquid transition scenarios.

Properties of high-density matter in the electroweak symmetric phase

International Nuclear Information System (INIS)

Chandra, D.; Goyal, A.

1992-01-01

We examine the bulk properties of matter at high densities and finite temperatures in the phase where electroweak symmetry is exact and fermions are massless, by taking the strong interactions into account perturbatively to lowest order in the quark-gluon chromodynamic coupling constant α c . We also discuss the possibility of a phase transition of strange quark matter into this high-density matter in the electroweak symmetric phase at densities likely to be present in the core of dense neutron stars or collapsing stars. Finally, we study the properties of finite-size chunks of this matter by taking surface effects into account and give an estimate of the surface tension

High-energy-density physics foundation of inertial fusion and experimental astrophysics

CERN Document Server

Drake, R Paul

2018-01-01

The raw numbers of high-energy-density physics are amazing: shock waves at hundreds of km/s (approaching a million km per hour), temperatures of millions of degrees, and pressures that exceed 100 million atmospheres. This title surveys the production of high-energy-density conditions, the fundamental plasma and hydrodynamic models that can describe them and the problem of scaling from the laboratory to the cosmos. Connections to astrophysics are discussed throughout. The book is intended to support coursework in high-energy-density physics, to meet the needs of new researchers in this field, and also to serve as a useful reference on the fundamentals. Specifically the book has been designed to enable academics in physics, astrophysics, applied physics and engineering departments to provide in a single-course, an introduction to fluid mechanics and radiative transfer, with dramatic applications in the field of high-energy-density systems. This second edition includes pedagogic improvements to the presentation ...

Analysis of JC virus DNA replication using a quantitative and high-throughput assay

Science.gov (United States)

Shin, Jong; Phelan, Paul J.; Chhum, Panharith; Bashkenova, Nazym; Yim, Sung; Parker, Robert; Gagnon, David; Gjoerup, Ole; Archambault, Jacques; Bullock, Peter A.

2015-01-01

Progressive Multifocal Leukoencephalopathy (PML) is caused by lytic replication of JC virus (JCV) in specific cells of the central nervous system. Like other polyomaviruses, JCV encodes a large T-antigen helicase needed for replication of the viral DNA. Here, we report the development of a luciferase-based, quantitative and high-throughput assay of JCV DNA replication in C33A cells, which, unlike the glial cell lines Hs 683 and U87, accumulate high levels of nuclear T-ag needed for robust replication. Using this assay, we investigated the requirement for different domains of T-ag, and for specific sequences within and flanking the viral origin, in JCV DNA replication. Beyond providing validation of the assay, these studies revealed an important stimulatory role of the transcription factor NF1 in JCV DNA replication. Finally, we show that the assay can be used for inhibitor testing, highlighting its value for the identification of antiviral drugs targeting JCV DNA replication. PMID:25155200

High-density polymorphisms analysis of 23 candidate genes for association with bone mineral density.

Science.gov (United States)

Giroux, Sylvie; Elfassihi, Latifa; Clément, Valérie; Bussières, Johanne; Bureau, Alexandre; Cole, David E C; Rousseau, François

2010-11-01

Osteoporosis is a bone disease characterized by low bone mineral density (BMD), a highly heritable and polygenic trait. Women are more prone than men to develop osteoporosis due to a lower peak bone mass and accelerated bone loss at menopause. Peak bone mass has been convincingly shown to be due to genetic factors with heritability up to 80%. Menopausal bone loss has been shown to have around 38% to 49% heritability depending on the site studied. To have more statistical power to detect small genetic effects we focused on premenopausal women. We studied 23 candidate genes, some involved in calcium and vitamin-D regulation and others because estrogens strongly induced their gene expression in mice where it was correlated with humerus trabecular bone density. High-density polymorphisms were selected to cover the entire gene variability and 231 polymorphisms were genotyped in a first sample of 709 premenopausal women. Positive associations were retested in a second, independent, sample of 673 premenopausal women. Ten polymorphisms remained associated with BMD in the combined samples and one was further associated in a large sample of postmenopausal women (1401 women). This associated polymorphism was located in the gene CSF3R (granulocyte colony stimulating factor receptor) that had never been associated with BMD before. The results reported in this study suggest a role for CSF3R in the determination of bone density in women. Copyright © 2010 Elsevier Inc. All rights reserved.

Kinetics of the high- to low-density amorphous water transition

International Nuclear Information System (INIS)

Koza, M M; Schober, H; Fischer, H E; Hansen, T; Fujara, F

2003-01-01

In situ neutron diffraction experiments have been carried out to study the kinetics of the transformation of high-density amorphous (HDA) water into its low-density amorphous state at temperatures 87 K ≤ T ≤ 110 K. It is found that three different stages are comprised in this transformation, namely an annealing process of the high-density matrix followed by a first-order-like transition into a low-density state, which can be further annealed at higher temperatures T ≤ 127 K. The annealing kinetics of the HDA state follows the logarithm of time as found in other systems showing polyamorphism. According to the theory of transformation by nucleation and growth the apparent first-order transition follows an Avrami-Kolmogorov behaviour. An energy barrier ΔE ∼ 33 k Jmol -1 is estimated from the temperature dependence of this transition

Noise reduction in muon tomography for detecting high density objects

International Nuclear Information System (INIS)

Benettoni, M; Checchia, P; Cossutta, L; Furlan, M; Gonella, F; Pegoraro, M; Garola, A Rigoni; Ronchese, P; Vanini, S; Viesti, G; Bettella, G; Bonomi, G; Donzella, A; Subieta, M; Zenoni, A; Calvagno, G; Cortelazzo, G; Zanuttigh, P; Calvini, P; Squarcia, S

2013-01-01

The muon tomography technique, based on multiple Coulomb scattering of cosmic ray muons, has been proposed as a tool to detect the presence of high density objects inside closed volumes. In this paper a new and innovative method is presented to handle the density fluctuations (noise) of reconstructed images, a well known problem of this technique. The effectiveness of our method is evaluated using experimental data obtained with a muon tomography prototype located at the Legnaro National Laboratories (LNL) of the Istituto Nazionale di Fisica Nucleare (INFN). The results reported in this paper, obtained with real cosmic ray data, show that with appropriate image filtering and muon momentum classification, the muon tomography technique can detect high density materials, such as lead, albeit surrounded by light or medium density material, in short times. A comparison with algorithms published in literature is also presented

Low-frequency oscillations at high density in JFT-2

International Nuclear Information System (INIS)

Maeno, Masaki; Katagiri, Masaki; Suzuki, Norio; Fujisawa, Noboru

1977-12-01

Low-frequency oscillations in a plasma were measured with magnetic probes and Si surface-barrier detectors, and behaviour of the high density plasmas was studied. The plasma current profile in the phase of decreasing density after the interruption of gas input is more peaked than during gas input. The introduction of hydrogen during a discharge results in a reduction of the impurities flux. The increase of density by fast gas input is limited with a negative voltage spike. Immediately before a negative voltage spike, oscillations of m=1,2 grow, leading to the spike. (auth.)

High-resolution DNA content analysis of microbiopsy samples in oral lichen planus.

Science.gov (United States)

Pentenero, M; Monticone, M; Marino, R; Aiello, C; Marchitto, G; Malacarne, D; Giaretti, W; Gandolfo, S; Castagnola, P

2017-04-01

DNA aneuploidy has been reported to be a predictor of poor prognosis in both premalignant and malignant lesions. In oral lichen planus (OLP), this hypothesis remains to be proved. This study aimed to determine the rate of occurrence of DNA aneuploidy in patients with OLP by high-resolution DNA flow cytometry. Patients with OLP were consecutively enrolled. Tissue samples were subdivided for formalin fixation and routine histological assessment and for immediate storage at -20°C for later DNA ploidy analysis, which was performed by DAPI staining of the extracted nuclei and excitation with a UV lamp. The DNA aneuploid sublines were characterized by the DNA Index. A DNA aneuploid status was observed in two of 77 patients with OLP (2.6%). When considering the clinical aspect of the OLP lesions, both DNA aneuploid cases had a reticular clinical aspect. DNA aneuploidy is an uncommon event in OLP and less frequent compared to other non-dysplastic and non-OLP oral potentially malignant disorders. The extremely low rate of DNA aneuploidy could represent an occasional finding or reflect the low rate of malignant transformation observed in patients with OLP even if the real prognostic value of DNA ploidy analysis in patients with OLP remains to be confirmed. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Volume generation of negative ions in high density hydrogen discharges

International Nuclear Information System (INIS)

Hiskes, J.R.; Karo, A.M.

1983-01-01

A parametric survey is made of a high-density tandem two-chamber hydrogen negative ion system. The optimum extracted negative ion current densities are sensitive to the atom concentration in the discharge and to the system scale length. For scale lengths ranging from 10 cm to 0.1 cm optimum current densities range from of order 1 to 100 mA cm -2 , respectively

A high-throughput and quantitative method to assess the mutagenic potential of translesion DNA synthesis

Science.gov (United States)

Taggart, David J.; Camerlengo, Terry L.; Harrison, Jason K.; Sherrer, Shanen M.; Kshetry, Ajay K.; Taylor, John-Stephen; Huang, Kun; Suo, Zucai

2013-01-01

Cellular genomes are constantly damaged by endogenous and exogenous agents that covalently and structurally modify DNA to produce DNA lesions. Although most lesions are mended by various DNA repair pathways in vivo, a significant number of damage sites persist during genomic replication. Our understanding of the mutagenic outcomes derived from these unrepaired DNA lesions has been hindered by the low throughput of existing sequencing methods. Therefore, we have developed a cost-effective high-throughput short oligonucleotide sequencing assay that uses next-generation DNA sequencing technology for the assessment of the mutagenic profiles of translesion DNA synthesis catalyzed by any error-prone DNA polymerase. The vast amount of sequencing data produced were aligned and quantified by using our novel software. As an example, the high-throughput short oligonucleotide sequencing assay was used to analyze the types and frequencies of mutations upstream, downstream and at a site-specifically placed cis–syn thymidine–thymidine dimer generated individually by three lesion-bypass human Y-family DNA polymerases. PMID:23470999

Achieving High-Energy-High-Power Density in a Flexible Quasi-Solid-State Sodium Ion Capacitor.

Science.gov (United States)

Li, Hongsen; Peng, Lele; Zhu, Yue; Zhang, Xiaogang; Yu, Guihua

2016-09-14

Simultaneous integration of high-energy output with high-power delivery is a major challenge for electrochemical energy storage systems, limiting dual fine attributes on a device. We introduce a quasi-solid-state sodium ion capacitor (NIC) based on a battery type urchin-like Na2Ti3O7 anode and a capacitor type peanut shell derived carbon cathode, using a sodium ion conducting gel polymer as electrolyte, achieving high-energy-high-power characteristics in solid state. Energy densities can reach 111.2 Wh kg(-1) at power density of 800 W kg(-1), and 33.2 Wh kg(-1) at power density of 11200 W kg(-1), which are among the best reported state-of-the-art NICs. The designed device also exhibits long-term cycling stability over 3000 cycles with capacity retention ∼86%. Furthermore, we demonstrate the assembly of a highly flexible quasi-solid-state NIC and it shows no obvious capacity loss under different bending conditions.

Isolation and characterization of high affinity aptamers against DNA polymerase iota.

Science.gov (United States)

Lakhin, Andrei V; Kazakov, Andrei A; Makarova, Alena V; Pavlov, Yuri I; Efremova, Anna S; Shram, Stanislav I; Tarantul, Viacheslav Z; Gening, Leonid V

2012-02-01

Human DNA-polymerase iota (Pol ι) is an extremely error-prone enzyme and the fidelity depends on the sequence context of the template. Using the in vitro systematic evolution of ligands by exponential enrichment (SELEX) procedure, we obtained an oligoribonucleotide with a high affinity to human Pol ι, named aptamer IKL5. We determined its dissociation constant with homogenous preparation of Pol ι and predicted its putative secondary structure. The aptamer IKL5 specifically inhibits DNA-polymerase activity of the purified enzyme Pol ι, but did not inhibit the DNA-polymerase activities of human DNA polymerases beta and kappa. IKL5 suppressed the error-prone DNA-polymerase activity of Pol ι also in cellular extracts of the tumor cell line SKOV-3. The aptamer IKL5 is useful for studies of the biological role of Pol ι and as a potential drug to suppress the increase of the activity of this enzyme in malignant cells.

Transport analysis of high radiation and high density plasmas in the ASDEX Upgrade tokamak

Directory of Open Access Journals (Sweden)

Casali L.

2014-01-01

Full Text Available Future fusion reactors, foreseen in the “European road map” such as DEMO, will operate under more demanding conditions compared to present devices. They will require high divertor and core radiation by impurity seeding to reduce heat loads on divertor target plates. In addition, DEMO will have to work at high core densities to reach adequate fusion performance. The performance of fusion reactors depends on three essential parameters: temperature, density and energy confinement time. The latter characterizes the loss rate due to both radiation and transport processes. The DEMO foreseen scenarios described above were not investigated so far, but are now addressed at the ASDEX Upgrade tokamak. In this work we present the transport analysis of such scenarios. Plasma with high radiation by impurity seeding: transport analysis taking into account the radiation distribution shows no change in transport during impurity seeding. The observed confinement improvement is an effect of higher pedestal temperatures which extend to the core via stiffness. A non coronal radiation model was developed and compared to the bolometric measurements in order to provide a reliable radiation profile for transport calculations. High density plasmas with pellets: the analysis of kinetic profiles reveals a transient phase at the start of the pellet fuelling due to a slower density build up compared to the temperature decrease. The low particle diffusion can explain the confinement behaviour.

