A Substrate Bias Effect on Recovery of the Threshold Voltage Shift of Amorphous Silicon Thin-Film Transistors

NASA Astrophysics Data System (ADS)

Han, Chang-Wook; Han, Min-Koo; Choi, Nack-Bong; Kim, Chang-Dong; Kim, Ki-Yong; Chung, In-Jae

2007-07-01

Hydrogenated amorphous silicon (a-Si:H) thin-film transistors (TFTs) were fabricated on a flexible stainless-steel (SS) substrate. The stability of the a-Si:H TFT is a key issue for active matrix organic light-emitting diodes (AMOLEDs). The drain current decreases because of the threshold voltage shift (Δ VTH) during OLED driving. A negative voltage at a floated gate can be induced by a negative substrate bias through a capacitor between the substrate and the gate electrode without additional circuits. The negative voltage biased at the SS substrate can recover Δ VTH and reduced drain current of the driving TFT. The VTH of the TFT increased by 2.3 V under a gate bias of +15 V and a drain bias of +15 V at 65 °C applied for 3,500 s. The VTH decreased by -2.3 V and the drain current recovered 97% of its initial value under a substrate bias of -23 V at 65 °C applied for 3,500 s.

Fully depleted back illuminated CCD

DOEpatents

Holland, Stephen Edward

2001-01-01

A backside illuminated charge coupled device (CCD) is formed of a relatively thick high resistivity photon sensitive silicon substrate, with frontside electronic circuitry, and an optically transparent backside ohmic contact for applying a backside voltage which is at least sufficient to substantially fully deplete the substrate. A greater bias voltage which overdepletes the substrate may also be applied. One way of applying the bias voltage to the substrate is by physically connecting the voltage source to the ohmic contact. An alternate way of applying the bias voltage to the substrate is to physically connect the voltage source to the frontside of the substrate, at a point outside the depletion region. Thus both frontside and backside contacts can be used for backside biasing to fully deplete the substrate. Also, high resistivity gaps around the CCD channels and electrically floating channel stop regions can be provided in the CCD array around the CCD channels. The CCD array forms an imaging sensor useful in astronomy.

Influence of Substrate Biasing on (Ba,Sr)TiO3 Films Prepared by Electron Cyclotron Resonance Plasma Sputtering

NASA Astrophysics Data System (ADS)

Matsumoto, Takeshi; Niino, Atsushi; Ohtsu, Yasunori; Misawa, Tatsuya; Yonesu, Akira; Fujita, Hiroharu; Miyake, Shoji

2004-03-01

(Ba,Sr)TiO3 (BST) films were deposited by electron cyclotron resonance (ECR) plasma sputtering with mirror confinement. DC bias voltage was applied to Pt/Ti/SiO2/Si substrates during deposition to vary the intensity of bombardment of energetic ions and to modify film properties. BST films deposited on the substrates at floating potential (approximately +20 V) were found to be amorphous, while films deposited on +40 V-biased substrates were crystalline in spite of a low substrate temperature below 648 K. In addition, atomic diffusion, which causes deterioration in the electrical properties of the films, was hardly observed in the crystallized films deposited with +40 V bias perhaps due to the low substrate temperature. Plasma diagnoses revealed that application of a positive bias to the substrate reduced the energy of ion bombardment and increased the density of excited neutral particles, which was assumed to result in the promotion of chemical reactions during deposition and the crystallization of BST films at a low temperature.

Mapping protease substrates using a biotinylated phage substrate library.

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

Scholle, M. D.; Kriplani, U.; Pabon, A.

We describe a bacteriophage M13 substrate library encoding the AviTag (BirA substrate) and combinatorial heptamer peptides displayed at the N terminus of the mature form of capsid protein III. Phages are biotinylated efficiently (> or = 50%) when grown in E. coli cells coexpressing BirA, and such viral particles can be immobilized on a streptavidin-coated support and released by protease cleavage within the combinatorial peptide. We have used this library to map the specificity of human Factor Xa and a neuropeptidase, neurolysin (EC3.4.24.16). Validation by analysis of isolated peptide substrates has revealed that neurolysin recognizes the motif hydrophobic-X-Pro-Arg-hydrophobic, where Arg-hydrophobicmore » is the scissile bond.« less

Effect of Substrate Bias on Friction Coefficient, Adhesion Strength and Hardness of TiN-COATED Tool Steel

NASA Astrophysics Data System (ADS)

Hamzah, Esah; Ali, Mubarak; Toff, Mohd Radzi Hj. Mohd

In the present study, TiN coatings have been deposited on D2 tool steel substrates by using cathodic arc physical vapor deposition technique. The objective of this research work is to determine the usefulness of TiN coatings in order to improve the micro-Vickers hardness and friction coefficient of TiN coating deposited on D2 tool steel, which is widely used in tooling applications. A Pin-on-Disc test was carried out to study the coefficient of friction versus sliding distance of TiN coating deposited at various substrate biases. The standard deviation parameter during tribo-test result showed that the coating deposited at substrate bias of -75 V was the most stable coating. A significant increase in micro-Vickers hardness was recorded, when substrate bias was reduced from -150 V to zero. Scratch tester was used to compare the critical loads for coatings deposited at different bias voltages and the adhesion achievable was demonstrated with relevance to the various modes, scratch macroscopic analysis, critical load, acoustic emission and penetration depth. A considerable improvement in TiN coatings was observed as a function of various substrate bias voltages.

Design of ultrasensitive probes for human neutrophil elastase through hybrid combinatorial substrate library profiling

PubMed Central

Kasperkiewicz, Paulina; Poreba, Marcin; Snipas, Scott J.; Parker, Heather; Winterbourn, Christine C.; Salvesen, Guy S.; Drag, Marcin

2014-01-01

The exploration of protease substrate specificity is generally restricted to naturally occurring amino acids, limiting the degree of conformational space that can be surveyed. We substantially enhanced this by incorporating 102 unnatural amino acids to explore the S1–S4 pockets of human neutrophil elastase. This approach provides hybrid natural and unnatural amino acid sequences, and thus we termed it the Hybrid Combinatorial Substrate Library. Library results were validated by the synthesis of individual tetrapeptide substrates, with the optimal substrate demonstrating more than three orders of magnitude higher catalytic efficiency than commonly used substrates of elastase. This optimal substrate was converted to an activity-based probe that demonstrated high selectivity and revealed the specific presence of active elastase during the process of neutrophil extracellular trap formation. We propose that this approach can be successfully used for any type of endopeptidase to deliver high activity and selectivity in substrates and probes. PMID:24550277

Calibrating genomic and allelic coverage bias in single-cell sequencing.

PubMed

Zhang, Cheng-Zhong; Adalsteinsson, Viktor A; Francis, Joshua; Cornils, Hauke; Jung, Joonil; Maire, Cecile; Ligon, Keith L; Meyerson, Matthew; Love, J Christopher

2015-04-16

Artifacts introduced in whole-genome amplification (WGA) make it difficult to derive accurate genomic information from single-cell genomes and require different analytical strategies from bulk genome analysis. Here, we describe statistical methods to quantitatively assess the amplification bias resulting from whole-genome amplification of single-cell genomic DNA. Analysis of single-cell DNA libraries generated by different technologies revealed universal features of the genome coverage bias predominantly generated at the amplicon level (1-10 kb). The magnitude of coverage bias can be accurately calibrated from low-pass sequencing (∼0.1 × ) to predict the depth-of-coverage yield of single-cell DNA libraries sequenced at arbitrary depths. We further provide a benchmark comparison of single-cell libraries generated by multi-strand displacement amplification (MDA) and multiple annealing and looping-based amplification cycles (MALBAC). Finally, we develop statistical models to calibrate allelic bias in single-cell whole-genome amplification and demonstrate a census-based strategy for efficient and accurate variant detection from low-input biopsy samples.

Calibrating genomic and allelic coverage bias in single-cell sequencing

PubMed Central

Francis, Joshua; Cornils, Hauke; Jung, Joonil; Maire, Cecile; Ligon, Keith L.; Meyerson, Matthew; Love, J. Christopher

2016-01-01

Artifacts introduced in whole-genome amplification (WGA) make it difficult to derive accurate genomic information from single-cell genomes and require different analytical strategies from bulk genome analysis. Here, we describe statistical methods to quantitatively assess the amplification bias resulting from whole-genome amplification of single-cell genomic DNA. Analysis of single-cell DNA libraries generated by different technologies revealed universal features of the genome coverage bias predominantly generated at the amplicon level (1–10 kb). The magnitude of coverage bias can be accurately calibrated from low-pass sequencing (~0.1 ×) to predict the depth-of-coverage yield of single-cell DNA libraries sequenced at arbitrary depths. We further provide a benchmark comparison of single-cell libraries generated by multi-strand displacement amplification (MDA) and multiple annealing and looping-based amplification cycles (MALBAC). Finally, we develop statistical models to calibrate allelic bias in single-cell whole-genome amplification and demonstrate a census-based strategy for efficient and accurate variant detection from low-input biopsy samples. PMID:25879913

The Contingent Valuation Method in Public Libraries

ERIC Educational Resources Information Center

Chung, Hye-Kyung

2008-01-01

This study aims to present a new model measuring the economic value of public libraries, combining the dissonance minimizing (DM) and information bias minimizing (IBM) format in the contingent valuation (CV) surveys. The possible biases which are tied to the conventional CV surveys are reviewed. An empirical study is presented to compare the model…

Large-scale Topographical Screen for Investigation of Physical Neural-Guidance Cues

NASA Astrophysics Data System (ADS)

Li, Wei; Tang, Qing Yuan; Jadhav, Amol D.; Narang, Ankit; Qian, Wei Xian; Shi, Peng; Pang, Stella W.

2015-03-01

A combinatorial approach was used to present primary neurons with a large library of topographical features in the form of micropatterned substrate for high-throughput screening of physical neural-guidance cues that can effectively promote different aspects of neuronal development, including axon and dendritic outgrowth. Notably, the neuronal-guidance capability of specific features was automatically identified using a customized image processing software, thus significantly increasing the screening throughput with minimal subjective bias. Our results indicate that the anisotropic topographies promote axonal and in some cases dendritic extension relative to the isotropic topographies, while dendritic branching showed preference to plain substrates over the microscale features. The results from this work can be readily applied towards engineering novel biomaterials with precise surface topography that can serve as guidance conduits for neuro-regenerative applications. This novel topographical screening strategy combined with the automated processing capability can also be used for high-throughput screening of chemical or genetic regulatory factors in primary neurons.

Engineering peptide ligase specificity by proteomic identification of ligation sites.

PubMed

Weeks, Amy M; Wells, James A

2018-01-01

Enzyme-catalyzed peptide ligation is a powerful tool for site-specific protein bioconjugation, but stringent enzyme-substrate specificity limits its utility. We developed an approach for comprehensively characterizing peptide ligase specificity for N termini using proteome-derived peptide libraries. We used this strategy to characterize the ligation efficiency for >25,000 enzyme-substrate pairs in the context of the engineered peptide ligase subtiligase and identified a family of 72 mutant subtiligases with activity toward N-terminal sequences that were previously recalcitrant to modification. We applied these mutants individually for site-specific bioconjugation of purified proteins, including antibodies, and in algorithmically selected combinations for sequencing of the cellular N terminome with reduced sequence bias. We also developed a web application to enable algorithmic selection of the most efficient subtiligase variant(s) for bioconjugation to user-defined sequences. Our methods provide a new toolbox of enzymes for site-specific protein modification and a general approach for rapidly defining and engineering peptide ligase specificity.

Species richness in soil bacterial communities: a proposed approach to overcome sample size bias.

PubMed

Youssef, Noha H; Elshahed, Mostafa S

2008-09-01

Estimates of species richness based on 16S rRNA gene clone libraries are increasingly utilized to gauge the level of bacterial diversity within various ecosystems. However, previous studies have indicated that regardless of the utilized approach, species richness estimates obtained are dependent on the size of the analyzed clone libraries. We here propose an approach to overcome sample size bias in species richness estimates in complex microbial communities. Parametric (Maximum likelihood-based and rarefaction curve-based) and non-parametric approaches were used to estimate species richness in a library of 13,001 near full-length 16S rRNA clones derived from soil, as well as in multiple subsets of the original library. Species richness estimates obtained increased with the increase in library size. To obtain a sample size-unbiased estimate of species richness, we calculated the theoretical clone library sizes required to encounter the estimated species richness at various clone library sizes, used curve fitting to determine the theoretical clone library size required to encounter the "true" species richness, and subsequently determined the corresponding sample size-unbiased species richness value. Using this approach, sample size-unbiased estimates of 17,230, 15,571, and 33,912 were obtained for the ML-based, rarefaction curve-based, and ACE-1 estimators, respectively, compared to bias-uncorrected values of 15,009, 11,913, and 20,909.

Massively parallel rRNA gene sequencing exacerbates the potential for biased community diversity comparisons due to variable library sizes

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

Gihring, Thomas; Green, Stefan; Schadt, Christopher Warren

2011-01-01

Technologies for massively parallel sequencing are revolutionizing microbial ecology and are vastly increasing the scale of ribosomal RNA (rRNA) gene studies. Although pyrosequencing has increased the breadth and depth of possible rRNA gene sampling, one drawback is that the number of reads obtained per sample is difficult to control. Pyrosequencing libraries typically vary widely in the number of sequences per sample, even within individual studies, and there is a need to revisit the behaviour of richness estimators and diversity indices with variable gene sequence library sizes. Multiple reports and review papers have demonstrated the bias in non-parametric richness estimators (e.g.more » Chao1 and ACE) and diversity indices when using clone libraries. However, we found that biased community comparisons are accumulating in the literature. Here we demonstrate the effects of sample size on Chao1, ACE, CatchAll, Shannon, Chao-Shen and Simpson's estimations specifically using pyrosequencing libraries. The need to equalize the number of reads being compared across libraries is reiterated, and investigators are directed towards available tools for making unbiased diversity comparisons.« less

Influence of substrate bias voltage on structure and properties of the CrAlN films deposited by unbalanced magnetron sputtering

NASA Astrophysics Data System (ADS)

Lv, Yanhong; Ji, Li; Liu, Xiaohong; Li, Hongxuan; Zhou, Huidi; Chen, Jianmin

2012-02-01

The CrAlN films were deposited on silicon and stainless steel substrates by unbalanced magnetron sputtering system. The influence of substrate bias on deposition rate, composition, structure, morphology and properties of the CrAlN films was investigated. The results showed that, with the increase of the substrate bias voltage, the deposition rate decreased accompanied by a change of the preferred orientation of the CrAlN film from (2 2 0) to (2 0 0). The grain size and the average surface roughness of the CrAlN films declined as the bias voltage increases above -100 V. The morphology of the films changed from obviously columnar to dense glass-like structure with the increase of the bias voltage from -50 to -250 V. Meanwhile, the films deposited at moderate bias voltage had better mechanical and tribological properties, while the films deposited at higher bias voltage showed better corrosion resistance. It was found that the corrosion resistance improvement was not only attributed to the low pinhole density of the film, but also to chemical composition of films.

DNA polymerase preference determines PCR priming efficiency.

PubMed

Pan, Wenjing; Byrne-Steele, Miranda; Wang, Chunlin; Lu, Stanley; Clemmons, Scott; Zahorchak, Robert J; Han, Jian

2014-01-30

Polymerase chain reaction (PCR) is one of the most important developments in modern biotechnology. However, PCR is known to introduce biases, especially during multiplex reactions. Recent studies have implicated the DNA polymerase as the primary source of bias, particularly initiation of polymerization on the template strand. In our study, amplification from a synthetic library containing a 12 nucleotide random portion was used to provide an in-depth characterization of DNA polymerase priming bias. The synthetic library was amplified with three commercially available DNA polymerases using an anchored primer with a random 3' hexamer end. After normalization, the next generation sequencing (NGS) results of the amplified libraries were directly compared to the unamplified synthetic library. Here, high throughput sequencing was used to systematically demonstrate and characterize DNA polymerase priming bias. We demonstrate that certain sequence motifs are preferred over others as primers where the six nucleotide sequences at the 3' end of the primer, as well as the sequences four base pairs downstream of the priming site, may influence priming efficiencies. DNA polymerases in the same family from two different commercial vendors prefer similar motifs, while another commercially available enzyme from a different DNA polymerase family prefers different motifs. Furthermore, the preferred priming motifs are GC-rich. The DNA polymerase preference for certain sequence motifs was verified by amplification from single-primer templates. We incorporated the observed DNA polymerase preference into a primer-design program that guides the placement of the primer to an optimal location on the template. DNA polymerase priming bias was characterized using a synthetic library amplification system and NGS. The characterization of DNA polymerase priming bias was then utilized to guide the primer-design process and demonstrate varying amplification efficiencies among three commercially available DNA polymerases. The results suggest that the interaction of the DNA polymerase with the primer:template junction during the initiation of DNA polymerization is very important in terms of overall amplification bias and has broader implications for both the primer design process and multiplex PCR.

Ligation Bias in Illumina Next-Generation DNA Libraries: Implications for Sequencing Ancient Genomes

PubMed Central

Seguin-Orlando, Andaine; Schubert, Mikkel; Clary, Joel; Stagegaard, Julia; Alberdi, Maria T.; Prado, José Luis; Prieto, Alfredo; Willerslev, Eske; Orlando, Ludovic

2013-01-01

Ancient DNA extracts consist of a mixture of endogenous molecules and contaminant DNA templates, often originating from environmental microbes. These two populations of templates exhibit different chemical characteristics, with the former showing depurination and cytosine deamination by-products, resulting from post-mortem DNA damage. Such chemical modifications can interfere with the molecular tools used for building second-generation DNA libraries, and limit our ability to fully characterize the true complexity of ancient DNA extracts. In this study, we first use fresh DNA extracts to demonstrate that library preparation based on adapter ligation at AT-overhangs are biased against DNA templates starting with thymine residues, contrarily to blunt-end adapter ligation. We observe the same bias on fresh DNA extracts sheared on Bioruptor, Covaris and nebulizers. This contradicts previous reports suggesting that this bias could originate from the methods used for shearing DNA. This also suggests that AT-overhang adapter ligation efficiency is affected in a sequence-dependent manner and results in an uneven representation of different genomic contexts. We then show how this bias could affect the base composition of ancient DNA libraries prepared following AT-overhang ligation, mainly by limiting the ability to ligate DNA templates starting with thymines and therefore deaminated cytosines. This results in particular nucleotide misincorporation damage patterns, deviating from the signature generally expected for authenticating ancient sequence data. Consequently, we show that models adequate for estimating post-mortem DNA damage levels must be robust to the molecular tools used for building ancient DNA libraries. PMID:24205269

Optimizing Illumina next-generation sequencing library preparation for extremely AT-biased genomes.

PubMed

Oyola, Samuel O; Otto, Thomas D; Gu, Yong; Maslen, Gareth; Manske, Magnus; Campino, Susana; Turner, Daniel J; Macinnis, Bronwyn; Kwiatkowski, Dominic P; Swerdlow, Harold P; Quail, Michael A

2012-01-03

Massively parallel sequencing technology is revolutionizing approaches to genomic and genetic research. Since its advent, the scale and efficiency of Next-Generation Sequencing (NGS) has rapidly improved. In spite of this success, sequencing genomes or genomic regions with extremely biased base composition is still a great challenge to the currently available NGS platforms. The genomes of some important pathogenic organisms like Plasmodium falciparum (high AT content) and Mycobacterium tuberculosis (high GC content) display extremes of base composition. The standard library preparation procedures that employ PCR amplification have been shown to cause uneven read coverage particularly across AT and GC rich regions, leading to problems in genome assembly and variation analyses. Alternative library-preparation approaches that omit PCR amplification require large quantities of starting material and hence are not suitable for small amounts of DNA/RNA such as those from clinical isolates. We have developed and optimized library-preparation procedures suitable for low quantity starting material and tolerant to extremely high AT content sequences. We have used our optimized conditions in parallel with standard methods to prepare Illumina sequencing libraries from a non-clinical and a clinical isolate (containing ~53% host contamination). By analyzing and comparing the quality of sequence data generated, we show that our optimized conditions that involve a PCR additive (TMAC), produces amplified libraries with improved coverage of extremely AT-rich regions and reduced bias toward GC neutral templates. We have developed a robust and optimized Next-Generation Sequencing library amplification method suitable for extremely AT-rich genomes. The new amplification conditions significantly reduce bias and retain the complexity of either extremes of base composition. This development will greatly benefit sequencing clinical samples that often require amplification due to low mass of DNA starting material.

Measuring the Global Substrate Specificity of Mycobacterial Serine Hydrolases Using a Library of Fluorogenic Ester Substrates.

PubMed

Bassett, Braden; Waibel, Brent; White, Alex; Hansen, Heather; Stephens, Dominique; Koelper, Andrew; Larsen, Erik M; Kim, Charles; Glanzer, Adam; Lavis, Luke D; Hoops, Geoffrey C; Johnson, R Jeremy

2018-04-16

Among the proteins required for lipid metabolism in Mycobacterium tuberculosis are a significant number of uncharacterized serine hydrolases, especially lipases and esterases. Using a streamlined synthetic method, a library of immolative fluorogenic ester substrates was expanded to better represent the natural lipidomic diversity of Mycobacterium. This expanded fluorogenic library was then used to rapidly characterize the global structure activity relationship (SAR) of mycobacterial serine hydrolases in M. smegmatis under different growth conditions. Confirmation of fluorogenic substrate activation by mycobacterial serine hydrolases was performed using nonspecific serine hydrolase inhibitors and reinforced the biological significance of the SAR. The hydrolases responsible for the global SAR were then assigned using gel-resolved activity measurements, and these assignments were used to rapidly identify the relative substrate specificity of previously uncharacterized mycobacterial hydrolases. These measurements provide a global SAR of mycobacterial hydrolase activity, a picture of cycling hydrolase activity, and a detailed substrate specificity profile for previously uncharacterized hydrolases.

Unnatural amino acids increase sensitivity and provide for the design of highly selective caspase substrates

PubMed Central

Poreba, M; Kasperkiewicz, P; Snipas, S J; Fasci, D; Salvesen, G S; Drag, M

2014-01-01

Traditional combinatorial peptidyl substrate library approaches generally utilize natural amino acids, limiting the usefulness of this tool in generating selective substrates for proteases that share similar substrate specificity profiles. To address this limitation, we synthesized a Hybrid Combinatorial Substrate Library (HyCoSuL) with the general formula of Ac-P4-P3-P2-Asp-ACC, testing the approach on a family of closely related proteases – the human caspases. The power of this library for caspase discrimination extends far beyond traditional PS-SCL approach, as in addition to 19 natural amino acids we also used 110 diverse unnatural amino acids that can more extensively explore the chemical space represented by caspase-active sites. Using this approach we identified and employed peptide-based substrates that provided excellent discrimination between individual caspases, allowing us to simultaneously resolve the individual contribution of the apical caspase-9 and the executioner caspase-3 and caspase-7 in the development of cytochrome-c-dependent apoptosis for the first time. PMID:24832467

Comparative study of ITO and TiN fabricated by low-temperature RF biased sputtering

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

Simon, Daniel K., E-mail: daniel.simon@namlab.com; Schenk, Tony; Dirnstorfer, Ingo

2016-03-15

Radio frequency (RF) biasing induced by a second plasma source at the substrate is applied to low-temperature sputtering processes for indium tin oxide (ITO) and titanium nitride (TiN) thin films. Investigations on crystal structure and surface morphology show that RF-biased substrate plasma processes result in a changed growth regime with different grain sizes and orientations than those produced by processes without a substrate bias. The influence of the RF bias is shown comparatively for reactive RF-sputtered ITO and reactive direct-current-sputtered TiN. The ITO layers exhibit an improved electrical resistivity of 0.5 mΩ cm and an optical absorption coefficient of 0.5 × 10{sup 4 }cm{supmore » −1} without substrate heating. Room-temperature sputtered TiN layers are deposited that possess a resistivity (0.1 mΩ cm) of 3 orders of magnitude lower than, and a density (5.4 g/cm{sup 3}) up to 45% greater than, those obtained from layers grown using the standard process without a substrate plasma.« less

Sex, Salaries, and Library Support--1981.

ERIC Educational Resources Information Center

Heim, Kathleen M.; Kacena, Carolyn

1981-01-01

Notes that library support kept pace with inflation during 1980 and indicates a continuing sex bias with respect to women library directors. Women are neither proportionately represented nor paid as well as their male counterparts and their libraries suffer from lower per capita financial support. Data and references are provided. (RAA)

Optimization of design and production strategies for novel adeno-associated viral display peptide libraries.

PubMed

Körbelin, J; Hunger, A; Alawi, M; Sieber, T; Binder, M; Trepel, M

2017-08-01

Libraries displaying random peptides on the surface of adeno-associated virus (AAV) are powerful tools for the generation of target-specific gene therapy vectors. However, for unknown reasons the success rate of AAV library screenings is variable and the influence of the production procedure has not been thoroughly evaluated. During library screenings, the capsid variants with the most favorable tropism are enriched over several selection rounds on a target of choice and identified by subsequent sequencing of the encapsidated viral genomes encoding the library capsids with targeting peptide insertions. Thus, a high capsid-genome correlation is crucial to obtain the correct information about the selected capsid variants. Producing AAV libraries by a two-step protocol with pseudotyped library transfer shuttles has been proposed as one way to ensure such a correlation. Here we show that AAV2 libraries produced by such a protocol via transfer shuttles display an unexpected additional bias in the amino-acid composition which confers increased heparin affinity and thus similarity to wildtype AAV2 tropism. This bias may fundamentally impair the intended use of AAV libraries, discouraging the use of transfer shuttles for the production of AAV libraries in the future.

T7 lytic phage-displayed peptide libraries exhibit less sequence bias than M13 filamentous phage-displayed peptide libraries.

PubMed

Krumpe, Lauren R H; Atkinson, Andrew J; Smythers, Gary W; Kandel, Andrea; Schumacher, Kathryn M; McMahon, James B; Makowski, Lee; Mori, Toshiyuki

2006-08-01

We investigated whether the T7 system of phage display could produce peptide libraries of greater diversity than the M13 system of phage display due to the differing processes of lytic and filamentous phage morphogenesis. Using a bioinformatics-assisted computational approach, collections of random peptide sequences obtained from a T7 12-mer library (X(12)) and a T7 7-mer disulfide-constrained library (CX(7)C) were analyzed and compared with peptide populations obtained from New England BioLabs' M13 Ph.D.-12 and Ph.D.-C7C libraries. Based on this analysis, peptide libraries constructed with the T7 system have fewer amino acid biases, increased peptide diversity, and more normal distributions of peptide net charge and hydropathy than the M13 libraries. The greater diversity of T7-displayed libraries provides a potential resource of novel binding peptides for new as well as previously studied molecular targets. To demonstrate their utility, several of the T7-displayed peptide libraries were screened for streptavidin- and neutravidin-binding phage. Novel binding motifs were identified for each protein.

Compact ion accelerator source

DOEpatents

Schenkel, Thomas; Persaud, Arun; Kapadia, Rehan; Javey, Ali

2014-04-29

An ion source includes a conductive substrate, the substrate including a plurality of conductive nanostructures with free-standing tips formed on the substrate. A conductive catalytic coating is formed on the nanostructures and substrate for dissociation of a molecular species into an atomic species, the molecular species being brought in contact with the catalytic coating. A target electrode placed apart from the substrate, the target electrode being biased relative to the substrate with a first bias voltage to ionize the atomic species in proximity to the free-standing tips and attract the ionized atomic species from the substrate in the direction of the target electrode.

Rapid Analysis of Protein Farnesyltransferase Substrate Specificity Using Peptide Libraries and Isoprenoid Diphosphate Analogues

PubMed Central

2015-01-01

Protein farnesytransferase (PFTase) catalyzes the farnesylation of proteins with a carboxy-terminal tetrapeptide sequence denoted as a Ca1a2X box. To explore the specificity of this enzyme, an important therapeutic target, solid-phase peptide synthesis in concert with a peptide inversion strategy was used to prepare two libraries, each containing 380 peptides. The libraries were screened using an alkyne-containing isoprenoid analogue followed by click chemistry with biotin azide and subsequent visualization with streptavidin-AP. Screening of the CVa2X and CCa2X libraries with Rattus norvegicus PFTase revealed reaction by many known recognition sequences as well as numerous unknown ones. Some of the latter occur in the genomes of bacteria and viruses and may be important for pathogenesis, suggesting new targets for therapeutic intervention. Screening of the CVa2X library with alkyne-functionalized isoprenoid substrates showed that those prepared from C10 or C15 precursors gave similar results, whereas the analogue synthesized from a C5 unit gave a different pattern of reactivity. Lastly, the substrate specificities of PFTases from three organisms (R. norvegicus, Saccharomyces cerevisiae, and Candida albicans) were compared using CVa2X libraries. R. norvegicus PFTase was found to share more peptide substrates with S. cerevisiae PFTase than with C. albicans PFTase. In general, this method is a highly efficient strategy for rapidly probing the specificity of this important enzyme. PMID:24841702

Biofragments: An Approach towards Predicting Protein Function Using Biologically Related Fragments and its Application to Mycobacterium tuberculosis CYP126

PubMed Central

Hudson, Sean A; Mashalidis, Ellene H; Bender, Andreas; McLean, Kirsty J; Munro, Andrew W; Abell, Chris

2014-01-01

We present a novel fragment-based approach that tackles some of the challenges for chemical biology of predicting protein function. The general approach, which we have termed biofragments, comprises two key stages. First, a biologically relevant fragment library (biofragment library) can be designed and constructed from known sets of substrate-like ligands for a protein class of interest. Second, the library can be screened for binding to a novel putative ligand-binding protein from the same or similar class, and the characterization of hits provides insight into the basis of ligand recognition, selectivity, and function at the substrate level. As a proof-of-concept, we applied the biofragments approach to the functionally uncharacterized Mycobacterium tuberculosis (Mtb) cytochrome P450 isoform, CYP126. This led to the development of a tailored CYP biofragment library with notable 3D characteristics and a significantly higher screening hit rate (14 %) than standard drug-like fragment libraries screened previously against Mtb CYP121 and 125 (4 % and 1 %, respectively). Biofragment hits were identified that make both substrate-like type-I and inhibitor-like type-II interactions with CYP126. A chemical-fingerprint-based substrate model was built from the hits and used to search a virtual TB metabolome, which led to the discovery that CYP126 has a strong preference for the recognition of aromatics and substrate-like type-I binding of chlorophenol moieties within the active site near the heme. Future catalytic analyses will be focused on assessing CYP126 for potential substrate oxidative dehalogenation. PMID:24677424

Collection Development and the Psychology of Bias

ERIC Educational Resources Information Center

Quinn, Brian

2012-01-01

The library literature addressing the role of bias in collection development emphasizes a philosophical approach. It is based on the notion that bias can be controlled by the conscious act of believing in certain values and adhering to a code of ethics. It largely ignores the psychological research on bias, which suggests that bias is a more…

RF plasma MOCVD of Y2O3 thin films: Effect of RF self-bias on the substrates during deposition

NASA Astrophysics Data System (ADS)

Chopade, S. S.; Barve, S. A.; Thulasi Raman, K. H.; Chand, N.; Deo, M. N.; Biswas, A.; Rai, Sanjay; Lodha, G. S.; Rao, G. M.; Patil, D. S.

2013-11-01

Yttrium oxide (Y2O3) thin films have been deposited by radio frequency plasma assisted metal organic chemical vapor deposition (MOCVD) process using (2,2,6,6-tetramethyl-3,5-heptanedionate) yttrium (commonly known as Y(thd)3) precursor in a plasma of argon and oxygen gases at a substrate temperature of 350 °C. The films have been deposited under influence of varying RF self-bias (-50 V to -175 V) on silicon, quartz, stainless steel and tantalum substrates. The deposited coatings are characterized by glancing angle X-ray diffraction (GIXRD), Fourier transform infrared spectroscopy (FTIR), X-ray photoelectron spectroscopy (XPS), spectroscopic ellipsometry and scanning electron microscopy (SEM). GIXRD and FTIR results indicate deposition of Y2O3 (BCC structure) in all cases. However, XPS results indicate nonstoichiometric cubic phase deposition on the surface of deposited films. The degree of nonstoichiometry varies with bias during deposition. Ellipsometry results indicate that the refractive index for the deposited films is varying from 1.70 to 1.83 that is typical for Y2O3. All films are transparent in the investigated wavelength range 300-1200 nm. SEM results indicate that the microstructure of the films is changing with applied bias. Results indicate that it is possible to deposit single phase cubic Y2O3 thin films at low substrate temperature by RF plasma MOCVD process. RF self-bias that decides about the energy of impinging ions on the substrates plays an important role in controlling the texture of deposited Y2O3 films on the substrates. Results indicate that to control the structure of films and its texture, it is important to control the bias on the substrate during deposition. The films deposited at high bias level show degradation in the crystallinity and reduction of thickness.