Structure solution of DNA-binding proteins and complexes with ARCIMBOLDO libraries

Energy Technology Data Exchange (ETDEWEB)

Pröpper, Kevin [University of Göttingen, (Germany); Instituto de Biologia Molecular de Barcelona (IBMB-CSIC), (Spain); Meindl, Kathrin; Sammito, Massimo [Instituto de Biologia Molecular de Barcelona (IBMB-CSIC), (Spain); Dittrich, Birger; Sheldrick, George M. [University of Göttingen, (Germany); Pohl, Ehmke, E-mail: ehmke.pohl@durham.ac.uk [Durham University, (United Kingdom); Usón, Isabel, E-mail: ehmke.pohl@durham.ac.uk [Instituto de Biologia Molecular de Barcelona (IBMB-CSIC), (Spain); Institucio Catalana de Recerca i Estudis Avancats (ICREA), (Spain); University of Göttingen, (Germany)

2014-06-01

The structure solution of DNA-binding protein structures and complexes based on the combination of location of DNA-binding protein motif fragments with density modification in a multi-solution frame is described. Protein–DNA interactions play a major role in all aspects of genetic activity within an organism, such as transcription, packaging, rearrangement, replication and repair. The molecular detail of protein–DNA interactions can be best visualized through crystallography, and structures emphasizing insight into the principles of binding and base-sequence recognition are essential to understanding the subtleties of the underlying mechanisms. An increasing number of high-quality DNA-binding protein structure determinations have been witnessed despite the fact that the crystallographic particularities of nucleic acids tend to pose specific challenges to methods primarily developed for proteins. Crystallographic structure solution of protein–DNA complexes therefore remains a challenging area that is in need of optimized experimental and computational methods. The potential of the structure-solution program ARCIMBOLDO for the solution of protein–DNA complexes has therefore been assessed. The method is based on the combination of locating small, very accurate fragments using the program Phaser and density modification with the program SHELXE. Whereas for typical proteins main-chain α-helices provide the ideal, almost ubiquitous, small fragments to start searches, in the case of DNA complexes the binding motifs and DNA double helix constitute suitable search fragments. The aim of this work is to provide an effective library of search fragments as well as to determine the optimal ARCIMBOLDO strategy for the solution of this class of structures.

High-Resolution Melting (HRM) of Hypervariable Mitochondrial DNA Regions for Forensic Science.

Science.gov (United States)

Dos Santos Rocha, Alípio; de Amorim, Isis Salviano Soares; Simão, Tatiana de Almeida; da Fonseca, Adenilson de Souza; Garrido, Rodrigo Grazinoli; Mencalha, Andre Luiz

2018-03-01

Forensic strategies commonly are proceeding by analysis of short tandem repeats (STRs); however, new additional strategies have been proposed for forensic science. Thus, this article standardized the high-resolution melting (HRM) of DNA for forensic analyzes. For HRM, mitochondrial DNA (mtDNA) from eight individuals were extracted from mucosa swabs by DNAzol reagent, samples were amplified by PCR and submitted to HRM analysis to identify differences in hypervariable (HV) regions I and II. To confirm HRM, all PCR products were DNA sequencing. The data suggest that is possible discriminate DNA from different samples by HRM curves. Also, uncommon dual-dissociation was identified in a single PCR product, increasing HRM analyzes by evaluation of melting peaks. Thus, HRM is accurate and useful to screening small differences in HVI and HVII regions from mtDNA and increase the efficiency of laboratory routines based on forensic genetics. © 2017 American Academy of Forensic Sciences.

Metal hydrides based high energy density thermal battery

International Nuclear Information System (INIS)

Fang, Zhigang Zak; Zhou, Chengshang; Fan, Peng; Udell, Kent S.; Bowman, Robert C.; Vajo, John J.; Purewal, Justin J.; Kekelia, Bidzina

2015-01-01

Highlights: • The principle of the thermal battery using advanced metal hydrides was demonstrated. • The thermal battery used MgH 2 and TiMnV as a working pair. • High energy density can be achieved by the use of MgH 2 to store thermal energy. - Abstract: A concept of thermal battery based on advanced metal hydrides was studied for heating and cooling of cabins in electric vehicles. The system utilized a pair of thermodynamically matched metal hydrides as energy storage media. The pair of hydrides that was identified and developed was: (1) catalyzed MgH 2 as the high temperature hydride material, due to its high energy density and enhanced kinetics; and (2) TiV 0.62 Mn 1.5 alloy as the matching low temperature hydride. Further, a proof-of-concept prototype was built and tested, demonstrating the potential of the system as HVAC for transportation vehicles

Hydrate-melt electrolytes for high-energy-density aqueous batteries

Science.gov (United States)

Yamada, Yuki; Usui, Kenji; Sodeyama, Keitaro; Ko, Seongjae; Tateyama, Yoshitaka; Yamada, Atsuo

2016-10-01

Aqueous Li-ion batteries are attracting increasing attention because they are potentially low in cost, safe and environmentally friendly. However, their low energy density (water and the limited selection of suitable negative electrodes, is problematic for their future widespread application. Here, we explore optimized eutectic systems of several organic Li salts and show that a room-temperature hydrate melt of Li salts can be used as a stable aqueous electrolyte in which all water molecules participate in Li+ hydration shells while retaining fluidity. This hydrate-melt electrolyte enables a reversible reaction at a commercial Li4Ti5O12 negative electrode with a low reaction potential (1.55 V versus Li+/Li) and a high capacity (175 mAh g-1). The resultant aqueous Li-ion batteries with high energy density (>130 Wh kg-1) and high voltage (˜2.3-3.1 V) represent significant progress towards performance comparable to that of commercial non-aqueous batteries (with energy densities of ˜150-400 Wh kg-1 and voltages of ˜2.4-3.8 V).

Highly Sensitive DNA Sensor Based on Upconversion Nanoparticles and Graphene Oxide.

Science.gov (United States)

Alonso-Cristobal, P; Vilela, P; El-Sagheer, A; Lopez-Cabarcos, E; Brown, T; Muskens, O L; Rubio-Retama, J; Kanaras, A G

2015-06-17

In this work we demonstrate a DNA biosensor based on fluorescence resonance energy transfer (FRET) between NaYF4:Yb,Er nanoparticles and graphene oxide (GO). Monodisperse NaYF4:Yb,Er nanoparticles with a mean diameter of 29.1 ± 2.2 nm were synthesized and coated with a SiO2 shell of 11 nm, which allowed the attachment of single strands of DNA. When these DNA-functionalized NaYF4:Yb,Er@SiO2 nanoparticles were in the proximity of the GO surface, the π-π stacking interaction between the nucleobases of the DNA and the sp(2) carbons of the GO induced a FRET fluorescence quenching due to the overlap of the fluorescence emission of the NaYF4:Yb,Er@SiO2 and the absorption spectrum of GO. By contrast, in the presence of the complementary DNA strands, the hybridization leads to double-stranded DNA that does not interact with the GO surface, and thus the NaYF4:Yb,Er@SiO2 nanoparticles remain unquenched and fluorescent. The high sensitivity and specificity of this sensor introduces a new method for the detection of DNA with a detection limit of 5 pM.

Toward quantitative fluorescence microscopy with DNA origami nanorulers.

Science.gov (United States)

Beater, Susanne; Raab, Mario; Tinnefeld, Philip

2014-01-01

The dynamic development of fluorescence microscopy has created a large number of new techniques, many of which are able to overcome the diffraction limit. This chapter describes the use of DNA origami nanostructures as scaffold for quantifying microscope properties such as sensitivity and resolution. The DNA origami technique enables placing of a defined number of fluorescent dyes in programmed geometries. We present a variety of DNA origami nanorulers that include nanorulers with defined labeling density and defined distances between marks. The chapter summarizes the advantages such as practically free choice of dyes and labeling density and presents examples of nanorulers in use. New triangular DNA origami nanorulers that do not require photoinduced switching by imaging transient binding to DNA nanostructures are also reported. Finally, we simulate fluorescence images of DNA origami nanorulers and reveal that the optimal DNA nanoruler for a specific application has an intermark distance that is roughly 1.3-fold the expected optical resolution. © 2014 Elsevier Inc. All rights reserved.

Evaporation of carbon using electrons of a high density plasma

International Nuclear Information System (INIS)

Muhl, S.; Camps, E.; Escobar A, L.; Garcia E, J.L.; Olea, O.

1999-01-01

The high density plasmas are used frequently in the preparation of thin films or surface modification, for example to nitridation. In these processes, are used mainly the ions and the neutrals which compose the plasma. However, the electrons present in the plasma are not used, except in the case of chemical reactions induced by collisions, although the electron bombardment usually get hot the work piece. Through the adequate polarization of a conductor material, it is possible to extract electrons from a high density plasma at low pressure, that could be gotten the evaporation of this material. As result of the interaction between the plasma and the electron flux with the vapor produced, this last will be ionized. In this work, it is reported the use of this novelty arrangement to prepare carbon thin films using a high density argon plasma and a high purity graphite bar as material to evaporate. It has been used substrates outside plasma and immersed in the plasma. Also it has been reported the plasma characteristics (temperature and electron density, energy and ions flux), parameters of the deposit process (deposit rate and ion/neutral rate) as well as the properties of the films obtained (IR absorption spectra and UV/Vis, elemental analysis, hardness and refractive index. (Author)

POLYSACCHARIDES AND eDNA AID BACTERIAL ATTACHMENT TO POLYMER BRUSH COATINGS (PLL-g-PEG)

DEFF Research Database (Denmark)

Zeng, Guanghong; Ogaki, Ryosuke; Regina, Viduthalai R.

measured the adsorption of peptides, polysaccharides and DNA to these coatings, as they represent bacterial adhesins with very different properties. While protein adsorption was minimized, we found considerable adsorption of polysaccharides, and exposure to DNA resulted in complete desorption...... of the conventional coating. These results explain why S. epidermidis, which produces polysaccharides and extracellular DNA, could successfully colonize the conventional PLL-g-PEG coatings. The ability of high-density PLL-g-PEG to resist polysaccharides, DNA, and bacterial adhesion of all strains is thus highly......Polymer brush coatings of poly(ethylene glycol) are considered the gold standard for nonfouling surfaces, but nevertheless, a few bacteria manage to attach and initiate biofilm formation on these coatings. To achieve robust resistance against bacterial adhesion and biofilm formation, grafting...

Lower hybrid current drive at ITER-relevant high plasma densities

International Nuclear Information System (INIS)

Cesario, R.; Amicucci, L.; Cardinali, A.; Castaldo, C.; Marinucci, M.; Panaccione, L.; Pericoli-Ridolfini, V.; Tuccillo, A. A.; Tudisco, O.; Calabro, G.

2009-01-01

Recent experiments indicated that a further non-inductive current, besides bootstrap, should be necessary for developing advanced scenario for ITER. The lower hybrid current drive (LHCD) should provide such tool, but its effectiveness was still not proved in operations with ITER-relevant density of the plasma column periphery. Progress of the LH deposition modelling is presented, performed considering the wave physics of the edge, and different ITER-relevant edge parameters. Operations with relatively high edge electron temperatures are expected to reduce the LH || spectral broadening and, consequently, enabling the LH power to propagate also in high density plasmas ( || is the wavenumber component aligned to the confinement magnetic field). New results of FTU experiments are presented, performed by following the aforementioned modeling: they indicate that, for the first time, the LHCD conditions are established by operating at ITER-relevant high edge densities.

A Robust Highly Aligned DNA Nanowire Array-Enabled Lithography for Graphene Nanoribbon Transistors.

Science.gov (United States)

Kang, Seok Hee; Hwang, Wan Sik; Lin, Zhiqun; Kwon, Se Hun; Hong, Suck Won

2015-12-09

Because of its excellent charge carrier mobility at the Dirac point, graphene possesses exceptional properties for high-performance devices. Of particular interest is the potential use of graphene nanoribbons or graphene nanomesh for field-effect transistors. Herein, highly aligned DNA nanowire arrays were crafted by flow-assisted self-assembly of a drop of DNA aqueous solution on a flat polymer substrate. Subsequently, they were exploited as "ink" and transfer-printed on chemical vapor deposited (CVD)-grown graphene substrate. The oriented DNA nanowires served as the lithographic resist for selective removal of graphene, forming highly aligned graphene nanoribbons. Intriguingly, these graphene nanoribbons can be readily produced over a large area (i.e., millimeter scale) with a high degree of feature-size controllability and a low level of defects, rendering the fabrication of flexible two terminal devices and field-effect transistors.

Binary self-assembly of highly symmetric DNA nanocages via sticky-end engineering

Institute of Scientific and Technical Information of China (English)

Xiao-Rong Wu; Chen-Wei Wu; Fei Ding; Cheng Tian; Wen Jiang; Cheng-De Mao; Chuan Zhang

2017-01-01

Discrete and symmetric three-dimensional (3D) DNA nanocages have been revoked as excellent candidates for various applications,such as guest component encapsulation and organization (e.g.dye molecules,proteins,inorganic nanoparticles,etc.) to construct new materials and devices.To date,a large variety of DNA nanocages has been synthesized through assembling small individual DNA motifs into predesigned structures in a bottom-up fashion.Most of them rely on the assembly using multiple copies of single type of motifs and a few sophisticated nanostructures have been engineered by co-assembling multi-types of DNA tiles simultaneously.However,the availability of complex DNA nanocages is still limited.Herein,we demonstrate that highly symmetric DNA nanocages consisted of binary DNA pointstar motifs can be easily assembled by deliberately engineering the sticky-end interaction between the component building blocks.As such,DNA nanocages with new geometries,including elongated tetrahedron (E-TET),rhombic dodecahedron (R-DOD),and rhombic triacontahedron (R-TRI) are successfully synthesized.Moreover,their design principle,assembly process,and structural features are revealed by polyacryalmide gel electrophoresis (PAGE),atomic force microscope (AFM) imaging,and cryogenic transmission electron microscope imaging (cryo-TEM) associated with single particle reconstruction.

Workshop on extremely high energy density plasmas and their diagnostics

Energy Technology Data Exchange (ETDEWEB)

Ishii, Shozo (ed.)

2001-09-01

Compiled are the papers presented at the workshop on 'Extremely High Energy Density Plasmas and Their Diagnostics' held at National Institute for Fusion Science. The papers cover physics and applications of extremely high-energy density plasmas such as dense z-pinch, plasma focus, and intense pulsed charged beams. Separate abstracts were presented for 7 of the papers in this report. The remaining 25 were considered outside the subject scope of INIS. (author)

Workshop on extremely high energy density plasmas and their diagnostics

International Nuclear Information System (INIS)

Ishii, Shozo

2001-09-01

Compiled are the papers presented at the workshop on 'Extremely High Energy Density Plasmas and Their Diagnostics' held at National Institute for Fusion Science. The papers cover physics and applications of extremely high-energy density plasmas such as dense z-pinch, plasma focus, and intense pulsed charged beams. Separate abstracts were presented for 7 of the papers in this report. The remaining 25 were considered outside the subject scope of INIS. (author)

Sequence of a cDNA encoding turtle high mobility group 1 protein.

Science.gov (United States)

Zheng, Jifang; Hu, Bi; Wu, Duansheng

2005-07-01

In order to understand sequence information about turtle HMG1 gene, a cDNA encoding HMG1 protein of the Chinese soft-shell turtle (Pelodiscus sinensis) was amplified by RT-PCR from kidney total RNA, and was cloned, sequenced and analyzed. The results revealed that the open reading frame (ORF) of turtle HMG1 cDNA is 606 bp long. The ORF codifies 202 amino acid residues, from which two DNA-binding domains and one polyacidic region are derived. The DNA-binding domains share higher amino acid identity with homologues sequences of chicken (96.5%) and mammalian (74%) than homologues sequence of rainbow trout (67%). The polyacidic region shows 84.6% amino acid homology with the equivalent region of chicken HMG1 cDNA. Turtle HMG1 protein contains 3 Cys residues located at completely conserved positions. Conservation in sequence and structure suggests that the functions of turtle HMG1 cDNA may be highly conserved during evolution. To our knowledge, this is the first report of HMG1 cDNA sequence in any reptilian.

Polypyrrole–gold nanoparticle composites for highly sensitive DNA detection

International Nuclear Information System (INIS)

Spain, Elaine; Keyes, Tia E.; Forster, Robert J.

2013-01-01

DNA capture surfaces represent a powerful approach to developing highly sensitive sensors for identifying the cause of infection. Electrochemically deposited polypyrrole, PPy, films have been functionalized with electrodeposited gold nanoparticles to give a nanocomposite material, PPy–AuNP. Thiolated capture strand DNA, that is complementary to the sequence from the pathogen Staphylococcus aureus that causes mammary gland inflammation, was then immobilized onto the gold nanoparticles and any of the underlying gold electrode that is exposed. A probe strand, labelled with horse radish peroxidase, HRP, was then hybridized to the target. The concentration of the target was determined by measuring the current generated by reducing benzoquinone produced by the HRP label. Semi-log plots of the pathogen DNA concentration vs. faradaic current are linear from 150 pM to 1 μM and pM concentrations can be detected without the need for molecular, e.g., PCR or NASBA, amplification. The nanocomposite also exhibits excellent selectivity and single base mismatches in a 30 mer sequence can be detected

Fueling requirements of super-high-density plasmas towards innovative ignition regime

International Nuclear Information System (INIS)

Sakamoto, Ryuichi; Yamada, Hiroshi

2014-01-01

Highlights: • Self-burning scenario with internal diffusion barrier is investigated. • Peaked density profiles allow to sustain self-burning plasma at lower temperature. • Core fueling beyond internal diffusion barrier is essential to sustain peaked density. • Acceptable pellet size becomes small to prevent fusion out perturbation. • Very high velocity pellet injection beyond 10 km/s is inevitable for this scenario. - Abstract: Super-high-density plasma with an internal diffusion barrier which is observed in the Large Helical Device has been extrapolated to a fusion reactor grade plasma to explore an innovative ignition regime and to clarify essential requirements for pellet fueling. The peaked density profiles due to the internal diffusion barrier formation allow reduction in the required minimum temperature to sustain a self-burning plasma down to 10 keV. Direct core fueling beyond the internal diffusion barrier is essential to sustain the peaked density profile. Furthermore, the acceptable pellet size becomes small in terms of fusion output perturbation because the effective volume of the burning plasma becomes small with the peaked density profile. In order to sustain a self-burning plasma with an internal diffusion barrier, therefore, extremely high velocity pellet injection beyond 10 km/s is inevitable unless another solution to the core fueling is found

How stable are the mutagenic tautomers of DNA bases?

Directory of Open Access Journals (Sweden)

Brovarets’ O. O.

2010-02-01

Full Text Available Aim. To determine the lifetime of the mutagenic tautomers of DNA base pairs through the investigation of the physicochemical mechanisms of their intramolecular proton transfer. Methods. Non-empirical quantum chemistry, the analysis of the electron density by means of Bader’s atom in molecules (AIM theory and physicochemical kinetics were used. Results. Physicochemical character of the transition state of the intramolecular tautomerisation of DNA bases was investigated, the lifetime of mutagenic tautomers was calculated. Conclusions. The lifetime of the DNA bases mutagenic tautomers by 3–10 orders exceeds typical time of DNA replication in the cell (~103 s. This fact confirms that the postulate, on which the Watson-Crick tautomeric hypothesis of spontaneous transitions grounds, is adequate. The absence of intramolecular H-bonds in the canonical and mutagenic tautomeric forms determine their high stability

StreamMap: Smooth Dynamic Visualization of High-Density Streaming Points.

Science.gov (United States)

Li, Chenhui; Baciu, George; Han, Yu

2018-03-01

Interactive visualization of streaming points for real-time scatterplots and linear blending of correlation patterns is increasingly becoming the dominant mode of visual analytics for both big data and streaming data from active sensors and broadcasting media. To better visualize and interact with inter-stream patterns, it is generally necessary to smooth out gaps or distortions in the streaming data. Previous approaches either animate the points directly or present a sampled static heat-map. We propose a new approach, called StreamMap, to smoothly blend high-density streaming points and create a visual flow that emphasizes the density pattern distributions. In essence, we present three new contributions for the visualization of high-density streaming points. The first contribution is a density-based method called super kernel density estimation that aggregates streaming points using an adaptive kernel to solve the overlapping problem. The second contribution is a robust density morphing algorithm that generates several smooth intermediate frames for a given pair of frames. The third contribution is a trend representation design that can help convey the flow directions of the streaming points. The experimental results on three datasets demonstrate the effectiveness of StreamMap when dynamic visualization and visual analysis of trend patterns on streaming points are required.

High-Density Lipoproteins and the Immune System

Directory of Open Access Journals (Sweden)

Hidesuke Kaji

2013-01-01

Full Text Available High-density lipoprotein (HDL plays a major role in vasodilation and in the reduction of low-density lipoprotein (LDL oxidation, inflammation, apoptosis, thrombosis, and infection; however, HDL is now less functional in these roles under certain conditions. This paper focuses on HDL, its anti-inflammation behavior, and the mechanisms by which HDL interacts with components of the innate and adaptive immune systems. Genome-wide association studies (GWAS and proteomic studies have elucidated important molecules involved in the interaction between HDL and the immune system. An understanding of these mechanisms is expected to be useful for the prevention and treatment of chronic inflammation due to metabolic syndrome, atherosclerosis, or various autoimmune diseases.

TEMPO-based catholyte for high-energy density nonaqueous redox flow batteries.

Science.gov (United States)

Wei, Xiaoliang; Xu, Wu; Vijayakumar, Murugesan; Cosimbescu, Lelia; Liu, Tianbiao; Sprenkle, Vincent; Wang, Wei

2014-12-03

A TEMPO-based non-aqueous electrolyte with the TEMPO concentration as high as 2.0 m is demonstrated as a high-energy-density catholyte for redox flow battery applications. With a hybrid anode, Li|TEMPO flow cells using this electrolyte deliver an energy efficiency of ca. 70% and an impressively high energy density of 126 W h L(-1) . © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Kaon Condensation in Neutron Stars and High Density Behaviour of Nuclear Symmetry Energy

International Nuclear Information System (INIS)

Kubis, S.; Kutschera, M.

1999-01-01

We study the influence of a high density behaviour of the nuclear symmetry energy on a kaon condensation in neutron stars. We find that the symmetry energy typical for several realistic nuclear potentials, which decreases at high densities, inhibits kaon condensation for weaker kaon-nucleon couplings at any density. There exists a threshold coupling above which the kaon condensate forms at densities exceeding some critical value. This is in contrast to the case of rising symmetry energy, as e.g. for relativistic mean field models, when the kaon condensate can form for any coupling at a sufficiently high density. Properties of the condensate are also different in both cases. (author)

Kaon Condensation in Neutron Stars and High Density Behaviour of Nuclear Symmetry Energy

International Nuclear Information System (INIS)

Kubis, S.; Kutschera, M.

1999-04-01

We study the influence of a high density behaviour of the nuclear symmetry energy on a kaon condensation in neutron stars. We find that the symmetry energy typical for several realistic nuclear potentials, which decreases at high densities, inhibits kaon condensation for weaker kaon-nucleon couplings at any density. There exists a threshold coupling above which the kaon condensate forms at densities exceeding some critical value. This is in contrast to the case of rising symmetry energy, as e.g. for relativistic mean field models, when the kaon condensate can form for any coupling at a sufficiently high density. Properties of the condensate are also different in both cases

Pioglitazone retrieves hepatic antioxidant DNA repair in a mice model of high fat diet

Directory of Open Access Journals (Sweden)

Yang Ching-Hsiu

2008-09-01

Full Text Available Abstract Background Pioglitazone was reported to improve hepatic steatosis and necroinflammation in human studies. To investigate whether the hepato-protective effect of pioglitazone was associated with an improvement of antioxidant defense mechanism, oxidative DNA damage and repair activity were determined in a high fat diet model. Male C57BL/6 mice were respectively fed with a 30% fat diet, the same diet with pioglitazone 100 mg/kg/day, or a chow diet as control for 8 weeks. Tissue oxidative stress was indicated by malondialdehyde concentration. Oxidative DNA damage was detected by immunohistochemical 8-oxoG staining. Enzymatic antioxidant defense was detected by the real-time PCR of superoxide dismutase (Sod1, Sod2 and DNA glycosylase (Ogg1, MutY. Oxidative DNA repair was detected by immunohistochemical staining and western blotting of OGG1 expression. Results Our results show that hepatic steatosis was induced by a high-fat diet and improved by adding pioglitazone. Malondialdehyde concentration and 8-oxoG staining were strongly increased in the high-fat diet group, but attenuated by pioglitazone. Gene expressions of antioxidant defense mechanism: Sod1, Sod2, Ogg1 and MutY significantly decreased in the high-fat diet group but reversed by pioglitazone co-administration. Conclusion The attenuation of hepatic oxidative DNA damage by pioglitazone in a high-fat diet may be mediated by up-regulation of the antioxidant defense mechanism and oxidative DNA repair activity. The diminution of oxidative damage may explain the clinical benefit of pioglitazone treatment in patients with non-alcoholic fatty liver disease.