SPICE Modeling of Body Bias Effect in 4H-SiC Integrated Circuit Resistors

NASA Technical Reports Server (NTRS)

Neudeck, Philip G.

2017-01-01

The DC electrical behavior of n-type 4H-SiC resistors used for realizing 500C durable integrated circuits (ICs) is studied as a function of substrate bias and temperature. Improved fidelity electrical simulation is described using SPICE NMOS model to simulate resistor substrate body bias effect that is absent from the SPICE semiconductor resistor model.

Synthesis and evaluation of a series of 6-chloro-4-methylumbelliferyl glycosides as fluorogenic reagents for screening metagenomic libraries for glycosidase activity.

PubMed

Chen, Hong-Ming; Armstrong, Zachary; Hallam, Steven J; Withers, Stephen G

2016-02-08

Screening of large enzyme libraries such as those derived from metagenomic sources requires sensitive substrates. Fluorogenic glycosides typically offer the best sensitivity but typically must be used in a stopped format to generate good signal. Use of fluorescent phenols of pKa < 7, such as halogenated coumarins, allows direct screening at neutral pH. The synthesis and characterisation of a set of nine different glycosides of 6-chloro-4-methylumbelliferone are described. The use of these substrates in a pooled format for screening of expressed metagenomic libraries yielded a "hit rate" of 1 in 60. Hits were then readily deconvoluted with the individual substrates in a single plate to identify specific activities within each clone. The use of such a collection of substrates greatly accelerates the screening process. Copyright © 2015 Elsevier Ltd. All rights reserved.

PEGylated substrates of NSP4 protease: A tool to study protease specificity

NASA Astrophysics Data System (ADS)

Wysocka, Magdalena; Gruba, Natalia; Grzywa, Renata; Giełdoń, Artur; Bąchor, Remigiusz; Brzozowski, Krzysztof; Sieńczyk, Marcin; Dieter, Jenne; Szewczuk, Zbigniew; Rolka, Krzysztof; Lesner, Adam

2016-03-01

Herein we present the synthesis of a novel type of peptidomimetics composed of repeating diaminopropionic acid residues modified with structurally diverse heterobifunctional polyethylene glycol chains (abbreviated as DAPEG). Based on the developed compounds, a library of fluorogenic substrates was synthesized. Further library deconvolution towards human neutrophil serine protease 4 (NSP4) yielded highly sensitive and selective internally quenched peptidomimetic substrates. In silico analysis of the obtained peptidomimetics revealed the presence of an interaction network with distant subsites located on the enzyme surface.

Substrate bias effects on composition and coercivity of CoCrTa/Cr thin films on canasite and glass

NASA Astrophysics Data System (ADS)

Deng, Y.; Lambeth, D. N.; Sui, X.; Lee, L.-L.; Laughlin, D. E.

1993-05-01

CoCrTa/Cr thin films were prepared by rf diode sputtering onto canasite and glass substrates at various bias voltages from two targets of different compositions (Co82.8Cr14.6Ta2.6 and Co86Cr12Ta2). While Auger depth profile analysis indicates that there is some broadening at the CoCrTa-Cr interface, x-ray fluorescence spectroscopy reveals that changes in alloy composition due to the resputtering processes are even more prominent. For both targets, as the substrate bias increases the Co content in the films declines, and the magnetization decreases. The maximum film coercivity appears to correlate to the final film composition. By investigating the results from both targets, it is concluded that the coercivity reaches a maximum when the film composition is in the neighborhood of Co84Cr13Ta3. Thus, to optimize the coercivity different bias voltages are required for each target. Excessive substrate bias, however, leads to films with low magnetization and coercivity.

Inclusion of Body Bias Effect in SPICE Modeling of 4H-SiC Integrated Circuit Resistors

NASA Technical Reports Server (NTRS)

Neudeck, Philip G.

2017-01-01

The DC electrical behavior of n-type 4H-SiC resistors used for realizing 500 degrees Celsius durable integrated circuits (ICs) is studied as a function of substrate bias and temperature. Improved fidelity electrical simulation is described using SPICE NMOS model to simulate resistor substrate body bias effect that is absent from the SPICE semiconductor resistor model.

Inclusion of Body-Bias Effect in SPICE Modeling of 4H-SiC Integrated Circuit Resistors

NASA Technical Reports Server (NTRS)

Neudeck, Philip G.

2017-01-01

The DC electrical behavior of n-type 4H-SiC resistors used for realizing 500 C durable integrated circuits (ICs) is studied as a function of substrate bias and temperature. Improved fidelity electrical simulation is described using SPICE NMOS model to simulate resistor substrate body bias effect that is absent from the SPICE semiconductor resistor model.

High throughput sequencing analysis of RNA libraries reveals the influences of initial library and PCR methods on SELEX efficiency.

PubMed

Takahashi, Mayumi; Wu, Xiwei; Ho, Michelle; Chomchan, Pritsana; Rossi, John J; Burnett, John C; Zhou, Jiehua

2016-09-22

The systemic evolution of ligands by exponential enrichment (SELEX) technique is a powerful and effective aptamer-selection procedure. However, modifications to the process can dramatically improve selection efficiency and aptamer performance. For example, droplet digital PCR (ddPCR) has been recently incorporated into SELEX selection protocols to putatively reduce the propagation of byproducts and avoid selection bias that result from differences in PCR efficiency of sequences within the random library. However, a detailed, parallel comparison of the efficacy of conventional solution PCR versus the ddPCR modification in the RNA aptamer-selection process is needed to understand effects on overall SELEX performance. In the present study, we took advantage of powerful high throughput sequencing technology and bioinformatics analysis coupled with SELEX (HT-SELEX) to thoroughly investigate the effects of initial library and PCR methods in the RNA aptamer identification. Our analysis revealed that distinct "biased sequences" and nucleotide composition existed in the initial, unselected libraries purchased from two different manufacturers and that the fate of the "biased sequences" was target-dependent during selection. Our comparison of solution PCR- and ddPCR-driven HT-SELEX demonstrated that PCR method affected not only the nucleotide composition of the enriched sequences, but also the overall SELEX efficiency and aptamer efficacy.

High throughput sequencing analysis of RNA libraries reveals the influences of initial library and PCR methods on SELEX efficiency

PubMed Central

Takahashi, Mayumi; Wu, Xiwei; Ho, Michelle; Chomchan, Pritsana; Rossi, John J.; Burnett, John C.; Zhou, Jiehua

2016-01-01

The systemic evolution of ligands by exponential enrichment (SELEX) technique is a powerful and effective aptamer-selection procedure. However, modifications to the process can dramatically improve selection efficiency and aptamer performance. For example, droplet digital PCR (ddPCR) has been recently incorporated into SELEX selection protocols to putatively reduce the propagation of byproducts and avoid selection bias that result from differences in PCR efficiency of sequences within the random library. However, a detailed, parallel comparison of the efficacy of conventional solution PCR versus the ddPCR modification in the RNA aptamer-selection process is needed to understand effects on overall SELEX performance. In the present study, we took advantage of powerful high throughput sequencing technology and bioinformatics analysis coupled with SELEX (HT-SELEX) to thoroughly investigate the effects of initial library and PCR methods in the RNA aptamer identification. Our analysis revealed that distinct “biased sequences” and nucleotide composition existed in the initial, unselected libraries purchased from two different manufacturers and that the fate of the “biased sequences” was target-dependent during selection. Our comparison of solution PCR- and ddPCR-driven HT-SELEX demonstrated that PCR method affected not only the nucleotide composition of the enriched sequences, but also the overall SELEX efficiency and aptamer efficacy. PMID:27652575

Heteroepitaxial growth of Pt and Au thin films on MgO single crystals by bias-assisted sputtering

DOE PAGES

Tolstova, Yulia; Omelchenko, Stefan T.; Shing, Amanda M.; ...

2016-03-17

The crystallographic orientation of a metal affects its surface energy and structure, and has profound implications for surface chemical reactions and interface engineering, which are important in areas ranging from optoelectronic device fabrication to catalysis. However, it can be very difficult and expensive to manufacture, orient, and cut single crystal metals along different crystallographic orientations, especially in the case of precious metals. One approach is to grow thin metal films epitaxially on dielectric substrates. In this work, we report on growth of Pt and Au films on MgO single crystal substrates of (100) and (110) surface orientation for use asmore » epitaxial templates for thin film photovoltaic devices. We develop bias-assisted sputtering for deposition of oriented Pt and Au films with sub-nanometer roughness. We show that biasing the substrate decreases the substrate temperature necessary to achieve epitaxial orientation, with temperature reduction from 600 to 350 °C for Au, and from 750 to 550 °C for Pt, without use of transition metal seed layers. Additionally, this temperature can be further reduced by reducing the growth rate. Biased deposition with varying substrate bias power and working pressure also enables control of the film morphology and surface roughness.« less

Collection Evaluation Techniques: A Short, Selective, Practical, Current, Annotated Bibliography, 1990-1998. RUSA Occasional Papers Number 24.

ERIC Educational Resources Information Center

Strohl, Bonnie, Comp.

This bibliography contains annotations of 110 journal articles on topics related to library collection evaluation techniques, including academic library collections, access-vs-ownership, "Books for College Libraries," business collections, the OCLC/AMIGOS Collection Analysis CD, circulation data, citation-checking, collection bias,…

Gas cushion control of OVJP print head position

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

Forrest, Stephen R

An OVJP apparatus and method for applying organic vapor or other flowable material to a substrate using a printing head mechanism in which the print head spacing from the substrate is controllable using a cushion of air or other gas applied between the print head and substrate. The print head is mounted for translational movement towards and away from the substrate and is biased toward the substrate by springs or other means. A gas cushion feed assembly supplies a gas under pressure between the print head and substrate which opposes the biasing of the print head toward the substrate somore » as to form a space between the print head and substrate. By controlling the pressure of gas supplied, the print head separation from the substrate can be precisely controlled.« less

Preparation of 24 ternary thin film materials libraries on a single substrate in one experiment for irreversible high-throughput studies.

PubMed

Buenconsejo, Pio John S; Siegel, Alexander; Savan, Alan; Thienhaus, Sigurd; Ludwig, Alfred

2012-01-09

For different areas of combinatorial materials science, it is desirable to have multiple materials libraries: especially for irreversible high-throughput studies, like, for example, corrosion resistance testing in different media or annealing of complete materials libraries at different temperatures. Therefore a new combinatorial sputter-deposition process was developed which yields 24 materials libraries in one experiment on a single substrate. It is discussed with the example of 24 Ti-Ni-Ag materials libraries. They are divided based on the composition coverage and orientation of composition gradient into two sets of 12 nearly identical materials libraries. Each materials library covers at least 30-40% of the complete ternary composition range. An acid etch test in buffered-HF solution was performed, illustrating the feasibility of our approach for destructive materials characterization. The results revealed that within the composition range of Ni < 30 at.%, the films were severely etched. The composition range which shows reversible martensitic transformations was confirmed to be outside this region. The high output of the present method makes it attractive for combinatorial studies requiring multiple materials libraries.

Surface Modification by Physical Vapour Deposition,

DTIC Science & Technology

1983-07-13

Fe) are used usually to a thickness of 20 to 106 micrometres [541. MCrAlY coatings are designed to produce protective scales of either A12 0 3 or...I on plating, 2 )Q bias-- e- D rnj I 88V bias --- pu terir -- A -Vcuum evaporation 10 - % 0 -, 0. 1 0- 1000- 9 .6 50-~N 10 10 0 10’ 101 106 Cycles...Library Hawker de Havilland Aust. Pty Ltd, Bankstown, Library Major Furnace and Combustion Engineers Pty Ltd, Manager Australian Institute of Petroleum

Improving RNA-Seq expression estimates by correcting for fragment bias

PubMed Central

2011-01-01

The biochemistry of RNA-Seq library preparation results in cDNA fragments that are not uniformly distributed within the transcripts they represent. This non-uniformity must be accounted for when estimating expression levels, and we show how to perform the needed corrections using a likelihood based approach. We find improvements in expression estimates as measured by correlation with independently performed qRT-PCR and show that correction of bias leads to improved replicability of results across libraries and sequencing technologies. PMID:21410973

Probe-Directed Degradation (PDD) for Flexible Removal of Unwanted cDNA Sequences from RNA-Seq Libraries.

PubMed

Archer, Stuart K; Shirokikh, Nikolay E; Preiss, Thomas

2015-04-01

Most applications for RNA-seq require the depletion of abundant transcripts to gain greater coverage of the underlying transcriptome. The sequences to be targeted for depletion depend on application and species and in many cases may not be supported by commercial depletion kits. This unit describes a method for generating RNA-seq libraries that incorporates probe-directed degradation (PDD), which can deplete any unwanted sequence set, with the low-bias split-adapter method of library generation (although many other library generation methods are in principle compatible). The overall strategy is suitable for applications requiring customized sequence depletion or where faithful representation of fragment ends and lack of sequence bias is paramount. We provide guidelines to rapidly design specific probes against the target sequence, and a detailed protocol for library generation using the split-adapter method including several strategies for streamlining the technique and reducing adapter dimer content. Copyright © 2015 John Wiley & Sons, Inc.

Substrate bias induced synthesis of flowered-like bunched carbon nanotube directly on bulk nickel

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

Bisht, Atul; Academy of Scientific and Innovative Research; Chockalingam, S.

2016-02-15

Highlights: • Flowered-like bunched MWCNTs have been synthesized by MW PECVD technique. • Effect of substrate bias on the properties of MWCNT has been studied. • Minimum E{sub T} = 1.9 V/μm with β = 4770 has been obtained in the film deposited at −350 V. - Abstract: This paper reports the effect of substrate bias on the multiwalled carbon nanotube (MWCNT) deposited on nickel foil by microwave plasma enhanced chemical vapor deposition technique. The MWCNTs have been characterized by the scanning electron microscopy (SEM), high resolution transmission electron microscopy (HRTEM), Raman spectroscopy, field emission and current–voltage characteristic of themore » heterojunction diode. The SEM images exhibit unique hierarchical flowered-like bunched and conformally coated MWCNTs. Substrate bias induced ion bombardment helps in the enhancement of hydrocarbon dissociation and is responsible for flowered-like MWCNTs growth. The HRTEM micrographs show the base growth mechanism for MWCNTs. The value of turn on field for emission decreases from 5.5 to 1.9 V/μm and field enhancement factor increases from 927 to 4770, respectively, with the increase of substrate bias. The diode ideality factor of CNT/ n-Si heterojunction is evaluated as 2.4 and the on/off current ratio is found to be 7 at ±2 V, respectively.« less

Everything You Need To Know about Bias Incidents. The Need To Know Library.

ERIC Educational Resources Information Center

Osborn, Kevin

Bias-related violence and harassment are increasing throughout the world. This book for children explores the causes and incidence of bias and also discusses what people are doing to defeat hatred and promote respect for the ways in which people differ. A bias incident or hate crime is any crime committed against a person because of his or her…

Design of a Selective Substrate and Activity Based Probe for Human Neutrophil Serine Protease 4

PubMed Central

Kasperkiewicz, Paulina; Poreba, Marcin; Snipas, Scott J.; Lin, S. Jack; Kirchhofer, Daniel; Salvesen, Guy S.; Drag, Marcin

2015-01-01

Human neutrophil serine protease 4 (NSP4), also known as PRSS57, is a recently discovered fourth member of the neutrophil serine proteases family. Although its biological function is not precisely defined, it is suggested to regulate neutrophil response and innate immune reactions. To create optimal substrates and visualization probes for NSP4 that distinguish it from other NSPs we have employed a Hybrid Combinatorial Substrate Library approach that utilizes natural and unnatural amino acids to explore protease subsite preferences. Library results were validated by synthesizing individual substrates, leading to the identification of an optimal substrate peptide. This substrate was converted to a covalent diphenyl phosphonate probe with an embedded biotin tag. This probe demonstrated high inhibitory activity and stringent specificity and may be suitable for visualizing NSP4 in the background of other NSPs. PMID:26172376

Altered Substrate Specificity of Drug-Resistant Human Immunodeficiency Virus Type 1 Protease

PubMed Central

Dauber, Deborah S.; Ziermann, Rainer; Parkin, Neil; Maly, Dustin J.; Mahrus, Sami; Harris, Jennifer L.; Ellman, Jon A.; Petropoulos, Christos; Craik, Charles S.

2002-01-01

Resistance to human immunodeficiency virus type 1 protease (HIV PR) inhibitors results primarily from the selection of multiple mutations in the protease region. Because many of these mutations are selected for the ability to decrease inhibitor binding in the active site, they also affect substrate binding and potentially substrate specificity. This work investigates the substrate specificity of a panel of clinically derived protease inhibitor-resistant HIV PR variants. To compare protease specificity, we have used positional-scanning, synthetic combinatorial peptide libraries as well as a select number of individual substrates. The subsite preferences of wild-type HIV PR determined by using the substrate libraries are consistent with prior reports, validating the use of these libraries to compare specificity among a panel of HIV PR variants. Five out of seven protease variants demonstrated subtle differences in specificity that may have significant impacts on their abilities to function in viral maturation. Of these, four variants demonstrated up to fourfold changes in the preference for valine relative to alanine at position P2 when tested on individual peptide substrates. This change correlated with a common mutation in the viral NC/p1 cleavage site. These mutations may represent a mechanism by which severely compromised, drug-resistant viral strains can increase fitness levels. Understanding the altered substrate specificity of drug-resistant HIV PR should be valuable in the design of future generations of protease inhibitors as well as in elucidating the molecular basis of regulation of proteolysis in HIV. PMID:11773410

The effect of substrate bias voltages on impact resistance of CrAlN coatings deposited by modified ion beam enhanced magnetron sputtering

NASA Astrophysics Data System (ADS)

Chunyan, Yu; Linhai, Tian; Yinghui, Wei; Shebin, Wang; Tianbao, Li; Bingshe, Xu

2009-01-01

CrAlN coatings were deposited on silicon and AISI H13 steel substrates using a modified ion beam enhanced magnetron sputtering system. The effect of substrate negative bias voltages on the impact property of the CrAlN coatings was studied. The X-ray diffraction (XRD) data show that all CrAlN coatings were crystallized in the cubic NaCl B1 structure, with the (1 1 1), (2 0 0) (2 2 0) and (2 2 2) diffraction peaks observed. Two-dimensional surface morphologies of CrAlN coatings were investigated by atomic force microscope (AFM). The results show that with increasing substrate bias voltage the coatings became more compact and denser, and the microhardness and fracture toughness of the coatings increased correspondingly. In the dynamic impact resistance tests, the CrAlN coatings displayed better impact resistance with the increase of bias voltage, due to the reduced emergence and propagation of the cracks in coatings with a very dense structure and the increase of hardness and fracture toughness in coatings.

Filtered cathodic arc deposition with ion-species-selective bias.

PubMed

Anders, André; Pasaja, Nitisak; Sansongsiri, Sakon

2007-06-01

A dual-cathode arc plasma source was combined with a computer-controlled bias amplifier to synchronize substrate bias with the pulsed production of plasma. In this way, bias can be applied in a material-selective way. The principle has been applied to the synthesis of metal-doped diamondlike carbon films, where the bias was applied and adjusted when the carbon plasma was condensing and the substrate was at ground when the metal was incorporated. In doing so, excessive sputtering by energetic metal ions can be avoided while the sp(3)sp(2) ratio can be adjusted. It is shown that the resistivity of the film can be tuned by this species-selective bias; Raman spectroscopy was used to confirm expected changes of the amorphous ta-C:Mo films. The species-selective bias principle could be extended to multiple material plasma sources and complex materials.

Application of High-Throughput Seebeck Microprobe Measurements on Thermoelectric Half-Heusler Thin Film Combinatorial Material Libraries.

PubMed

Ziolkowski, Pawel; Wambach, Matthias; Ludwig, Alfred; Mueller, Eckhard

2018-01-08

In view of the variety and complexity of thermoelectric (TE) material systems, combinatorial approaches to materials development come to the fore for identifying new promising compounds. The success of this approach is related to the availability and reliability of high-throughput characterization methods for identifying interrelations between materials structures and properties within the composition spread libraries. A meaningful characterization starts with determination of the Seebeck coefficient as a major feature of TE materials. Its measurement, and hence the accuracy and detectability of promising material compositions, may be strongly affected by thermal and electrical measurement conditions. This work illustrates the interrelated effects of the substrate material, the layer thickness, and spatial property distributions of thin film composition spread libraries, which are studied experimentally by local thermopower scans by means of the Potential and Seebeck Microprobe (PSM). The study is complemented by numerical evaluation. Material libraries of the half-Heusler compound system Ti-Ni-Sn were deposited on selected substrates (Si, AlN, Al 2 O 3 ) by magnetron sputtering. Assuming homogeneous properties of a film, significant decrease of the detected thermopower S m can be expected on substrates with higher thermal conductivity, yielding an underestimation of materials thermopower between 15% and 50%, according to FEM (finite element methods) simulations. Thermally poor conducting substrates provide a better accuracy with thermopower underestimates lower than 8%, but suffer from a lower spatial resolution. According to FEM simulations, local scanning of sharp thermopower peaks on lowly conductive substrates is linked to an additional deviation of the measured thermopower of up to 70% compared to homogeneous films, which is 66% higher than for corresponding cases on substrates with higher thermal conductivity of this study.

Field emission from bias-grown diamond thin films in a microwave plasma

DOEpatents

Gruen, Dieter M.; Krauss, Alan R.; Ding, Ming Q.; Auciello, Orlando

2002-01-01

A method of producing diamond or diamond like films in which a negative bias is established on a substrate with an electrically conductive surface in a microwave plasma chemical vapor deposition system. The atmosphere that is subjected to microwave energy includes a source of carbon, nitrogen and hydrogen. The negative bias is maintained on the substrate through both the nucleation and growth phase of the film until the film is continuous. Biases between -100V and -200 are preferred. Carbon sources may be one or more of CH.sub.4, C.sub.2 H.sub.2 other hydrocarbons and fullerenes.

Nanohardness and Residual Stress in TiN Coatings.

PubMed

Hernández, Luis Carlos; Ponce, Luis; Fundora, Abel; López, Enrique; Pérez, Eduardo

2011-05-17

TiN films were prepared by the Cathodic arc evaporation deposition method under different negative substrate bias. AFM image analyses show that the growth mode of biased coatings changes from 3D island to lateral when the negative bias potential is increased. Nanohardness of the thin films was measured by nanoindentation, and residual stress was determined using Grazing incidence X ray diffraction. The maximum value of residual stress is reached at -100 V substrate bias coinciding with the biggest values of adhesion and nanohardness. Nanoindentation measurement proves that the force-depth curve shifts due to residual stress. The experimental results demonstrate that nanohardness is seriously affected by the residual stress.

Controlled growth of aligned carbon nanotube using pulsed glow barrier discharge

NASA Astrophysics Data System (ADS)

Nozaki, Tomohiro; Kimura, Yoshihito; Okazaki, Ken

2002-10-01

We first achieved a catalytic growth of aligned carbon nanotube (CNT) using atmospheric pressure pulsed glow barrier discharge combined with DC bias (1000 V). Aligned CNT can grow with the directional electric field, and this is a big challenge in barrier discharges since dielectric barrier does not allow DC bias and forces to use AC voltage to maintain stable plasma conditions. To overcome this, we developed a power source generating Gaussian-shape pulses at 20 kpps with 4% duty, and DC bias was applied to the GND electrode where Ni-, Fe-coated substrate existed. With positive pulse, i.e. substrate was the cathode, random growth of CNT was observed at about 10^9 cm-2. Growth rate significantly reduced when applied negative pulse; Negative glow formation near substrate is essential for sufficient supply of radical species to the catalyst. If -DC was biased, aligned CNT with 20 nm was synthesized because negative bias enhanced negative glow formation. Interestingly, 2 to 3 CNTs stuck each other with +DC bias, resulting in 50-70 nm and non-aligned CNT. Atmospheric pressure glow barrier discharges can be highly controlled and be a potential alternative to vacuum plasmas for CVD, micro-scale, nano-scale fabrication.

Single-Point Mutation with a Rotamer Library Toolkit: Toward Protein Engineering.

PubMed

Pottel, Joshua; Moitessier, Nicolas

2015-12-28

Protein engineers have long been hard at work to harness biocatalysts as a natural source of regio-, stereo-, and chemoselectivity in order to carry out chemistry (reactions and/or substrates) not previously achieved with these enzymes. The extreme labor demands and exponential number of mutation combinations have induced computational advances in this domain. The first step in our virtual approach is to predict the correct conformations upon mutation of residues (i.e., rebuilding side chains). For this purpose, we opted for a combination of molecular mechanics and statistical data. In this work, we have developed automated computational tools to extract protein structural information and created conformational libraries for each amino acid dependent on a variable number of parameters (e.g., resolution, flexibility, secondary structure). We have also developed the necessary tool to apply the mutation and optimize the conformation accordingly. For side-chain conformation prediction, we obtained overall average root-mean-square deviations (RMSDs) of 0.91 and 1.01 Å for the 18 flexible natural amino acids within two distinct sets of over 3000 and 1500 side-chain residues, respectively. The commonly used dihedral angle differences were also evaluated and performed worse than the state of the art. These two metrics are also compared. Furthermore, we generated a family-specific library for kinases that produced an average 2% lower RMSD upon side-chain reconstruction and a residue-specific library that yielded a 17% improvement. Ultimately, since our protein engineering outlook involves using our docking software, Fitted/Impacts, we applied our mutation protocol to a benchmarked data set for self- and cross-docking. Our side-chain reconstruction does not hinder our docking software, demonstrating differences in pose prediction accuracy of approximately 2% (RMSD cutoff metric) for a set of over 200 protein/ligand structures. Similarly, when docking to a set of over 100 kinases, side-chain reconstruction (using both general and biased conformation libraries) had minimal detriment to the docking accuracy.

Peptide microarray analysis of substrate specificity of the transmembrane Ser/Thr kinase KPI-2 reveals reactivity with cystic fibrosis transmembrane conductance regulator and phosphorylase.

PubMed

Wang, Hong; Brautigan, David L

2006-11-01

Human lemur (Lmr) kinases are predicted to be Tyr kinases based on sequences and are related to neurotrophin receptor Trk kinases. This study used homogeneous recombinant KPI-2 (Lmr2, LMTK2, Cprk, brain-enriched protein kinase) kinase domain and a library of 1,154 peptides on a microarray to analyze substrate specificity. We found that KPI-2 is strictly a Ser/Thr kinase that reacts with Ser either preceded by or followed by Pro residues but unlike other Pro-directed kinases does not strictly require an adjacent Pro residue. The most reactive peptide in the library corresponds to Ser-737 of cystic fibrosis transmembrane conductance regulator, and the recombinant R domain of cystic fibrosis transmembrane conductance regulator was a preferred substrate. Furthermore the KPI-2 kinase phosphorylated peptides corresponding to the single site in phosphorylase and purified phosphorylase b, making this only the second known phosphorylase b kinase. Phosphorylase was used as a specific substrate to show that KPI-2 is inhibited in living cells by addition of nerve growth factor or serum. The results demonstrate the utility of the peptide library to probe specificity and discover kinase substrates and offer a specific assay that reveals hormonal regulation of the activity of this unusual transmembrane kinase.

Method and apparatus for sputtering utilizing an apertured electrode and a pulsed substrate bias

NASA Technical Reports Server (NTRS)

Przybyszewski, J. S.; Shaltens, R. K. (Inventor)

1973-01-01

The method and equipment used for sputtering by use of an apertured electrode and a pulsed substrate bias are discussed. The technique combines the advantages of ion plating with the versatility of a radio frequency sputtered source. Electroplating is accomplished by passing a pulsed high voltage direct current to the article being plated during radio frequency sputtering.

The heterogeneity statistic I(2) can be biased in small meta-analyses.

PubMed

von Hippel, Paul T

2015-04-14

Estimated effects vary across studies, partly because of random sampling error and partly because of heterogeneity. In meta-analysis, the fraction of variance that is due to heterogeneity is estimated by the statistic I(2). We calculate the bias of I(2), focusing on the situation where the number of studies in the meta-analysis is small. Small meta-analyses are common; in the Cochrane Library, the median number of studies per meta-analysis is 7 or fewer. We use Mathematica software to calculate the expectation and bias of I(2). I(2) has a substantial bias when the number of studies is small. The bias is positive when the true fraction of heterogeneity is small, but the bias is typically negative when the true fraction of heterogeneity is large. For example, with 7 studies and no true heterogeneity, I(2) will overestimate heterogeneity by an average of 12 percentage points, but with 7 studies and 80 percent true heterogeneity, I(2) can underestimate heterogeneity by an average of 28 percentage points. Biases of 12-28 percentage points are not trivial when one considers that, in the Cochrane Library, the median I(2) estimate is 21 percent. The point estimate I(2) should be interpreted cautiously when a meta-analysis has few studies. In small meta-analyses, confidence intervals should supplement or replace the biased point estimate I(2).

A novel ultra high-throughput 16S rRNA gene amplicon sequencing library preparation method for the Illumina HiSeq platform.

PubMed

de Muinck, Eric J; Trosvik, Pål; Gilfillan, Gregor D; Hov, Johannes R; Sundaram, Arvind Y M

2017-07-06

Advances in sequencing technologies and bioinformatics have made the analysis of microbial communities almost routine. Nonetheless, the need remains to improve on the techniques used for gathering such data, including increasing throughput while lowering cost and benchmarking the techniques so that potential sources of bias can be better characterized. We present a triple-index amplicon sequencing strategy to sequence large numbers of samples at significantly lower c ost and in a shorter timeframe compared to existing methods. The design employs a two-stage PCR protocol, incorpo rating three barcodes to each sample, with the possibility to add a fourth-index. It also includes heterogeneity spacers to overcome low complexity issues faced when sequencing amplicons on Illumina platforms. The library preparation method was extensively benchmarked through analysis of a mock community in order to assess biases introduced by sample indexing, number of PCR cycles, and template concentration. We further evaluated the method through re-sequencing of a standardized environmental sample. Finally, we evaluated our protocol on a set of fecal samples from a small cohort of healthy adults, demonstrating good performance in a realistic experimental setting. Between-sample variation was mainly related to batch effects, such as DNA extraction, while sample indexing was also a significant source of bias. PCR cycle number strongly influenced chimera formation and affected relative abundance estimates of species with high GC content. Libraries were sequenced using the Illumina HiSeq and MiSeq platforms to demonstrate that this protocol is highly scalable to sequence thousands of samples at a very low cost. Here, we provide the most comprehensive study of performance and bias inherent to a 16S rRNA gene amplicon sequencing method to date. Triple-indexing greatly reduces the number of long custom DNA oligos required for library preparation, while the inclusion of variable length heterogeneity spacers minimizes the need for PhiX spike-in. This design results in a significant cost reduction of highly multiplexed amplicon sequencing. The biases we characterize highlight the need for highly standardized protocols. Reassuringly, we find that the biological signal is a far stronger structuring factor than the various sources of bias.