Pioglitazone retrieves hepatic antioxidant DNA repair in a mice model of high fat diet

Science.gov (United States)

Hsiao, Pi-Jung; Hsieh, Tusty-Jiuan; Kuo, Kung-Kai; Hung, Wei-Wen; Tsai, Kun-Bow; Yang, Ching-Hsiu; Yu, Ming-Lung; Shin, Shyi-Jang

2008-01-01

Background Pioglitazone was reported to improve hepatic steatosis and necroinflammation in human studies. To investigate whether the hepato-protective effect of pioglitazone was associated with an improvement of antioxidant defense mechanism, oxidative DNA damage and repair activity were determined in a high fat diet model. Male C57BL/6 mice were respectively fed with a 30% fat diet, the same diet with pioglitazone 100 mg/kg/day, or a chow diet as control for 8 weeks. Tissue oxidative stress was indicated by malondialdehyde concentration. Oxidative DNA damage was detected by immunohistochemical 8-oxoG staining. Enzymatic antioxidant defense was detected by the real-time PCR of superoxide dismutase (Sod1, Sod2) and DNA glycosylase (Ogg1, MutY). Oxidative DNA repair was detected by immunohistochemical staining and western blotting of OGG1 expression. Results Our results show that hepatic steatosis was induced by a high-fat diet and improved by adding pioglitazone. Malondialdehyde concentration and 8-oxoG staining were strongly increased in the high-fat diet group, but attenuated by pioglitazone. Gene expressions of antioxidant defense mechanism: Sod1, Sod2, Ogg1 and MutY significantly decreased in the high-fat diet group but reversed by pioglitazone co-administration. Conclusion The attenuation of hepatic oxidative DNA damage by pioglitazone in a high-fat diet may be mediated by up-regulation of the antioxidant defense mechanism and oxidative DNA repair activity. The diminution of oxidative damage may explain the clinical benefit of pioglitazone treatment in patients with non-alcoholic fatty liver disease. PMID:18822121

Metal hydrides based high energy density thermal battery

Energy Technology Data Exchange (ETDEWEB)

Fang, Zhigang Zak, E-mail: zak.fang@utah.edu [Department of Metallurgical Engineering, The University of Utah, 135 South 1460 East, Room 412, Salt Lake City, UT 84112-0114 (United States); Zhou, Chengshang; Fan, Peng [Department of Metallurgical Engineering, The University of Utah, 135 South 1460 East, Room 412, Salt Lake City, UT 84112-0114 (United States); Udell, Kent S. [Department of Metallurgical Engineering, The University of Utah, 50 S. Central Campus Dr., Room 2110, Salt Lake City, UT 84112-0114 (United States); Bowman, Robert C. [Department of Metallurgical Engineering, The University of Utah, 135 South 1460 East, Room 412, Salt Lake City, UT 84112-0114 (United States); Vajo, John J.; Purewal, Justin J. [HRL Laboratories, LLC, 3011 Malibu Canyon Road, Malibu, CA 90265 (United States); Kekelia, Bidzina [Department of Metallurgical Engineering, The University of Utah, 50 S. Central Campus Dr., Room 2110, Salt Lake City, UT 84112-0114 (United States)

2015-10-05

Highlights: • The principle of the thermal battery using advanced metal hydrides was demonstrated. • The thermal battery used MgH{sub 2} and TiMnV as a working pair. • High energy density can be achieved by the use of MgH{sub 2} to store thermal energy. - Abstract: A concept of thermal battery based on advanced metal hydrides was studied for heating and cooling of cabins in electric vehicles. The system utilized a pair of thermodynamically matched metal hydrides as energy storage media. The pair of hydrides that was identified and developed was: (1) catalyzed MgH{sub 2} as the high temperature hydride material, due to its high energy density and enhanced kinetics; and (2) TiV{sub 0.62}Mn{sub 1.5} alloy as the matching low temperature hydride. Further, a proof-of-concept prototype was built and tested, demonstrating the potential of the system as HVAC for transportation vehicles.

High energy-density science on the National Ignition Facility

Energy Technology Data Exchange (ETDEWEB)

Campbell, E.M.; Cauble, R.; Remington, B.A.

1997-08-01

The National Ignition Facility, as well as its French counterpart Le Laser Megajoule, have been designed to confront one of the most difficult and compelling problem in shock physics - the creation of a hot, compassed DT plasma surrounded and confined by cold, nearly degenerate DT fuel. At the same time, these laser facilities will present the shock physics community with unique tools for the study of high energy density matter at states unreachable by any other laboratory technique. Here we describe how these lasers can contribute to investigations of high energy density in the area of material properties and equations of state, extend present laboratory shock techniques such as high-speed jets to new regimes, and allow study of extreme conditions found in astrophysical phenomena.

Frontiers for Discovery in High Energy Density Physics

Energy Technology Data Exchange (ETDEWEB)

Davidson, R. C.; Katsouleas, T.; Arons, J.; Baring, M.; Deeney, C.; Di Mauro, L.; Ditmire, T.; Falcone, R.; Hammer, D.; Hill, W.; Jacak, B.; Joshi, C.; Lamb, F.; Lee, R.; Logan, B. G.; Melissinos, A.; Meyerhofer, D.; Mori, W.; Murnane, M.; Remington, B.; Rosner, R.; Schneider, D.; Silvera, I.; Stone, J.; Wilde, B.; Zajc. W.

2004-07-20

The report is intended to identify the compelling research opportunities of high intellectual value in high energy density physics. The opportunities for discovery include the broad scope of this highly interdisciplinary field that spans a wide range of physics areas including plasma physics, laser and particle beam physics, nuclear physics, astrophysics, atomic and molecular physics, materials science and condensed matter physics, intense radiation-matter interaction physics, fluid dynamics, and magnetohydrodynamics

Visualization of DNA in highly processed botanical materials.

Science.gov (United States)

Lu, Zhengfei; Rubinsky, Maria; Babajanian, Silva; Zhang, Yanjun; Chang, Peter; Swanson, Gary

2018-04-15

DNA-based methods have been gaining recognition as a tool for botanical authentication in herbal medicine; however, their application in processed botanical materials is challenging due to the low quality and quantity of DNA left after extensive manufacturing processes. The low amount of DNA recovered from processed materials, especially extracts, is "invisible" by current technology, which has casted doubt on the presence of amplifiable botanical DNA. A method using adapter-ligation and PCR amplification was successfully applied to visualize the "invisible" DNA in botanical extracts. The size of the "invisible" DNA fragments in botanical extracts was around 20-220 bp compared to fragments of around 600 bp for the more easily visualized DNA in botanical powders. This technique is the first to allow characterization and visualization of small fragments of DNA in processed botanical materials and will provide key information to guide the development of appropriate DNA-based botanical authentication methods in the future. Copyright © 2017 Elsevier Ltd. All rights reserved.

High Performance Systolic Array Core Architecture Design for DNA Sequencer

Directory of Open Access Journals (Sweden)

Saiful Nurdin Dayana

2018-01-01

Full Text Available This paper presents a high performance systolic array (SA core architecture design for Deoxyribonucleic Acid (DNA sequencer. The core implements the affine gap penalty score Smith-Waterman (SW algorithm. This time-consuming local alignment algorithm guarantees optimal alignment between DNA sequences, but it requires quadratic computation time when performed on standard desktop computers. The use of linear SA decreases the time complexity from quadratic to linear. In addition, with the exponential growth of DNA databases, the SA architecture is used to overcome the timing issue. In this work, the SW algorithm has been captured using Verilog Hardware Description Language (HDL and simulated using Xilinx ISIM simulator. The proposed design has been implemented in Xilinx Virtex -6 Field Programmable Gate Array (FPGA and improved in the core area by 90% reduction.

High energy density Z-pinch plasmas using flow stabilization

Energy Technology Data Exchange (ETDEWEB)

Shumlak, U., E-mail: shumlak@uw.edu; Golingo, R. P., E-mail: shumlak@uw.edu; Nelson, B. A., E-mail: shumlak@uw.edu; Bowers, C. A., E-mail: shumlak@uw.edu; Doty, S. A., E-mail: shumlak@uw.edu; Forbes, E. G., E-mail: shumlak@uw.edu; Hughes, M. C., E-mail: shumlak@uw.edu; Kim, B., E-mail: shumlak@uw.edu; Knecht, S. D., E-mail: shumlak@uw.edu; Lambert, K. K., E-mail: shumlak@uw.edu; Lowrie, W., E-mail: shumlak@uw.edu; Ross, M. P., E-mail: shumlak@uw.edu; Weed, J. R., E-mail: shumlak@uw.edu [Aerospace and Energetics Research Program, University of Washington, Seattle, Washington, 98195-2250 (United States)

2014-12-15

The ZaP Flow Z-Pinch research project[1] at the University of Washington investigates the effect of sheared flows on MHD instabilities. Axially flowing Z-pinch plasmas are produced that are 100 cm long with a 1 cm radius. The plasma remains quiescent for many radial Alfvén times and axial flow times. The quiescent periods are characterized by low magnetic mode activity measured at several locations along the plasma column and by stationary visible plasma emission. Plasma evolution is modeled with high-resolution simulation codes – Mach2, WARPX, NIMROD, and HiFi. Plasma flow profiles are experimentally measured with a multi-chord ion Doppler spectrometer. A sheared flow profile is observed to be coincident with the quiescent period, and is consistent with classical plasma viscosity. Equilibrium is determined by diagnostic measurements: interferometry for density; spectroscopy for ion temperature, plasma flow, and density[2]; Thomson scattering for electron temperature; Zeeman splitting for internal magnetic field measurements[3]; and fast framing photography for global structure. Wall stabilization has been investigated computationally and experimentally by removing 70% of the surrounding conducting wall to demonstrate no change in stability behavior.[4] Experimental evidence suggests that the plasma lifetime is only limited by plasma supply and current waveform. The flow Z-pinch concept provides an approach to achieve high energy density plasmas,[5] which are large, easy to diagnose, and persist for extended durations. A new experiment, ZaP-HD, has been built to investigate this approach by separating the flow Z-pinch formation from the radial compression using a triaxial-electrode configuration. This innovation allows more detailed investigations of the sheared flow stabilizing effect, and it allows compression to much higher densities than previously achieved on ZaP by reducing the linear density and increasing the pinch current. Experimental results and

High density aseismic spent fuel storage racks

International Nuclear Information System (INIS)

Louvat, J.P.

1985-05-01

After the reasons of the development of high density aseismic spent fuel racks by FRAMATOME and LEMER, a description is presented, as also the codes, standards and regulations used to design this FRAMATOME storage rack. Tests have been carried out concerning criticality, irradiation of Cadminox, corrosion of the cell, and the seismic behaviour

Charge transfer in pi-stacked systems including DNA

International Nuclear Information System (INIS)

Siebbeles, L.D.A.

2003-01-01

Charge migration in DNA is a subject of intense current study motivated by long-range detection of DNA damage and the potential application of DNA as a molecular wire in nanoscale electronic devices. A key structural element, which makes DNA a medium for long-range charge transfer, is the array of stacked base pairs in the interior of the double helix. The overlapping pi-orbitals of the nucleobases provide a pathway for motion of charge carriers generated on the stack. This 'pi-pathway' resembles the columnarly stacked macrocyclic cores in discotic materials such as triphenylenes. The structure of these pi-stacked systems is highly disordered with dynamic fluctuations occurring on picosecond to nanosecond time scales. Theoretical calculations, concerning the effects of structural disorder and nucleobase sequence in DNA, on the dynamics of charge carriers are presented. Electronic couplings and localization energies of charge carriers were calculated using density functional theory (DFT). Results for columnarly stacked triphenylenes and DNA nucleobases are compared. The results are used to provide insight into the factors that control the mobility of charge carriers. Further, experimental results on the site-selective oxidation of guanine nucleobases in DNA (hot spots for DNA damage) are analyzed on basis of the theoretical results

High-resolution NMR studies of chimeric DNA-RNA-DNA duplexes, heteronomous base pairing, and continuous base stacking at junctions

International Nuclear Information System (INIS)

Chou, Shanho; Flynn, P.; Wang, A.; Reid, B.

1991-01-01

Two symmetrical DNA-RNA-DNA duplex chimeras, d(CGCG)r(AAUU)d(CGCG) (designated rAAUU) and d(CGCG)r(UAUA)d(CGCG) (designated rUAUA), and a nonsymmetrical chimeric duplex, d(CGTT)r(AUAA)d(TGCG)/d(CGCA)r(UUAU)d(AACG) (designated rAUAA), as well as their pure DNA analogues, containing dU instead of T, have been synthesized by solid-phase phosphoramidite methods and studied by high-resolution NMR techniques. The 1D imino proton NOE spectra of these d-r-d chimeras indicate normal Watson-Crick hydrogen bonding and base stacking at the junction region. Preliminary qualitative NOESY, COSY, and chemical shift data suggest that the internal RNA segment contains C3'-endo (A-type) sugar conformations except for the first RNA residues (position 5 and 17) following the 3' end of the DNA block, which, unlike the other six ribonucleotides, exhibit detectable H1'-H2' J coupling. The nucleosides of the two flanking DNA segments appear to adopt a fairly normal C2'-endo B-DNA conformation except at the junction with the RNA blocks (residues 4 and 16), where the last DNA residue appears to adopt an intermediate sugar conformation. The data indicate that A-type and B-type conformations can coexist in a single short continuous nucleic acid duplex, but these results differ somewhat from previous theoretical model studies

High-density cervical ureaplasma urealyticum colonization in pregnant women

Directory of Open Access Journals (Sweden)

Ranđelović Gordana

2006-01-01

Full Text Available Background/aim: Ureaplasma urealyticum, a common commensal of the female lower genital tract, has been observed as an important opportunistic pathogen during pregnancy. The aims of this study were to determine the degree of cervical colonization with U. urealyticum in pregnant women with risk pregnancy and in pregnant women with normal term delivery and to evaluate the correlation between high-density cervical U. urealyticum colonization and premature rupture of membranes (PROM as well. Methods. This research was conducted on the samples comprising 130 hospitalized pregnant women with threatening preterm delivery and premature rupture of membranes. The control group consisted of 39 pregnant women with term delivery without PROM. In addition to standard bacteriological examination and performing direct immunofluorescence test to detect Chlamydia trachomatis, cervical swabs were also examined for the presence of U. urealyticum and Mycoplasma hominis by commercially available Mycofast Evolution 2 test (International Microbio, France. Results. The number of findings with isolated high-density U. urealyticum in the target group was 69 (53.08%, while in the control group was 14 (35.90%. Premature rupture of membranes (PROM occurred in 43 (33.08% examinees: 29 were pPROM, and 14 were PROM. The finding of U.urealyticum ≥104 was determined in 25 (58.14% pregnant women with rupture, 17 were pPROM, and 8 were PROM. There was statistically significant difference in the finding of high-density U. urealyticum between the pregnant women with PROM and the control group (χ² = 4.06, p < 0.05. U. urealyticum was predominant bacterial species found in 62.79% of isolates in the PROM cases, while in 32.56% it was isolated alone. Among the 49 pregnant women with preterm delivery, pPROM occurred in 29 (59.18% examinees, and in 70.83% of pregnant women with findings of high-density U. urealyticum pPROM was observed. Conclusion. Cervical colonization with U

Bremsstrahlung spectra for Al, Cs, and Au atoms in high-temperature, high-density plasmas

International Nuclear Information System (INIS)

Kim, L.; Pratt, R.H.; Tseng, H.K.