Poisson Statistics of Combinatorial Library Sampling Predict False Discovery Rates of Screening

PubMed Central

2017-01-01

Microfluidic droplet-based screening of DNA-encoded one-bead-one-compound combinatorial libraries is a miniaturized, potentially widely distributable approach to small molecule discovery. In these screens, a microfluidic circuit distributes library beads into droplets of activity assay reagent, photochemically cleaves the compound from the bead, then incubates and sorts the droplets based on assay result for subsequent DNA sequencing-based hit compound structure elucidation. Pilot experimental studies revealed that Poisson statistics describe nearly all aspects of such screens, prompting the development of simulations to understand system behavior. Monte Carlo screening simulation data showed that increasing mean library sampling (ε), mean droplet occupancy, or library hit rate all increase the false discovery rate (FDR). Compounds identified as hits on k > 1 beads (the replicate k class) were much more likely to be authentic hits than singletons (k = 1), in agreement with previous findings. Here, we explain this observation by deriving an equation for authenticity, which reduces to the product of a library sampling bias term (exponential in k) and a sampling saturation term (exponential in ε) setting a threshold that the k-dependent bias must overcome. The equation thus quantitatively describes why each hit structure’s FDR is based on its k class, and further predicts the feasibility of intentionally populating droplets with multiple library beads, assaying the micromixtures for function, and identifying the active members by statistical deconvolution. PMID:28682059

Queering the Catalog: Queer Theory and the Politics of Correction

ERIC Educational Resources Information Center

Drabinski, Emily

2013-01-01

Critiques of hegemonic library classification structures and controlled vocabularies have a rich history in information studies. This project has pointed out the trouble with classification and cataloging decisions that are framed as objective and neutral but are always ideological and worked to correct bias in library structures. Viewing…

Design and isolation of ribozyme-substrate pairs using RNase P-based ribozymes containing altered substrate binding sites.

PubMed Central

Mobley, E M; Pan, T

1999-01-01

Substrate recognition and cleavage by the bacterial RNase P RNA requires two domains, a specificity domain, or S-domain, and a catalytic domain, or C-domain. The S-domain binds the T stem-loop region in a pre-tRNA substrate to confer specificity for tRNA substrates. In this work, the entire S-domain of the Bacillus subtilis RNase P RNA is replaced with an artificial substrate binding module. New RNA substrates are isolated by in vitro selection using two libraries containing random regions of 60 nt. At the end of the selection, the cleavage rates of the substrate library are approximately 0.7 min(-1)in 10 mM MgCl(2)at 37 degrees C, approximately 4-fold better than the cleavage of a pre-tRNA substrate by the wild-type RNase P RNA under the same conditions. The contribution of the S-domain replacement to the catalytic efficiency is from 6- to 22 000-fold. Chemical and nuclease mapping of two ribozyme-product complexes shows that this contribution correlates with direct interactions between the S-domain replacement and the selected substrate. These results demonstrate the feasibility of design and isolation of RNase P-based, matching ribozyme-substrate pairs without prior knowledge of the sequence or structure of the interactive modules in the ribozyme or substrate. PMID:10518624

Biased selection of propagation-related TUPs from phage display peptide libraries.

PubMed

Zade, Hesam Motaleb; Keshavarz, Reihaneh; Shekarabi, Hosna Sadat Zahed; Bakhshinejad, Babak

2017-08-01

Phage display is rapidly advancing as a screening strategy in drug discovery and drug delivery. Phage-encoded combinatorial peptide libraries can be screened through the affinity selection procedure of biopanning to find pharmaceutically relevant cell-specific ligands. However, the unwanted enrichment of target-unrelated peptides (TUPs) with no true affinity for the target presents an important barrier to the successful screening of phage display libraries. Propagation-related TUPs (Pr-TUPs) are an emerging but less-studied category of phage display-derived false-positive hits that are displayed on the surface of clones with faster propagation rates. Despite long regarded as an unbiased selection system, accumulating evidence suggests that biopanning may create biological bias toward selection of phage clones with certain displayed peptides. This bias can be dependent on or independent of the displayed sequence and may act as a major driving force for the isolation of fast-growing clones. Sequence-dependent bias is reflected by censorship or over-representation of some amino acids in the displayed peptide and sequence-independent bias is derived from either point mutations or rare recombination events occurring in the phage genome. It is of utmost interest to clean biopanning data by identifying and removing Pr-TUPs. Experimental and bioinformatic approaches can be exploited for Pr-TUP discovery. With no doubt, obtaining deeper insight into how Pr-TUPs emerge during biopanning and how they could be detected provides a basis for using cell-targeting peptides isolated from phage display screening in the development of disease-specific diagnostic and therapeutic platforms.

Image sensor with motion artifact supression and anti-blooming

NASA Technical Reports Server (NTRS)

Pain, Bedabrata (Inventor); Wrigley, Chris (Inventor); Yang, Guang (Inventor); Yadid-Pecht, Orly (Inventor)

2006-01-01

An image sensor includes pixels formed on a semiconductor substrate. Each pixel includes a photoactive region in the semiconductor substrate, a sense node, and a power supply node. A first electrode is disposed near a surface of the semiconductor substrate. A bias signal on the first electrode sets a potential in a region of the semiconductor substrate between the photoactive region and the sense node. A second electrode is disposed near the surface of the semiconductor substrate. A bias signal on the second electrode sets a potential in a region of the semiconductor substrate between the photoactive region and the power supply node. The image sensor includes a controller that causes bias signals to be provided to the electrodes so that photocharges generated in the photoactive region are accumulated in the photoactive region during a pixel integration period, the accumulated photocharges are transferred to the sense node during a charge transfer period, and photocharges generated in the photoactive region are transferred to the power supply node during a third period without passing through the sense node. The imager can operate at high shutter speeds with simultaneous integration of pixels in the array. High quality images can be produced free from motion artifacts. High quantum efficiency, good blooming control, low dark current, low noise and low image lag can be obtained.

High speed CMOS imager with motion artifact supression and anti-blooming

NASA Technical Reports Server (NTRS)

Pain, Bedabrata (Inventor); Wrigley, Chris (Inventor); Yang, Guang (Inventor); Yadid-Pecht, Orly (Inventor)

2001-01-01

An image sensor includes pixels formed on a semiconductor substrate. Each pixel includes a photoactive region in the semiconductor substrate, a sense node, and a power supply node. A first electrode is disposed near a surface of the semiconductor substrate. A bias signal on the first electrode sets a potential in a region of the semiconductor substrate between the photoactive region and the sense node. A second electrode is disposed near the surface of the semiconductor substrate. A bias signal on the second electrode sets a potential in a region of the semiconductor substrate between the photoactive region and the power supply node. The image sensor includes a controller that causes bias signals to be provided to the electrodes so that photocharges generated in the photoactive region are accumulated in the photoactive region during a pixel integration period, the accumulated photocharges are transferred to the sense node during a charge transfer period, and photocharges generated in the photoactive region are transferred to the power supply node during a third period without passing through the sense node. The imager can operate at high shutter speeds with simultaneous integration of pixels in the array. High quality images can be produced free from motion artifacts. High quantum efficiency, good blooming control, low dark current, low noise and low image lag can be obtained.

Subtraction of cap-trapped full-length cDNA libraries to select rare transcripts.

PubMed

Hirozane-Kishikawa, Tomoko; Shiraki, Toshiyuki; Waki, Kazunori; Nakamura, Mari; Arakawa, Takahiro; Kawai, Jun; Fagiolini, Michela; Hensch, Takao K; Hayashizaki, Yoshihide; Carninci, Piero

2003-09-01

The normalization and subtraction of highly expressed cDNAs from relatively large tissues before cloning dramatically enhanced the gene discovery by sequencing for the mouse full-length cDNA encyclopedia, but these methods have not been suitable for limited RNA materials. To normalize and subtract full-length cDNA libraries derived from limited quantities of total RNA, here we report a method to subtract plasmid libraries excised from size-unbiased amplified lambda phage cDNA libraries that avoids heavily biasing steps such as PCR and plasmid library amplification. The proportion of full-length cDNAs and the gene discovery rate are high, and library diversity can be validated by in silico randomization.

Capturing the 'ome': the expanding molecular toolbox for RNA and DNA library construction.

PubMed

Boone, Morgane; De Koker, Andries; Callewaert, Nico

2018-04-06

All sequencing experiments and most functional genomics screens rely on the generation of libraries to comprehensively capture pools of targeted sequences. In the past decade especially, driven by the progress in the field of massively parallel sequencing, numerous studies have comprehensively assessed the impact of particular manipulations on library complexity and quality, and characterized the activities and specificities of several key enzymes used in library construction. Fortunately, careful protocol design and reagent choice can substantially mitigate many of these biases, and enable reliable representation of sequences in libraries. This review aims to guide the reader through the vast expanse of literature on the subject to promote informed library generation, independent of the application.

Optimal estimation of diffusion coefficients from single-particle trajectories

NASA Astrophysics Data System (ADS)

Vestergaard, Christian L.; Blainey, Paul C.; Flyvbjerg, Henrik

2014-02-01

How does one optimally determine the diffusion coefficient of a diffusing particle from a single-time-lapse recorded trajectory of the particle? We answer this question with an explicit, unbiased, and practically optimal covariance-based estimator (CVE). This estimator is regression-free and is far superior to commonly used methods based on measured mean squared displacements. In experimentally relevant parameter ranges, it also outperforms the analytically intractable and computationally more demanding maximum likelihood estimator (MLE). For the case of diffusion on a flexible and fluctuating substrate, the CVE is biased by substrate motion. However, given some long time series and a substrate under some tension, an extended MLE can separate particle diffusion on the substrate from substrate motion in the laboratory frame. This provides benchmarks that allow removal of bias caused by substrate fluctuations in CVE. The resulting unbiased CVE is optimal also for short time series on a fluctuating substrate. We have applied our estimators to human 8-oxoguanine DNA glycolase proteins diffusing on flow-stretched DNA, a fluctuating substrate, and found that diffusion coefficients are severely overestimated if substrate fluctuations are not accounted for.

Near-zero IR transmission of VO2 thin films deposited on Si substrate

NASA Astrophysics Data System (ADS)

Zhang, Chunzi; Koughia, Cyril; Li, Yuanshi; Cui, Xiaoyu; Ye, Fan; Shiri, Sheida; Sanayei, Mohsen; Wen, Shi-Jie; Yang, Qiaoqin; Kasap, Safa

2018-05-01

Vanadium dioxide (VO2) thin films of different thickness have been deposited on Si substrates by using DC magnetron sputtering. The effects of substrate pre-treatment by means of seeding (spin coating and ultrasonic bathing) and biasing on the structure and optical properties were investigated. Seeding results in a smaller grain size in the oxide film, whereas biasing results in square-textured crystals. VO2 thin films of 150 nm thick show a near-zero IR transmission in switched state. Especially, the 150 nm thick VO2 thin film with seeding treatment shows an enhanced switching efficiency.

Randomization Methods in Emergency Setting Trials: A Descriptive Review

ERIC Educational Resources Information Center

Corbett, Mark Stephen; Moe-Byrne, Thirimon; Oddie, Sam; McGuire, William

2016-01-01

Background: Quasi-randomization might expedite recruitment into trials in emergency care settings but may also introduce selection bias. Methods: We searched the Cochrane Library and other databases for systematic reviews of interventions in emergency medicine or urgent care settings. We assessed selection bias (baseline imbalances) in prognostic…

Influence of substrate bias voltage on the properties of TiO2 deposited by radio-frequency magnetron sputtering on 304L for biomaterials applications

NASA Astrophysics Data System (ADS)

Bait, L.; Azzouz, L.; Madaoui, N.; Saoula, N.

2017-02-01

The aim of this paper is to investigate the effect of the substrate bias, varied from 0 to -100 V, on the structure and properties of the TiO2 thin films for biomaterials applications. The TiO2 films were grown onto 304L stainless steel substrate using radio-frequency (rf) magnetron sputtering from a pure titanium target in Ar-O2 gas mixture. The variation of substrate bias voltage from 0 to -100 V produces variations of structure and mechanical properties of the films. The deposited films were characterized by X-rays diffraction, nanoindentation and potentiodynamic polarization. Also, the friction and wear properties of TiO2 films sliding against alumina ball in air were investigated. Experimental results showed that the thickness increases for non-biased substrate voltage to Vs = -100 V from 820 nm to 1936 nm respectively. The roughness is in the range of 50 nm and 14 nm. XRD results show that all structures of the films are crystalline and changed with varying the bias voltage. The anatase phase is predominant in the low negative bias range (0-50 V). The hardness significantly increased from 2.2 to 6.4 GPa when the bias voltage was increased from 0 to 75 V and then slightly decrease to 5.1 GPa as further increased to 100 V. At the same time, the results indicate that TiO2 films deposited at -100 V exhibited better wear resistance compared to the other samples, i.e. the minimum wear rates and the lower coefficient of friction of 0.16. In order to simulate natural biological conditions, physiological serum (pH = 6.3), thermostatically controlled at 37 °C, was used as the electrolyte for the study of the electrochemical properties. Comparison between the corrosion resistance of the uncoated and coated samples showed a reduction in corrosion current density for coated samples compared to the uncoated one. The best corrosion current density of the film deposited at -75 V was 5.9 nA/cm2, which is about 11 times less than that of the uncoated steel 68.3 nA/cm2). The optimum anti-corrosion performance and hardness was obtained for TiO2 deposited at a bias of-75 V.

Identification and removal of low-complexity sites in allele-specific analysis of ChIP-seq data.

PubMed

Waszak, Sebastian M; Kilpinen, Helena; Gschwind, Andreas R; Orioli, Andrea; Raghav, Sunil K; Witwicki, Robert M; Migliavacca, Eugenia; Yurovsky, Alisa; Lappalainen, Tuuli; Hernandez, Nouria; Reymond, Alexandre; Dermitzakis, Emmanouil T; Deplancke, Bart

2014-01-15

High-throughput sequencing technologies enable the genome-wide analysis of the impact of genetic variation on molecular phenotypes at unprecedented resolution. However, although powerful, these technologies can also introduce unexpected artifacts. We investigated the impact of library amplification bias on the identification of allele-specific (AS) molecular events from high-throughput sequencing data derived from chromatin immunoprecipitation assays (ChIP-seq). Putative AS DNA binding activity for RNA polymerase II was determined using ChIP-seq data derived from lymphoblastoid cell lines of two parent-daughter trios. We found that, at high-sequencing depth, many significant AS binding sites suffered from an amplification bias, as evidenced by a larger number of clonal reads representing one of the two alleles. To alleviate this bias, we devised an amplification bias detection strategy, which filters out sites with low read complexity and sites featuring a significant excess of clonal reads. This method will be useful for AS analyses involving ChIP-seq and other functional sequencing assays. The R package abs filter for library clonality simulations and detection of amplification-biased sites is available from http://updepla1srv1.epfl.ch/waszaks/absfilter

Examining the Presidential Libraries: Students Find Biases and Recommend a Multicultural Perspective

ERIC Educational Resources Information Center

Baptiste, H. Prentice; Townsend, Katie

2008-01-01

The primary focus of research that the authors have undertaken at New Mexico State University for the past several years can be summed up with the question--are Presidential Libraries educational institutions or are they simply political monuments and messages? The authors have conducted extensive investigations involving visitations to ten…

Impact of library preparation protocols and template quantity on the metagenomic reconstruction of a mock microbial community

DOE PAGES

Bowers, Robert M.; Clum, Alicia; Tice, Hope; ...

2015-10-24

Background: The rapid development of sequencing technologies has provided access to environments that were either once thought inhospitable to life altogether or that contain too few cells to be analyzed using genomics approaches. While 16S rRNA gene microbial community sequencing has revolutionized our understanding of community composi tion and diversity over time and space, it only provides a crude estimate of microbial functional and metabolic potential. Alternatively, shotgun metagenomics allows comprehensive sampling of all genetic material in an environment, without any underlying primer biases. Until recently, one of the major bottlenecks of shotgun metagenomics has been the requirement for largemore » initial DNA template quantities during library preparation. Results: Here, we investigate the effects of varying template concentrations across three low biomass library preparation protocols on their ability to accurately reconstruct a mock microbial community of known composition. We analyze the effects of input DNA quantity and library preparation method on library insert size, GC content, community composition, assembly quality and metagenomic binning. We found that library preparation method and the amount of starting material had significant impacts on the mock community metagenomes. In particular, GC content shifted towards more GC rich sequences at the lower input quantities regardless of library prep method, the number of low quality reads that could not be mapped to the reference genomes increased with decreasing input quantities, and the different library preparation methods had an impact on overall metagenomic community composition. Conclusions: This benchmark study provides recommendations for library creation of representative and minimally biased metagenome shotgun sequencing, enabling insights into functional attributes of low biomass ecosystem microbial communities.« less

Impact of library preparation protocols and template quantity on the metagenomic reconstruction of a mock microbial community

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

Bowers, Robert M.; Clum, Alicia; Tice, Hope

Background: The rapid development of sequencing technologies has provided access to environments that were either once thought inhospitable to life altogether or that contain too few cells to be analyzed using genomics approaches. While 16S rRNA gene microbial community sequencing has revolutionized our understanding of community composi tion and diversity over time and space, it only provides a crude estimate of microbial functional and metabolic potential. Alternatively, shotgun metagenomics allows comprehensive sampling of all genetic material in an environment, without any underlying primer biases. Until recently, one of the major bottlenecks of shotgun metagenomics has been the requirement for largemore » initial DNA template quantities during library preparation. Results: Here, we investigate the effects of varying template concentrations across three low biomass library preparation protocols on their ability to accurately reconstruct a mock microbial community of known composition. We analyze the effects of input DNA quantity and library preparation method on library insert size, GC content, community composition, assembly quality and metagenomic binning. We found that library preparation method and the amount of starting material had significant impacts on the mock community metagenomes. In particular, GC content shifted towards more GC rich sequences at the lower input quantities regardless of library prep method, the number of low quality reads that could not be mapped to the reference genomes increased with decreasing input quantities, and the different library preparation methods had an impact on overall metagenomic community composition. Conclusions: This benchmark study provides recommendations for library creation of representative and minimally biased metagenome shotgun sequencing, enabling insights into functional attributes of low biomass ecosystem microbial communities.« less

Error Analysis of Deep Sequencing of Phage Libraries: Peptides Censored in Sequencing

PubMed Central

Matochko, Wadim L.; Derda, Ratmir

2013-01-01

Next-generation sequencing techniques empower selection of ligands from phage-display libraries because they can detect low abundant clones and quantify changes in the copy numbers of clones without excessive selection rounds. Identification of errors in deep sequencing data is the most critical step in this process because these techniques have error rates >1%. Mechanisms that yield errors in Illumina and other techniques have been proposed, but no reports to date describe error analysis in phage libraries. Our paper focuses on error analysis of 7-mer peptide libraries sequenced by Illumina method. Low theoretical complexity of this phage library, as compared to complexity of long genetic reads and genomes, allowed us to describe this library using convenient linear vector and operator framework. We describe a phage library as N × 1 frequency vector n = ||ni||, where ni is the copy number of the ith sequence and N is the theoretical diversity, that is, the total number of all possible sequences. Any manipulation to the library is an operator acting on n. Selection, amplification, or sequencing could be described as a product of a N × N matrix and a stochastic sampling operator (S a). The latter is a random diagonal matrix that describes sampling of a library. In this paper, we focus on the properties of S a and use them to define the sequencing operator (S e q). Sequencing without any bias and errors is S e q = S a IN, where IN is a N × N unity matrix. Any bias in sequencing changes IN to a nonunity matrix. We identified a diagonal censorship matrix (C E N), which describes elimination or statistically significant downsampling, of specific reads during the sequencing process. PMID:24416071

Effects of bias voltage on diamond like carbon coatings deposited using titanium isopropoxide (TIPOT) and acetylene/argon mixtures onto various substrate materials.

PubMed

Said, R; Ghumman, C A A; Teodoro, M N D; Ahmed, W; Abuazza, A; Gracio, J

2010-04-01

RF-PECVD was used to prepare amorphous of carbon (DLC) onto stainless steel 316 and glass substrates. The substrates were negatively biased at between 100 V to 400 V. Thin films of DLC have been deposited using C2H2 and titanium isopropoxide (TIPOT). Argon was used to generate the plasma in the PECVD system chamber. DEKTAK 8 surface stylus profilometer was used to measure the film thickness and the deposition rate was calculated. Micro Raman spectroscopy was employed to determine the chemical structure and bonding present in the films. Composition analysis of the samples was carried out using VGTOF SIMS (IX23LS) instrument. In addition, X-ray photoelectron spectroscopy (XPS) was used to analyze the composition and chemical state of the films. The wettability of the films was examined using the optical contact angle meter (CAM200) system. Two types of liquids with different polarities were used to study changes in the surface energy. The as-grown films were in the thickness range of 200-400 nm. Raman spectroscopy results showed that the I(D)/I(G) ratio decreased when the bias voltage on the stainless steel substrates was increased. This indicates an increase in the graphitic nature of the film deposited. In contrast, on the glass substrates the I(D)/I(G) ratio increased when the bias voltage was increased indicates a greater degree of diamond like character. Chemical composition determined using XPS showed the presence of carbon and oxygen in both samples on glass and stainless steel substrates. Both coatings the contact angle of the films decreased except for 400 V which showed a slight increase. The oxygen is thought to play an important role on the polar component of a-C.

Partially Ionized Beam Deposition of Silicon-Dioxide and Aluminum Thin Films - Defects Generation.

NASA Astrophysics Data System (ADS)

Wong, Justin Wai-Chow

1987-09-01

Detect formation in SiO_2 and Al thin films and interfaces were studied using a partially ionized beam (PIB) deposition technique. The evaporated species (the deposition material) were partially ionized to give an ion/atom ratio of <=q0.1% and the substrate was biased at 0-5kV during the deposition. The results suggest that due to the ion bombardment, stoichiometric SiO_2 films can be deposited at a low substrate temperature (~300 ^circC) and low oxygen pressure (<=q10^{-4} Torr). Such deposition cannot be achieved using conventional evaporation-deposition techniques. However, traps and mobile ions were observed in the oxide and local melt-down was observed when a sufficiently high electric field was applied to the film. For the PIB Al deposition on the Si substrate, stable Al/Si Schottky contact was formed when the substrate bias was <=q1kV. For a substrate bias of 2.5kV, the capacitance of the Al/Si interface increased dramatically. A model of self-ion implantation with a p-n junction created by the Al^+ ion implantation was proposed and tested to explain the increase of the interface capacitance. Several deep level states at the Al/Si interface were observed using Deep Level Transient Spectroscopy (DLTS) technique when the film was deposited at a bias of 3kV. The PIB Al films deposited on the Si substrate showed unusually strong electromigration resistance under high current density operation. This phenomenon was explained by the highly oriented microstructure of the Al films created by the self-ion bombardment during deposition. These findings show that PIB has potential applications in a number of areas, including low temperature thin film deposition, and epitaxial growth of thin films in the microelectronics thin film industry.

High-voltage compatible, full-depleted CCD

DOEpatents

Holland, Stephen Edward

2007-09-18

A charge coupled device for detecting electromagnetic and particle radiation is described. The device includes a high-resistivity semiconductor substrate, buried channel regions, gate electrode circuitry, and amplifier circuitry. For good spatial resolution and high performance, especially when operated at high voltages with full or nearly full depletion of the substrate, the device can also include a guard ring positioned near channel regions, a biased channel stop, and a biased polysilicon electrode over the channel stop.

Mechanical and tribological properties of crystalline aluminum nitride coatings deposited on stainless steel by magnetron sputtering

NASA Astrophysics Data System (ADS)

Choudhary, R. K.; Mishra, S. C.; Mishra, P.; Limaye, P. K.; Singh, K.

2015-11-01

Aluminum nitride (AlN) coating is a potential candidate for addressing the problems of MHD pressure drop, tritium permeation and liquid metal corrosion of the test blanket module of fusion reactor. In this work, AlN coatings were grown on stainless steel by magnetron sputtering. Grazing incidence X-ray diffraction measurement revealed that formation of mixed phase (wurtzite and rock salt) AlN was favored at low discharge power and substrate negative biasing. However, at sufficiently high discharge power and substrate bias, (100) oriented wurtzite AlN was obtained. Secondary ion mass spectroscopy showed presence of oxygen in the coatings. The highest value of hardness and Young's modulus were 14.1 GPa and 215 GPa, respectively. Scratch test showed adhesive failure at a load of about 20 N. Wear test showed improved wear resistance of the coatings obtained at higher substrate bias.

Charge movement in a GaN-based hetero-structure field effect transistor structure with carbon doped buffer under applied substrate bias

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

Pooth, Alexander, E-mail: a.pooth@bristol.ac.uk; IQE; Uren, Michael J.

2015-12-07

Charge trapping and transport in the carbon doped GaN buffer of a GaN-based hetero-structure field effect transistor (HFET) has been investigated under both positive and negative substrate bias. Clear evidence of redistribution of charges in the carbon doped region by thermally generated holes is seen, with electron injection and capture observed during positive bias. Excellent agreement is found with simulations. It is shown that these effects are intrinsic to the carbon doped GaN and need to be controlled to provide reliable and efficient GaN-based power HFETs.

An XPS study of the adherence of refractory carbide, silicide, and boride RF-sputtered wear-resistant coatings. [X-ray Photoelectron Spectroscopy of steel surfaces

NASA Technical Reports Server (NTRS)

Brainard, W. A.; Wheeler, D. R.

1978-01-01

Radio frequency sputtering was used to deposit refractory carbide, silicide, and boride coatings on 440-C steel substrates. Both sputter etched and pre-oxidized substrates were used and the films were deposited with and without a substrate bias. The composition of the coatings was determined as a function of depth by X-ray photoelectron spectroscopy combined with argon ion etching. Friction and wear tests were conducted to evaluate coating adherence. In the interfacial region there was evidence that bias may produce a graded interface for some compounds. Biasing, while generally improving bulk film stoichiometry, can adversely affect adherence by removing interfacial oxide layers. Oxides of all film constituents except carbon and iron were present in all cases but the iron oxide coverage was only complete on the preoxidized substrates. The film and iron oxides were mixed in the MoSi2 and Mo2C films but layered in the Mo2B5 films. In the case of mixed oxides, preoxidation enhanced film adherence. In the layered case it did not.

A room temperature strategy towards enhanced performance and bias stability of oxide thin film transistor with a sandwich structure channel layer

NASA Astrophysics Data System (ADS)

Zeng, Yong; Ning, Honglong; Zheng, Zeke; Zhang, Hongke; Fang, Zhiqiang; Yao, Rihui; Xu, Miao; Wang, Lei; Lan, Linfeng; Peng, Junbiao; Lu, Xubing

2017-04-01

Thermal annealing is a conventional and effective way to improve the bias stress stability of oxide thin film transistors (TFT) on solid substrates. However, it is still a challenge for enhancing the bias stress stability of oxide TFTs on flexible substrates by high-temperature post-treatment due to the thermal sensitivity of flexible substrates. Here, a room temperature strategy is presented towards enhanced performance and bias stability of oxide TFTs by intentionally engineering a sandwich structure channel layer consisting of a superlattice with aluminum doped zinc oxide (AZO) and Al2O3 thin films. The Al2O3/AZO/Al2O3-TFTs not only exhibit a saturation mobility of 9.27 cm2 V-1 s-1 and a linear mobility of 11.38 cm2 V-1 s-1 but also demonstrate a better bias stress stability than AZO/Al2O3-TFT. Moreover, the underlying mechanism of this enhanced electrical performance of TFTs with a sandwich structure channel layer is that the bottom Al2O3 thin films can obviously improve the crystalline phase of AZO films while decreasing electrical trapping centers and adsorption sites for undesirable molecules such as water and oxygen.

Method and apparatus for increasing resistance of bipolar buried layer integrated circuit devices to single-event upsets

NASA Technical Reports Server (NTRS)

Zoutendyk, John A. (Inventor)

1991-01-01

Bipolar transistors fabricated in separate buried layers of an integrated circuit chip are electrically isolated with a built-in potential barrier established by doping the buried layer with a polarity opposite doping in the chip substrate. To increase the resistance of the bipolar transistors to single-event upsets due to ionized particle radiation, the substrate is biased relative to the buried layer with an external bias voltage selected to offset the built-in potential just enough (typically between about +0.1 to +0.2 volt) to prevent an accumulation of charge in the buried-layer-substrate junction.

The properties and performance of moisture/oxygen barrier layers deposited by remote plasma sputtering

NASA Astrophysics Data System (ADS)

Brown, Hayley Louise

The development of flexible lightweight OLED devices requires oxygen/moisture barrier layer thin films with water vapour transmission rates (WVTR) of < 10-6 g/m2/day. This thesis reports on single and multilayer architecture barrier layers (mostly based on SiO2, Al2O3 and TiO2) deposited onto glass, Si and polymeric substrates using remote plasma sputtering. The reactive sputtering depositions were performed on Plasma Quest S500 based sputter systems and the morphology, nanostructure and composition of the coatings have been examined using SEM, EDX, STEM, XPS, XRD and AFM. The WVTR has been determined using industry standard techniques (e.g. MOCON) but, for rapid screening of the deposited layers, an in-house permeation test was also developed. SEM, XRD and STEM results showed that the coatings exhibited a dense, amorphous structure with no evidence of columnar growth. However, all of the single and multilayer coatings exhibited relatively poor WVTRs of > 1 x 10-1 g/m2/day at 38 °C and 85 % RH. Further characterisation indicated that the barrier films were failing due to the presence of substrate asperities and airborne particulates. Different mechanisms were investigated in an attempt to reduce the density of film defects including incorporation of a getter layer, modification of growth kinetics, plasma treatment and polymer planarising, but none were successful in lowering the WVTR. Review of this issue indicated that the achievement of good barrier layers was likely to be problematic in commercial practice due to the cost implications of adequately reducing particulate density and the need to cover deliberately non-planar surfaces and fabricated 3D structures. Conformal coverage would therefore be required to bury surface structures and to mitigate particulate issues. Studies of the remote plasma system showed that it both inherently delivered an ionised physical vapour deposition (IPVD) process and was compatible with bias re-sputtering of substrates. Accordingly, a process using RF substrate bias to conformally coat surfaces was developed to encapsulate surface particulates and seal associated permeation paths. An order of magnitude improvement in WVTR (6.7 x 10-2 g/m2/day) was measured for initial Al2O3 coatings deposited with substrate bias. The development of substrate bias to enhance conformal coverage provides significant new commercial benefit. Furthermore, conformal coverage of 5:1 aspect ratio structures have been demonstrated by alternating the substrate bias between -222 V and -267 V, with a 50 % dwell time at each voltage. Further development and optimisation of the substrate bias technique is required to fully explore the potential for further improving barrier properties and conformal coverage of high aspect ratio and other 3D structures.

Modeling liquid organic thin films on substrates

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

Bernacki, Bruce E.; Johnson, Timothy J.; Myers, Tanya L.

We present the rationale, methods, and results of modeling of thin film organic liquids on various substrates. These liquids may coat surfaces (substrates) either as a result of their production, dispersal via aerosols or spills. Identification of unknown coated surfaces using either reflectance or emittance spectroscopy cannot be accomplished simply through reference to reflectance signature libraries since neither the thickness of the liquid layer nor the substrate type is known beforehand and both contribute to the signature. Liquid spectral libraries offer the complex index of refraction (n,k) as a function of wavelength which by itself is useful only for thickmore » (bulk) liquid layers via computation of reflectance and transmittance coefficients using the Fresnel equations. Thin liquid layers both reflect and refract incident light in combination with reflectance from the substrate. We show modeling of various organic liquids on substrates using commercial thin film design and modeling software, as well as Monte Carlo ray tracing software to demonstrate the variety of potential signatures encountered that depend on the thickness of the liquid layer as well as the characteristics of the substrate (metal or dielectric). These substrates give rise to transflectance behavior, while many dielectric substrates have rich absorption features that provide complex signatures that combine attributes of both the liquid and the substrate. Knowledge of the complex index of refraction of both target liquids and substrates is essential in order to synthesize spectra necessary in the application of target identification algorithms.« less

Apparatus and method for selective area deposition of thin films on electrically biased substrates

DOEpatents

Zuhr, R.A.; Haynes, T.E.; Golanski, A.

1994-10-11

An ion beam deposition process for selective area deposition on a polarized substrate uses a potential applied to the substrate which allows the ionized particles to reach into selected areas for film deposition. Areas of the substrate to be left uncoated are held at a potential that repels the ionized particles. 3 figs.

Apparatus and method for selective area deposition of thin films on electrically biased substrates

DOEpatents

Zuhr, R.A.; Haynes, T.E.; Golanski, A.

1999-06-08

An ion beam deposition process for selective area deposition on a polarized substrate uses a potential applied to the substrate which allows the ionized particles to reach into selected areas for film deposition. Areas of the substrate to be left uncoated are held at a potential that repels the ionized particles. 3 figs.

Apparatus and method for selective area deposition of thin films on electrically biased substrates

DOEpatents

Zuhr, Raymond A.; Haynes, Tony E.; Golanski, Andrzej

1999-01-01

An ion beam deposition process for selective area deposition on a polarized substrate uses a potential applied to the substrate which allows the ionized particles to reach into selected areas for film deposition. Areas of the substrate to be left uncoated are held at a potential that repells the ionized particles.

Apparatus and method for selective area deposition of thin films on electrically biased substrates

DOEpatents

Zuhr, Raymond A.; Haynes, Tony E.; Golanski, Andrzej

1994-01-01

An ion beam deposition process for selective area deposition on a polarized substrate uses a potential applied to the substrate which allows the ionized particles to reach into selected areas for film deposition. Areas of the substrate to be left uncoated are held at a potential that repells the ionized particles.

Immune Antibody Libraries: Manipulating The Diverse Immune Repertoire for Antibody Discovery.

PubMed

Lim, Theam Soon; Chan, Soo Khim

2016-01-01

Antibody phage display is highly dependent on the availability of antibody libraries. There are several forms of libraries depending mainly on the origin of the source materials. There are three major classes of libraries, mainly the naïve, immune and synthetic libraries. Immune antibody libraries are designed to isolate specific and high affinity antibodies against disease antigens. The pre-exposure of the host to an infection results in the production of a skewed population of antibodies against the particular infection. This characteristic takes advantage of the in vivo editing machinery to generate bias and specific immune repertoire. The skewed but diverse repertoire of immune libraries has been adapted successfully in the generation of antibodies against a wide range of diseases. We envisage immune antibody libraries to play a greater role in the discovery of antibodies for diseases in the near future. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Optimization of exchange bias in Co/CoO magnetic nanocaps by tuning deposition parameters

NASA Astrophysics Data System (ADS)

Sharma, A.; Tripathi, J.; Ugochukwu, K. C.; Tripathi, S.

2017-03-01

In the present work, we report exchange bias tuning by varying thin film deposition parameters such as synthesis method and underlying layer patterning. The patterned substrates for this study were prepared by self-assembly of polystyrene (PS) latex spheres ( 530 nm) on Si (100) substrate. The desired magnetic nanocaps composed of CoO/Co bilayer film on these patterned substrates were prepared by molecular beam epitaxy technique under ultra-high vacuum conditions. For this, a Co layer of 10 nm thickness was deposited on the substrates and then oxidized in-situ to form CoO/Co/PS in-situ oxidized film or ex-situ in ambiance which also gives CoO/Co/PS naturally oxidized film. Simultaneously, reference thin films of Co ( 10 nm) were also prepared on plane Si substrate and similar oxidation treatments were performed on them respectively. The magnetic properties studied using SQUID technique revealed higher exchange bias ( 1736 Oe) in the in-situ oxidized Co/PS film as compared to that in naturally oxidized Co/PS film ( 1544 Oe) and also compared to the reference film. The observed variations in the magnetic properties are explained in terms of surface patterning induced structural changes of the deposited films and different oxidation methods.

Caught in the middle with multiple displacement amplification: the myth of pooling for avoiding multiple displacement amplification bias in a metagenome.

PubMed

Marine, Rachel; McCarren, Coleen; Vorrasane, Vansay; Nasko, Dan; Crowgey, Erin; Polson, Shawn W; Wommack, K Eric

2014-01-30

Shotgun metagenomics has become an important tool for investigating the ecology of microorganisms. Underlying these investigations is the assumption that metagenome sequence data accurately estimates the census of microbial populations. Multiple displacement amplification (MDA) of microbial community DNA is often used in cases where it is difficult to obtain enough DNA for sequencing; however, MDA can result in amplification biases that may impact subsequent estimates of population census from metagenome data. Some have posited that pooling replicate MDA reactions negates these biases and restores the accuracy of population analyses. This assumption has not been empirically tested. Using mock viral communities, we examined the influence of pooling on population-scale analyses. In pooled and single reaction MDA treatments, sequence coverage of viral populations was highly variable and coverage patterns across viral genomes were nearly identical, indicating that initial priming biases were reproducible and that pooling did not alleviate biases. In contrast, control unamplified sequence libraries showed relatively even coverage across phage genomes. MDA should be avoided for metagenomic investigations that require quantitative estimates of microbial taxa and gene functional groups. While MDA is an indispensable technique in applications such as single-cell genomics, amplification biases cannot be overcome by combining replicate MDA reactions. Alternative library preparation techniques should be utilized for quantitative microbial ecology studies utilizing metagenomic sequencing approaches.

Assay development and case history of a 32K-biased library high-content MK2-EGFP translocation screen to identify p38 mitogen-activated protein kinase inhibitors on the ArrayScan 3.1 imaging platform.

PubMed

Trask, Oscar J; Baker, Audrey; Williams, Rhonda Gates; Nickischer, Debra; Kandasamy, Ramani; Laethem, Carmen; Johnston, Patricia A; Johnston, Paul A

2006-01-01

This chapter describes the conversion and assay development of a 96-well MK2-EGFP translocation assay into a higher density 384-well format high-content assay to be screened on the ArrayScan 3.1 imaging platform. The assay takes advantage of the well-substantiated hypothesis that mitogen-activated protein kinase-activating protein kinase-2 (MK2) is a substrate of p38 MAPK kinase and that p38-induced phosphorylation of MK-2 induces a nucleus-to-cytoplasm translocation. This chapter also presents a case history of the performance of the MK2-EGFP translocation assay, run as a "high-content" screen of a 32K kinase-biased library to identify p38 inhibitors. The assay performed very well and a number of putative p38 inhibitor hits were identified. Through the use of multiparameter data provided by the nuclear translocation algorithm and by checking images, a number of compounds were identified that were potential artifacts due to interference with the imaging format. These included fluorescent compounds, or compounds that dramatically reduced cell numbers due to cytotoxicity or by disrupting cell adherence. A total of 145 compounds produced IC(50) values <50.0 muM in the MK2-EGFP translocation assay, and a cross target query of the Lilly-RTP HTS database confirmed their inhibitory activity against in vitro kinase targets, including p38a. Compounds were confirmed structurally by LCMS analysis and profiled in cell-based imaging assays for MAPK signaling pathway selectivity. Three of the hit scaffolds identified in the MK2-EGFP translocation HCS run on the ArrayScan were selected for a p38a inhibitor hit-to-lead structure activity relationship (SAR) chemistry effort.

Functional protease profiling for diagnosis of malignant disease.

PubMed

Findeisen, Peter; Neumaier, Michael

2012-01-01

Clinical proteomic profiling by mass spectrometry (MS) aims at uncovering specific alterations within mass profiles of clinical specimens that are of diagnostic value for the detection and classification of various diseases including cancer. However, despite substantial progress in the field, the clinical proteomic profiling approaches have not matured into routine diagnostic applications so far. Their limitations are mainly related to high-abundance proteins and their complex processing by a multitude of endogenous proteases thus making rigorous standardization difficult. MS is biased towards the detection of low-molecular-weight peptides. Specifically, in serum specimens, the particular fragments of proteolytically degraded proteins are amenable to MS analysis. Proteases are known to be involved in tumour progression and tumour-specific proteases are released into the blood stream presumably as a result of invasive progression and metastasis. Thus, the determination of protease activity in clinical specimens from patients with malignant disease can offer diagnostic and also therapeutic options. The identification of specific substrates for tumour proteases in complex biological samples is challenging, but proteomic screens for proteases/substrate interactions are currently experiencing impressive progress. Such proteomic screens include peptide-based libraries, differential isotope labelling in combination with MS, quantitative degradomic analysis of proteolytically generated neo-N-termini, monitoring the degradation of exogenous reporter peptides with MS, and activity-based protein profiling. In the present article, we summarize and discuss the current status of proteomic techniques to identify tumour-specific protease-substrate interactions for functional protease profiling. Thereby, we focus on the potential diagnostic use of the respective approaches. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Fabrication and characterization of thin-film phosphor combinatorial libraries

NASA Astrophysics Data System (ADS)

Mordkovich, V. Z.; Jin, Zhengwu; Yamada, Y.; Fukumura, T.; Kawasaki, M.; Koinuma, H.

2002-05-01

The laser molecular beam epitaxy method was employed to fabricate thin-film combinatorial libraries of ZnO-based phosphors on different substrates. Fabrication of both pixel libraries, on the example of Fe-doped ZnO, and spread libraries, on the example of Eu-doped ZnO, has been demonstrated. Screening of the Fe-doped ZnO libraries led to the discovery of weak green cathodoluminescence with the maximum efficiency at the Fe content of 0.58 mol %. Screening of the Eu-doped ZnO libraries led to the discovery of unusual reddish-violet cathodoluminescence which is observed in a broad range of Eu concentration. No photoluminescence was registered in either system.

A novel esterase gene cloned from a metagenomic library from neritic sediments of the South China Sea

PubMed Central

2011-01-01

Background Marine microbes are a large and diverse group, which are exposed to a wide variety of pressure, temperature, salinity, nutrient availability and other environmental conditions. They provide a huge potential source of novel enzymes with unique properties that may be useful in industry and biotechnology. To explore the lipolytic genetic resources in the South China Sea, 23 sediment samples were collected in the depth < 100 m marine areas. Results A metagenomic library of South China Sea sediments assemblage in plasmid vector containing about 194 Mb of community DNA was prepared. Screening of a part of the unamplified library resulted in isolation of 15 unique lipolytic clones with the ability to hydrolyze tributyrin. A positive recombinant clone (pNLE1), containing a novel esterase (Est_p1), was successfully expressed in E. coli and purified. In a series of assays, Est_p1 displayed maximal activity at pH 8.57, 40°C, with ρ-Nitrophenyl butyrate (C4) as substrate. Compared to other metagenomic esterases, Est_p1 played a notable role in specificity for substrate C4 (kcat/Km value 11,500 S-1m M-1) and showed no inhibited by phenylmethylsulfonyl fluoride, suggested that the substrate binding pocket was suitable for substrate C4 and the serine active-site residue was buried at the bottom of substrate binding pocket which sheltered by a lid structure. Conclusions Esterase, which specificity towards short chain fatty acids, especially butanoic acid, is commercially available as potent flavoring tools. According the outstanding activity and specificity for substrate C4, Est_p1 has potential application in flavor industries requiring hydrolysis of short chain esters. PMID:22067554

Composition of RF-sputtered refractory compounds determined by X-ray photoelectron spectroscopy

NASA Technical Reports Server (NTRS)

Wheeler, D. R.; Brainard, W. A.

1978-01-01

RF-sputtered coatings of CrB2, MoSi2, Mo2C, TiC, and MoS2 were examined by X-ray photoelectron spectroscopy (XPS). Data on stoichiometry, impurity content, and chemical bonding were obtained. The influences of sputtering target history, deposition time, RF power level, and substrate bias were studied. Significant deviations from stoichiometry and high oxide levels were related to target outgassing. The effect of substrate bias depended on the particular coating material studied.

The Impact of Library Resource Utilization on Undergraduate Students' Academic Performance: A Propensity Score Matching Design

ERIC Educational Resources Information Center

Kot, Felly Chiteng; Jones, Jennifer L.

2015-01-01

This study uses three cohorts of first-time, full-time undergraduate students (N = 8,652) at a large, metropolitan, public research university to examine the impact of student use of three library resources (workstations, study rooms, and research clinics) on academic performance. To deal with self-selection bias and estimate this impact more…

Substrate Stiffness Regulates the Development of Left-Right Asymmetry in Cell Orientation.

PubMed

Bao, Yuanye; Huang, Yaozhun; Lam, Miu Ling; Xu, Ting; Zhu, Ninghao; Guo, Zhaobin; Cui, Xin; Lam, Raymond H W; Chen, Ting-Hsuan

2016-07-20

Left-right (LR) asymmetry of tissue/organ structure is a morphological feature essential for many tissue functions. The ability to incorporate the LR formation in constructing tissue/organ replacement is important for recapturing the inherent tissue structure and functions. However, how LR asymmetry is formed remains largely underdetermined, which creates significant hurdles to reproduce and regulate the formation of LR asymmetry in an engineering context. Here, we report substrate rigidity functioning as an effective switch that turns on the development of LR asymmetry. Using micropatterned cell-adherent stripes on rigid substrates, we found that cells collectively oriented at a LR-biased angle relative to the stripe boundary. This LR asymmetry was initiated by a LR-biased migration of cells at stripe boundary, which later generated a velocity gradient propagating from stripe boundary to the center. After a series of cell translocations and rotations, ultimately, an LR-biased cell orientation within the micropatterned stripe was formed. Importantly, this initiation and propagation of LR asymmetry was observed only on rigid but not on soft substrates, suggesting that the LR asymmetry was regulated by rigid substrate probably through the organization of actin cytoskeleton. Together, we demonstrated substrate rigidity as a determinant factor that mediates the self-organizing LR asymmetry being unfolded from single cells to multicellular organization. More broadly, we anticipate that our findings would pave the way for rebuilding artificial tissue constructs with inherent LR asymmetry in the future.

Analysing the substrate multispecificity of a proton-coupled oligopeptide transporter using a dipeptide library

PubMed Central

Ito, Keisuke; Hikida, Aya; Kawai, Shun; Lan, Vu Thi Tuyet; Motoyama, Takayasu; Kitagawa, Sayuri; Yoshikawa, Yuko; Kato, Ryuji; Kawarasaki, Yasuaki

2013-01-01

Peptide uptake systems that involve members of the proton-coupled oligopeptide transporter (POT) family are conserved across all organisms. POT proteins have characteristic substrate multispecificity, with which one transporter can recognize as many as 8,400 types of di/tripeptides and certain peptide-like drugs. Here we characterize the substrate multispecificity of Ptr2p, a major peptide transporter of Saccharomyces cerevisiae, using a dipeptide library. The affinities (Ki) of di/tripeptides toward Ptr2p show a wide distribution range from 48 mM to 0.020 mM. This substrate multispecificity indicates that POT family members have an important role in the preferential uptake of vital amino acids. In addition, we successfully establish high performance ligand affinity prediction models (97% accuracy) using our comprehensive dipeptide screening data in conjunction with simple property indices for describing ligand molecules. Our results provide an important clue to the development of highly absorbable peptides and their derivatives including peptide-like drugs. PMID:24060756

Low dislocation density InAlN/AlN/GaN heterostructures grown on GaN substrates and the effects on gate leakage characteristics

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

Kotani, Junji, E-mail: kotani.junji-01@jp.fujitsu.com; Yamada, Atsushi; Ishiguro, Tetsuro

2016-04-11

This paper reports on the electrical characterization of Ni/Au Schottky diodes fabricated on InAlN high-electron-mobility transistor (HEMT) structures grown on low dislocation density free-standing GaN substrates. InAlN HEMT structures were grown on sapphire and GaN substrates by metal-organic vapor phase epitaxy, and the effects of threading dislocation density on the leakage characteristics of Ni/Au Schottky diodes were investigated. Threading dislocation densities were determined to be 1.8 × 10{sup 4 }cm{sup −2} and 1.2 × 10{sup 9 }cm{sup −2} by the cathodoluminescence measurement for the HEMT structures grown on GaN and sapphire substrates, respectively. Leakage characteristics of Ni/Au Schottky diodes were compared between the two samples, andmore » a reduction of the leakage current of about three to four orders of magnitude was observed in the forward bias region. For the high reverse bias region, however, no significant improvement was confirmed. We believe that the leakage current in the low bias region is governed by a dislocation-related Frenkel–Poole emission, and the leakage current in the high reverse bias region originates from field emission due to the large internal electric field in the InAlN barrier layer. Our results demonstrated that the reduction of dislocation density is effective in reducing leakage current in the low bias region. At the same time, it was also revealed that another approach will be needed, for instance, band modulation by impurity doping and insertion of insulating layers beneath the gate electrodes for a substantial reduction of the gate leakage current.« less

Electronic access to scientific nursing knowledge: the Virginia Henderson International Nursing Library.

PubMed

Graves, J R

2001-02-01

To inform oncology nurses about the electronic knowledge resources offered by the Sigma Theta Tau International Virginia Henderson International Nursing Library. Published articles and research studies. Clinical nursing research dissemination has been seriously affected by publication bias. The Virginia Henderson International Nursing Library has introduced both a new publishing paradigm for research and a new knowledge indexing strategy for improving electronic access to research knowledge (findings). The ability of oncology nursing to evolve, as an evidence-based practice, is largely dependent on access to research findings.

High throughput assay for cytochrome P450 BM3 for screening libraries of substrates and combinatorial mutants.

PubMed

Tsotsou, Georgia Eleni; Cass, Anthony Edward George; Gilardi, Gianfranco

2002-01-01

A rapid method for identifying compounds that are potential substrates for the drug metabolising enzyme cytochrome P450 is described. The strategy is based on the detection of a degradation product of NAD(P)H oxidation during substrate turnover by the enzyme expressed in Escherichia coli cells spontaneously lysed under the experimental conditions. The performance of the method has been tested on two known substrates of the wild-type cytochrome P450 BM3, arachidonic (AA) and lauric (LA) acids, and two substrates with environmental significance, the anionic surfactant sodium dodecyl sulfate (SDS), and the solvent 1,1,2,2-tetrachloroethane (TCE). The minimal background signal given from cells expressing cytochrome P450 BM3 in the absence of added substrate is only 3% of the signal in the presence of saturating substrate. Control experiments have proven that this method is specifically detecting NADPH oxidation by catalytic turnover of P450 BM3. The assay has been adapted to a microtitre plate format and used to screen a series of furazan derivatives as potential substrates. Three derivatives were identified as substrates. The method gave a significant different signal for two isomeric furazan derivatives. All results found on the cell lysate were verified and confirmed with the purified enzyme. This strategy opens the way to automated high throughput screening of NAD(P)H-linked enzymatic activity of molecules of pharmacological and biotechnological interest and libraries of random mutants of NAD(P)H-dependent biocatalysts.

Sequencing on the SOLiD 5500xl System - in-depth characterization of the GC bias.

PubMed

Roeh, Simone; Weber, Peter; Rex-Haffner, Monika; Deussing, Jan M; Binder, Elisabeth B; Jakovcevski, Mira

2017-07-04

Different types of sequencing biases have been described and subsequently improved for a variety of sequencing systems, mostly focusing on the widely used Illumina systems. Similar studies are missing for the SOLiD 5500xl system, a sequencer which produced many data sets available to researchers today. Describing and understanding the bias is important to accurately interpret and integrate these published data in various ongoing research projects. We report a particularly strong GC bias for this sequencing system when analyzing a defined gDNA mix of 5 microbes with a wide range of different GC contents (20-72%) when comparing to the expected distribution and Illumina MiSeq data from the same DNA pool. Since we observed this bias already under PCR-free conditions, changing the PCR conditions during library preparation - a common strategy to handle bias in the Illumina system - was not relevant. Source of the bias appeared to be an uneven heat distribution during the SOLiD emulsion PCR (ePCR) - for enrichment of libraries prior loading - since ePCR in either small pouches or in 96-well plates improved the GC bias. Sequencing of chromatin immunoprecipitated DNA (ChIP-seq) is a common approach in epigenetics. ChIP-seq of the mixed source histone mark H3K9ac (acetyl Histone H3 lysine 9), typically found on promoter regions and on gene bodies, including CpG islands, performed on a SOLiD 5500xl machine, resulted in major loss of reads at GC rich loci (GC content ≥ 62%), not explained by low sequencing depth. This was improved with adaptations of the ePCR.

Effects of substrate voltage on noise characteristics and hole lifetime in SOI metal-oxide-semiconductor field-effect transistor photon detector.

PubMed

Putranto, Dedy Septono Catur; Priambodo, Purnomo Sidi; Hartanto, Djoko; Du, Wei; Satoh, Hiroaki; Ono, Atsushi; Inokawa, Hiroshi

2014-09-08

Low-frequency noise and hole lifetime in silicon-on-insulator (SOI) metal-oxide-semiconductor field-effect transistors (MOSFETs) are analyzed, considering their use in photon detection based on single-hole counting. The noise becomes minimum at around the transition point between front- and back-channel operations when the substrate voltage is varied, and increases largely on both negative and positive sides of the substrate voltage showing peculiar Lorentzian (generation-recombination) noise spectra. Hole lifetime is evaluated by the analysis of drain current histogram at different substrate voltages. It is found that the peaks in the histogram corresponding to the larger number of stored holes become higher as the substrate bias becomes larger. This can be attributed to the prolonged lifetime caused by the higher electric field inside the body of SOI MOSFET. It can be concluded that, once the inversion channel is induced for detection of the photo-generated holes, the small absolute substrate bias is favorable for short lifetime and low noise, leading to high-speed operation.

Product-induced gene expression, a product-responsive reporter assay used to screen metagenomic libraries for enzyme-encoding genes.

PubMed

Uchiyama, Taku; Miyazaki, Kentaro

2010-11-01

A reporter assay-based screening method for enzymes, which we named product-induced gene expression (PIGEX), was developed and used to screen a metagenomic library for amidases. A benzoate-responsive transcriptional activator, BenR, was placed upstream of the gene encoding green fluorescent protein and used as a sensor. Escherichia coli sensor cells carrying the benR-gfp gene cassette fluoresced in response to benzoate concentrations as low as 10 μM but were completely unresponsive to the substrate benzamide. An E. coli metagenomic library consisting of 96,000 clones was grown in 96-well format in LB medium containing benzamide. The library cells were then cocultivated with sensor cells. Eleven amidase genes were recovered from 143 fluorescent wells; eight of these genes were homologous to known bacterial amidase genes while three were novel genes. In addition to their activity toward benzamide, the enzymes were active toward various substrates, including d- and l-amino acid amides, and displayed enantioselectivity. Thus, we demonstrated that PIGEX is an effective approach for screening novel enzymes based on product detection.

Application of Biocatalysis to on-DNA Carbohydrate Library Synthesis.

PubMed

Thomas, Baptiste; Lu, Xiaojie; Birmingham, William R; Huang, Kun; Both, Peter; Reyes Martinez, Juana Elizabeth; Young, Robert J; Davie, Christopher P; Flitsch, Sabine L

2017-05-04

DNA-encoded libraries are increasingly used for the discovery of bioactive lead compounds in high-throughput screening programs against specific biological targets. Although a number of libraries are now available, they cover limited chemical space due to bias in ease of synthesis and the lack of chemical reactions that are compatible with DNA tagging. For example, compound libraries rarely contain complex biomolecules such as carbohydrates with high levels of functionality, stereochemistry, and hydrophilicity. By using biocatalysis in combination with chemical methods, we aimed to significantly expand chemical space and generate generic libraries with potentially better biocompatibility. For DNA-encoded libraries, biocatalysis is particularly advantageous, as it is highly selective and can be performed in aqueous environments, which is an essential feature for this split-and-mix library technology. In this work, we demonstrated the application of biocatalysis for the on-DNA synthesis of carbohydrate-based libraries by using enzymatic oxidation and glycosylation in combination with traditional organic chemistry. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Light emitting diode with porous SiC substrate and method for fabricating

DOEpatents

Li, Ting; Ibbetson, James; Keller, Bernd

2005-12-06

A method and apparatus for forming a porous layer on the surface of a semiconductor material wherein an electrolyte is provided and is placed in contact with one or more surfaces of a layer of semiconductor material. The electrolyte is heated and a bias is introduced across said electrolyte and the semiconductor material causing a current to flow between the electrolyte and the semiconductor material. The current forms a porous layer on the one or more surfaces of the semiconductor material in contact with the electrolyte. The semiconductor material with its porous layer can serve as a substrate for a light emitter. A semiconductor emission region can be formed on the substrate. The emission region is capable of emitting light omnidirectionally in response to a bias, with the porous layer enhancing extraction of the emitting region light passing through the substrate.

Deposition of diamond-like films by ECR microwave plasma

NASA Technical Reports Server (NTRS)

Shing, Yuh-Han (Inventor); Pool, Frederick S. (Inventor)

1995-01-01

Hard amorphous hydrogenated carbon, diamond-like films are deposited using an electron cyclotron resonance microwave plasma with a separate radio frequency power bias applied to a substrate stage. The electron cyclotron resonance microwave plasma yields low deposition pressure and creates ion species otherwise unavailable. A magnetic mirror configuration extracts special ion species from a plasma chamber. Different levels of the radio frequency power bias accelerate the ion species of the ECR plasma impinging on a substrate to form different diamond-like films. During the deposition process, a sample stage is maintained at an ambient temperature of less than 100.degree. C. No external heating is applied to the sample stage. The deposition process enables diamond-like films to be deposited on heat-sensitive substrates.

Informatic selection of a neural crest-melanocyte cDNA set for microarray analysis

PubMed Central

Loftus, S. K.; Chen, Y.; Gooden, G.; Ryan, J. F.; Birznieks, G.; Hilliard, M.; Baxevanis, A. D.; Bittner, M.; Meltzer, P.; Trent, J.; Pavan, W.

1999-01-01

With cDNA microarrays, it is now possible to compare the expression of many genes simultaneously. To maximize the likelihood of finding genes whose expression is altered under the experimental conditions, it would be advantageous to be able to select clones for tissue-appropriate cDNA sets. We have taken advantage of the extensive sequence information in the dbEST expressed sequence tag (EST) database to identify a neural crest-derived melanocyte cDNA set for microarray analysis. Analysis of characterized genes with dbEST identified one library that contained ESTs representing 21 neural crest-expressed genes (library 198). The distribution of the ESTs corresponding to these genes was biased toward being derived from library 198. This is in contrast to the EST distribution profile for a set of control genes, characterized to be more ubiquitously expressed in multiple tissues (P < 1 × 10−9). From library 198, a subset of 852 clustered ESTs were selected that have a library distribution profile similar to that of the 21 neural crest-expressed genes. Microarray analysis demonstrated the majority of the neural crest-selected 852 ESTs (Mel1 array) were differentially expressed in melanoma cell lines compared with a non-neural crest kidney epithelial cell line (P < 1 × 10−8). This was not observed with an array of 1,238 ESTs that was selected without library origin bias (P = 0.204). This study presents an approach for selecting tissue-appropriate cDNAs that can be used to examine the expression profiles of developmental processes and diseases. PMID:10430933

Bias stress instability of double-gate a-IGZO TFTs on polyimide substrate

NASA Astrophysics Data System (ADS)

Cho, Won-Ju; Ahn, Min-Ju

2017-09-01

In this study, flexible double-gate thin-film transistor (TFT)-based amorphous indium-galliumzinc- oxide (a-IGZO) was fabricated on a polyimide substrate. Double-gate operation with connected front and back gates was compared with a single-gate operation. As a result, the double-gate a- IGZO TFT exhibited enhanced electrical characteristics as well as improved long-term reliability. Under positive- and negative-bias temperature stress, the threshold voltage shift of the double-gate operation was much smaller than that of the single-gate operation.

Substrate specificity of mitochondrial intermediate peptidase analysed by a support-bound peptide library

PubMed Central

Marcondes, M.F.M.; Alves, F.M.; Assis, D.M.; Hirata, I.Y.; Juliano, L.; Oliveira, V.; Juliano, M.A.

2015-01-01

The substrate specificity of recombinant human mitochondrial intermediate peptidase (hMIP) using a synthetic support-bound FRET peptide library is presented. The collected fluorescent beads, which contained the hydrolysed peptides generated by hMIP, were sequenced by Edman degradation. The results showed that this peptidase presents a remarkable preference for polar uncharged residues at P1 and P1′ substrate positions: Ser = Gln > Thr at P1 and Ser > Thr at P1′. Non-polar residues were frequent at the substrate P3, P2, P2′ and P3′ positions. Analysis of the predicted MIP processing sites in imported mitochondrial matrix proteins shows these cleavages indeed occur between polar uncharged residues. Previous analysis of these processing sites indicated the importance of positions far from the MIP cleavage site, namely the presence of a hydrophobic residue (Phe or Leu) at P8 and a polar uncharged residue (Ser or Thr) at P5. To evaluate this, additional kinetic analyses were carried out, using fluorogenic substrates synthesized based on the processing sites attributed to MIP. The results described here underscore the importance of the P1 and P1′ substrate positions for the hydrolytic activity of hMIP. The information presented in this work will help in the design of new substrate-based inhibitors for this peptidase. PMID:26082885

Control of Surface Chemistry, Substrate Stiffness, and Cell Function in a Novel Terpolymer Methacrylate Library

PubMed Central

Joy, Abraham; Cohen, Daniel M.; Luk, Arnold; Anim-Danso, Emmanuel; Chen, Christopher; Kohn, Joachim

2011-01-01

A focused library of methacrylate terpolymers was synthesized to explore the effects of varying surface chemistry and adhesive peptide ligands on cell function. The chemical diversity of methacrylate monomers enabled construction of a library of polymers in which one can systematically vary the chemical composition to achieve a wide range of contact angle, Young's modulus, and Tg values. Furthermore, the materials were designed to allow surface immobilization of bioactive peptides. We then examined the effects of these material compositions on protein adsorption and cell attachment, proliferation, and differentiation. We observed that chemical composition of the polymers was an important determinant for NIH 3T3 cell attachment and proliferation, as well as human mesenchymal stem cell differentiation, and correlated directly with the ability of the polymers to adsorb proteins that mediate cell adhesion. Importantly, functionalization of the methacrylate terpolymer library with an adhesive GRGDS peptide normalized cellular responses. RGD-functionalized polymers uniformly exhibited robust attachment, proliferation, and differentiation irrespective of the underlying substrate chemistry. These studies provide a library-based approach to rapidly explore the biological functionality of biomaterials with a wide range of compositions, and highlights the importance of cell and protein cell adhesion in predicting their performance. PMID:21226505

Erkitinib, a novel EGFR tyrosine kinase inhibitor screened using a ProteoChip system from a phytochemical library

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

Kim, Eung-Yoon; Choi, Young-Jin; Innopharmascreen, Inc., Asan 336-795

2009-11-20

Receptor tyrosine kinases (PTKs) play key roles in the pathogenesis of numerous human diseases, including cancer. Therefore PTK inhibitors are currently under intensive investigation as potential drug candidates. Herein, we report on a ProteoChip-based screening of an epidermal growth factor receptor (EGFR) tyrosine kinase (TK) inhibitor, Erkitinibs, from phytochemical libraries. PLC-{gamma}-1 was used as a substrate immobilized on a ProteoChip and incubated with an EGFR kinase to phosphorylate tyrosine residues of the substrate, followed by a fluorescence detection of the substrate recognized by a phospho-specific monoclonal antibody. Erkitinibs inhibited HeLa cell proliferation in a dose-dependent manner. In conclusion, these datamore » suggest that Erkitinibs can be a specific inhibitor of an EGFR kinase and can be further developed as a potent anti-tumor agent.« less

The neural substrates of in-group bias: a functional magnetic resonance imaging investigation.

PubMed

Van Bavel, Jay J; Packer, Dominic J; Cunningham, William A

2008-11-01

Classic minimal-group studies found that people arbitrarily assigned to a novel group quickly display a range of perceptual, affective, and behavioral in-group biases. We randomly assigned participants to a mixed-race team and used functional magnetic resonance imaging to identify brain regions involved in processing novel in-group and out-group members independently of preexisting attitudes, stereotypes, or familiarity. Whereas previous research on intergroup perception found amygdala activity--typically interpreted as negativity--in response to stigmatized social groups, we found greater activity in the amygdala, fusiform gyri, orbitofrontal cortex, and dorsal striatum when participants viewed novel in-group faces than when they viewed novel out-group faces. Moreover, activity in orbitofrontal cortex mediated the in-group bias in self-reported liking for the faces. These in-group biases in neural activity were not moderated by race or by whether participants explicitly attended to team membership or race, a finding suggesting that they may occur automatically. This study helps clarify the role of neural substrates involved in perceptual and affective in-group biases.

Anomalous response of supported few-layer hexagonal boron nitride to DC electric fields: a confined water effect?