1985-01-01

Results are presented from a numerical calculation for the bremsstrahlung spectrum and Gaunt factors of Al, Cs, and Au atoms in high-temperature (-T), high-density (-rho) plasmas. Plasma temperatures kT = 0.1 and 1.0 keV and plasma densities rho = rho 0 (the normal solid density) and rho = 100rho 0 are considered. This allows us to determine the generality and identify the origins of features which we had previously identified in calculations for Cs. We also now present results for the total energy loss of an electron in such a plasma. We use a relativistic multipole code which treats the bremsstrahlung process as a single-electron transition in a static screened central potential. We take for the static potential corresponding to an atom in a hot dense plasma the finite-temperature, finite-density Thomas-Fermi model. This approach corresponds to an average atom in local thermodynamic equilibrium. In comparison to isolated-neutral-atom results we observe general suppression of cross sections and a particular suppression in the tip region of the spectrum. Within this model, both superscreening and shape resonances are found in the circumstances of extreme density. At more normal densities and except for the soft-photon end, the spectrum at these energies for an atom in a hot plasma (characterized by an average degree of ionization) can be well represented by the spectrum of the corresponding isolated ion, which has a similar potential shape at the distances which characterize the process

Ultrasensitive DNA sequence detection using nanoscale ZnO sensor arrays

Energy Technology Data Exchange (ETDEWEB)

Kumar, Nitin; Dorfman, Adam; Hahm, Jong-in [Department of Chemical Engineering, Pennsylvania State University, 160 Fenske Laboratory, University Park, PA 16802 (United States)

2006-06-28

We report that engineered nanoscale zinc oxide structures can be effectively used for the identification of the biothreat agent, Bacillus anthracis by successfully discriminating its DNA sequence from other genetically related species. We explore both covalent and non-covalent linking schemes in order to couple probe DNA strands to the zinc oxide nanostructures. Hybridization reactions are performed with various concentrations of target DNA strands whose sequence is unique to Bacillus anthracis. The use of zinc oxide nanomaterials greatly enhances the fluorescence signal collected after carrying out duplex formation reaction. Specifically, the covalent strategy allows detection of the target species at sample concentrations at a level as low as a few femtomolar as compared to the detection sensitivity in the tens of nanomolar range when using the non-covalent scheme. The presence of the underlying zinc oxide nanomaterials is critical in achieving increased fluorescence detection of hybridized DNA and, therefore, accomplishing rapid and extremely sensitive identification of the biothreat agent. We also demonstrate the easy integration potential of nanoscale zinc oxide into high density arrays by using various types of zinc oxide sensor prototypes in the DNA sequence detection. When combined with conventional automatic sample handling apparatus and computerized fluorescence detection equipment, our approach can greatly promote the use of zinc oxide nanomaterials as signal enhancing platforms for rapid, multiplexed, high-throughput, highly sensitive, DNA sensor arrays.

Ultrasensitive DNA sequence detection using nanoscale ZnO sensor arrays

International Nuclear Information System (INIS)

Kumar, Nitin; Dorfman, Adam; Hahm, Jong-in

2006-01-01

We report that engineered nanoscale zinc oxide structures can be effectively used for the identification of the biothreat agent, Bacillus anthracis by successfully discriminating its DNA sequence from other genetically related species. We explore both covalent and non-covalent linking schemes in order to couple probe DNA strands to the zinc oxide nanostructures. Hybridization reactions are performed with various concentrations of target DNA strands whose sequence is unique to Bacillus anthracis. The use of zinc oxide nanomaterials greatly enhances the fluorescence signal collected after carrying out duplex formation reaction. Specifically, the covalent strategy allows detection of the target species at sample concentrations at a level as low as a few femtomolar as compared to the detection sensitivity in the tens of nanomolar range when using the non-covalent scheme. The presence of the underlying zinc oxide nanomaterials is critical in achieving increased fluorescence detection of hybridized DNA and, therefore, accomplishing rapid and extremely sensitive identification of the biothreat agent. We also demonstrate the easy integration potential of nanoscale zinc oxide into high density arrays by using various types of zinc oxide sensor prototypes in the DNA sequence detection. When combined with conventional automatic sample handling apparatus and computerized fluorescence detection equipment, our approach can greatly promote the use of zinc oxide nanomaterials as signal enhancing platforms for rapid, multiplexed, high-throughput, highly sensitive, DNA sensor arrays

Positron camera with high-density avalanche chambers

International Nuclear Information System (INIS)

Manfrass, D.; Enghardt, W.; Fromm, W.D.; Wohlfarth, D.; Hennig, K.

1988-01-01

The results of an extensive investigation of the properties of high-density avalanche chambers (HIDAC) are presented. This study has been performed in order to optimize the layout of HIDAC detectors, since they are intended to be applied as position sensitive detectors for annihilation radiation in a positron emission tomograph being under construction. (author)

Transcription of highly repetitive tandemly organized DNA in amphibians and birds: A historical overview and modern concepts.

Science.gov (United States)

Trofimova, Irina; Krasikova, Alla

2016-12-01

Tandemly organized highly repetitive DNA sequences are crucial structural and functional elements of eukaryotic genomes. Despite extensive evidence, satellite DNA remains an enigmatic part of the eukaryotic genome, with biological role and significance of tandem repeat transcripts remaining rather obscure. Data on tandem repeats transcription in amphibian and avian model organisms is fragmentary despite their genomes being thoroughly characterized. Review systematically covers historical and modern data on transcription of amphibian and avian satellite DNA in somatic cells and during meiosis when chromosomes acquire special lampbrush form. We highlight how transcription of tandemly repetitive DNA sequences is organized in interphase nucleus and on lampbrush chromosomes. We offer LTR-activation hypotheses of widespread satellite DNA transcription initiation during oogenesis. Recent explanations are provided for the significance of high-yield production of non-coding RNA derived from tandemly organized highly repetitive DNA. In many cases the data on the transcription of satellite DNA can be extrapolated from lampbrush chromosomes to interphase chromosomes. Lampbrush chromosomes with applied novel technical approaches such as superresolution imaging, chromosome microdissection followed by high-throughput sequencing, dynamic observation in life-like conditions provide amazing opportunities for investigation mechanisms of the satellite DNA transcription.

Effect of high density lipoproteins on permeability of rabbit aorta to low density lipoproteins

International Nuclear Information System (INIS)

Klimov, A.N.; Popov, V.A.; Nagornev, V.A.; Pleskov, V.M.

1985-01-01

A study was made on the effect of high density lipoproteins (HDL) on the permeability of rabbit aorta to low density lipoproteins (LDL) after intravenous administration of human HDL and human ( 125 I)LDL to normal and hypercholesterolemic rabbits. Evaluation of radioactivity in plasma and aorta has shown that the administration of a large dose of HDL decreased the aorta permeability rate for ( 125 I)LDL on an average by 19% in normal rabbits, and by 45% in rabbits with moderate hypercholesterolemia. A historadiographic study showed that HDL also decreased the vessel wall permeability to ( 125 I)LDL in normal and particularly in hypercholesterolemic animals. The suggestion was made that HDL at very high molar concentration can hamper LDL transportation through the intact endothelial layer into the intima due to the ability of HDL to compete with LDL in sites of low affinity on the surface of endothelial cells. (author)

Slow crack growth in post-consumer recycled high-density polyethylene

OpenAIRE

Sciammarella, Cesar A.; Yang, Y.

2015-01-01

An experimental study of slow crack growth behavior of post-consumer recycled high-density polyethylene blended with virgin high-density polyethylene copolymer has been done. The study has been performed under constant load and in baths of distilled water at 40, 60, 80°C. The specimen used is notched with side grooves. The test results of crack growth have been analyzed using linear fracture mechanics and the rate process theory. The results show that the resistance to crack growth increases ...

Optimized mtDNA Control Region Primer Extension Capture Analysis for Forensically Relevant Samples and Highly Compromised mtDNA of Different Age and Origin

Directory of Open Access Journals (Sweden)

Mayra Eduardoff

2017-09-01

Full Text Available The analysis of mitochondrial DNA (mtDNA has proven useful in forensic genetics and ancient DNA (aDNA studies, where specimens are often highly compromised and DNA quality and quantity are low. In forensic genetics, the mtDNA control region (CR is commonly sequenced using established Sanger-type Sequencing (STS protocols involving fragment sizes down to approximately 150 base pairs (bp. Recent developments include Massively Parallel Sequencing (MPS of (multiplex PCR-generated libraries using the same amplicon sizes. Molecular genetic studies on archaeological remains that harbor more degraded aDNA have pioneered alternative approaches to target mtDNA, such as capture hybridization and primer extension capture (PEC methods followed by MPS. These assays target smaller mtDNA fragment sizes (down to 50 bp or less, and have proven to be substantially more successful in obtaining useful mtDNA sequences from these samples compared to electrophoretic methods. Here, we present the modification and optimization of a PEC method, earlier developed for sequencing the Neanderthal mitochondrial genome, with forensic applications in mind. Our approach was designed for a more sensitive enrichment of the mtDNA CR in a single tube assay and short laboratory turnaround times, thus complying with forensic practices. We characterized the method using sheared, high quantity mtDNA (six samples, and tested challenging forensic samples (n = 2 as well as compromised solid tissue samples (n = 15 up to 8 kyrs of age. The PEC MPS method produced reliable and plausible mtDNA haplotypes that were useful in the forensic context. It yielded plausible data in samples that did not provide results with STS and other MPS techniques. We addressed the issue of contamination by including four generations of negative controls, and discuss the results in the forensic context. We finally offer perspectives for future research to enable the validation and accreditation of the PEC MPS

DNA detection on ultrahigh-density optical fiber-based nanoarrays.

Science.gov (United States)

Tam, Jenny M; Song, Linan; Walt, David R

2009-04-15

Nanoarrays for DNA detection were fabricated on etched nanofiber bundles based on recently developed techniques for microscale arrays. Two different-sized nanoarrays were created: one with 700 nm feature sizes and a 1 microm center-to-center pitch (approximately 1x10(6) array elements/mm(2)) and one with 300 nm feature sizes and a 500 nm center-to-center pitch (4.6x10(6) array elements/mm(2)). A random, multiplexed array composed of oligonucleotide-functionalized nanospheres was constructed and used for parallel detection and analysis of fluorescently labeled DNA targets. We have used these arrays to detect a variety of target sequences including Bacillus thuringiensis kurstaki and vaccina virus sequences, two potential biowarfare agents, as well as interleukin-2 sequences, an immune system modulator that has been used for the diagnosis of HIV.

Series asymmetric supercapacitors based on free-standing inner-connection electrodes for high energy density and high output voltage

Science.gov (United States)

Tao, Jiayou; Liu, Nishuang; Rao, Jiangyu; Ding, Longwei; Al Bahrani, Majid Raissan; Li, Luying; Su, Jun; Gao, Yihua

2014-11-01

Asymmetric supercapacitors (ASCs) based on free-standing membranes with high energy density and high output voltage are reported. MnO2 nanowire/carbon nanotube (CNT) composites and MoO3 nanobelt/CNT composites are selected as the anode and the cathode materials of the devices, respectively. The ASC has a high volumetric capacitance of 50.2 F cm-3 at a scan rate of 2 mV s-1 and a high operation voltage window of 2.0 V. Especially, after a middle layer with an inner-connection structure was inserted between the anode and the cathode, the output voltage of the whole device can achieve 4.0 V. The full cell of series ASCs (SASC) with an inner-connection middle layer has a high energy density of 28.6 mW h cm-3 at a power density of 261.4 mW cm-3, and exhibits excellent cycling performance of 99.6% capacitance retention over 10 000 cycles. This strategy of designing the hybridized structure for SASCs provides a promising route for next-generation SCs with high energy density and high output voltage.Asymmetric supercapacitors (ASCs) based on free-standing membranes with high energy density and high output voltage are reported. MnO2 nanowire/carbon nanotube (CNT) composites and MoO3 nanobelt/CNT composites are selected as the anode and the cathode materials of the devices, respectively. The ASC has a high volumetric capacitance of 50.2 F cm-3 at a scan rate of 2 mV s-1 and a high operation voltage window of 2.0 V. Especially, after a middle layer with an inner-connection structure was inserted between the anode and the cathode, the output voltage of the whole device can achieve 4.0 V. The full cell of series ASCs (SASC) with an inner-connection middle layer has a high energy density of 28.6 mW h cm-3 at a power density of 261.4 mW cm-3, and exhibits excellent cycling performance of 99.6% capacitance retention over 10 000 cycles. This strategy of designing the hybridized structure for SASCs provides a promising route for next-generation SCs with high energy density and high

Targeted DNA Methylation Analysis by High Throughput Sequencing in Porcine Peri-attachment Embryos

OpenAIRE

MORRILL, Benson H.; COX, Lindsay; WARD, Anika; HEYWOOD, Sierra; PRATHER, Randall S.; ISOM, S. Clay

2013-01-01

Abstract The purpose of this experiment was to implement and evaluate the effectiveness of a next-generation sequencing-based method for DNA methylation analysis in porcine embryonic samples. Fourteen discrete genomic regions were amplified by PCR using bisulfite-converted genomic DNA derived from day 14 in vivo-derived (IVV) and parthenogenetic (PA) porcine embryos as template DNA. Resulting PCR products were subjected to high-throughput sequencing using the Illumina Genome Analyzer IIx plat...