NASA Astrophysics Data System (ADS)

Oliveira, Camilla; Matos, Matheus; Mazzoni, Mário; Chacham, Hélio; Neves, Bernardo

2013-03-01

Hexagonal boron nitride (h-BN) is a two-dimensional compound from III-V family, with the atoms of boron and nitrogen arranged in a honeycomb lattice, similar to graphene. Unlike graphene though, h-BN is an insulator material, with a gap larger than 5 eV. Here, we use Electric Force Microscopy (EFM) to study the electrical response of mono and few-layers of h-BN to an electric field applied by the EFM tip. Our results show an anomalous behavior in the dielectric response for h-BN for different bias orientation: for a positive bias applied to the tip, h-BN layers respond with a larger dielectric constant than the dielectric constant of the silicon dioxide substrate; while for a negative bias, the h-BN dielectric constant is smaller than the dielectric constant of the substrate. Based on first-principles calculations, we showed that this anomalous response may be interpreted as a macroscopic consequence of confinement of a thin water layer between h-BN and substrate. These results were confirmed by sample annealing and also also by a comparative analysis with h-BN on a non-polar substrate. All the authors acknowledge financial support from CNPq, Fapemig, Rede Nacional de Pesquisa em Nanotubos de Carbono and INCT-Nano-Carbono.

The ‘Goldilocks’ effect: preservation bias in vertebrate track assemblages

PubMed Central

Falkingham, P. L.; Bates, K. T.; Margetts, L.; Manning, P. L.

2011-01-01

Finite-element analysis was used to investigate the extent of bias in the ichnological fossil record attributable to body mass. Virtual tracks were simulated for four dinosaur taxa of different sizes (Struthiomimus, Tyrannosaurus, Brachiosaurus and Edmontosaurus), in a range of substrate conditions. Outlines of autopodia were generated based upon osteology and published soft-tissue reconstructions. Loads were applied vertically to the feet equivalent to the weight of the animal, and distributed accordingly to fore- and hindlimbs where relevant. Ideal, semi-infinite elastic–plastic substrates displayed a ‘Goldilocks’ quality where only a narrow range of loads could produce tracks, given that small animals failed to indent the substrate, and larger animals would be unable to traverse the area without becoming mired. If a firm subsurface layer is assumed, a more complete assemblage is possible, though there is a strong bias towards larger, heavier animals. The depths of fossil tracks within an assemblage may indicate thicknesses of mechanically distinct substrate layers at the time of track formation, even when the lithified strata appear compositionally homogeneous. This work increases the effectiveness of using vertebrate tracks as palaeoenvironmental indicators in terms of inferring substrate conditions at the time of track formation. Additionally, simulated undertracks are examined, and it is shown that complex deformation beneath the foot may not be indicative of limb kinematics as has been previously interpreted, but instead ridges and undulations at the base of a track may be a function of sediment displacement vectors and pedal morphology. PMID:21233145

High-conductance low-voltage organic thin film transistor with locally rearranged poly(3-hexylthiophene) domain by current annealing on plastic substrate

NASA Astrophysics Data System (ADS)

Pei, Zingway; Tsai, Hsing-Wang; Lai, Hsin-Cheng

2016-02-01

The organic material based thin film transistors (TFTs) are attractive for flexible optoelectronics applications due to the ability of lager area fabrication by solution and low temperature process on plastic substrate. Recently, the research of organic TFT focus on low operation voltage and high output current to achieve a low power organic logic circuit for optoelectronic device,such as e-paper or OLED displayer. To obtain low voltage and high output current, high gate capacitance and high channel mobility are key factors. The well-arranged polymer chain by a high temperature postannealing, leading enhancement conductivity of polymer film was a general method. However, the thermal annealing applying heat for all device on the substrate and may not applicable to plastic substrate. Therefore, in this work, the low operation voltage and high output current of polymer TFTs was demonstrated by locally electrical bias annealing. The poly(styrene-comethyl methacrylate) (PS-r-PMMA) with ultra-thin thickness is used as gate dielectric that the thickness is controlled by thermal treatment after spin coated on organic electrode. In electrical bias-annealing process, the PS-r- PMMA is acted a heating layer. After electrical bias-annealing, the polymer TFTs obtain high channel mobility at low voltage that lead high output current by a locally annealing of P3HT film. In the future, the locally electrical biasannealing method could be applied on plastic substrate for flexible optoelectronic application.

Using oriented peptide array libraries to evaluate methylarginine-specific antibodies and arginine methyltransferase substrate motifs

PubMed Central

Gayatri, Sitaram; Cowles, Martis W.; Vemulapalli, Vidyasiri; Cheng, Donghang; Sun, Zu-Wen; Bedford, Mark T.

2016-01-01

Signal transduction in response to stimuli relies on the generation of cascades of posttranslational modifications that promote protein-protein interactions and facilitate the assembly of distinct signaling complexes. Arginine methylation is one such modification, which is catalyzed by a family of nine protein arginine methyltransferases, or PRMTs. Elucidating the substrate specificity of each PRMT will promote a better understanding of which signaling networks these enzymes contribute to. Although many PRMT substrates have been identified, and their methylation sites mapped, the optimal target motif for each of the nine PRMTs has not been systematically addressed. Here we describe the use of Oriented Peptide Array Libraries (OPALs) to methodically dissect the preferred methylation motifs for three of these enzymes – PRMT1, CARM1 and PRMT9. In parallel, we show that an OPAL platform with a fixed methylarginine residue can be used to validate the methyl-specific and sequence-specific properties of antibodies that have been generated against different PRMT substrates, and can also be used to confirm the pan nature of some methylarginine-specific antibodies. PMID:27338245

Community analysis of hydrogen-producing extreme thermophilic anaerobic microflora enriched from cow manure with five substrates.

PubMed

Yokoyama, Hiroshi; Moriya, Naoko; Ohmori, Hideyuki; Waki, Miyoko; Ogino, Akifumi; Tanaka, Yasuo

2007-11-01

The present study analyzed the community structures of anaerobic microflora producing hydrogen under extreme thermophilic conditions by two culture-independent methods: denaturing gradient gel electrophoresis (DGGE) and clone library analyses. Extreme thermophilic microflora (ETM) was enriched from cow manure by repeated batch cultures at 75 degrees C, using a substrate of xylose, glucose, lactose, cellobiose, or soluble starch, and produced hydrogen at yields of 0.56, 2.65, 2.17, 2.68, and 1.73 mol/mol-monosaccharide degraded, respectively. The results from the DGGE and clone library analyses were consistent and demonstrated that the community structures of ETM enriched with the four hexose-based substrates (glucose, lactose, cellobiose, and soluble starch) consisted of a single species, closely related to a hydrogen-producing extreme thermophile, Caldoanaerobacter subterraneus, with diversity at subspecies levels. The ETM enriched with xylose was more diverse than those enriched with the other substrates, and contained the bacterium related to C. subterraneus and an unclassified bacterium, distantly related to a xylan-degrading and hydrogen-producing extreme thermophile, Caloramator fervidus.

Universal Common Communication Substrate (UCCS) Specification; Universal Common Communication Substrate (UCCS) Implementation

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

Universal Common Communication Substrate (UCCS) is a low-level communication substrate that exposes high-performance communication primitives, while providing network interoperability. It is intended to support multiple upper layer protocol (ULPs) or programming models including SHMEM,UPC,Titanium,Co-Array Fortran,Global Arrays,MPI,GASNet, and File I/O. it provides various communication operations including one-sided and two-sided point-to-point, collectives, and remote atomic operations. In addition to operations for ULPs, it provides an out-of-band communication channel required typically required to wire-up communication libraries.

Junction-based field emission structure for field emission display

DOEpatents

Dinh, Long N.; Balooch, Mehdi; McLean, II, William; Schildbach, Marcus A.

2002-01-01

A junction-based field emission display, wherein the junctions are formed by depositing a semiconducting or dielectric, low work function, negative electron affinity (NEA) silicon-based compound film (SBCF) onto a metal or n-type semiconductor substrate. The SBCF can be doped to become a p-type semiconductor. A small forward bias voltage is applied across the junction so that electron transport is from the substrate into the SBCF region. Upon entering into this NEA region, many electrons are released into the vacuum level above the SBCF surface and accelerated toward a positively biased phosphor screen anode, hence lighting up the phosphor screen for display. To turn off, simply switch off the applied potential across the SBCF/substrate. May be used for field emission flat panel displays.

Economical analysis of saturation mutagenesis experiments

PubMed Central

Acevedo-Rocha, Carlos G.; Reetz, Manfred T.; Nov, Yuval

2015-01-01

Saturation mutagenesis is a powerful technique for engineering proteins, metabolic pathways and genomes. In spite of its numerous applications, creating high-quality saturation mutagenesis libraries remains a challenge, as various experimental parameters influence in a complex manner the resulting diversity. We explore from the economical perspective various aspects of saturation mutagenesis library preparation: We introduce a cheaper and faster control for assessing library quality based on liquid media; analyze the role of primer purity and supplier in libraries with and without redundancy; compare library quality, yield, randomization efficiency, and annealing bias using traditional and emergent randomization schemes based on mixtures of mutagenic primers; and establish a methodology for choosing the most cost-effective randomization scheme given the screening costs and other experimental parameters. We show that by carefully considering these parameters, laboratory expenses can be significantly reduced. PMID:26190439

A systematic review and meta-analysis of cognitive bias to food stimuli in people with disordered eating behaviour.

PubMed

Brooks, Samantha; Prince, Alexis; Stahl, Daniel; Campbell, Iain C; Treasure, Janet

2011-02-01

Maladaptive cognitions about food, weight and shape bias attention, memory and judgment and may be linked to disordered eating behaviour. This paper reviews information processing of food stimuli (words, pictures) in people with eating disorders (ED). PubMed, Ovid, ScienceDirect, PsychInfo, Web of Science, Cochrane Library and Google Scholar were searched to December 2009. 63 studies measured attention, memory and judgment bias towards food stimuli in women with ED. Stroop tasks had sufficient sample size for a meta-analyses and effects ranged from small to medium. Other studies of attention bias had variable effects (e.g. the Dot-Probe task, distracter tasks and Startle Eyeblink Modulation). A meta-analysis of memory bias studies in ED and RE yielded insignificant effect. Effect sizes for judgment bias ranged from negligible to large. People with ED have greater attentional bias to food stimuli than healthy controls (HC). Evidence for a memory and judgment bias in ED is limited. Copyright © 2010 Elsevier Ltd. All rights reserved.

Stepwise molding, etching, and imprinting to form libraries of nanopatterned substrates.

PubMed

Zhao, Zhi; Cai, Yangjun; Liao, Wei-Ssu; Cremer, Paul S

2013-06-04

Herein, we describe a novel colloidal lithographic strategy for the stepwise patterning of planar substrates with numerous complex and unique designs. In conjunction with colloidal self-assembly, imprint molding, and capillary force lithography, reactive ion etching was used to create complex libraries of nanoscale features. This combinatorial strategy affords the ability to develop an exponentially increasing number of two-dimensional nanoscale patterns with each sequential step in the process. Specifically, dots, triangles, circles, and lines could be assembled on the surface separately and in combination with each other. Numerous architectures are obtained for the first time with high uniformity and reproducibility. These hexagonal arrays were made from polystyrene and gold features, whereby each surface element could be tuned from the micrometer size scale down to line widths of ~35 nm. The patterned area could be 1 cm(2) or even larger. The techniques described herein can be combined with further steps to make even larger libraries. Moreover, these polymer and metal features may prove useful in optical, sensing, and electronic applications.

A multi-substrate approach for functional metagenomics-based screening for (hemi)cellulases in two wheat straw-degrading microbial consortia unveils novel thermoalkaliphilic enzymes.

PubMed

Maruthamuthu, Mukil; Jiménez, Diego Javier; Stevens, Patricia; van Elsas, Jan Dirk

2016-01-28

Functional metagenomics is a promising strategy for the exploration of the biocatalytic potential of microbiomes in order to uncover novel enzymes for industrial processes (e.g. biorefining or bleaching pulp). Most current methodologies used to screen for enzymes involved in plant biomass degradation are based on the use of single substrates. Moreover, highly diverse environments are used as metagenomic sources. However, such methods suffer from low hit rates of positive clones and hence the discovery of novel enzymatic activities from metagenomes has been hampered. Here, we constructed fosmid libraries from two wheat straw-degrading microbial consortia, denoted RWS (bred on untreated wheat straw) and TWS (bred on heat-treated wheat straw). Approximately 22,000 clones from each library were screened for (hemi)cellulose-degrading enzymes using a multi-chromogenic substrate approach. The screens yielded 71 positive clones for both libraries, giving hit rates of 1:440 and 1:1,047 for RWS and TWS, respectively. Seven clones (NT2-2, T5-5, NT18-17, T4-1, 10BT, NT18-21 and T17-2) were selected for sequence analyses. Their inserts revealed the presence of 18 genes encoding enzymes belonging to twelve different glycosyl hydrolase families (GH2, GH3, GH13, GH17, GH20, GH27, GH32, GH39, GH53, GH58, GH65 and GH109). These encompassed several carbohydrate-active gene clusters traceable mainly to Klebsiella related species. Detailed functional analyses showed that clone NT2-2 (containing a beta-galactosidase of ~116 kDa) had highest enzymatic activity at 55 °C and pH 9.0. Additionally, clone T5-5 (containing a beta-xylosidase of ~86 kDa) showed > 90% of enzymatic activity at 55 °C and pH 10.0. This study employed a high-throughput method for rapid screening of fosmid metagenomic libraries for (hemi)cellulose-degrading enzymes. The approach, consisting of screens on multi-substrates coupled to further analyses, revealed high hit rates, as compared with recent other studies. Two clones, 10BT and T4-1, required the presence of multiple substrates for detectable activity, indicating a new avenue in library activity screening. Finally, clones NT2-2, T5-5 and NT18-17 were found to encode putative novel thermo-alkaline enzymes, which could represent a starting point for further biotechnological applications.

Optoelectrical Properties of a Heterojunction with Amorphous InGaZnO Film on n-Silicon Substrate

NASA Astrophysics Data System (ADS)

Jiang, D. L.; Ma, X. Z.; Li, L.; Xu, Z. K.

2017-10-01

An a-IGZO/ n-Si heterojunction device has been fabricated at room temperature by depositing amorphous InGaZnO (a-IGZO) film on n-type silicon substrate by plasma-assisted pulsed laser deposition and its optoelectrical properties studied in detail. The heterojunction showed distinct rectifying characteristic with rectification ratio of 1.93 × 103 at ±2 V bias and reverse leakage current density of 1.6 × 10-6 A cm-2 at -2 V bias. More interestingly, the heterojunction not only showed the characteristic of unbiased photoresponse, but could also detect either ultraviolet or ultraviolet-visible light by simply changing the polarity of the bias applied to the heterojunction. The variable photoresponse phenomenon and the charge transport mechanisms in the heterojunction are explained based on the energy band diagram of the heterojunction.

X-ray photoelectron spectroscopy study of radiofrequency-sputtered refractory compound steel interfaces

NASA Technical Reports Server (NTRS)

Wheeler, D. R.; Brainard, W. A.

1978-01-01

Radiofrequency sputtering was used to deposit Mo2C, Mo2B5, and MoSi2 coatings on 440C steel substrates. Both sputter etched and preoxidized substrates were used, and the films were deposited with and without a substrate bias of -300 V. The composition of the coatings was measured as a function of depth by X-ray photoelectron spectroscopy combined with argon ion etching. In the interfacial region there was evidence that bias produced a graded interface in Mo2B5 but not in Mo2C. Oxides of iron and of all film constituents except carbon were presented in all cases but the iron oxide concentration was higher and the layer thicker on the preoxidized substrates. The film and iron oxides were mixed in the MoSi2 and Mo2C films but layered in the Mo2B5 film. The presence of mixed oxides correlates with enhanced film adhesion.

Combinatorial synthesis of ceramic materials

DOEpatents

Lauf, Robert J [Oak Ridge, TN; Walls, Claudia A [Oak Ridge, TN; Boatner, Lynn A [Oak Ridge, TN

2010-02-23

A combinatorial library includes a gelcast substrate defining a plurality of cavities in at least one surface thereof; and a plurality of gelcast test materials in the cavities, at least two of the test materials differing from the substrate in at least one compositional characteristic, the two test materials differing from each other in at least one compositional characteristic.

Combinatorial synthesis of ceramic materials

DOEpatents

Lauf, Robert J.; Walls, Claudia A.; Boatner, Lynn A.

2006-11-14

A combinatorial library includes a gelcast substrate defining a plurality of cavities in at least one surface thereof; and a plurality of gelcast test materials in the cavities, at least two of the test materials differing from the substrate in at least one compositional characteristic, the two test materials differing from each other in at least one compositional characteristic.

Self-biased magnetoelectric charge coupling in transducer of SmFe2, Pb(Zr,Ti)O3 stack, and stepped horn substrate with multi-frequency effect

NASA Astrophysics Data System (ADS)

Tang, Chengpei; Lu, Caijiang; Gao, Hongli; Fu, Guoqiang

2017-10-01

This paper presents a broadband, self-biased magnetoelectric (ME) charge coupling in a transducer comprising of a negative magnetostrictive SmFe2 plate, a piezoelectric Pb(Zr,Ti)O3 (PZT) stack, and a stepped horn substrate. By using the SmFe2 plate with a large anisotropic field, an outstanding self-biased piezomagnetic effect is realized. The horn serves as a waveguide with multiple resonances and converges vibrating energy excited by the SmFe2 plate from the wide side to the narrow side, which results in a higher vibrating magnification at the position of the PZT-stack. Then, a strong mechanical-electric coupling is realized by the use of the PZT-stack with high capacitance. Consequently, several large peaks of ME charge response with magnitudes of 1.02-18.99 nC/Oe in the 0.1-50 kHz range are observed at zero-biased magnetic field. This demonstrates that the proposed broadband self-biased structure may be useful for multifunctional devices such as low frequency AC magnetic field sensors or multi-frequency energy harvesters.

An AlGaN/GaN high-electron-mobility transistor with an AlN sub-buffer layer

NASA Astrophysics Data System (ADS)

Shealy, J. R.; Kaper, V.; Tilak, V.; Prunty, T.; Smart, J. A.; Green, B.; Eastman, L. F.

2002-04-01

The AlGaN/GaN high-electron-mobility transistor requires a thermally conducting, semi-insulating substrate to achieve the best possible microwave performance. The semi-insulating SiC substrate is currently the best choice for this device technology; however, fringing fields which penetrate the GaN buffer layer at pinch-off introduce significant substrate conduction at modest drain bias if channel electrons are not well confined to the nitride structure. The addition of an insulating AlN sub-buffer on the semi-insulating SiC substrate suppresses this parasitic conduction, which results in dramatic improvements in the AlGaN/GaN transistor performance. A pronounced reduction in both the gate-lag and the gate-leakage current are observed for structures with the AlN sub-buffer layer. These structures operate up to 50 V drain bias under drive, corresponding to a peak voltage of 80 V, for a 0.30 µm gate length device. The devices have achieved high-efficiency operation at 10 GHz (>70% power-added efficiency in class AB mode at 15 V drain bias) and the highest output power density observed thus far (11.2 W mm-1). Large-periphery devices (1.5 mm gate width) deliver 10 W (continuous wave) of maximum saturated output power at 10 GHz. The growth, processing, and performance of these devices are briefly reviewed.

Mechanism for and method of biasing magnetic sensor

DOEpatents

Kautz, David R.

2007-12-04

A magnetic sensor package having a biasing mechanism involving a coil-generated, resistor-controlled magnetic field for providing a desired biasing effect. In a preferred illustrated embodiment, the package broadly comprises a substrate; a magnetic sensor element; a biasing mechanism, including a coil and a first resistance element; an amplification mechanism; a filter capacitor element; and an encapsulant. The sensor is positioned within the coil. A current applied to the coil produces a biasing magnetic field. The biasing magnetic field is controlled by selecting a resistance value for the first resistance element which achieves the desired biasing effect. The first resistance element preferably includes a plurality of selectable resistors, the selection of one or more of which sets the resistance value.

An in vivo library-versus-library selection of optimized protein-protein interactions.

PubMed

Pelletier, J N; Arndt, K M; Plückthun, A; Michnick, S W

1999-07-01

We describe a rapid and efficient in vivo library-versus-library screening strategy for identifying optimally interacting pairs of heterodimerizing polypeptides. Two leucine zipper libraries, semi-randomized at the positions adjacent to the hydrophobic core, were genetically fused to either one of two designed fragments of the enzyme murine dihydrofolate reductase (mDHFR), and cotransformed into Escherichia coli. Interaction between the library polypeptides reconstituted enzymatic activity of mDHFR, allowing bacterial growth. Analysis of the resulting colonies revealed important biases in the zipper sequences relative to the original libraries, which are consistent with selection for stable, heterodimerizing pairs. Using more weakly associating mDHFR fragments, we increased the stringency of selection. We enriched the best-performing leucine zipper pairs by multiple passaging of the pooled, selected colonies in liquid culture, as the best pairs allowed for better bacterial propagation. This competitive growth allowed small differences among the pairs to be amplified, and different sequence positions were enriched at different rates. We applied these selection processes to a library-versus-library sample of 2.0 x 10(6) combinations and selected a novel leucine zipper pair that may be appropriate for use in further in vivo heterodimerization strategies.

Structural and mechanistic analysis of a β-glycoside phosphorylase identified by screening a metagenomic library.

PubMed

Macdonald, Spencer S; Patel, Ankoor; Larmour, Veronica L C; Morgan-Lang, Connor; Hallam, Steven J; Mark, Brian L; Withers, Stephen G

2018-03-02

Glycoside phosphorylases have considerable potential as catalysts for the assembly of useful glycans for products ranging from functional foods and prebiotics to novel materials. However, the substrate diversity of currently identified phosphorylases is relatively small, limiting their practical applications. To address this limitation, we developed a high-throughput screening approach using the activated substrate 2,4-dinitrophenyl β-d-glucoside (DNPGlc) and inorganic phosphate for identifying glycoside phosphorylase activity and used it to screen a large insert metagenomic library. The initial screen, based on release of 2,4-dinitrophenyl from DNPGlc in the presence of phosphate, identified the gene bglP, encoding a retaining β-glycoside phosphorylase from the CAZy GH3 family. Kinetic and mechanistic analysis of the gene product, BglP, confirmed a double displacement ping-pong mechanism involving a covalent glycosyl-enzyme intermediate. X-ray crystallographic analysis provided insights into the phosphate-binding mode and identified a key glutamine residue in the active site important for substrate recognition. Substituting this glutamine for a serine swapped the substrate specificity from glucoside to N -acetylglucosaminide. In summary, we present a high-throughput screening approach for identifying β-glycoside phosphorylases, which was robust, simple to implement, and useful in identifying active clones within a metagenomics library. Implementation of this screen enabled discovery of a new glycoside phosphorylase class and has paved the way to devising simple ways in which enzyme specificity can be encoded and swapped, which has implications for biotechnological applications. © 2018 by The American Society for Biochemistry and Molecular Biology, Inc.

Pay Equal, But Not Opportunities

ERIC Educational Resources Information Center

Chapman, Liz

1978-01-01

Women librarians in Great Britain are struggling to eliminate the historical bias against married women continuing to work. Also, while the number of women working in libraries has increased, the number in top positions has decreased. (JAB)

A lanthipeptide library used to identify a protein-protein interaction inhibitor.

PubMed

Yang, Xiao; Lennard, Katherine R; He, Chang; Walker, Mark C; Ball, Andrew T; Doigneaux, Cyrielle; Tavassoli, Ali; van der Donk, Wilfred A

2018-04-01

In this article we describe the production and screening of a genetically encoded library of 10 6 lanthipeptides in Escherichia coli using the substrate-tolerant lanthipeptide synthetase ProcM. This plasmid-encoded library was combined with a bacterial reverse two-hybrid system for the interaction of the HIV p6 protein with the UEV domain of the human TSG101 protein, which is a critical protein-protein interaction for HIV budding from infected cells. Using this approach, we identified an inhibitor of this interaction from the lanthipeptide library, whose activity was verified in vitro and in cell-based virus-like particle-budding assays. Given the variety of lanthipeptide backbone scaffolds that may be produced with ProcM, this method may be used for the generation of genetically encoded libraries of natural product-like lanthipeptides containing substantial structural diversity. Such libraries may be combined with any cell-based assay to identify lanthipeptides with new biological activities.

Reliability Prediction Modeling of New Devices.

DTIC Science & Technology

1980-07-01

film of magnetic material on a nonmagnetic garnet crystal substrate with a surround- ing magnetic bias field mechanism to complete the basic hybrid...semiconductor processes. The magnetic domain centers are formed in a magnetic epitaxial film of garnet crystal on a nonmagnetic garnet substrate, and...polarity. The most widely used basic substrate is a high-purity gadolinium garnet . The thin- film magnetic layer is of the same crystal class with a

Propagation Characteristics of Finite Ground Coplanar Waveguide on Si Substrates With Porous Si and Polyimide Interface Layers

NASA Technical Reports Server (NTRS)

Ponchak, George E.; Itotia, Isaac K.; Drayton, Rhonda Franklin

2003-01-01

Measured and modeled propagation characteristics of Finite Ground Coplanar (FGC) waveguide fabricated on a 15 ohm-cm Si substrate with a 23 micron thick, 68% porous Si layer and a 20 micron thick polyimide interface layer are presented for the first time. Attenuation and effective permittivity as function of the FGC geometry and the bias between the center conductor and the ground planes are presented. It is shown that the porous Si reduces the attenuation by 1 dB/cm compared to FGC lines with only polyimide interface layers, and the polyimide on porous silicon demonstrates negligible bias dependence.

Ion-induced crystal damage during plasma-assisted MBE growth of GaN layers

NASA Astrophysics Data System (ADS)

Kirchner, V.; Heinke, H.; Birkle, U.; Einfeldt, S.; Hommel, D.; Selke, H.; Ryder, P. L.

1998-12-01

Gallium nitride layers were grown by plasma-assisted molecular-beam epitaxy on (0001)-oriented sapphire substrates using an electron cyclotron resonance (ECR) and a radio frequency (rf) plasma source. An applied substrate bias was varied from -200 to +250 V, resulting in a change of the density and energy of nitrogen ions impinging the growth surface. The layers were investigated by high-resolution x-ray diffractometry and high-resolution transmission electron microscopy (HRTEM). Applying a negative bias during growth has a marked detrimental effect on the crystal perfection of the layers grown with an ECR plasma source. This is indicated by a change in shape and width of (0002) and (202¯5) reciprocal lattice points as monitored by triple axis x-ray measurements. In HRTEM images, isolated basal plane stacking faults were found, which probably result from precipitation of interstitial atoms. The crystal damage in layers grown with a highly negative substrate bias is comparable to that observed for ion implantation processes at orders of magnitude larger ion energies. This is attributed to the impact of ions on the growing surface. None of the described phenomena was observed for the samples grown with the rf plasma source.

Pretreatment process for forming a smooth surface diamond film on a carbon-coated substrate

DOEpatents

Feng, Zhu; Brewer, Marilee; Brown, Ian; Komvopoulos, Kyriakos

1994-01-01

A process is disclosed for the pretreatment of a carbon-coated substrate to provide a uniform high density of nucleation sites thereon for the subsequent deposition of a continuous diamond film without the application of a bias voltage to the substrate. The process comprises exposing the carbon-coated substrate, in a microwave plasma enhanced chemical vapor deposition system, to a mixture of hydrogen-methane gases, having a methane gas concentration of at least about 4% (as measured by partial pressure), while maintaining the substrate at a pressure of about 10 to about 30 Torr during the pretreatment.

Non-biased and efficient global amplification of a single-cell cDNA library

PubMed Central

Huang, Huan; Goto, Mari; Tsunoda, Hiroyuki; Sun, Lizhou; Taniguchi, Kiyomi; Matsunaga, Hiroko; Kambara, Hideki

2014-01-01

Analysis of single-cell gene expression promises a more precise understanding of molecular mechanisms of a living system. Most techniques only allow studies of the expressions for limited numbers of gene species. When amplification of cDNA was carried out for analysing more genes, amplification biases were frequently reported. A non-biased and efficient global-amplification method, which uses a single-cell cDNA library immobilized on beads, was developed for analysing entire gene expressions for single cells. Every step in this analysis from reverse transcription to cDNA amplification was optimized. By removing degrading excess primers, the bias due to the digestion of cDNA was prevented. Since the residual reagents, which affect the efficiency of each subsequent reaction, could be removed by washing beads, the conditions for uniform and maximized amplification of cDNAs were achieved. The differences in the amplification rates for randomly selected eight genes were within 1.5-folds, which could be negligible for most of the applications of single-cell analysis. The global amplification gives a large amount of amplified cDNA (>100 μg) from a single cell (2-pg mRNA), and that amount is enough for downstream analysis. The proposed global-amplification method was used to analyse transcript ratios of multiple cDNA targets (from several copies to several thousand copies) quantitatively. PMID:24141095

Lead-Tin Telluride Sputtered Thin Films for Infrared Sensors

DTIC Science & Technology

1975-06-01

Concentrations in Pfa .78Sn,22Te Fllms " Tar8et *10 Effect of Substrate Bias Voltage on As-Deposited Carrier Concentration - Target #12 Effect of...be laid down in one deposition run with one target by simple bias voltage control. 3252 Sorption Coef"^^ *"* Energy Gaps. Typical plots

Understanding sources of uncertainty and bias error in models of human response to low amplitude sonic booms

NASA Astrophysics Data System (ADS)

Collmar, M.; Cook, B. G.; Cowart, R.; Freund, D.; Gavin, J.

2015-10-01

A pool of 240 subjects was exposed to a library of waveforms consisting of example signatures of low boom aircraft. The signature library included intentional variations in both loudness and spectral content, and were auralized using the Gulfstream SASS-II sonic boom simulator. Post-processing was used to quantify the impacts of test design decisions on the "quality" of the resultant database. Specific lessons learned from this study include insight regarding potential for bias error due to variations in loudness or peak over-pressure, sources of uncertainty and their relative importance on objective measurements and robustness of individual metrics to wide variations in spectral content. Results provide clear guidance for design of future large scale community surveys, where one must optimize the complex tradeoffs between the size of the surveyed population, spatial footprint of those participants, and the fidelity/density of objective measurements.

Superluminescence from an optically pumped molecular tunneling junction by injection of plasmon induced hot electrons

PubMed Central

Braun, Kai; Wang, Xiao; Kern, Andreas M; Adler, Hilmar; Peisert, Heiko; Chassé, Thomas; Zhang, Dai

2015-01-01

Summary Here, we demonstrate a bias-driven superluminescent point light-source based on an optically pumped molecular junction (gold substrate/self-assembled molecular monolayer/gold tip) of a scanning tunneling microscope, operating at ambient conditions and providing almost three orders of magnitude higher electron-to-photon conversion efficiency than electroluminescence induced by inelastic tunneling without optical pumping. A positive, steadily increasing bias voltage induces a step-like rise of the Stokes shifted optical signal emitted from the junction. This emission is strongly attenuated by reversing the applied bias voltage. At high bias voltage, the emission intensity depends non-linearly on the optical pump power. The enhanced emission can be modelled by rate equations taking into account hole injection from the tip (anode) into the highest occupied orbital of the closest substrate-bound molecule (lower level) and radiative recombination with an electron from above the Fermi level (upper level), hence feeding photons back by stimulated emission resonant with the gap mode. The system reflects many essential features of a superluminescent light emitting diode. PMID:26171286

Quantitative characterization of crude oils and fuels in mineral substrates using reflectance spectroscopy: Implications for remote sensing

NASA Astrophysics Data System (ADS)

Scafutto, Rebecca Del'Papa Moreira; Souza Filho, Carlos Roberto de

2016-08-01

The near and shortwave infrared spectral reflectance properties of several mineral substrates impregnated with crude oils (°APIs 19.2, 27.5 and 43.2), diesel, gasoline and ethanol were measured and assembled in a spectral library. These data were examined using Principal Component Analysis (PCA) and Partial Least Squares (PLS) Regression. Unique and characteristic absorption features were identified in the mixtures, besides variations of the spectral signatures related to the compositional difference of the crude oils and fuels. These features were used for qualitative and quantitative determination of the contaminant impregnated in the substrates. Specific wavelengths, where key absorption bands occur, were used for the individual characterization of oils and fuels. The intensity of these features can be correlated to the abundance of the contaminant in the mixtures. Grain size and composition of the impregnated substrate directly influence the variation of the spectral signatures. PCA models applied to the spectral library proved able to differentiate the type and density of the hydrocarbons. The calibration models generated by PLS are robust, of high quality and can also be used to predict the concentration of oils and fuels in mixtures with mineral substrates. Such data and models are employable as a reference for classifying unknown samples of contaminated substrates. The results of this study have important implications for onshore exploration and environmental monitoring of oil and fuels leaks using proximal and far range multispectral, hyperspectral and ultraespectral remote sensing.