Correspondence: chromosomal localization of uv-induced unscheduled DNA synthesis

International Nuclear Information System (INIS)

Berliner, J.; Mello, R.S.; Norman, A.

1976-01-01

We have measured the grain density - the number of grains per unit length - over the centromere and noncentromere regions of metaphase chromosomes in autoradiographs of human lymphocytes. When the chromosomes were labeled in G 0 by uv-induced unscheduled DNA synthesis, the grain density was two to four times larger over the centromere than over the noncentromere regions. When the labeling was done by scheduled DNA synthesis in S or unscheduled synthesis in M, the grain densities were approximately equal over both regions

Ultra-stretchable Interconnects for high-density stretchable electronics

NARCIS (Netherlands)

Shafqat, S.; Hoefnagels, J.P.M.; Savov, A.; Joshi, S.; Dekker, R.; Geers, M.G.D.

2017-01-01

The exciting field of stretchable electronics (SE) promises numerous novel applications, particularly in-body and medical diagnostics devices. However, future advanced SE miniature devices will require high-density, extremely stretchable interconnects with micron-scale footprints, which calls for

Membrane receptors for very low density lipoprotein (VLDL) inhibitor of lymphocyte proliferation

International Nuclear Information System (INIS)

Yi, P.I.; Beck, G.; Zucker, S.

1981-01-01

Physiologic concentrations of human plasma very low density lipoproteins inhibit the DNA synthesis of lymphocytes stimulated by allogeneic cells or lectins. In this report reachers have compared the effects of isolated lipoproteins [very low density lipoproteins (VLDL), low density lipoproteins (LDL), and high density lipoproteins (HDL)] and lipoprotein-depleted plasma (LDP) on DNA synthesis by phytohemagglutinin-stimulated human lymphocytes. The relative potency for the inhibition of lymphocyte proliferation was VLDL greater than LDL greater than HDL greater than LDP. Fifty percent inhibition of DNA synthesis was observed at a VLDL protein concentration of 1.5--2.0 microgram/ml. Researchers have further demonstrated the presence of specific receptors for VLDL on human lymphocytes. Native VLDL was more effective than LDL in competing for 125I-VLDL binding sites. Subsequent to binding to lymphocytes, 125I-VLDL was internalized and degraded to acid-soluble products. Based on a Scatchard analysis of VLDL binding at 4 degrees C, the number of VLDL receptors per lymphocyte was estimated at 28,000 +/- 1300. Based on an estimated mean binding affinity for the VLDL receptor complex at half saturation of approximately 8.8 X 10(7) liter/mole, it is estimated that 91% of lymphocyte VLDL receptors are occupied at physiologic VLDL concentrations in blood. Although the immune regulatory role of plasma lipoproteins is uncertain, researchers suggest tha VLDL and LDL-In may maintain circulating blood lymphocytes in a nonproliferative state via their respective cell receptor mechanisms

High-resolution proxies for wood density variations in Terminalia superba

Science.gov (United States)

De Ridder, Maaike; Van den Bulcke, Jan; Vansteenkiste, Dries; Van Loo, Denis; Dierick, Manuel; Masschaele, Bert; De Witte, Yoni; Mannes, David; Lehmann, Eberhard; Beeckman, Hans; Van Hoorebeke, Luc; Van Acker, Joris

2011-01-01

Background and Aims Density is a crucial variable in forest and wood science and is evaluated by a multitude of methods. Direct gravimetric methods are mostly destructive and time-consuming. Therefore, faster and semi- to non-destructive indirect methods have been developed. Methods Profiles of wood density variations with a resolution of approx. 50 µm were derived from one-dimensional resistance drillings, two-dimensional neutron scans, and three-dimensional neutron and X-ray scans. All methods were applied on Terminalia superba Engl. & Diels, an African pioneer species which sometimes exhibits a brown heart (limba noir). Key Results The use of X-ray tomography combined with a reference material permitted direct estimates of wood density. These X-ray-derived densities overestimated gravimetrically determined densities non-significantly and showed high correlation (linear regression, R2 = 0·995). When comparing X-ray densities with the attenuation coefficients of neutron scans and the amplitude of drilling resistance, a significant linear relation was found with the neutron attenuation coefficient (R2 = 0·986) yet a weak relation with drilling resistance (R2 = 0·243). When density patterns are compared, all three methods are capable of revealing the same trends. Differences are mainly due to the orientation of tree rings and the different characteristics of the indirect methods. Conclusions High-resolution X-ray computed tomography is a promising technique for research on wood cores and will be explored further on other temperate and tropical species. Further study on limba noir is necessary to reveal the causes of density variations and to determine how resistance drillings can be further refined. PMID:21131386

Lexical Density Of English Reading Texts For Senior High School

OpenAIRE

Nesia, Bersyebah Herljimsi; Ginting, Siti Aisah

2014-01-01

This study deals with the lexical density especially the lexical items of English reading texts in the textbook for senior high school. The objectives of the study are to find out the lexical density especially the lexical items which formed in the reading texts of Look Ahead textbook and the type of genre which has the highest lexical density of the reading texts. This study was conducted by descriptive method with qualitative approach. The data of this research were the English reading text...

PRODUCTION OF HIGH DENSITY PARTICLEBOARD USING MELAMINE-UREA-FORMALDEHYDE RESIN

Directory of Open Access Journals (Sweden)

Setsuo Iwakiri

2005-12-01

Full Text Available This research was developed aiming to evaluate the effects of board density and melamine-urea-formaldehyde resin onthe properties of particleboard for semi-structural applications. The boards were manufactured with nominal density of 0.65 g/cm³and 0.90 g/cm³ using urea-formaldehyde resin as control and melamine-urea-formaldehyde. The results showed a better dimensionallystability and mechanical properties of the boards manufactured with higher density and MUF resin content. The fine furnish usedfor external layer of particleboard in the industrial process, could be used for high density homogeneous board to semi-strucuturaluses, such as flooring applications.

High-Sensitivity Measurement of Density by Magnetic Levitation.

Science.gov (United States)

Nemiroski, Alex; Kumar, A A; Soh, Siowling; Harburg, Daniel V; Yu, Hai-Dong; Whitesides, George M

2016-03-01

This paper presents methods that use Magnetic Levitation (MagLev) to measure very small differences in density of solid diamagnetic objects suspended in a paramagnetic medium. Previous work in this field has shown that, while it is a convenient method, standard MagLev (i.e., where the direction of magnetization and gravitational force are parallel) cannot resolve differences in density mm) because (i) objects close in density prevent each other from reaching an equilibrium height due to hard contact and excluded volume, and (ii) using weaker magnets or reducing the magnetic susceptibility of the medium destabilizes the magnetic trap. The present work investigates the use of weak magnetic gradients parallel to the faces of the magnets as a means of increasing the sensitivity of MagLev without destabilization. Configuring the MagLev device in a rotated state (i.e., where the direction of magnetization and gravitational force are perpendicular) relative to the standard configuration enables simple measurements along the axes with the highest sensitivity to changes in density. Manipulating the distance of separation between the magnets or the lengths of the magnets (along the axis of measurement) enables the sensitivity to be tuned. These modifications enable an improvement in the resolution up to 100-fold over the standard configuration, and measurements with resolution down to 10(-6) g/cm(3). Three examples of characterizing the small differences in density among samples of materials having ostensibly indistinguishable densities-Nylon spheres, PMMA spheres, and drug spheres-demonstrate the applicability of rotated Maglev to measuring the density of small (0.1-1 mm) objects with high sensitivity. This capability will be useful in materials science, separations, and quality control of manufactured objects.

Ultra-Stretchable Interconnects for High-Density Stretchable Electronics

Directory of Open Access Journals (Sweden)

Salman Shafqat

2017-09-01

Full Text Available The exciting field of stretchable electronics (SE promises numerous novel applications, particularly in-body and medical diagnostics devices. However, future advanced SE miniature devices will require high-density, extremely stretchable interconnects with micron-scale footprints, which calls for proven standardized (complementary metal-oxide semiconductor (CMOS-type process recipes using bulk integrated circuit (IC microfabrication tools and fine-pitch photolithography patterning. Here, we address this combined challenge of microfabrication with extreme stretchability for high-density SE devices by introducing CMOS-enabled, free-standing, miniaturized interconnect structures that fully exploit their 3D kinematic freedom through an interplay of buckling, torsion, and bending to maximize stretchability. Integration with standard CMOS-type batch processing is assured by utilizing the Flex-to-Rigid (F2R post-processing technology to make the back-end-of-line interconnect structures free-standing, thus enabling the routine microfabrication of highly-stretchable interconnects. The performance and reproducibility of these free-standing structures is promising: an elastic stretch beyond 2000% and ultimate (plastic stretch beyond 3000%, with <0.3% resistance change, and >10 million cycles at 1000% stretch with <1% resistance change. This generic technology provides a new route to exciting highly-stretchable miniature devices.

Nanocomposites with increased energy density through high aspect ratio PZT nanowires.

Science.gov (United States)

Tang, Haixiong; Lin, Yirong; Andrews, Clark; Sodano, Henry A

2011-01-07

High energy storage plays an important role in the modern electric industry. Herein, we investigated the role of filler aspect ratio in nanocomposites for energy storage. Nanocomposites were synthesized using lead zirconate titanate (PZT) with two different aspect ratio (nanowires, nanorods) fillers at various volume fractions dispersed in a polyvinylidene fluoride (PVDF) matrix. The permittivity constants of composites containing nanowires (NWs) were higher than those with nanorods (NRs) at the same inclusion volume fraction. It was also indicated that the high frequency loss tangent of samples with PZT nanowires was smaller than for those with nanorods, demonstrating the high electrical energy storage efficiency of the PZT NW nanocomposite. The high aspect ratio PZT NWs showed a 77.8% increase in energy density over the lower aspect ratio PZT NRs, under an electric field of 15 kV mm(-1) and 50% volume fraction. The breakdown strength was found to decrease with the increasing volume fraction of PZT NWs, but to only change slightly from a volume fraction of around 20%-50%. The maximum calculated energy density of nanocomposites is as high as 1.158 J cm(-3) at 50% PZT NWs in PVDF. Since the breakdown strength is lower compared to a PVDF copolymer such as poly(vinylidene fluoride-tertrifluoroethylene-terchlorotrifluoroethylene) P(VDF-TreEE-CTFE) and poly(vinylidene fluoride-co-hexafluoropropylene) P(VDF-HFP), the energy density of the nanocomposite could be significantly increased through the use of PZT NWs and a polymer with greater breakdown strength. These results indicate that higher aspect ratio fillers show promising potential to improve the energy density of nanocomposites, leading to the development of advanced capacitors with high energy density.

Diffusive dynamics during the high-to-low density transition in amorphous ice

Science.gov (United States)

Perakis, Fivos; Amann-Winkel, Katrin; Lehmkühler, Felix; Sprung, Michael; Mariedahl, Daniel; Sellberg, Jonas A.; Pathak, Harshad; Späh, Alexander; Cavalca, Filippo; Schlesinger, Daniel; Ricci, Alessandro; Jain, Avni; Massani, Bernhard; Aubree, Flora; Benmore, Chris J.; Loerting, Thomas; Grübel, Gerhard; Pettersson, Lars G. M.; Nilsson, Anders

2017-08-01

Water exists in high- and low-density amorphous ice forms (HDA and LDA), which could correspond to the glassy states of high- (HDL) and low-density liquid (LDL) in the metastable part of the phase diagram. However, the nature of both the glass transition and the high-to-low-density transition are debated and new experimental evidence is needed. Here we combine wide-angle X-ray scattering (WAXS) with X-ray photon-correlation spectroscopy (XPCS) in the small-angle X-ray scattering (SAXS) geometry to probe both the structural and dynamical properties during the high-to-low-density transition in amorphous ice at 1 bar. By analyzing the structure factor and the radial distribution function, the coexistence of two structurally distinct domains is observed at T = 125 K. XPCS probes the dynamics in momentum space, which in the SAXS geometry reflects structural relaxation on the nanometer length scale. The dynamics of HDA are characterized by a slow component with a large time constant, arising from viscoelastic relaxation and stress release from nanometer-sized heterogeneities. Above 110 K a faster, strongly temperature-dependent component appears, with momentum transfer dependence pointing toward nanoscale diffusion. This dynamical component slows down after transition into the low-density form at 130 K, but remains diffusive. The diffusive character of both the high- and low-density forms is discussed among different interpretations and the results are most consistent with the hypothesis of a liquid-liquid transition in the ultraviscous regime.

A high-density genetic map and QTL analysis of agronomic traits in foxtail millet [Setaria italica (L.) P. Beauv.] using RAD-seq.