Utilizing pulsed laser deposition lateral inhomogeneity as a tool in combinatorial material science.

PubMed

Keller, David A; Ginsburg, Adam; Barad, Hannah-Noa; Shimanovich, Klimentiy; Bouhadana, Yaniv; Rosh-Hodesh, Eli; Takeuchi, Ichiro; Aviv, Hagit; Tischler, Yaakov R; Anderson, Assaf Y; Zaban, Arie

2015-04-13

Pulsed laser deposition (PLD) is widely used in combinatorial material science, as it enables rapid fabrication of different composite materials. Nevertheless, this method was usually limited to small substrates, since PLD deposition on large substrate areas results in severe lateral inhomogeneity. A few technical solutions for this problem have been suggested, including the use of different designs of masks, which were meant to prevent inhomogeneity in the thickness, density, and oxidation state of a layer, while only the composition is allowed to be changed. In this study, a possible way to take advantage of the large scale deposition inhomogeneity is demonstrated, choosing an iron oxide PLD-deposited library with continuous compositional spread (CCS) as a model system. An Fe₂O₃-Nb₂O₅ library was fabricated using PLD, without any mask between the targets and the substrate. The library was measured using high-throughput scanners for electrical, structural, and optical properties. A decrease in electrical resistivity that is several orders of magnitude lower than pure α-Fe₂O₃ was achieved at ∼20% Nb-O (measured at 47 and 267 °C) but only at points that are distanced from the center of the PLD plasma plume. Using hierarchical clustering analysis, we show that the PLD inhomogeneity can be used as an additional degree of freedom, helping, in this case, to achieve iron oxide with much lower resistivity.

Molecular Library Synthesis Using Complex Substrates: Expanding the Framework of Triterpenoids

PubMed Central

Ignatenko, Vasily A.; Han, Yong; Tochtrop, Gregory P.

2013-01-01

The remodelling of a natural product core framework by means of diversity-oriented synthesis (DOS) is a valuable approach to access diverse/biologically relevant chemical space and to overcome the limitations of combinatorial-type compounds. Here we provide proof of principle and a thorough conformational analysis for a general strategy whereby the inherent complexity of a starting material is used to define the regio- and stereochemical outcomes of reactions in chemical library construction. This is in contrast to the traditional DOS logic employing reaction development and catalysis to drive library diversity PMID:23245400

Characterization of Bleomycin-Mediated Cleavage of a Hairpin DNA Library

PubMed Central

Segerman, Zachary J.; Roy, Basab; Hecht, Sidney M.

2013-01-01

A study of BLM A5 was conducted using a previously isolated library of hairpin DNAs found to bind strongly to metal free BLM. The ability of Fe(II)•BLM to effect cleavage on both the 3' and 5'-arms of the hairpin DNAs was characterized. The strongly bound DNAs were found to be efficient substrates for Fe•BLM A5-mediated hairpin DNA cleavage. Surprisingly, the most prevalent site of BLM-mediated cleavage was found to be the 5′-AT-3′ dinucleotide sequence. This dinucleotide sequence, and other sequences generally not cleaved well by BLM when examined using arbitrarily chosen DNA substrates, were apparent when examining the library of ten hairpin DNAs. In total, 132 sites of DNA cleavage were produced by exposure of the hairpin DNA library to Fe•BLM A5. The existence of multiple sites of cleavage on both the 3′- and 5′-arms of the hairpin DNAs suggested that some of these might be double-strand cleavage events. Accordingly, an assay was developed with which to test the propensity of the hairpin DNAs to undergo double-strand DNA damage. One hairpin DNA was characterized using this method, and gave results consistent with earlier reports of double-strand DNA cleavage, but with a sequence selectivity different from those reported previously. PMID:23834496

Many-body design of highly strained GaInNAs electroabsorption modulators on GaInAs ternary substrates

NASA Astrophysics Data System (ADS)

Fujisawa, Takeshi; Arai, Masakazu; Kano, Fumiyoshi

2010-05-01

Electroabsorption in highly strained GaInAs and GaInNAs quantum wells (QWs) grown on GaInAs or quasi-GaInAs substrates is investigated by using microscopic many-body theory. The effects of various parameters, such as strain, barrier height, substrate composition, and temperature are thoroughly examined. It is shown that the value of the absorption coefficient strongly depends on the depth of the QWs under large bias electric field due to the small overlap integral of wave functions between the conduction and valence bands. The use of GaInNAs QWs makes the strain in the well layer very small. Further, the effective quantum-well depth is increased in GaInNAs QWs due to the anticrossing interaction between the conduction and N-resonant bands, making it possible to obtain larger absorption coefficient under large bias electric fields without using wide-band gap materials for barriers.

Tribological synthesis method for producing low-friction surface film coating

DOEpatents

Ajayi, Oyelayo O.; Lorenzo-Martin, Maria De La; Fenske, George R.

2016-10-25

An article of method of manufacture of a low friction tribological film on a substrate. The article includes a substrate of a steel or ceramic which has been tribologically processed with a lubricant containing selected additives and the additives, temperature, load and time of processing can be selectively controlled to bias formation of a film on the substrate where the film is an amorphous structure exhibiting highly advantageous low friction properties.

Engineering on-chip nanoporous gold material libraries via precision photothermal treatment [Precision Photothermal Annealing of Nanoporous Gold Thin Films for the Microfabrication of a Single-ship Material Libraries

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

Chapman, Christopher A. R.; Wang, Ling; Biener, Juergen

Single-chip material libraries of thin films of nanostructured materials are a promising approach for high throughput studies of structure-property relationship in the fields of physics and biology. Nanoporous gold (np-Au), produced by an alloy corrosion process, is a nanostructured material of specific interest in both these fields. One attractive property of np-Au is its self-similar coarsening behavior by thermally induced surface diffusion. However, traditional heat application techniques for the modification of np-Au are bulk processes that cannot be used to generate a library of different pore sizes on a single chip. Laser micromachining offers an attractive solution to this problemmore » by providing a means to apply energy with high spatial and temporal resolution. In our present study we use finite element multiphysics simulations to predict the effects of laser mode (continuous-wave vs. pulsed) and supporting substrate thermal conductivity on the local np-Au film temperatures during photothermal annealing and subsequently investigate the mechanisms by which the np-Au network is coarsening. Our simulations predict that continuous-wave mode laser irradiation on a silicon supporting substrate supports the widest range of morphologies that can be created through the photothermal annealing of thin film np-Au. Using this result we successfully fabricate a single-chip material library consisting of 81 np-Au samples of 9 different morphologies for use in increased throughput material interaction studies.« less

Engineering on-chip nanoporous gold material libraries via precision photothermal treatment [Precision Photothermal Annealing of Nanoporous Gold Thin Films for the Microfabrication of a Single-ship Material Libraries

DOE PAGES

Chapman, Christopher A. R.; Wang, Ling; Biener, Juergen; ...

2016-01-01

Single-chip material libraries of thin films of nanostructured materials are a promising approach for high throughput studies of structure-property relationship in the fields of physics and biology. Nanoporous gold (np-Au), produced by an alloy corrosion process, is a nanostructured material of specific interest in both these fields. One attractive property of np-Au is its self-similar coarsening behavior by thermally induced surface diffusion. However, traditional heat application techniques for the modification of np-Au are bulk processes that cannot be used to generate a library of different pore sizes on a single chip. Laser micromachining offers an attractive solution to this problemmore » by providing a means to apply energy with high spatial and temporal resolution. In our present study we use finite element multiphysics simulations to predict the effects of laser mode (continuous-wave vs. pulsed) and supporting substrate thermal conductivity on the local np-Au film temperatures during photothermal annealing and subsequently investigate the mechanisms by which the np-Au network is coarsening. Our simulations predict that continuous-wave mode laser irradiation on a silicon supporting substrate supports the widest range of morphologies that can be created through the photothermal annealing of thin film np-Au. Using this result we successfully fabricate a single-chip material library consisting of 81 np-Au samples of 9 different morphologies for use in increased throughput material interaction studies.« less

Plasmonic Library Based on Substrate-Supported Gradiential Plasmonic Arrays

PubMed Central

2014-01-01

We present a versatile approach to produce macroscopic, substrate-supported arrays of plasmonic nanoparticles with well-defined interparticle spacing and a continuous particle size gradient. The arrays thus present a “plasmonic library” of locally noncoupling plasmonic particles of different sizes, which can serve as a platform for future combinatorial screening of size effects. The structures were prepared by substrate assembly of gold-core/poly(N-isopropylacrylamide)-shell particles and subsequent post-modification. Coupling of the localized surface plasmon resonance (LSPR) could be avoided since the polymer shell separates the encapsulated gold cores. To produce a particle array with a broad range of well-defined but laterally distinguishable particle sizes, the substrate was dip-coated in a growth solution, which resulted in an overgrowth of the gold cores controlled by the local exposure time. The kinetics was quantitatively analyzed and found to be diffusion rate controlled, allowing for precise tuning of particle size by adjusting the withdrawal speed. We determined the kinetics of the overgrowth process, investigated the LSPRs along the gradient by UV–vis extinction spectroscopy, and compared the spectroscopic results to the predictions from Mie theory, indicating the absence of local interparticle coupling. We finally discuss potential applications of these substrate-supported plasmonic particle libraries and perspectives toward extending the concept from size to composition variation and screening of plasmonic coupling effects. PMID:25137554

Non-Cell-Adhesive Substrates for Printing of Arrayed Biomaterials

PubMed Central

Appel, Eric A.; Larson, Benjamin L.; Luly, Kathryn M.; Kim, Jinseong D.

2015-01-01

Cellular microarrays have become extremely useful in expediting the investigation of large libraries of (bio)materials for both in vitro and in vivo biomedical applications. We have developed an exceedingly simple strategy for the fabrication of non-cell-adhesive substrates supporting the immobilization of diverse (bio)material features, including both monomeric and polymeric adhesion molecules (e.g. RGD and polylysine), hydrogels, and polymers. PMID:25430948

Fabrication and deformation behaviour of multilayer Al2O3/Ti/TiO2 nanotube arrays.

PubMed

Baradaran, S; Basirun, W J; Zalnezhad, E; Hamdi, M; Sarhan, Ahmed A D; Alias, Y

2013-04-01

In this study, titanium thin films were deposited on alumina substrates by radio frequency (RF) magnetron sputtering. The mechanical properties of the Ti coatings were evaluated in terms of adhesion strength at various RF powers, temperatures, and substrate bias voltages. The coating conditions of 400W of RF power, 250°C, and a 75V substrate bias voltage produced the strongest coating adhesion, as obtained by the Taguchi optimisation method. TiO2 nanotube arrays were grown as a second layer on the Ti substrates using electrochemical anodisation at a constant potential of 20V and anodisation times of 15min, 45min, and 75min in a NH4F electrolyte solution (75 ethylene glycol: 25 water). The anodised titanium was annealed at 450°C and 650°C in a N2 gas furnace to obtain different phases of titania, anatase and rutile, respectively. The mechanical properties of the anodised layer were investigated by nanoindentation. The results indicate that Young's modulus and hardness increased with annealing temperature to 650°C. Copyright © 2013 Elsevier Ltd. All rights reserved.

Engineering on-chip nanoporous gold material libraries via precision photothermal treatment

NASA Astrophysics Data System (ADS)

Chapman, Christopher A. R.; Wang, Ling; Biener, Juergen; Seker, Erkin; Biener, Monika M.; Matthews, Manyalibo J.

2015-12-01

Libraries of nanostructured materials on a single chip are a promising platform for high throughput and combinatorial studies of structure-property relationships in the fields of physics and biology. Nanoporous gold (np-Au), produced by an alloy corrosion process, is a nanostructured material specifically suited for such studies because of its self-similar thermally induced coarsening behavior. However, traditional heat application techniques for the modification of np-Au are bulk processes that cannot be used to generate a library of different pore sizes on a single chip. Here, laser micro-processing offers an attractive solution to this problem by providing a means to apply energy with high spatial and temporal resolution. In the present study we use finite element multiphysics simulations to predict the effects of laser mode (continuous-wave vs. pulsed) and thermal conductivity of the supporting substrate on the local np-Au film temperatures during photothermal annealing. Based on these results we discuss the mechanisms by which the np-Au network is coarsened. Thermal transport simulations predict that continuous-wave mode laser irradiation of np-Au thin films on a silicon substrate supports the widest range of morphologies that can be created through photothermal annealing of np-Au. Using the guidance provided by simulations, we successfully fabricate an on-chip material library consisting of 81 np-Au samples of 9 different morphologies for use in the parallel study of structure-property relationships.Libraries of nanostructured materials on a single chip are a promising platform for high throughput and combinatorial studies of structure-property relationships in the fields of physics and biology. Nanoporous gold (np-Au), produced by an alloy corrosion process, is a nanostructured material specifically suited for such studies because of its self-similar thermally induced coarsening behavior. However, traditional heat application techniques for the modification of np-Au are bulk processes that cannot be used to generate a library of different pore sizes on a single chip. Here, laser micro-processing offers an attractive solution to this problem by providing a means to apply energy with high spatial and temporal resolution. In the present study we use finite element multiphysics simulations to predict the effects of laser mode (continuous-wave vs. pulsed) and thermal conductivity of the supporting substrate on the local np-Au film temperatures during photothermal annealing. Based on these results we discuss the mechanisms by which the np-Au network is coarsened. Thermal transport simulations predict that continuous-wave mode laser irradiation of np-Au thin films on a silicon substrate supports the widest range of morphologies that can be created through photothermal annealing of np-Au. Using the guidance provided by simulations, we successfully fabricate an on-chip material library consisting of 81 np-Au samples of 9 different morphologies for use in the parallel study of structure-property relationships. Electronic supplementary information (ESI) available: Details of sample preparation, fabrication of material libraries, as well as further analysis and supporting scanning electron micrographs can be found in ESI. See DOI: 10.1039/c5nr04580k

Comparison of large-insert, small-insert and pyrosequencing libraries for metagenomic analysis.

PubMed

Danhorn, Thomas; Young, Curtis R; DeLong, Edward F

2012-11-01

The development of DNA sequencing methods for characterizing microbial communities has evolved rapidly over the past decades. To evaluate more traditional, as well as newer methodologies for DNA library preparation and sequencing, we compared fosmid, short-insert shotgun and 454 pyrosequencing libraries prepared from the same metagenomic DNA samples. GC content was elevated in all fosmid libraries, compared with shotgun and 454 libraries. Taxonomic composition of the different libraries suggested that this was caused by a relative underrepresentation of dominant taxonomic groups with low GC content, notably Prochlorales and the SAR11 cluster, in fosmid libraries. While these abundant taxa had a large impact on library representation, we also observed a positive correlation between taxon GC content and fosmid library representation in other low-GC taxa, suggesting a general trend. Analysis of gene category representation in different libraries indicated that the functional composition of a library was largely a reflection of its taxonomic composition, and no additional systematic biases against particular functional categories were detected at the level of sequencing depth in our samples. Another important but less predictable factor influencing the apparent taxonomic and functional library composition was the read length afforded by the different sequencing technologies. Our comparisons and analyses provide a detailed perspective on the influence of library type on the recovery of microbial taxa in metagenomic libraries and underscore the different uses and utilities of more traditional, as well as contemporary 'next-generation' DNA library construction and sequencing technologies for exploring the genomics of the natural microbial world.

Capturing diversity of marine heterotrophic protists: one cell at a time

PubMed Central

Heywood, Jane L; Sieracki, Michael E; Bellows, Wendy; Poulton, Nicole J; Stepanauskas, Ramunas

2011-01-01

Recent applications of culture-independent, molecular methods have revealed unexpectedly high diversity in a variety of functional and phylogenetic groups of microorganisms in the ocean. However, none of the existing research tools are free from significant limitations, such as PCR and cloning biases, low phylogenetic resolution and others. Here, we employed novel, single-cell sequencing techniques to assess the composition of small (<10 μm diameter), heterotrophic protists from the Gulf of Maine. Single cells were isolated by flow cytometry, their genomes amplified, and 18S rRNA marker genes were amplified and sequenced. We compared the results to traditional environmental PCR cloning of sorted cells. The diversity of heterotrophic protists was significantly higher in the library of single amplified genomes (SAGs) than in environmental PCR clone libraries of the 18S rRNA gene, obtained from the same coastal sample. Libraries of SAGs, but not clones contained several recently discovered, uncultured groups, including picobiliphytes and novel marine stramenopiles. Clone, but not SAG, libraries contained several large clusters of identical and nearly identical sequences of Dinophyceae, Cercozoa and Stramenopiles. Similar results were obtained using two alternative primer sets, suggesting that PCR biases may not be the only explanation for the observed patterns. Instead, differences in the number of 18S rRNA gene copies among the various protist taxa probably had a significant role in determining the PCR clone composition. These results show that single-cell sequencing has the potential to more accurately assess protistan community composition than previously established methods. In addition, the creation of SAG libraries opens opportunities for the analysis of multiple genes or entire genomes of the uncultured protist groups. PMID:20962875

High-Throughput Ligand Discovery Reveals a Sitewise Gradient of Diversity in Broadly Evolved Hydrophilic Fibronectin Domains

PubMed Central

Woldring, Daniel R.; Holec, Patrick V.; Zhou, Hong; Hackel, Benjamin J.

2015-01-01

Discovering new binding function via a combinatorial library in small protein scaffolds requires balance between appropriate mutations to introduce favorable intermolecular interactions while maintaining intramolecular integrity. Sitewise constraints exist in a non-spatial gradient from diverse to conserved in evolved antibody repertoires; yet non-antibody scaffolds generally do not implement this strategy in combinatorial libraries. Despite the fact that biased amino acid distributions, typically elevated in tyrosine, serine, and glycine, have gained wider use in synthetic scaffolds, these distributions are still predominantly applied uniformly to diversified sites. While select sites in fibronectin domains and DARPins have shown benefit from sitewise designs, they have not been deeply evaluated. Inspired by this disparity between diversity distributions in natural libraries and synthetic scaffold libraries, we hypothesized that binders resulting from discovery and evolution would exhibit a non-spatial, sitewise gradient of amino acid diversity. To identify sitewise diversities consistent with efficient evolution in the context of a hydrophilic fibronectin domain, >105 binders to six targets were evolved and sequenced. Evolutionarily favorable amino acid distributions at 25 sites reveal Shannon entropies (range: 0.3–3.9; median: 2.1; standard deviation: 1.1) supporting the diversity gradient hypothesis. Sitewise constraints in evolved sequences are consistent with complementarity, stability, and consensus biases. Implementation of sitewise constrained diversity enables direct selection of nanomolar affinity binders validating an efficient strategy to balance inter- and intra-molecular interaction demands at each site. PMID:26383268

Surface treatment of ceramic articles

DOEpatents

Komvopoulos, Kyriakos; Brown, Ian G.; Wei, Bo; Anders, Simone; Anders, Andre; Bhatia, C. Singh

1998-01-01

A process for producing an article with improved ceramic surface properties including providing an article having a ceramic surface, and placing the article onto a conductive substrate holder in a hermetic enclosure. Thereafter a low pressure ambient is provided in the hermetic enclosure. A plasma including ions of solid materials is produced the ceramic surface of the article being at least partially immersed in a macroparticle free region of the plasma. While the article is immersed in the macroparticle free region, a bias of the substrate holder is biased between a low voltage at which material from the plasma condenses on the surface of the article and a high negative voltage at which ions from the plasma are implanted into the article.

Pretreatment process for forming a smooth surface diamond film on a carbon-coated substrate

DOEpatents

Feng, Z.; Brewer, M.; Brown, I.; Komvopoulos, K.

1994-05-03

A process is disclosed for the pretreatment of a carbon-coated substrate to provide a uniform high density of nucleation sites thereon for the subsequent deposition of a continuous diamond film without the application of a bias voltage to the substrate. The process comprises exposing the carbon-coated substrate, in a microwave plasma enhanced chemical vapor deposition system, to a mixture of hydrogen-methane gases, having a methane gas concentration of at least about 4% (as measured by partial pressure), while maintaining the substrate at a pressure of about 10 to about 30 Torr during the pretreatment. 6 figures.

A Fast Solution to NGS Library Prep with Low Nanogram DNA Input

PubMed Central

Liu, Pingfang; Lohman, Gregory J.S.; Cantor, Eric; Langhorst, Bradley W.; Yigit, Erbay; Apone, Lynne M.; Munafo, Daniela B.; Stewart, Fiona J.; Evans, Thomas C.; Nichols, Nicole; Dimalanta, Eileen T.; Davis, Theodore B.; Sumner, Christine

2013-01-01

Next Generation Sequencing (NGS) has significantly impacted human genetics, enabling a comprehensive characterization of the human genome as well as a better understanding of many genomic abnormalities. By delivering massive DNA sequences at unprecedented speed and cost, NGS promises to make personalized medicine a reality in the foreseeable future. To date, library construction with clinical samples has been a challenge, primarily due to the limited quantities of sample DNA available. Our objective here was to overcome this challenge by developing NEBNext® Ultra DNA Library Prep Kit, a fast library preparation method. Specifically, we streamlined the workflow utilizing novel NEBNext reagents and adaptors, including a new DNA polymerase that has been optimized to minimize GC bias. As a result of this work, we have developed a simple method for library construction from an amount of DNA as low as 5 ng, which can be used for both intact and fragmented DNA. Moreover, the workflow is compatible with multiple NGS platforms.

Influence of microstructure and chemical composition of sputter deposited TiO2 thin films on in vitro bioactivity.

PubMed

Lilja, Mirjam; Genvad, Axel; Astrand, Maria; Strømme, Maria; Enqvist, Håkan

2011-12-01

Functionalisation of biomedical implants via surface modifications for tailored tissue response is a growing field of research. Crystalline TiO(2) has been proven to be a bone bioactive, non-resorbable material. In contact with body fluids a hydroxyapaptite (HA) layer forms on its surface facilitating the bone contact. Thus, the path of improving biomedical implants via deposition of crystalline TiO(2) on the surface is interesting to follow. In this study we have evaluated the influence of microstructure and chemical composition of sputter deposited titanium oxide thin films on the in vitro bioactivity. We find that both substrate bias, topography and the flow ratio of the gases used during sputtering affect the HA layer formed on the films after immersion in simulated body fluid at 37°C. A random distribution of anatase and rutile crystals, formed at negative substrate bias and low Ar to O(2) gas flow ratios, are shown to favor the growth of flat HA crystal structures whereas higher flow ratios and positive substrate bias induced growth of more spherical HA structures. These findings should provide valuable information when optimizing the bioactivity of titanium oxide coatings as well as for tailoring process parameters for sputtered-based production of bioactive titanium oxide implant surfaces.

Growing Neural PC-12 Cell on Crosslinked Silica Aerogels Increases Neurite Extension in the Presence of an Electric Field.

PubMed

Lynch, Kyle J; Skalli, Omar; Sabri, Firouzeh

2018-04-20

Externally applied electrical stimulation (ES) has been shown to enhance the nerve regeneration process and to influence the directionality of neurite outgrowth. In addition, the physical and chemical properties of the substrate used for nerve-cell regeneration is critical in fostering regeneration. Previously, we have shown that polyurea-crosslinked silica aerogels (PCSA) exert a positive influence on the extension of neurites by PC-12 cells, a cell-line model widely used to study neurite extension and electrical excitability. In this work, we have examined how an externally applied electric field (EF) influences the extension of neurites in PC-12 cells grown on two substrates: collagen-coated dishes versus collagen-coated crosslinked silica aerogels. The externally applied direct current (DC) bias was applied in vitro using a custom-designed chamber containing polydimethysiloxane (PDMS) embedded copper electrodes to create an electric field across the substrate for the cultured PC-12 cells. Results suggest orientation preference towards the anode, and, on average, longer neurites in the presence of the applied DC bias than with 0 V DC bias. In addition, neurite length was increased in cells grown on silica-crosslinked aerogel when compared to cells grown on regular petri-dishes. These results further support the notion that PCSA is a promising material for nerve regeneration.

Cushing's syndrome mutant PKA L205R exhibits altered substrate specificity

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

Lubner, Joshua M.; Dodge-Kafka, Kimberly L.; Carlson, Cathrine R.

The PKA L205R hotspot mutation has been implicated in Cushing's syndrome through hyperactive gain-of-function PKA signaling; however, its influence on substrate specificity has not been investigated. Here, we employ the Proteomic Peptide Library (ProPeL) approach to create high-resolution models for PKA WT and PKA L205R substrate specificity. We reveal that the L205R mutation reduces canonical hydrophobic preference at the substrate P + 1 position, and increases acidic preference in downstream positions. Using these models, we designed peptide substrates that exhibit altered selectivity for specific PKA variants, and demonstrate the feasibility of selective PKA L205R loss-of-function signaling. Through these results, wemore » suggest that substrate rewiring may contribute to Cushing's syndrome disease etiology, and introduce a powerful new paradigm for investigating mutation-induced kinase substrate rewiring in human disease.« less

Cushing's syndrome mutant PKA L205R exhibits altered substrate specificity

DOE PAGES

Lubner, Joshua M.; Dodge-Kafka, Kimberly L.; Carlson, Cathrine R.; ...

2017-02-01

The PKA L205R hotspot mutation has been implicated in Cushing's syndrome through hyperactive gain-of-function PKA signaling; however, its influence on substrate specificity has not been investigated. Here, we employ the Proteomic Peptide Library (ProPeL) approach to create high-resolution models for PKA WT and PKA L205R substrate specificity. We reveal that the L205R mutation reduces canonical hydrophobic preference at the substrate P + 1 position, and increases acidic preference in downstream positions. Using these models, we designed peptide substrates that exhibit altered selectivity for specific PKA variants, and demonstrate the feasibility of selective PKA L205R loss-of-function signaling. Through these results, wemore » suggest that substrate rewiring may contribute to Cushing's syndrome disease etiology, and introduce a powerful new paradigm for investigating mutation-induced kinase substrate rewiring in human disease.« less

Accurate and predictive antibody repertoire profiling by molecular amplification fingerprinting.

PubMed

Khan, Tarik A; Friedensohn, Simon; Gorter de Vries, Arthur R; Straszewski, Jakub; Ruscheweyh, Hans-Joachim; Reddy, Sai T

2016-03-01

High-throughput antibody repertoire sequencing (Ig-seq) provides quantitative molecular information on humoral immunity. However, Ig-seq is compromised by biases and errors introduced during library preparation and sequencing. By using synthetic antibody spike-in genes, we determined that primer bias from multiplex polymerase chain reaction (PCR) library preparation resulted in antibody frequencies with only 42 to 62% accuracy. Additionally, Ig-seq errors resulted in antibody diversity measurements being overestimated by up to 5000-fold. To rectify this, we developed molecular amplification fingerprinting (MAF), which uses unique molecular identifier (UID) tagging before and during multiplex PCR amplification, which enabled tagging of transcripts while accounting for PCR efficiency. Combined with a bioinformatic pipeline, MAF bias correction led to measurements of antibody frequencies with up to 99% accuracy. We also used MAF to correct PCR and sequencing errors, resulting in enhanced accuracy of full-length antibody diversity measurements, achieving 98 to 100% error correction. Using murine MAF-corrected data, we established a quantitative metric of recent clonal expansion-the intraclonal diversity index-which measures the number of unique transcripts associated with an antibody clone. We used this intraclonal diversity index along with antibody frequencies and somatic hypermutation to build a logistic regression model for prediction of the immunological status of clones. The model was able to predict clonal status with high confidence but only when using MAF error and bias corrected Ig-seq data. Improved accuracy by MAF provides the potential to greatly advance Ig-seq and its utility in immunology and biotechnology.

Accurate and predictive antibody repertoire profiling by molecular amplification fingerprinting

PubMed Central

Khan, Tarik A.; Friedensohn, Simon; de Vries, Arthur R. Gorter; Straszewski, Jakub; Ruscheweyh, Hans-Joachim; Reddy, Sai T.

2016-01-01

High-throughput antibody repertoire sequencing (Ig-seq) provides quantitative molecular information on humoral immunity. However, Ig-seq is compromised by biases and errors introduced during library preparation and sequencing. By using synthetic antibody spike-in genes, we determined that primer bias from multiplex polymerase chain reaction (PCR) library preparation resulted in antibody frequencies with only 42 to 62% accuracy. Additionally, Ig-seq errors resulted in antibody diversity measurements being overestimated by up to 5000-fold. To rectify this, we developed molecular amplification fingerprinting (MAF), which uses unique molecular identifier (UID) tagging before and during multiplex PCR amplification, which enabled tagging of transcripts while accounting for PCR efficiency. Combined with a bioinformatic pipeline, MAF bias correction led to measurements of antibody frequencies with up to 99% accuracy. We also used MAF to correct PCR and sequencing errors, resulting in enhanced accuracy of full-length antibody diversity measurements, achieving 98 to 100% error correction. Using murine MAF-corrected data, we established a quantitative metric of recent clonal expansion—the intraclonal diversity index—which measures the number of unique transcripts associated with an antibody clone. We used this intraclonal diversity index along with antibody frequencies and somatic hypermutation to build a logistic regression model for prediction of the immunological status of clones. The model was able to predict clonal status with high confidence but only when using MAF error and bias corrected Ig-seq data. Improved accuracy by MAF provides the potential to greatly advance Ig-seq and its utility in immunology and biotechnology. PMID:26998518

Activity-Based Profiling of a Physiologic Aglycone Library Reveals Sugar Acceptor Promiscuity of Family 1 UDP-Glucosyltransferases from Grape1[W

PubMed Central

Bönisch, Friedericke; Frotscher, Johanna; Stanitzek, Sarah; Rühl, Ernst; Wüst, Matthias; Bitz, Oliver; Schwab, Wilfried

2014-01-01

Monoterpenols serve various biological functions and accumulate in grape (Vitis vinifera), where a major fraction occurs as nonvolatile glycosides. We have screened the grape genome for sequences with similarity to terpene URIDINE DIPHOSPHATE GLYCOSYLTRANSFERASES (UGTs) from Arabidopsis (Arabidopsis thaliana). A ripening-related expression pattern was shown for three candidates by spatial and temporal expression analyses in five grape cultivars. Transcript accumulation correlated with the production of monoterpenyl β-d-glucosides in grape exocarp during ripening and was low in vegetative tissue. Targeted functional screening of the recombinant UGTs for their biological substrates was performed by activity-based metabolite profiling (ABMP) employing a physiologic library of aglycones built from glycosides isolated from grape. This approach led to the identification of two UDP-glucose:monoterpenol β-d-glucosyltransferases. Whereas VvGT14a glucosylated geraniol, R,S-citronellol, and nerol with similar efficiency, the three allelic forms VvGT15a, VvGT15b, and VvGT15c preferred geraniol over nerol. Kinetic resolution of R,S-citronellol and R,S-linalool was shown for VvGT15a and VvGT14a, respectively. ABMP revealed geraniol as the major biological substrate but also disclosed that these UGTs may add to the production of further glycoconjugates in planta. ABMP of aglycone libraries provides a versatile tool to uncover novel biologically relevant substrates of small-molecule glycosyltransferases that often show broad sugar acceptor promiscuity. PMID:25073706

Creating a Canonical Scientific and Technical Information Classification System for NCSTRL+

NASA Technical Reports Server (NTRS)

Tiffany, Melissa E.; Nelson, Michael L.

1998-01-01

The purpose of this paper is to describe the new subject classification system for the NCSTRL+ project. NCSTRL+ is a canonical digital library (DL) based on the Networked Computer Science Technical Report Library (NCSTRL). The current NCSTRL+ classification system uses the NASA Scientific and Technical (STI) subject classifications, which has a bias towards the aerospace, aeronautics, and engineering disciplines. Examination of other scientific and technical information classification systems showed similar discipline-centric weaknesses. Traditional, library-oriented classification systems represented all disciplines, but were too generalized to serve the needs of a scientific and technically oriented digital library. Lack of a suitable existing classification system led to the creation of a lightweight, balanced, general classification system that allows the mapping of more specialized classification schemes into the new framework. We have developed the following classification system to give equal weight to all STI disciplines, while being compact and lightweight.

Effect of nonsinusoidal bias waveforms on ion energy distributions and fluorocarbon plasma etch selectivity

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

Agarwal, Ankur; Kushner, Mark J.; Iowa State University, Department of Electrical and Computer Engineering, 104 Marston Hall, Ames, Iowa 50011-2151

2005-09-15

The distributions of ion energies incident on the wafer significantly influence feature profiles and selectivity during plasma etching. Control of ion energies is typically obtained by varying the amplitude or frequency of a radio frequency sinusoidal bias voltage applied to the substrate. The resulting ion energy distribution (IED), though, is generally broad. Controlling the width and shape of the IED can potentially improve etch selectivity by distinguishing between threshold energies of surface processes. In this article, control of the IED was computationally investigated by applying a tailored, nonsinusoidal bias waveform to the substrate of an inductively coupled plasma. The waveformmore » we investigated, a quasi-dc negative bias having a short positive pulse each cycle, produced a narrow IED whose width was controllable based on the length of the positive spike and frequency. We found that the selectivity between etching Si and SiO{sub 2} in fluorocarbon plasmas could be controlled by adjusting the width and energy of the IED. Control of the energy of a narrow IED enables etching recipes that transition between speed and selectivity without change of gas mixture.« less

Mixed-mode high-power impulse magnetron sputter deposition of tetrahedral amorphous carbon with pulse-length control of ionization

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

Tucker, M. D.; Marks, N. A.; Ganesan, R.

2016-04-21

High-power impulse magnetron sputtering (HiPIMS) is used to deposit amorphous carbon thin films with sp{sup 3} fractions of 13% to 82%. Increasing the pulse length results in a transition from conventional HiPIMS deposition to a “mixed-mode” in which an arc triggers on the target surface, resulting in a large flux of carbon ions. The films are characterized using X-ray photoelectron spectroscopy, Raman spectroscopy, ellipsometry, nanoindentation, elastic recoil detection analysis, and measurements of stress and contact angle. All properties vary in a consistent manner, showing a high tetrahedral character only for long pulses, demonstrating that mixed-mode deposition is the source ofmore » the high carbon ion flux. Varying the substrate bias reveals an “energy window” effect, where the sp{sup 3} fraction of the films is greatest for a substrate bias around −100 V and decreases for higher or lower bias values. In the absence of bias, the films' properties show little dependence on the pulse length, showing that energetic ions are the origin of the highly tetrahedral character.« less

Compact ion source neutron generator

DOEpatents

Schenkel, Thomas; Persaud, Arun; Kapadia, Rehan; Javey, Ali; Chang-Hasnain, Constance; Rangelow, Ivo; Kwan, Joe

2015-10-13

A neutron generator includes a conductive substrate comprising a plurality of conductive nanostructures with free-standing tips and a source of an atomic species to introduce the atomic species in proximity to the free-standing tips. A target placed apart from the substrate is voltage biased relative to the substrate to ionize and accelerate the ionized atomic species toward the target. The target includes an element capable of a nuclear fusion reaction with the ionized atomic species to produce a one or more neutrons as a reaction by-product.

The analysis of ion-selective field-effect transistor operation in chemical sensors

NASA Astrophysics Data System (ADS)

Hotra, Zenon; Holyaka, Roman; Hladun, Michael; Humenuk, Iryna

2003-09-01

In this paper we present the research results of influence of substrate potential in ion-selective field-effect transistors (ISFET) on output signal of chemical sensors, e.g. PH-meters. It is shown that the instability of substrate-source p-n junction bias in well-known chemical sensors, which use grounded reference electrode - ISFET gate, affect on sensor characteristics in negative way. The analytical description and research results of 'substrate effect' on ISFET characteristics are considered.

Nanostructured Ti-Ta thin films synthesized by combinatorial glancing angle sputter deposition

NASA Astrophysics Data System (ADS)

Motemani, Yahya; Khare, Chinmay; Savan, Alan; Hans, Michael; Paulsen, Alexander; Frenzel, Jan; Somsen, Christoph; Mücklich, Frank; Eggeler, Gunther; Ludwig, Alfred

2016-12-01

Ti-Ta alloys are attractive materials for applications in actuators as well as biomedical implants. When fabricated as thin films, these alloys can potentially be employed as microactuators, components for micro-implantable devices and coatings on surgical implants. In this study, Ti100-x Ta x (x = 21, 30) nanocolumnar thin films are fabricated by glancing angle deposition (GLAD) at room temperature using Ti73Ta27 and Ta sputter targets. Crystal structure, morphology and microstructure of the nanostructured thin films are systematically investigated by XRD, SEM and TEM, respectively. Nanocolumns of ˜150-160 nm in width are oriented perpendicular to the substrate for both Ti79Ta21 and Ti70Ta30 compositions. The disordered α″ martensite phase with orthorhombic structure is formed in room temperature as-deposited thin films. The columns are found to be elongated small single crystals which are aligned perpendicular to the (20\\bar{4}) and (204) planes of α″ martensite, indicating that the films’ growth orientation is mainly dominated by these crystallographic planes. Laser pre-patterned substrates are utilized to obtain periodic nanocolumnar arrays. The differences in seed pattern, and inter-seed distances lead to growth of multi-level porous nanostructures. Using a unique sputter deposition geometry consisting of Ti73Ta27 and Ta sputter sources, a nanocolumnar Ti-Ta materials library was fabricated on a static substrate by a co-deposition process (combinatorial-GLAD approach). In this library, a composition spread developed between Ti72.8Ta27.2 and Ti64.4Ta35.6, as confirmed by high-throughput EDX analysis. The morphology over the materials library varies from well-isolated nanocolumns to fan-like nanocolumnar structures. The influence of two sputter sources is investigated by studying the resulting column angle on the materials library. The presented nanostructuring methods including the use of the GLAD technique along with pre-patterning and a combinatorial materials library fabrication strategy offer a promising technological approach for investigating Ti-Ta thin films for a range of applications. The proposed approaches can be similarly implemented for other materials systems which can benefit from the formation of a nanocolumnar morphology.

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

Sharma, Shailesh, E-mail: shailesh.sharma6@mail.dcu.ie; Impedans Limited, Chase House, City Junction Business Park, Northern Cross, D17 AK63, Dublin 17; Gahan, David, E-mail: david.gahan@impedans.com

A compact retarding field analyzer with embedded quartz crystal microbalance has been developed to measure deposition rate, ionized flux fraction, and ion energy distribution arriving at the substrate location. The sensor can be placed on grounded, electrically floating, or radio frequency (rf) biased electrodes. A calibration method is presented to compensate for temperature effects in the quartz crystal. The metal deposition rate, metal ionization fraction, and energy distribution of the ions arriving at the substrate location are investigated in an asymmetric bipolar pulsed dc magnetron sputtering reactor under grounded, floating, and rf biased conditions. The diagnostic presented in this researchmore » work does not suffer from complications caused by water cooling arrangements to maintain constant temperature and is an attractive technique for characterizing a thin film deposition system.« less

An all-diamond X-ray position and flux monitor using nitrogen-incorporated ultra-nanocrystalline diamond contacts

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

Zou, Mengnan; Gaowei, Mengjia; Zhou, Tianyi

Diamond X-ray detectors with conducting nitrogen-incorporated ultra-nanocrystalline diamond (N-UNCD) films as electrodes were fabricated to measure X-ray beam flux and position. Structural characterization and functionality tests were performed for these devices. The N-UNCD films grown on unseeded diamond substrates were compared with N-UNCD films grown on a seeded silicon substrate. The feasibility of the N-UNCD films acting as electrodes for X-ray detectors was confirmed by the stable performance in a monochromatic X-ray beam. The fabrication process is able to change the surface status which may influence the signal uniformity under low bias, but this effect can be neglected under fullmore » collection bias.« less

Surface treatment of ceramic articles

DOEpatents

Komvopoulos, K.; Brown, I.G.; Wei, B.; Anders, S.; Anders, A.; Bhatia, C.S.

1998-12-22

A process is disclosed for producing an article with improved ceramic surface properties including providing an article having a ceramic surface, and placing the article onto a conductive substrate holder in a hermetic enclosure. Thereafter a low pressure ambient is provided in the hermetic enclosure. A plasma including ions of solid materials is produced the ceramic surface of the article being at least partially immersed in a macroparticle free region of the plasma. While the article is immersed in the macroparticle free region, a bias of the substrate holder is biased between a low voltage at which material from the plasma condenses on the surface of the article and a high negative voltage at which ions from the plasma are implanted into the article. 15 figs.

Heterojunction photodiode on cleaved SiC

NASA Astrophysics Data System (ADS)

Solovan, Mykhailo M.; Farah, John; Kovaliuk, Taras T.; Brus, Viktor V.; Mostovyi, Andrii I.; Maistruk, Eduard V.; Maryanchuk, Pavlo D.

2018-01-01

Graphite/n-SiC Shottky diodes were prepared by means of the recently proposed technique based on the transferring of drawn graphite films onto the n-SiC single crystal substrate. Current-voltage characteristics were measured and analyzed. High quality ohmic contancts were prepared by the DC magnetron sputtering of Ni thin films onto cleaved n-type SiC single crystal substrates. The height of the potential barrier and the series resistance of the graphite/n-SiC junctions were measured and analysed. The dominant current transport mechanisms through the diodes were determined. There was shown that the dominant current transport mechanisms through the graphite/n-SiC Shottky diodes were the multi-step tunnel-recombination at forward bias and the tunnelling mechanisms at reverse bias.

MEMS switches having non-metallic crossbeams

NASA Technical Reports Server (NTRS)

Scardelletti, Maximillian C (Inventor)

2009-01-01

A RF MEMS switch comprising a crossbeam of SiC, supported by at least one leg above a substrate and above a plurality of transmission lines forming a CPW. Bias is provided by at least one layer of metal disposed on a top surface of the SiC crossbeam, such as a layer of chromium followed by a layer of gold, and extending beyond the switch to a biasing pad on the substrate. The switch utilizes stress and conductivity-controlled non-metallic thin cantilevers or bridges, thereby improving the RF characteristics and operational reliability of the switch. The switch can be fabricated with conventional silicon integrated circuit (IC) processing techniques. The design of the switch is very versatile and can be implemented in many transmission line mediums.

Enhanced stability against bias-stress of metal-oxide thin film transistors deposited at elevated temperatures

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

Fakhri, M.; Goerrn, P.; Riedl, T.

2011-09-19

Transparent zinc-tin-oxide (ZTO) thin film transistors (TFTs) have been prepared by DC magnetron sputtering. Compared to reference devices with a channel deposited at room temperature and subsequently annealing at 400 deg. C, a substantially enhanced stability against bias stress is evidenced for devices with in-situ substrate heating during deposition (400 deg. C). A reduced density of sub-gap defect states in TFT channels prepared with in-situ substrate heating is found. Concomitantly, a reduced sensitivity to the adsorption of ambient gases is evidenced for the in-situ heated devices. This finding is of particular importance for an application as driver electronics for organicmore » light emitting diode displays.« less

Indium oxide-based transparent conductive films deposited by reactive sputtering using alloy targets

NASA Astrophysics Data System (ADS)

Miyazaki, Yusuke; Maruyama, Eri; Jia, Junjun; Machinaga, Hironobu; Shigesato, Yuzo

2017-04-01

High-quality transparent conductive oxide (TCO) films, Sn-doped In2O3 (ITO) and In2O3-ZnO (IZO), were successfully deposited on either synthetic silica or polyethylene terephthalate (PET) substrates in the “transition region” by reactive dc magnetron sputtering using In-Zn and In-Sn alloy targets, respectively, with a specially designed plasma emission feedback system. The composition, crystallinity, surface morphology, and electrical and optical properties of the films were analyzed. All of the IZO films were amorphous, whereas the ITO films were polycrystalline over a wide range of deposition conditions. The minimum resistivities of the IZO and ITO films deposited on the heated PET substrates at 150 °C were 3.3 × 10-4 and 5.4 × 10-4 Ω·cm, respectively. By applying rf bias to unheated PET substrates, ITO films with a resistivity of 4.4 × 10-4 Ω·cm were deposited at a dc self-bias voltage of -60 V.

Manual for the Jet Event and Background Simulation Library(JEBSimLib)

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

Heinz, Matthias; Soltz, Ron; Angerami, Aaron

Jets are the collimated streams of particles resulting from hard scattering in the initial state of high-energy collisions. In heavy-ion collisions, jets interact with the quark-gluon plasma (QGP) before freezeout, providing a probe into the internal structure and properties of the QGP. In order to study jets, background must be subtracted from the measured event, potentially introducing a bias. We aim to understand and quantify this subtraction bias. PYTHIA, a library to simulate pure jet events, is used to simulate a model for a signature with one pure jet (a photon) and one quenched jet, where all quenched particle momentamore » are reduced by a user-de ned constant fraction. Background for the event is simulated using multiplicity values generated by the TRENTO initial state model of heavy-ion collisions fed into a thermal model consisting of a 3-dimensional Boltzmann distribution for particle types and momenta. Data from the simulated events is used to train a statistical model, which computes a posterior distribution of the quench factor for a data set. The model was tested rst on pure jet events and then on full events including the background. This model will allow for a quantitative determination of biases induced by various methods of background subtraction.« less

Manual for the Jet Event and Background Simulation Library

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

Heinz, M.; Soltz, R.; Angerami, A.

Jets are the collimated streams of particles resulting from hard scattering in the initial state of high-energy collisions. In heavy-ion collisions, jets interact with the quark-gluon plasma (QGP) before freezeout, providing a probe into the internal structure and properties of the QGP. In order to study jets, background must be subtracted from the measured event, potentially introducing a bias. We aim to understand and quantify this subtraction bias. PYTHIA, a library to simulate pure jet events, is used to simulate a model for a signature with one pure jet (a photon) and one quenched jet, where all quenched particle momentamore » are reduced by a user-de ned constant fraction. Background for the event is simulated using multiplicity values generated by the TRENTO initial state model of heavy-ion collisions fed into a thermal model consisting of a 3-dimensional Boltzmann distribution for particle types and momenta. Data from the simulated events is used to train a statistical model, which computes a posterior distribution of the quench factor for a data set. The model was tested rst on pure jet events and then on full events including the background. This model will allow for a quantitative determination of biases induced by various methods of background subtraction.« less

Managing a Special Library. Parts I and II.

ERIC Educational Resources Information Center

Labovitz, Judy; Swanigan, Meryl

1985-01-01

Various concepts from "In Search of Excellence" are described in context of authors' personal styles. Discussions address thinking in terms of options, using statistics, learning value of corporate politics, a bias toward action, productivity through people, the "lean-machine" concept, staying close to client, entrepreneurship…

Evidence for an allosteric mechanism of substrate release from membrane-transporter accessory binding proteins.

PubMed

Marinelli, Fabrizio; Kuhlmann, Sonja I; Grell, Ernst; Kunte, Hans-Jörg; Ziegler, Christine; Faraldo-Gómez, José D

2011-12-06

Numerous membrane importers rely on accessory water-soluble proteins to capture their substrates. These substrate-binding proteins (SBP) have a strong affinity for their ligands; yet, substrate release onto the low-affinity membrane transporter must occur for uptake to proceed. It is generally accepted that release is facilitated by the association of SBP and transporter, upon which the SBP adopts a conformation similar to the unliganded state, whose affinity is sufficiently reduced. Despite the appeal of this mechanism, however, direct supporting evidence is lacking. Here, we use experimental and theoretical methods to demonstrate that an allosteric mechanism of enhanced substrate release is indeed plausible. First, we report the atomic-resolution structure of apo TeaA, the SBP of the Na(+)-coupled ectoine TRAP transporter TeaBC from Halomonas elongata DSM2581(T), and compare it with the substrate-bound structure previously reported. Conformational free-energy landscape calculations based upon molecular dynamics simulations are then used to dissect the mechanism that couples ectoine binding to structural change in TeaA. These insights allow us to design a triple mutation that biases TeaA toward apo-like conformations without directly perturbing the binding cleft, thus mimicking the influence of the membrane transporter. Calorimetric measurements demonstrate that the ectoine affinity of the conformationally biased triple mutant is 100-fold weaker than that of the wild type. By contrast, a control mutant predicted to be conformationally unbiased displays wild-type affinity. This work thus demonstrates that substrate release from SBPs onto their membrane transporters can be facilitated by the latter through a mechanism of allosteric modulation of the former.

Amorphous diamond films

DOEpatents

Falabella, S.

1998-06-09

Amorphous diamond films having a significant reduction in intrinsic stress are prepared by biasing a substrate to be coated and depositing carbon ions thereon under controlled temperature conditions. 1 fig.

A high throughput mutagenic analysis of yeast sumo structure and function

PubMed Central

Newman, Heather A.; Lu, Jian; Carson, Caryn; Boeke, Jef D.

2017-01-01

Sumoylation regulates a wide range of essential cellular functions through diverse mechanisms that remain to be fully understood. Using S. cerevisiae, a model organism with a single essential SUMO gene (SMT3), we developed a library of >250 mutant strains with single or multiple amino acid substitutions of surface or core residues in the Smt3 protein. By screening this library using plate-based assays, we have generated a comprehensive structure-function based map of Smt3, revealing essential amino acid residues and residues critical for function under a variety of genotoxic and proteotoxic stress conditions. Functionally important residues mapped to surfaces affecting Smt3 precursor processing and deconjugation from protein substrates, covalent conjugation to protein substrates, and non-covalent interactions with E3 ligases and downstream effector proteins containing SUMO-interacting motifs. Lysine residues potentially involved in formation of polymeric chains were also investigated, revealing critical roles for polymeric chains, but redundancy in specific chain linkages. Collectively, our findings provide important insights into the molecular basis of signaling through sumoylation. Moreover, the library of Smt3 mutants represents a valuable resource for further exploring the functions of sumoylation in cellular stress response and other SUMO-dependent pathways. PMID:28166236

Para-nitrobenzyl esterases with enhanced activity in aqueous and nonaqueous media

DOEpatents

Arnold, Frances H.; Moore, Jeffrey C.

1998-01-01

A method for isolating and identifying modified para-nitrobenzyl esterases which exhibit improved stability and/or esterase hydrolysis activity toward selected substrates and under selected reaction conditions relative to the unmodified para-nitrobenzyl esterase. The method involves preparing a library of modified para-nitrobenzyl esterase nucleic acid segments (genes) which have nucleotide sequences that differ from the nucleic acid segment which encodes for unmodified para-nitrobenzyl esterase. The library of modified para-nitrobenzyl nucleic acid segments is expressed to provide a plurality of modified enzymes. The clones expressing modified enzymes are then screened to identify which enzymes have improved esterase activity by measuring the ability of the enzymes to hydrolyze the selected substrate under the selected reaction conditions. Specific modified para-nitrobenzyl esterases are disclosed which have improved stability and/or ester hydrolysis activity in aqueous or aqueous-organic media relative to the stability and/or ester hydrolysis activity of unmodified naturally occurring para-nitrobenzyl esterase.

Para-nitrobenzyl esterases with enhanced activity in aqueous and nonaqueous media

DOEpatents

Arnold, Frances H.; Moore, Jeffrey C.

1999-01-01

A method for isolating and identifying modified para-nitrobenzyl esterases which exhibit improved stability and/or esterase hydrolysis activity toward selected substrates and under selected reaction conditions relative to the unmodified para-nitrobenzyl esterase. The method involves preparing a library of modified para-nitrobenzyl esterase nucleic acid segments (genes) which have nucleotide sequences that differ from the nucleic acid segment which encodes for unmodified para-nitrobenzyl esterase. The library of modified para-nitrobenzyl nucleic acid segments is expressed to provide a plurality of modified enzymes. The clones expressing modified enzymes are then screened to identify which enzymes have improved esterase activity by measuring the ability of the enzymes to hydrolyze the selected substrate under the selected reaction conditions. Specific modified para-nitrobenzyl esterases are disclosed which have improved stability and/or ester hydrolysis activity in aqueous or aqueous-organic media relative to the stability and/or ester hydrolysis activity of unmodified naturally occurring para-nitrobenzyl esterase.

Exchange bias and perpendicular anisotropy study of ultrathin Pt-Co-Pt-IrMn multilayers sputtered on float glass

NASA Astrophysics Data System (ADS)

Laval, M.; Lüders, U.; Bobo, J. F.

2007-09-01

We have prepared ultrathin Pt-Co-Pt-IrMn polycrystalline multilayers on float-glass substrates by DC magnetron sputtering. We have determined the optimal set of thickness for both Pt layers, the Co layer and the IrMn biasing layer so that these samples exhibit at the same time out-of-plane magnetic anisotropy and exchange bias. Kerr microscopy domain structure imaging evidences an increase of nucleation rate accompanied with inhomogeneous magnetic behavior in the case of exchange-biased films compared to Pt-Co-Pt trilayers. Polar hysteresis loops are measured in obliquely applied magnetic field conditions, allowing us to determine both perpendicular anisotropy effective constant Keff and exchange-bias coupling JE, which are significantly different from the ones determined by standard switching field measurements.

Mis-estimation and bias of hyperpolarized apparent diffusion coefficient measurements due to slice profile effects.

PubMed

Gordon, Jeremy W; Milshteyn, Eugene; Marco-Rius, Irene; Ohliger, Michael; Vigneron, Daniel B; Larson, Peder E Z

2017-09-01

The purpose of this work was to explore the impact of slice profile effects on apparent diffusion coefficient (ADC) mapping of hyperpolarized (HP) substrates. Slice profile effects were simulated using a Gaussian radiofrequency (RF) pulse with a variety of flip angle schedules and b-value ordering schemes. A long T 1 water phantom was used to validate the simulation results, and ADC mapping of HP [ 13 C, 15 N 2 ]urea was performed on the murine liver to assess these effects in vivo. Slice profile effects result in excess signal after repeated RF pulses, causing bias in HP measurements. The largest error occurs for metabolites with small ADCs, resulting in up to 10-fold overestimation for metabolites that are in more-restricted environments. A mixed b-value scheme substantially reduces this bias, whereas scaling the slice-select gradient can mitigate it completely. In vivo, the liver ADC of hyperpolarized [ 13 C, 15 N 2 ]urea is nearly 70% lower (0.99 ± 0.22 vs 1.69 ± 0.21 × 10 -3 mm 2 /s) when slice-select gradient scaling is used. Slice profile effects can lead to bias in HP ADC measurements. A mixed b-value ordering scheme can reduce this bias compared to sequential b-value ordering. Slice-select gradient scaling can also correct for this deviation, minimizing bias and providing more-precise ADC measurements of HP substrates. Magn Reson Med 78:1087-1092, 2017. © 2016 International Society for Magnetic Resonance in Medicine. © 2016 International Society for Magnetic Resonance in Medicine.

Phage display peptide libraries: deviations from randomness and correctives

PubMed Central

Ryvkin, Arie; Ashkenazy, Haim; Weiss-Ottolenghi, Yael; Piller, Chen; Pupko, Tal; Gershoni, Jonathan M

2018-01-01

Abstract Peptide-expressing phage display libraries are widely used for the interrogation of antibodies. Affinity selected peptides are then analyzed to discover epitope mimetics, or are subjected to computational algorithms for epitope prediction. A critical assumption for these applications is the random representation of amino acids in the initial naïve peptide library. In a previous study, we implemented next generation sequencing to evaluate a naïve library and discovered severe deviations from randomness in UAG codon over-representation as well as in high G phosphoramidite abundance causing amino acid distribution biases. In this study, we demonstrate that the UAG over-representation can be attributed to the burden imposed on the phage upon the assembly of the recombinant Protein 8 subunits. This was corrected by constructing the libraries using supE44-containing bacteria which suppress the UAG driven abortive termination. We also demonstrate that the overabundance of G stems from variant synthesis-efficiency and can be corrected using compensating oligonucleotide-mixtures calibrated by mass spectroscopy. Construction of libraries implementing these correctives results in markedly improved libraries that display random distribution of amino acids, thus ensuring that enriched peptides obtained in biopanning represent a genuine selection event, a fundamental assumption for phage display applications. PMID:29420788

Increased size selectivity of Si quantum dots on SiC at low substrate temperatures: An ion-assisted self-organization approach

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

Seo, D. H.; Das Arulsamy, A.; Rider, A. E.

A simple, effective, and innovative approach based on ion-assisted self-organization is proposed to synthesize size-selected Si quantum dots (QDs) on SiC substrates at low substrate temperatures. Using hybrid numerical simulations, the formation of Si QDs through a self-organization approach is investigated by taking into account two distinct cases of Si QD formation using the ionization energy approximation theory, which considers ionized in-fluxes containing Si{sup 3+} and Si{sup 1+} ions in the presence of a microscopic nonuniform electric field induced by a variable surface bias. The results show that the highest percentage of the surface coverage by 1 and 2 nmmore » size-selected QDs was achieved using a bias of -20 V and ions in the lowest charge state, namely, Si{sup 1+} ions in a low substrate temperature range (227-327 deg. C). As low substrate temperatures ({<=}500 deg. C) are desirable from a technological point of view, because (i) low-temperature deposition techniques are compatible with current thin-film Si-based solar cell fabrication and (ii) high processing temperatures can frequently cause damage to other components in electronic devices and destroy the tandem structure of Si QD-based third-generation solar cells, our results are highly relevant to the development of the third-generation all-Si tandem photovoltaic solar cells.« less

Increased size selectivity of Si quantum dots on SiC at low substrate temperatures: An ion-assisted self-organization approach

NASA Astrophysics Data System (ADS)

Seo, D. H.; Rider, A. E.; Das Arulsamy, A.; Levchenko, I.; Ostrikov, K.

2010-01-01

A simple, effective, and innovative approach based on ion-assisted self-organization is proposed to synthesize size-selected Si quantum dots (QDs) on SiC substrates at low substrate temperatures. Using hybrid numerical simulations, the formation of Si QDs through a self-organization approach is investigated by taking into account two distinct cases of Si QD formation using the ionization energy approximation theory, which considers ionized in-fluxes containing Si3+ and Si1+ ions in the presence of a microscopic nonuniform electric field induced by a variable surface bias. The results show that the highest percentage of the surface coverage by 1 and 2 nm size-selected QDs was achieved using a bias of -20 V and ions in the lowest charge state, namely, Si1+ ions in a low substrate temperature range (227-327 °C). As low substrate temperatures (≤500 °C) are desirable from a technological point of view, because (i) low-temperature deposition techniques are compatible with current thin-film Si-based solar cell fabrication and (ii) high processing temperatures can frequently cause damage to other components in electronic devices and destroy the tandem structure of Si QD-based third-generation solar cells, our results are highly relevant to the development of the third-generation all-Si tandem photovoltaic solar cells.

Fabrication of amorphous diamond films

DOEpatents

Falabella, S.

1995-12-12

Amorphous diamond films having a significant reduction in intrinsic stress are prepared by biasing a substrate to be coated and depositing carbon ions thereon under controlled temperature conditions. 1 fig.

A Systematic Review of Experimental Paradigms for Exploring Biased Interpretation of Ambiguous Information with Emotional and Neutral Associations.

PubMed

Schoth, Daniel E; Liossi, Christina

2017-01-01

Interpretation biases have been extensively explored in a range of populations, including patients with anxiety and depressive disorders where they have been argued to influence the onset and maintenance of such conditions. Other populations in which interpretation biases have been explored include patients with chronic pain, anorexia nervosa, and alcohol dependency among others, although this literature is more limited. In this research, stimuli with threatening/emotional and neutral meanings are presented, with participant responses indicative of ambiguity resolution. A large number of paradigms have been designed and implemented in the exploration of interpretation biases, some varying in minor features only. This article provides a review of experimental paradigms available for exploring interpretation biases, with the aim to stimulate and inform the design of future research exploring cognitive biases across a range of populations. A systematic search of the experimental literature was conducted in Medline, PsychINFO, Web of Science, CINAHL, and Cochrane Library databases. Search terms were information, stimuli , and ambiguous intersected with the terms interpretation and bias * . Forty-five paradigms were found, categorized into those using ambiguous words, ambiguous images, and ambiguous scenarios. The key features, strengths and limitations of the paradigms identified are discussed.

CORALINA: a universal method for the generation of gRNA libraries for CRISPR-based screening.

PubMed

Köferle, Anna; Worf, Karolina; Breunig, Christopher; Baumann, Valentin; Herrero, Javier; Wiesbeck, Maximilian; Hutter, Lukas H; Götz, Magdalena; Fuchs, Christiane; Beck, Stephan; Stricker, Stefan H

2016-11-14

The bacterial CRISPR system is fast becoming the most popular genetic and epigenetic engineering tool due to its universal applicability and adaptability. The desire to deploy CRISPR-based methods in a large variety of species and contexts has created an urgent need for the development of easy, time- and cost-effective methods enabling large-scale screening approaches. Here we describe CORALINA (comprehensive gRNA library generation through controlled nuclease activity), a method for the generation of comprehensive gRNA libraries for CRISPR-based screens. CORALINA gRNA libraries can be derived from any source of DNA without the need of complex oligonucleotide synthesis. We show the utility of CORALINA for human and mouse genomic DNA, its reproducibility in covering the most relevant genomic features including regulatory, coding and non-coding sequences and confirm the functionality of CORALINA generated gRNAs. The simplicity and cost-effectiveness make CORALINA suitable for any experimental system. The unprecedented sequence complexities obtainable with CORALINA libraries are a necessary pre-requisite for less biased large scale genomic and epigenomic screens.

Enzyme reversal to explore the function of yeast E3 ubiquitin-ligases.

PubMed

MacDonald, Chris; Winistorfer, Stanley; Pope, Robert M; Wright, Michael E; Piper, Robert C

2017-07-01

The covalent attachment of ubiquitin onto proteins can elicit a variety of downstream consequences. Attachment is mediated by a large array of E3 ubiquitin ligases, each thought be subject to regulatory control and to have a specific repertoire of substrates. Assessing the biological roles of ligases, and in particular, identifying their biologically relevant substrates has been a persistent yet challenging question. In this study, we describe tools that may help achieve both of these goals. We describe a strategy whereby the activity of a ubiquitin ligase has been enzymatically reversed, accomplished by fusing it to a catalytic domain of an exogenous deubiquitinating enzyme. We present a library of 72 "anti-ligases" that appear to work in a dominant-negative fashion to stabilize their cognate substrates against ubiquitin-dependent proteasomal and lysosomal degradation. We then used the ligase-deubiquitinating enzyme (DUb) library to screen for E3 ligases involved in post-Golgi/endosomal trafficking. We identify ligases previously implicated in these pathways (Rsp5 and Tul1), in addition to ligases previously localized to endosomes (Pib1 and Vps8). We also document an optimized workflow for isolating and analyzing the "ubiquitome" of yeast, which can be used with mass spectrometry to identify substrates perturbed by expression of particular ligase-DUb fusions. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Modeling of frequency agile devices: development of PKI neuromodeling library based on hierarchical network structure

NASA Astrophysics Data System (ADS)

Sanchez, P.; Hinojosa, J.; Ruiz, R.

2005-06-01

Recently, neuromodeling methods of microwave devices have been developed. These methods are suitable for the model generation of novel devices. They allow fast and accurate simulations and optimizations. However, the development of libraries makes these methods to be a formidable task, since they require massive input-output data provided by an electromagnetic simulator or measurements and repeated artificial neural network (ANN) training. This paper presents a strategy reducing the cost of library development with the advantages of the neuromodeling methods: high accuracy, large range of geometrical and material parameters and reduced CPU time. The library models are developed from a set of base prior knowledge input (PKI) models, which take into account the characteristics common to all the models in the library, and high-level ANNs which give the library model outputs from base PKI models. This technique is illustrated for a microwave multiconductor tunable phase shifter using anisotropic substrates. Closed-form relationships have been developed and are presented in this paper. The results show good agreement with the expected ones.