Science.gov (United States)

Wang, Jun; Wang, Zhilan; Du, Xiaofen; Yang, Huiqing; Han, Fang; Han, Yuanhuai; Yuan, Feng; Zhang, Linyi; Peng, Shuzhong; Guo, Erhu

2017-01-01

Foxtail millet (Setaria italica), a very important grain crop in China, has become a new model plant for cereal crops and biofuel grasses. Although its reference genome sequence was released recently, quantitative trait loci (QTLs) controlling complex agronomic traits remains limited. The development of massively parallel genotyping methods and next-generation sequencing technologies provides an excellent opportunity for developing single-nucleotide polymorphisms (SNPs) for linkage map construction and QTL analysis of complex quantitative traits. In this study, a high-throughput and cost-effective RAD-seq approach was employed to generate a high-density genetic map for foxtail millet. A total of 2,668,587 SNP loci were detected according to the reference genome sequence; meanwhile, 9,968 SNP markers were used to genotype 124 F2 progenies derived from the cross between Hongmiaozhangu and Changnong35; a high-density genetic map spanning 1648.8 cM, with an average distance of 0.17 cM between adjacent markers was constructed; 11 major QTLs for eight agronomic traits were identified; five co-dominant DNA markers were developed. These findings will be of value for the identification of candidate genes and marker-assisted selection in foxtail millet.

Design of highly oriented (HOR) media for extremely high density recording

International Nuclear Information System (INIS)

Hee, C.H.; Wang, J.P.; Chong, T.C.; Low, T.S.

2001-01-01

The magnetic properties and recording performance of highly oriented (HOR) longitudinal media are systematically studied via micromagnetic simulation. It was found that highly oriented longitudinal media could be achieved by controlling the anisotropy axes distribution. The effect of anisotropy constant, saturated magnetization and exchange coupling constants on the hysteresis loops are presented. It was further found that highly oriented media show an ultra-low transition noise. Another interesting observation made was that increasing M s for the HOR media decreases the coercivity, which suggests practical usage of this media with current head field. A 500 Gbit/in 2 recording media is simulated to support the application of the highly oriented longitudinal media for ultra high density recording

Mitochondrial DNA mutation screening of male patients with obstructive sleep apnea-hypopnea syndrome.

Science.gov (United States)

Huang, Xiao-Ying; Li, Hong; Xu, Xiao-Mei; Wang, Liang-Xing

2014-08-01

The aim of the present study was to analyze the differences between the genes of the mitochondrial DNA (mtDNA) displacement loop (D-loop) region and the Cambridge Reference sequence, in order to screen the mutation sites and investigate the correlation between mutations, clinical parameters and complications associated with obstructive sleep apnea-hypopnea syndrome (OSAHS). mtDNA was obtained from male patients with OSAHS in the Zhejiang Province. In total, 60 male patients with OSAHS and 102 healthy adults were assessed to determine the levels of fasting blood glucose, total cholesterol, triglyceride (TG) and high-density and low-density lipoproteins (LDL). Furthermore, peripheral mtDNA was extracted and bidirectional sequencing was conducted to enable mutation screening. In the mtDNA D-loop region, 178 mutation sites were identified, of which 115 sites were present in the two groups. The number of non-common sites in the OSAHS group was significantly higher compared with the control group (P0.05). A total of 21 cases in the severe OSAHS group exhibited mutation rates of >10%. In the control group, there were 24 cases where the np73A-G and np263A-G mutations were predominant. The np303-np315 region was identified to be the highly variable region and various mutation forms were observed. Statistically significant differences were observed in the neck perimeter, TG and LDL levels among the OSAHS-no-mutation subgroups (P<0.05) and LDL was shown to be associated with an mtDNA mutation in the OSAHS group. Numerous polymorphic mutation sites were identified in the mtDNA D-loop region of the OSAHS group. Therefore, mtDNA mutation sites may be closely associated with the clinical manifestations and complications of OSAHS.

Imaginary time density-density correlations for two-dimensional electron gases at high density

Energy Technology Data Exchange (ETDEWEB)

Motta, M.; Galli, D. E. [Dipartimento di Fisica, Università degli Studi di Milano, Via Celoria 16, 20133 Milano (Italy); Moroni, S. [IOM-CNR DEMOCRITOS National Simulation Center and SISSA, Via Bonomea 265, 34136 Trieste (Italy); Vitali, E. [Department of Physics, College of William and Mary, Williamsburg, Virginia 23187-8795 (United States)

2015-10-28

We evaluate imaginary time density-density correlation functions for two-dimensional homogeneous electron gases of up to 42 particles in the continuum using the phaseless auxiliary field quantum Monte Carlo method. We use periodic boundary conditions and up to 300 plane waves as basis set elements. We show that such methodology, once equipped with suitable numerical stabilization techniques necessary to deal with exponentials, products, and inversions of large matrices, gives access to the calculation of imaginary time correlation functions for medium-sized systems. We discuss the numerical stabilization techniques and the computational complexity of the methodology and we present the limitations related to the size of the systems on a quantitative basis. We perform the inverse Laplace transform of the obtained density-density correlation functions, assessing the ability of the phaseless auxiliary field quantum Monte Carlo method to evaluate dynamical properties of medium-sized homogeneous fermion systems.

ORDEM 3.0 and the Risk of High-Density Debris

Science.gov (United States)

Matney, Mark; Anz-Meador, Philip

2014-01-01

NASA’s Orbital Debris Engineering Model was designed to calculate orbital debris fluxes on spacecraft in order to assess collision risk. The newest of these models, ORDEM 3.0, has a number of features not present in previous models. One of the most important is that the populations and fluxes are now broken out into material density groups. Previous models concentrated on debris size alone, but a particle’s mass and density also determine the amount of damage it can cause. ORDEM 3.0 includes a high-density component, primarily consisting of iron/steel particles that drive much of the risk to spacecraft. This paper will outline the methods that were used to separate and identify the different densities of debris, and how these new densities affect the overall debris flux and risk.

Extract of mangosteen increases high density lipoprotein levels in rats fed high lipid

Directory of Open Access Journals (Sweden)

Dwi Laksono Adiputro

2013-04-01

Full Text Available Background In cardiovascular medicine, Garcinia mangostana has been used as an antioxidant to inhibit oxidation of low density lipoproteins and as an antiobesity agent. The effect of Garcinia mangostana on hyperlipidemia is unknown. The aim of this study was to evaluate the effect of an ethanolic extract of Garcinia mangostana pericarp on lipid profile in rats fed a high lipid diet. Methods A total of 40 rats were divided into five groups control, high lipid diet, and high lipid diet + ethanolic extract of Garcinia mangostana pericarp at dosages of 200, 400, and 800 mg/kg body weight. The control group received a standard diet for 60 days. The high lipid diet group received standard diet plus egg yolk, goat fat, cholic acid, and pig fat for 60 days with or without ethanolic extract of Garcinia mangostana pericarp by the oral route. After 60 days, rats were anesthesized with ether for collection of blood by cardiac puncture. Analysis of blood lipid profile comprised colorimetric determination of cholesterol, triglyceride, low density lipoprotein (LDL, and high density lipoprotein (HDL. Results From the results of one-way ANOVA it was concluded that there were significant between-group differences in cholesterol, trygliceride, LDL, and HDL levels (p=0.000. Ethanolic extract of Garcinia mangostana pericarp significantly decreased cholesterol, trygliceride, and LDL levels, starting at 400 mg/kg body weight (p=0.000. Ethanolic extract of Garcinia mangostana pericarp significantly increased HDL level starting at 200 mg/kg body weight (p=0.000. Conclusion Ethanolic extract of Garcinia mangostana pericarp has a beneficial effect on lipid profile in rats on a high lipid diet.

Extract of mangosteen increases high density lipoprotein levels in rats fed high lipid

Directory of Open Access Journals (Sweden)

Dwi Laksono Adiputro

2015-12-01

Full Text Available BACKGROUND In cardiovascular medicine, Garcinia mangostana has been used as an antioxidant to inhibit oxidation of low density lipoproteins and as an antiobesity agent. The effect of Garcinia mangostana on hyperlipidemia is unknown. The aim of this study was to evaluate the effect of an ethanolic extract of Garcinia mangostana pericarp on lipid profile in rats fed a high lipid diet. METHODS A total of 40 rats were divided into five groups control, high lipid diet, and high lipid diet + ethanolic extract of Garcinia mangostana pericarp at dosages of 200, 400, and 800 mg/kg body weight. The control group received a standard diet for 60 days. The high lipid diet group received standard diet plus egg yolk, goat fat, cholic acid, and pig fat for 60 days with or without ethanolic extract of Garcinia mangostana pericarp by the oral route. After 60 days, rats were anesthesized with ether for collection of blood by cardiac puncture. Analysis of blood lipid profile comprised colorimetric determination of cholesterol, triglyceride, low density lipoprotein (LDL, and high density lipoprotein (HDL. RESULTS From the results of one-way ANOVA it was concluded that there were significant between-group differences in cholesterol, trygliceride, LDL, and HDL levels (p=0.000. Ethanolic extract of Garcinia mangostana pericarp significantly decreased cholesterol, trygliceride, and LDL levels, starting at 400 mg/kg body weight (p=0.000. Ethanolic extract of Garcinia mangostana pericarp significantly increased HDL level starting at 200 mg/kg body weight (p=0.000. CONCLUSION Ethanolic extract of Garcinia mangostana pericarp has a beneficial effect on lipid profile in rats on a high lipid diet.

Sequential strand displacement beacon for detection of DNA coverage on functionalized gold nanoparticles.

Science.gov (United States)

Paliwoda, Rebecca E; Li, Feng; Reid, Michael S; Lin, Yanwen; Le, X Chris

2014-06-17

Functionalizing nanomaterials for diverse analytical, biomedical, and therapeutic applications requires determination of surface coverage (or density) of DNA on nanomaterials. We describe a sequential strand displacement beacon assay that is able to quantify specific DNA sequences conjugated or coconjugated onto gold nanoparticles (AuNPs). Unlike the conventional fluorescence assay that requires the target DNA to be fluorescently labeled, the sequential strand displacement beacon method is able to quantify multiple unlabeled DNA oligonucleotides using a single (universal) strand displacement beacon. This unique feature is achieved by introducing two short unlabeled DNA probes for each specific DNA sequence and by performing sequential DNA strand displacement reactions. Varying the relative amounts of the specific DNA sequences and spacing DNA sequences during their coconjugation onto AuNPs results in different densities of the specific DNA on AuNP, ranging from 90 to 230 DNA molecules per AuNP. Results obtained from our sequential strand displacement beacon assay are consistent with those obtained from the conventional fluorescence assays. However, labeling of DNA with some fluorescent dyes, e.g., tetramethylrhodamine, alters DNA density on AuNP. The strand displacement strategy overcomes this problem by obviating direct labeling of the target DNA. This method has broad potential to facilitate more efficient design and characterization of novel multifunctional materials for diverse applications.

Analysis of Active Methylotrophic Communities: When DNA-SIP Meets High-Throughput Technologies.

Science.gov (United States)

Taubert, Martin; Grob, Carolina; Howat, Alexandra M; Burns, Oliver J; Chen, Yin; Neufeld, Josh D; Murrell, J Colin

2016-01-01

Methylotrophs are microorganisms ubiquitous in the environment that can metabolize one-carbon (C1) compounds as carbon and/or energy sources. The activity of these prokaryotes impacts biogeochemical cycles within their respective habitats and can determine whether these habitats act as sources or sinks of C1 compounds. Due to the high importance of C1 compounds, not only in biogeochemical cycles, but also for climatic processes, it is vital to understand the contributions of these microorganisms to carbon cycling in different environments. One of the most challenging questions when investigating methylotrophs, but also in environmental microbiology in general, is which species contribute to the environmental processes of interest, or "who does what, where and when?" Metabolic labeling with C1 compounds substituted with (13)C, a technique called stable isotope probing, is a key method to trace carbon fluxes within methylotrophic communities. The incorporation of (13)C into the biomass of active methylotrophs leads to an increase in the molecular mass of their biomolecules. For DNA-based stable isotope probing (DNA-SIP), labeled and unlabeled DNA is separated by isopycnic ultracentrifugation. The ability to specifically analyze DNA of active methylotrophs from a complex background community by high-throughput sequencing techniques, i.e. targeted metagenomics, is the hallmark strength of DNA-SIP for elucidating ecosystem functioning, and a protocol is detailed in this chapter.

Low voltage electroosmotic pump for high density integration into microfabricated fluidic systems

NARCIS (Netherlands)

Heuck, F.C.A.; Staufer, U.

2011-01-01

A low voltage electroosmotic (eo) pump suitable for high density integration into microfabricated fluidic systems has been developed. The high density integration of the eo pump required a small footprint as well as a specific on-chip design to ventilate the electrolyzed gases emerging at the

X-ray spectroscopy for high energy-density X pinch density and temperature measurements (invited)

International Nuclear Information System (INIS)

Pikuz, S.A.; Shelkovenko, T.A.; Chandler, K.M.; Mitchell, M.D.; Hammer, D.A.; Skobelev, I.Y.; Shlyaptseva, A.S.; Hansen, S.B.

2004-01-01

X pinch plasmas produced from fine metal wires can reach near solid densities and temperatures of 1 keV or even more. Plasma conditions change on time scales as short as 5-10 ps as determined using an x-ray streak camera viewing a focusing crystal spectrograph or directly viewing the plasma through multiple filters on a single test. As a result, it is possible to determine plasma conditions from spectra with ∼10 ps time resolution. Experiments and theory are now coming together to give a consistent picture of the dynamics and kinetics of these high energy density plasmas with very high temporal and spatial precision. A set of diagnostic techniques used in experiments for spectrally, temporally, and spatially resolved measurements of X pinch plasmas is described. Results of plasma parameter determination from these measurements are presented. X ray backlighting of one x-pinch by another with ∼30 ps x-ray pulses enables the dynamics and kinetics to be correlated in time

High density hydrogen storage in nanocavities: Role of the electrostatic interaction

Energy Technology Data Exchange (ETDEWEB)

Reguera, L. [Centro de Investigacion en Ciencia Aplicada y Tecnologia Avanzada del IPN, Legaria 694, Mexico D.F (Mexico); Facultad de Quimica, Universidad de La Habana, La Habana (Cuba); Roque, J. [Centro de Investigacion en Ciencia Aplicada y Tecnologia Avanzada del IPN, Legaria 694, Mexico D.F (Mexico); Hernandez, J. [Centro de Investigacion en Ciencia Aplicada y Tecnologia Avanzada del IPN, Legaria 694, Mexico D.F (Mexico); Universidad de Pinar del Rio, Pinar del Rio (Cuba); Reguera, E. [Centro de Investigacion en Ciencia Aplicada y Tecnologia Avanzada del IPN, Legaria 694, Mexico D.F (Mexico); Instituto de Ciencia y Tecnologia de Materiales, Universidad de La Habana, La Habana (Cuba)

2010-12-15

High pressure H{sub 2} adsorption isotherms at N{sub 2} liquid temperature were recorded for the series of cubic nitroprussides, Ni{sub 1-x}Co{sub x}[Fe(CN){sub 5}NO] with x = 0, 0.5, 0.7, 1. The obtained data were interpreted according to the effective polarizing power for the metal found at the surface of the cavity. The cavity volume where the hydrogen molecules are accumulated was estimated from the amount of water molecules that are occupying that available space in the as-synthesized solids considering a water density of 1 g/cm{sup 3}. The calculated cavity volume was then used to obtain the density of H{sub 2} storage in the cavity. For the Ni-containing material the highest storage density was obtained, in a cavity volume of 448.5 A{sup 3} up to 10.4 hydrogen molecules are accumulated, for a local density of 77.6 g/L, above the density value corresponding to liquid hydrogen (71 g/L). Such high value of local density was interpreted as related to the electrostatic contribution to the adsorption potential for the hydrogen molecule within the cavity. (author)

Microstructure and critical current density in high-Tc metal oxide superconductors

International Nuclear Information System (INIS)

Johnson, S.M.; Gusman, M.I.

1992-03-01

Superconductor powders in the U-Ba-Cu-O (YBCO) and Bi-Pb-Sr-Ca-Cu-O (BSCCO) systems were synthesized by freeze-drying. Powders were characterized, and processed into samples for evaluation of superconducting behavior. Freeze-drying is attractive because the powders have high purity, are homogeneous, have a small size and are active. YBCO powders can be sintered to high density at 890 degrees C. Many compositions, processing approaches and heat treatments were explored in an effort to understand relations between microstructure and critical density, and to improve the critical current density. Powders were also formed into sputtering targets for coating preparation at Stanford University. The highest critical current density achieved with the YBCO powders was ∼15,000 A/cm 2 at 4.2K and 0.5T using powders treated to prevent carbon contamination. The BSCCO materials with the highest critical current density, ∼30,000 A/cm 2 at the same conditions were formed by heat treating melted and quenched samples. All critical current density measurements were made by Stanford University, a subcontractor to this effort. Stanford University also prepared coatings by off-axis magnetron sputtering

High-Density Near-Field Optical Disc Recording

Science.gov (United States)

Shinoda, Masataka; Saito, Kimihiro; Ishimoto, Tsutomu; Kondo, Takao; Nakaoki, Ariyoshi; Ide, Naoki; Furuki, Motohiro; Takeda, Minoru; Akiyama, Yuji; Shimouma, Takashi; Yamamoto, Masanobu

2005-05-01

We developed a high-density near-field optical recording disc system using a solid immersion lens. The near-field optical pick-up consists of a solid immersion lens with a numerical aperture of 1.84. The laser wavelength for recording is 405 nm. In order to realize the near-field optical recording disc, we used a phase-change recording media and a molded polycarbonate substrate. A clear eye pattern of 112 GB capacity with 160 nm track pitch and 50 nm bit length was observed. The equivalent areal density is 80.6 Gbit/in2. The bottom bit error rate of 3 tracks-write was 4.5× 10-5. The readout power margin and the recording power margin were ± 30.4% and ± 11.2%, respectively.

Density-dependent squeezing of excitons in highly excited semiconductors

International Nuclear Information System (INIS)

Nguyen Hong Quang.

1995-07-01

The time evolution from coherent states to squeezed states of high density excitons is studied theoretically based on the boson formalism and within the Random Phase Approximation. Both the mutual interaction between excitons and the anharmonic exciton-photon interaction due to phase-space filling of excitons are taken into account. It is shown that the exciton squeezing depends strongly on the exciton density in semiconductors and becomes smaller with increasing the latter. (author). 16 refs, 2 figs

Use of ancient sedimentary DNA as a novel conservation tool for high-altitude tropical biodiversity.

Science.gov (United States)

Boessenkool, Sanne; McGlynn, Gayle; Epp, Laura S; Taylor, David; Pimentel, Manuel; Gizaw, Abel; Nemomissa, Sileshi; Brochmann, Christian; Popp, Magnus

2014-04-01

Conservation of biodiversity may in the future increasingly depend upon the availability of scientific information to set suitable restoration targets. In traditional paleoecology, sediment-based pollen provides a means to define preanthropogenic impact conditions, but problems in establishing the exact provenance and ecologically meaningful levels of taxonomic resolution of the evidence are limiting. We explored the extent to which the use of sedimentary ancient DNA (sedaDNA) may complement pollen data in reconstructing past alpine environments in the tropics. We constructed a record of afro-alpine plants retrieved from DNA preserved in sediment cores from 2 volcanic crater sites in the Albertine Rift, eastern Africa. The record extended well beyond the onset of substantial anthropogenic effects on tropical mountains. To ensure high-quality taxonomic inference from the sedaDNA sequences, we built an extensive DNA reference library covering the majority of the afro-alpine flora, by sequencing DNA from taxonomically verified specimens. Comparisons with pollen records from the same sediment cores showed that plant diversity recovered with sedaDNA improved vegetation reconstructions based on pollen records by revealing both additional taxa and providing increased taxonomic resolution. Furthermore, combining the 2 measures assisted in distinguishing vegetation change at different geographic scales; sedaDNA almost exclusively reflects local vegetation, whereas pollen can potentially originate from a wide area that in highlands in particular can span several ecozones. Our results suggest that sedaDNA may provide information on restoration targets and the nature and magnitude of human-induced environmental changes, including in high conservation priority, biodiversity hotspots, where understanding of preanthropogenic impact (or reference) conditions is highly limited. © 2013 Society for Conservation Biology.

A DNA fingerprinting procedure for ultra high-throughput genetic analysis of insects.

Science.gov (United States)

Schlipalius, D I; Waldron, J; Carroll, B J; Collins, P J; Ebert, P R

2001-12-01

Existing procedures for the generation of polymorphic DNA markers are not optimal for insect studies in which the organisms are often tiny and background molecular information is often non-existent. We have used a new high throughput DNA marker generation protocol called randomly amplified DNA fingerprints (RAF) to analyse the genetic variability in three separate strains of the stored grain pest, Rhyzopertha dominica. This protocol is quick, robust and reliable even though it requires minimal sample preparation, minute amounts of DNA and no prior molecular analysis of the organism. Arbitrarily selected oligonucleotide primers routinely produced approximately 50 scoreable polymorphic DNA markers, between individuals of three independent field isolates of R. dominica. Multivariate cluster analysis using forty-nine arbitrarily selected polymorphisms generated from a single primer reliably separated individuals into three clades corresponding to their geographical origin. The resulting clades were quite distinct, with an average genetic difference of 37.5 +/- 6.0% between clades and of 21.0 +/- 7.1% between individuals within clades. As a prelude to future gene mapping efforts, we have also assessed the performance of RAF under conditions commonly used in gene mapping. In this analysis, fingerprints from pooled DNA samples accurately and reproducibly reflected RAF profiles obtained from individual DNA samples that had been combined to create the bulked samples.

Base damage within single-strand DNA underlies in vivo hypermutability induced by a ubiquitous environmental agent.

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Kin Chan

Full Text Available Chromosomal DNA must be in single-strand form for important transactions such as replication, transcription, and recombination to occur. The single-strand DNA (ssDNA is more prone to damage than double-strand DNA (dsDNA, due to greater exposure of chemically reactive moieties in the nitrogenous bases. Thus, there can be agents that damage regions of ssDNA in vivo while being inert toward dsDNA. To assess the potential hazard posed by such agents, we devised an ssDNA-specific mutagenesis reporter system in budding yeast. The reporter strains bear the cdc13-1 temperature-sensitive mutation, such that shifting to 37°C results in telomere uncapping and ensuing 5' to 3' enzymatic resection. This exposes the reporter region, containing three closely-spaced reporter genes, as a long 3' ssDNA overhang. We validated the ability of the system to detect mutagenic damage within ssDNA by expressing a modified human single-strand specific cytosine deaminase, APOBEC3G. APOBEC3G induced a high density of substitutions at cytosines in the ssDNA overhang strand, resulting in frequent, simultaneous inactivation of two reporter genes. We then examined the mutagenicity of sulfites, a class of reactive sulfur oxides to which humans are exposed frequently via respiration and food intake. Sulfites, at a concentration similar to that found in some foods, induced a high density of mutations, almost always as substitutions at cytosines in the ssDNA overhang strand, resulting in simultaneous inactivation of at least two reporter genes. Furthermore, sulfites formed a long-lived adducted 2'-deoxyuracil intermediate in DNA that was resistant to excision by uracil-DNA N-glycosylase. This intermediate was bypassed by error-prone translesion DNA synthesis, frequently involving Pol ζ, during repair synthesis. Our results suggest that sulfite-induced lesions in DNA can be particularly deleterious, since cells might not possess the means to repair or bypass such lesions

Measurement of spontaneous DNA damage and DNA repair capacity in healthy adult individuals from high and normal level natural radiation areas of Kerala, India

International Nuclear Information System (INIS)

Vivek Kumar, P.R.; Jaikrishan, G.; Das, Birajalaxmi

2014-01-01

Inhabitants of the south west coastal areas of Kerala receive high level natural radiation due to the presence of monazite ( 232 Th) in the beach sand. This provides a unique opportunity to investigate the biological effects of high level natural radiation on humans. This study evaluate basal DNA damage in 149 healthy adult male subjects (104 from high level natural radiation areas (HLNRA, > 1mSv year -1 ) and 45 from normal level natural radiation area (NLNRA, d''1mSv year -1 ) by the alkaline comet assay. Oxidative DNA damage (ENDO III, FPG and hOGG1-sensitive sites) was measured by the enzyme modified comet assay. Induction and rejoining of DNA strand breaks was measured after irradiating peripheral blood lymphocytes with 2 Gy or 4 Gy gamma radiation. Basal damage due to age and residential area of the donors showed significant interaction (P=0.001), when all subjects were analyzed using a general linear model (GLM). In subgroup analysis, basal damage increased with age in subjects from the NLNRA (P=0.007), while a significant negative correlation (P=0.01) was observed in subjects from HLNRA. Oxidative DNA damage was not influenced by age, smoking habit or residential area in the entire sample. Subjects of high dose group from HLNRA (>5.75 mSv/y, N=34) showed a significant reduction in the induction of DNA damage after 2 Gy (P=0.03) and 4 Gy (P=0.05) compared to subjects form NLNRA. The study showed increased rejoining of DNA strand breaks in subjects from HLNRA when measured at 7 minutes after irradiation (P=0.04). In this pilot study, a low basal damage in elderly subjects from HLNRA and a reduced induction of DNA damage after 2 Gy and 4 Gy irradiation in high dose group subjects from HLNRA might suggest a possible role of chronic low dose natural radiation on the induction of an in vivo radio adaptive response. However, our findings need more validation in a larger study population. (author)

Interplay of charge density wave and spin density wave in high-T{sub c} superconductors

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Pradhan, B. [Government Science College, Malkangiri 764 048 (India)], E-mail: brunda@iopb.res.in; Raj, B.K. [B.J.B. College, Bhubaneswar 751 014 (India); Rout, G.C. [Condensed Matter Physics Group, P.G. Department of Applied Physics and Ballistics, F.M. University, Balasore 756 019 (India)], E-mail: gcr@iopb.res.in

2008-12-01

We present a mean-field theory theoretical model study for the coexistence of the two strongly interacting charge density wave (CDW) and spin density wave (SDW) for high-T{sub c} cuprates in the underdoped region before the onset of the superconductivity in the system. The analytic expressions for the temperature dependence of the CDW and SDW order parameters are derived and solved self-consistently. Their interplay is studied by varying their respective coupling constants. It is observed that in the interplay region both the gap parameters exhibit very strong dependence of their gap values for the coupling constants. Further, the electronic density of states (DOS) for the conduction electrons, which represents the scanning tunneling data, show two gap parameters in the interplay region from these experimental data. Our model can help to determine separately the CDW and SDW parameters.

Novel PVA-DNA nanoparticles prepared by ultra high pressure technology for gene delivery