Microbial dynamics in upflow anaerobic sludge blanket (UASB) bioreactor granules in response to short-term changes in substrate feed

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

Kovacik, William P.; Scholten, Johannes C.; Culley, David E.

2010-08-01

The complexity and diversity of the microbial communities in biogranules from an upflow anaerobic sludge blanket (UASB) bioreactor were determined in response to short-term changes in substrate feeds. The reactor was fed simulated brewery wastewater (SBWW) (70% ethanol, 15% acetate, 15% propionate) for 1.5 months (phase 1), acetate / sulfate for 2 months (phase 2), acetate-alone for 3 months (phase 3), and then a return to SBWW for 2 months (phase 4). Performance of the reactor remained relatively stable throughout the experiment as shown by COD removal and gas production. 16S rDNA, methanogen-associated mcrA and sulfate reducer-associated dsrAB genes weremore » PCR amplified, then cloned and sequenced. Sequence analysis of 16S clone libraries showed a relatively simple community composed mainly of the methanogenic Archaea (Methanobacterium and Methanosaeta), members of the Green Non-Sulfur (Chloroflexi) group of Bacteria, followed by fewer numbers of Syntrophobacter, Spirochaeta, Acidobacteria and Cytophaga-related Bacterial sequences. Methanogen-related mcrA clone libraries were dominated throughout by Methanobacter and Methanospirillum related sequences. Although not numerous enough to be detected in our 16S rDNA libraries, sulfate reducers were detected in dsrAB clone libraries, with sequences related to Desulfovibrio and Desulfomonile. Community diversity levels (Shannon-Weiner index) generally decreased for all libraries in response to a change from SBWW to acetate-alone feed. But there was a large transitory increase noted in 16S diversity at the two-month sampling on acetate-alone, entirely related to an increase in Bacterial diversity. Upon return to SBWW conditions in phase 4, all diversity measures returned to near phase 1 levels.« less

Specificity profiling of protein-binding domains using one-bead-one-compound Peptide libraries.

PubMed

Kunys, Andrew R; Lian, Wenlong; Pei, Dehua

2012-12-01

One-bead-one-compound (OBOC) libraries consist of structurally related compounds (e.g., peptides) covalently attached to a solid support, with each resin bead carrying a unique compound. OBOC libraries of high structural diversity can be rapidly synthesized and screened without the need for any special equipment, and therefore can be employed in any chemical or biochemical laboratory. OBOC peptide libraries have been widely used to map the ligand specificity of proteins, to determine the substrate specificity of enzymes, and to develop inhibitors against macromolecular targets. They have proven particularly useful in profiling the binding specificity of protein modular domains (e.g., SH2 domains, BIR domains, and PDZ domains); subsequently, the specificity information can be used to predict the protein targets of these domains. The protocols outlined in this article describe the methodologies for synthesizing and screening OBOC peptide libraries against SH2 and PDZ domains, and the related data analysis. Curr. Protoc. Chem. Biol. 4:331-355 © 2012 by John Wiley & Sons, Inc.

Combinatorial Optimization of Heterogeneous Catalysts Used in the Growth of Carbon Nanotubes

NASA Technical Reports Server (NTRS)

Cassell, Alan M.; Verma, Sunita; Delzeit, Lance; Meyyappan, M.; Han, Jie

2000-01-01

Libraries of liquid-phase catalyst precursor solutions were printed onto iridium-coated silicon substrates and evaluated for their effectiveness in catalyzing the growth of multi-walled carbon nanotubes (MWNTs) by chemical vapor deposition (CVD). The catalyst precursor solutions were composed of inorganic salts and a removable tri-block copolymer (EO)20(PO)70(EO)20 (EO = ethylene oxide, PO = propylene oxide) structure-directing agent (SDA), dissolved in ethanol/methanol mixtures. Sample libraries were quickly assayed using scanning electron microscopy after CVD growth to identify active catalysts and CVD conditions. Composition libraries and focus libraries were then constructed around the active spots identified in the discovery libraries to understand how catalyst precursor composition affects the yield, density, and quality of the nanotubes. Successful implementation of combinatorial optimization methods in the development of highly active, carbon nanotube catalysts is demonstrated, as well as the identification of catalyst formulations that lead to varying densities and shapes of aligned nanotube towers.

Solid-Phase Synthesis of Diverse Peptide Tertiary Amides By Reductive Amination

PubMed Central

Pels, Kevin; Kodadek, Thomas

2015-01-01

The synthesis of libraries of conformationally-constrained peptide-like oligomers is an important goal in combinatorial chemistry. In this regard an attractive building block is the N-alkylated peptide, also known as peptide tertiary amide (PTA). PTAs are strongly biased conformationally due to allylic 1,3 strain interactions. We report here an improved synthesis of these species on solid supports through the use of reductive amination chemistry using amino acid-terminated, bead-displayed oligomers and diverse aldehydes. The utility of this chemistry is demonstrated by the synthesis of a library of 10,000 mixed peptoid-PTA oligomers. PMID:25695359

Development of Fluorescent Substrates and Assays for the Key Autophagy-Related Cysteine Protease Enzyme, ATG4B

PubMed Central

Nguyen, Thanh G.; Honson, Nicolette S.; Arns, Steven; Davis, Tara L.; Dhe-Paganon, Sirano; Kovacic, Suzana; Kumar, Nag S.; Pfeifer, Tom A.

2014-01-01

Abstract The cysteine protease ATG4B plays a role in key steps of the autophagy process and is of interest as a potential therapeutic target. At an early step, ATG4B cleaves proLC3 isoforms to form LC3-I for subsequent lipidation to form LC3-II and autophagosome membrane insertion. ATG4B also cleaves phosphatidylethanolamine (PE) from LC3-II to regenerate LC3-I, enabling its recycling for further membrane biogenesis. Here, we report several novel assays for monitoring the enzymatic activity of ATG4B. An assay based on mass spectrometric analysis and quantification of cleavage of the substrate protein LC3-B was developed and, while useful for mechanistic studies, was not suitable for high throughput screening (HTS). A doubly fluorescent fluorescence resonance energy transfer (FRET) ligand YFP-LC3B-EmGFP (FRET-LC3) was constructed and shown to be an excellent substrate for ATG4B with rates of cleavage similar to that for LC3B itself. A HTS assay to identify candidate inhibitors of ATG4B utilizing FRET-LC3 as a substrate was developed and validated with a satisfactory Z′ factor and high signal-to-noise ratio suitable for screening small molecule libraries. Pilot screens of the 1,280-member library of pharmacologically active compounds (LOPAC™) and a 3,481-member library of known drugs (KD2) gave hit rates of 0.6% and 0.5% respectively, and subsequent titrations confirmed ATG4B inhibitory activity for three compounds, both in the FRET and mass spectrometry assays. The FRET- and mass spectrometry–based assays we have developed will allow for both HTS for inhibitors of ATG4B and mechanistic approaches to study inhibition of a major component of the autophagy pathway. PMID:24735444

Validation of a weather forecast model at radiance level against satellite observations allowing quantification of temperature, humidity, and cloud-related biases

NASA Astrophysics Data System (ADS)

Bani Shahabadi, Maziar; Huang, Yi; Garand, Louis; Heilliette, Sylvain; Yang, Ping

2016-09-01

An established radiative transfer model (RTM) is adapted for simulating all-sky infrared radiance spectra from the Canadian Global Environmental Multiscale (GEM) model in order to validate its forecasts at the radiance level against Atmospheric InfraRed Sounder (AIRS) observations. Synthetic spectra are generated for 2 months from short-term (3-9 h) GEM forecasts. The RTM uses a monthly climatological land surface emissivity/reflectivity atlas. An updated ice particle optical property library was introduced for cloudy radiance calculations. Forward model brightness temperature (BT) biases are assessed to be of the order of ˜1 K for both clear-sky and overcast conditions. To quantify GEM forecast meteorological variables biases, spectral sensitivity kernels are generated and used to attribute radiance biases to surface and atmospheric temperatures, atmospheric humidity, and clouds biases. The kernel method, supplemented with retrieved profiles based on AIRS observations in collocation with a microwave sounder, achieves good closure in explaining clear-sky radiance biases, which are attributed mostly to surface temperature and upper tropospheric water vapor biases. Cloudy-sky radiance biases are dominated by cloud-induced radiance biases. Prominent GEM biases are identified as: (1) too low surface temperature over land, causing about -5 K bias in the atmospheric window region; (2) too high upper tropospheric water vapor, inducing about -3 K bias in the water vapor absorption band; (3) too few high clouds in the convective regions, generating about +10 K bias in window band and about +6 K bias in the water vapor band.

Precision Photothermal Annealing of Nanoporous Gold Thin Films for the Microfabrication of a Single-chip Material Libraries

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

Harris, C. D.; Shen, N.; Rubenchik, A.

2015-06-30

Single-chip material libraries of thin films of nanostructured materials are a promising approach for high throughput studies of structure-property relationship in the fields of physics and biology. Nanoporous gold (np-Au), produced by an alloy corrosion process, is a nanostructured material of specific interest in both these fields. One attractive property of np-Au is its self-similar coarsening behavior by thermally induced surface diffusion. However, traditional heat application techniques for the modification of np-Au are bulk processes that cannot be used to generate a library of different pore sizes on a single chip. Laser micromachining offers an attractive solution to this problemmore » by providing a means to apply energy with high spatial and temporal resolution. In the present study we use finite element multiphysics simulations to predict the effects of laser mode (continuous-wave vs. pulsed) and supporting substrate thermal conductivity on the local np-Au film temperatures during photothermal annealing and subsequently investigate the mechanisms by which the np-Au network is coarsening. Our simulations predict that continuous-wave mode laser irradiation on a silicon supporting substrate supports the widest range of morphologies that can be created through the photothermal annealing of thin film np-Au. Using this result we successfully fabricate a single-chip material library consisting of 81 np-Au samples of 9 different morphologies for use in increased throughput material interaction studies.« less

Direction of Perceived Motion and Eye Movements Show Similar Biases for Asymmetrically Windowed Moving Plaids

NASA Technical Reports Server (NTRS)

Beutter, B. R.; Mulligan, J. B.; Stone, L. S.; Hargens, Alan R. (Technical Monitor)

1995-01-01

We have shown that moving a plaid in an asymmetric window biases the perceived direction of motion (Beutter, Mulligan & Stone, ARVO 1994). We now explore whether these biased motion signals might also drive the smooth eye-movement response by comparing the perceived and tracked directions. The human smooth oculomotor response to moving plaids appears to be driven by the perceived rather than the veridical direction of motion. This suggests that human motion perception and smooth eye movements share underlying neural motion-processing substrates as has already been shown to be true for monkeys.

A Combinatorial Platform for the Optimization of Peptidomimetic Methyl-Lysine Reader Antagonists

NASA Astrophysics Data System (ADS)

Barnash, Kimberly D.

Post-translational modification of histone N-terminal tails mediates chromatin compaction and, consequently, DNA replication, transcription, and repair. While numerous post-translational modifications decorate histone tails, lysine methylation is an abundant mark important for both gene activation and repression. Methyl-lysine (Kme) readers function through binding mono-, di-, or trimethyl-lysine. Chemical intervention of Kme readers faces numerous challenges due to the broad surface-groove interactions between readers and their cognate histone peptides; yet, the increasing interest in understanding chromatin-modifying complexes suggests tractable lead compounds for Kme readers are critical for elucidating the mechanisms of chromatin dysregulation in disease states and validating the druggability of these domains and complexes. The successful discovery of a peptide-derived chemical probe, UNC3866, for the Polycomb repressive complex 1 (PRC1) chromodomain Kme readers has proven the potential for selective peptidomimetic inhibition of reader function. Unfortunately, the systematic modification of peptides-to-peptidomimetics is a costly and inefficient strategy for target-class hit discovery against Kme readers. Through the exploration of biased chemical space via combinatorial on-bead libraries, we have developed two concurrent methodologies for Kme reader chemical probe discovery. We employ biased peptide combinatorial libraries as a hit discovery strategy with subsequent optimization via iterative targeted libraries. Peptide-to-peptidomimetic optimization through targeted library design was applied based on structure-guided library design around the interaction of the endogenous peptide ligand with three target Kme readers. Efforts targeting the WD40 reader EED led to the discovery of the 3-mer peptidomimetic ligand UNC5115 while combinatorial repurposing of UNC3866 for off-target chromodomains resulted in the discovery of UNC4991, a CDYL/2-selective ligand, and UNC4848, a MPP8 and CDYL/2 ligand. Ultimately, our efforts demonstrate the generalizability of a peptidomimetic combinatorial platform for the optimization of Kme reader ligands in a target class manner.

Should fatty acid signature proportions sum to 1 for diet estimation?

USGS Publications Warehouse

Bromaghin, Jeffrey F.; Budge, Suzanne M.; Thiemann, Gregory W.

2016-01-01

Knowledge of predator diets, including how diets might change through time or differ among predators, provides essential insights into their ecology. Diet estimation therefore remains an active area of research within quantitative ecology. Quantitative fatty acid signature analysis (QFASA) is an increasingly common method of diet estimation. QFASA is based on a data library of prey signatures, which are vectors of proportions summarizing the fatty acid composition of lipids, and diet is estimated as the mixture of prey signatures that most closely approximates a predator’s signature. Diets are typically estimated using proportions from a subset of all fatty acids that are known to be solely or largely influenced by diet. Given the subset of fatty acids selected, the current practice is to scale their proportions to sum to 1.0. However, scaling signature proportions has the potential to distort the structural relationships within a prey library and between predators and prey. To investigate that possibility, we compared the practice of scaling proportions with two alternatives and found that the traditional scaling can meaningfully bias diet estimators under some conditions. Two aspects of the prey types that contributed to a predator’s diet influenced the magnitude of the bias: the degree to which the sums of unscaled proportions differed among prey types and the identifiability of prey types within the prey library. We caution investigators against the routine scaling of signature proportions in QFASA.

Generation of the V4.2m5 and AMPX and MPACT 51 and 252-Group Libraries with ENDF/B-VII.0 and VII.1

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

Kim, Kang Seog

The evaluated nuclear data file (ENDF)/B-7.0 v4.1m3 MPACT 47-group library has been used as a main library for the Consortium for Advanced Simulation of Light Water Reactors (CASL) neutronics simulator in simulating pressurized water reactor (PWR) problems. Recent analysis for the high void boiling water reactor (BWR) fuels and burnt fuels indicates that the 47-group library introduces relatively large reactivity bias. Since the 47- group structure does not match with the SCALE 6.2 252-group boundaries, the CASL Virtual Environment for Reactor Applications Core Simulator (VERA-CS) MPACT library must be maintained independently, which causes quality assurance concerns. In order to addressmore » this issue, a new 51-group structure has been proposed based on the MPACT 47- g and SCALE 252-g structures. In addition, the new CASL library will include a 19-group structure for gamma production and interaction cross section data based on the SCALE 19- group structure. New AMPX and MPACT 51-group libraries have been developed with the ENDF/B-7.0 and 7.1 evaluated nuclear data. The 19-group gamma data also have been generated for future use, but they are only available on the AMPX 51-g library. In addition, ENDF/B-7.0 and 7.1 MPACT 252-g libraries have been generated for verification purposes. Various benchmark calculations have been performed to verify and validate the newly developed libraries.« less

Robust Sub-nanomolar Library Preparation for High Throughput Next Generation Sequencing.

PubMed

Wu, Wells W; Phue, Je-Nie; Lee, Chun-Ting; Lin, Changyi; Xu, Lai; Wang, Rong; Zhang, Yaqin; Shen, Rong-Fong

2018-05-04

Current library preparation protocols for Illumina HiSeq and MiSeq DNA sequencers require ≥2 nM initial library for subsequent loading of denatured cDNA onto flow cells. Such amounts are not always attainable from samples having a relatively low DNA or RNA input; or those for which a limited number of PCR amplification cycles is preferred (less PCR bias and/or more even coverage). A well-tested sub-nanomolar library preparation protocol for Illumina sequencers has however not been reported. The aim of this study is to provide a much needed working protocol for sub-nanomolar libraries to achieve outcomes as informative as those obtained with the higher library input (≥ 2 nM) recommended by Illumina's protocols. Extensive studies were conducted to validate a robust sub-nanomolar (initial library of 100 pM) protocol using PhiX DNA (as a control), genomic DNA (Bordetella bronchiseptica and microbial mock community B for 16S rRNA gene sequencing), messenger RNA, microRNA, and other small noncoding RNA samples. The utility of our protocol was further explored for PhiX library concentrations as low as 25 pM, which generated only slightly fewer than 50% of the reads achieved under the standard Illumina protocol starting with > 2 nM. A sub-nanomolar library preparation protocol (100 pM) could generate next generation sequencing (NGS) results as robust as the standard Illumina protocol. Following the sub-nanomolar protocol, libraries with initial concentrations as low as 25 pM could also be sequenced to yield satisfactory and reproducible sequencing results.

Natural product-like virtual libraries: recursive atom-based enumeration.

PubMed

Yu, Melvin J

2011-03-28

A new molecular enumerator is described that allows chemically and architecturally diverse sets of natural product-like and drug-like structures to be generated from a core structure as simple as a single carbon atom or as complex as a polycyclic ring system. Integrated with a rudimentary machine-learning algorithm, the enumerator has the ability to assemble biased virtual libraries enriched in compounds predicted to meet target criteria. The ability to dynamically generate relatively small focused libraries in a recursive manner could reduce the computational time and infrastructure necessary to construct and manage extremely large static libraries. Depending on enumeration conditions, natural product-like structures can be produced with a wide range of heterocyclic and alicyclic ring assemblies. Because natural products represent a proven source of validated structures for identifying and designing new drug candidates, mimicking the structural and topological diversity found in nature with a dynamic set of virtual natural product-like compounds may facilitate the creation of new ideas for novel, biologically relevant lead structures in areas of uncharted chemical space.

Identification of Broad-Based HIV-1 Protease Inhibitors From Combinatorial Libraries

PubMed Central

Chang, Max W.; Giffin, Michael J.; Muller, Rolf; Savage, Jeremiah; Lin, Ying C.; Hong, Sukwon; Jin, Wei; Whitby, Landon R.; Elder, John H.; Boger, Dale L.; Torbett, Bruce E.

2011-01-01

Clinically approved inhibitors of HIV-1 protease function via a competitive mechanism. A particular vulnerability of competitive inhibitors is their sensitivity to increases in substrate concentration, as may occur during virion assembly, budding and processing into a mature, infectious viral particle. Advances in chemical synthesis have led to the development of new chemical libraries with high diversity using rapid in-solution syntheses. These libraries have been previously shown to be effective at disrupting protein-protein and protein-nucleic acid interfaces. We have screened 44,000 compounds from such a library to identify inhibitors of HIV-1 protease. One compound was identified that inhibits wild type protease, as well as a drug-resistant protease with 6 mutations. Moreover, analysis of this compound suggests an allosteric, non-competitive mechanism of inhibition and may represent a starting point for an additional strategy for anti-retroviral therapy. PMID:20507280

Investigating the chemical mist deposition technique for poly(3,4-ethylenedioxythiophene):poly(styrene sulfonate) on textured crystalline-silicon for organic/crystalline-silicon heterojunction solar cells

NASA Astrophysics Data System (ADS)

Hossain, Jaker; Ohki, Tatsuya; Ichikawa, Koki; Fujiyama, Kazuhiko; Ueno, Keiji; Fujii, Yasuhiko; Hanajiri, Tatsuro; Shirai, Hajime

2016-03-01

Chemical mist deposition (CMD) of poly(3,4-ethylenedioxythiophene):poly(styrene sulfonate) (PEDOT:PSS) was investigated in terms of cavitation frequency f, solvent, flow rate of nitrogen, substrate temperature Ts, and substrate dc bias Vs as variables for efficient PEDOT:PSS/crystalline silicon (c-Si) heterojunction solar cells. The high-speed-camera and differential mobility analysis characterizations revealed that the average size and flux of PEDOT:PSS mist depend on f, type of solvent, and Vs. Film deposition occurred when positive Vs was applied to the c-Si substrate at Ts of 30-40 °C, whereas no deposition of films occurred with negative Vs, implying that the film is deposited mainly from negatively charged mist. The uniform deposition of PEDOT:PSS films occurred on textured c-Si(100) substrates by adjusting Ts and Vs. The adhesion of CMD PEDOT:PSS film to c-Si was greatly enhanced by applying substrate dc bias Vs compared with that of spin-coated film. The CMD PEDOT:PSS/c-Si heterojunction solar cell devices on textured c-Si(100) in 2 × 2 cm2 exhibited a power conversion efficiency η of 11.0% with better uniformity of the solar cell parameters. Furthermore, η was increased to 12.5% by adding an AR coating layer of molybdenum oxide MoOx formed by CMD. These findings suggest that CMD with negatively charged mist has great potential for the uniform deposition of organic and inorganic materials on textured c-Si substrates by suitably adjusting Ts and Vs.

Ion Beam Analysis of the Thermal Stability of Hydrogenated Diamond-Like Carbon Thin Films on Si Substrate

NASA Astrophysics Data System (ADS)

Nandasiri, M. I.; Moore, A.; Garratt, E.; Wickey, K. J.; AlFaify, S.; Gao, X.; Kayani, A.; Ingram, D.

2009-03-01

Unbalanced magnetron sputtering deposition of C-H films has been performed with various levels of negative substrate bias and with a fixed flow rate of hydrogen. Argon was used as a sputtering gas and formed the majority of the gas in the plasma. The effect of hydrogenation on the final concentration of trapped elements and their thermal stability with respect to hydrogen content is studied using ion beam analysis (IBA) techniques. The elemental concentrations of the films were measured in the films deposited on silicon substrates with a 2.5 MeV of H+ beam, which is used to perform Rutherford Backscattering Spectrometry (RBS) and Non-Rutherford Backscattering spectrometry (NRBS) and with 16 MeV of O5+ beam, used to perform Elastic Recoil Detection Analysis (ERDA). Effect of bias on the thermal stability of trapped hydrogen in the films has been studied. As the films were heated in-situ in vacuum using a non-gassy button heater, hydrogen was found to be decreasing around 400° C.

Experimental and Theoretical Study of 4H-SiC JFET Threshold Voltage Body Bias Effect from 25 C to 500 C

NASA Technical Reports Server (NTRS)

Neudeck, Philip G.; Spry, David J.; Chen, Liangyu

2015-01-01

This work reports a theoretical and experimental study of 4H-SiC JFET threshold voltage as a function of substrate body bias, device position on the wafer, and temperature from 25 C (298K) to 500 C (773K). Based on these results, an alternative approach to SPICE circuit simulation of body effect for SiC JFETs is proposed.

Strategy to discover diverse optimal molecules in the small molecule universe.

PubMed

Rupakheti, Chetan; Virshup, Aaron; Yang, Weitao; Beratan, David N

2015-03-23

The small molecule universe (SMU) is defined as a set of over 10(60) synthetically feasible organic molecules with molecular weight less than ∼500 Da. Exhaustive enumerations and evaluation of all SMU molecules for the purpose of discovering favorable structures is impossible. We take a stochastic approach and extend the ACSESS framework ( Virshup et al. J. Am. Chem. Soc. 2013 , 135 , 7296 - 7303 ) to develop diversity oriented molecular libraries that can generate a set of compounds that is representative of the small molecule universe and that also biases the library toward favorable physical property values. We show that the approach is efficient compared to exhaustive enumeration and to existing evolutionary algorithms for generating such libraries by testing in the NKp fitness landscape model and in the fully enumerated GDB-9 chemical universe containing 3 × 10(5) molecules.

Strategy To Discover Diverse Optimal Molecules in the Small Molecule Universe

PubMed Central

2015-01-01

The small molecule universe (SMU) is defined as a set of over 1060 synthetically feasible organic molecules with molecular weight less than ∼500 Da. Exhaustive enumerations and evaluation of all SMU molecules for the purpose of discovering favorable structures is impossible. We take a stochastic approach and extend the ACSESS framework (Virshup et al. J. Am. Chem. Soc.2013, 135, 7296–730323548177) to develop diversity oriented molecular libraries that can generate a set of compounds that is representative of the small molecule universe and that also biases the library toward favorable physical property values. We show that the approach is efficient compared to exhaustive enumeration and to existing evolutionary algorithms for generating such libraries by testing in the NKp fitness landscape model and in the fully enumerated GDB-9 chemical universe containing 3 × 105 molecules. PMID:25594586

CARS Spectral Fitting with Multiple Resonant Species using Sparse Libraries

NASA Technical Reports Server (NTRS)

Cutler, Andrew D.; Magnotti, Gaetano

2010-01-01

The dual pump CARS technique is often used in the study of turbulent flames. Fast and accurate algorithms are needed for fitting dual-pump CARS spectra for temperature and multiple chemical species. This paper describes the development of such an algorithm. The algorithm employs sparse libraries, whose size grows much more slowly with number of species than a conventional library. The method was demonstrated by fitting synthetic "experimental" spectra containing 4 resonant species (N2, O2, H2 and CO2), both with noise and without it, and by fitting experimental spectra from a H2-air flame produced by a Hencken burner. In both studies, weighted least squares fitting of signal, as opposed to least squares fitting signal or square-root signal, was shown to produce the least random error and minimize bias error in the fitted parameters.

Scholarly Communication: ARL as a Catalyst for Change

ERIC Educational Resources Information Center

Case, Mary M.

2009-01-01

With the creation of the Office of Scholarly Communication (OSC) in 1990, the Association of Research Libraries (ARL) launched an initiative to focus widespread attention on the dysfunctions in the scholarly publishing system. Through the collection and dissemination of data documenting the serials crisis, a bias for action that led to the…

Analysis of Mycobacterium avium subspecies paratuberculosis mutant libraries reveals loci-dependent transposition biases and strategies to novel mutant discovery

USDA-ARS?s Scientific Manuscript database

Mycobacterium avium subsp. paratuberculosis (MAP), the etiologic agent of Johne’s disease, is one of the most important bacterial pathogens in ruminants. The lack of efficacious control measures demands a thorough understanding of MAP pathogenesis to develop new vaccines and diagnostic tests. The ge...

A Survey of the Experiences of African Librarians in American Academic Libraries

ERIC Educational Resources Information Center

Ibraheem, Abiodun I.; Devine, Christopher

2013-01-01

A national research study was undertaken to identify and clarify issues related to the employment in academic settings of African librarians who have relocated to the United States. It examined, by means of a survey, employment issues concerned with education, credentialing, language skills and cultural bias from the perspective of those…

Effects of magnetic flux density and substrate bias voltage on Ni films prepared on a flexible substrate material using unbalanced magnetron sputtering assisted by inductively coupled plasma

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

Koda, Tatsunori; Toyota, Hiroshi, E-mail: h.toyota.za@it-hiroshima.ac.jp

The authors fabricated Ni films on a flexible substrate material using unbalanced magnetron sputtering assisted by inductively coupled plasma. The effects of magnetic flux density B{sub C} and substrate DC bias voltage V{sub S} on the Ni film structures were investigated. For V{sub S} = −40 V, the average surface grain size D{sub G} measured by atomic force microscopy for B{sub C} = 0, 3, and 5 mT was 88.2, 95.4, and 104.4 nm, respectively. In addition, D{sub G} increased with V{sub S}. From x-ray diffraction measurements, the (111) and (200) peaks were clearly visible for the fabricated Ni films. The ratio of the integrated intensities ofmore » I(111)/I(200) increased with V{sub S}. For V{sub S} = −40 V and B{sub C} = 3 mT, a film resistivity ρ of 8.96 × 10{sup −6} Ω cm was observed, which is close to the Ni bulk value of 6.84 × 10{sup −6} Ω cm. From these results, the authors determined that the structure of the fabricated Ni films on the flexible substrate material was affected by the values of B{sub C} and V{sub S}.« less

RNA-SeQC: RNA-seq metrics for quality control and process optimization.

PubMed

DeLuca, David S; Levin, Joshua Z; Sivachenko, Andrey; Fennell, Timothy; Nazaire, Marc-Danie; Williams, Chris; Reich, Michael; Winckler, Wendy; Getz, Gad

2012-06-01

RNA-seq, the application of next-generation sequencing to RNA, provides transcriptome-wide characterization of cellular activity. Assessment of sequencing performance and library quality is critical to the interpretation of RNA-seq data, yet few tools exist to address this issue. We introduce RNA-SeQC, a program which provides key measures of data quality. These metrics include yield, alignment and duplication rates; GC bias, rRNA content, regions of alignment (exon, intron and intragenic), continuity of coverage, 3'/5' bias and count of detectable transcripts, among others. The software provides multi-sample evaluation of library construction protocols, input materials and other experimental parameters. The modularity of the software enables pipeline integration and the routine monitoring of key measures of data quality such as the number of alignable reads, duplication rates and rRNA contamination. RNA-SeQC allows investigators to make informed decisions about sample inclusion in downstream analysis. In summary, RNA-SeQC provides quality control measures critical to experiment design, process optimization and downstream computational analysis. See www.genepattern.org to run online, or www.broadinstitute.org/rna-seqc/ for a command line tool.

Discovery of Regulators of Receptor Internalization with High-Throughput Flow Cytometry

PubMed Central

Tapia, Phillip H.; Fisher, Gregory W.; Simons, Peter C.; Strouse, J. Jacob; Foutz, Terry; Waggoner, Alan S.; Jarvik, Jonathan; Sklar, Larry A.

2012-01-01

We developed a platform combining fluorogen-activating protein (FAP) technology with high-throughput flow cytometry to detect real-time protein trafficking to and from the plasma membrane in living cells. The hybrid platform facilitates drug discovery for trafficking receptors such as G protein-coupled receptors and was validated with the β2-adrenergic receptor (β2AR) system. When a chemical library containing ∼1200 off-patent drugs was screened against cells expressing FAP-tagged β2ARs, all 33 known β2AR-active ligands in the library were successfully identified, together with a number of compounds that might regulate receptor internalization in a nontraditional manner. Results indicated that the platform identified ligands of target proteins regardless of the associated signaling pathway; therefore, this approach presents opportunities to search for biased receptor modulators and is suitable for screening of multiplexed targets for improved efficiency. The results revealed that ligands may be biased with respect to the rate or duration of receptor internalization and that receptor internalization may be independent of activation of the mitogen-activated protein kinase pathway. PMID:22767611

A systematic review and meta-analysis on the effects of yoga on weight-related outcomes.

PubMed

Lauche, Romy; Langhorst, Jost; Lee, Myeong Soo; Dobos, Gustav; Cramer, Holger

2016-06-01

Overweight and obesity are among the most important modifiable risk factors for chronic diseases and premature death. The aim of this review was to systematically assess and analyze the effects of yoga on weight-related outcomes. Medline/PubMed, Scopus, and the Cochrane Library were screened through March 2015 for randomized controlled trials on yoga for weight-related outcomes in the general population or overweight/obese individuals. Risk of bias was assessed using the Cochrane risk of bias tool on the following domains: selection bias, performance bias, detection bias, attrition bias, reporting bias, and other bias. Out of 445 records identified during literature search, 30 trials with a total of 2173 participants were included. No effects on weight, body mass index, body fat percentage or waist circumference were found. In studies with healthy adult participants an effect of yoga compared to usual care was found regarding waist/hip ratio (SMD=--1.00; 95% CI=--1.44, -0.55; p<0.001). In studies with overweight/obese participants only, effects relative to usual care were found for body mass index (SMD=-0.99; 95% CI=-1.67, -0.31; p=0.004). Effects however were not robust against selection bias; and publication bias could not be ruled out. No intervention-related adverse events were reported. Despite methodological drawbacks, yoga can be preliminarily considered a safe and effective intervention to reduce body mass index in overweight or obese individuals. Copyright © 2016 Elsevier Inc. All rights reserved.

Strategies to Prevent or Reduce Gender Bias in Peer Review of Research Grants: A Rapid Scoping Review.

PubMed

Tricco, Andrea C; Thomas, Sonia M; Antony, Jesmin; Rios, Patricia; Robson, Reid; Pattani, Reena; Ghassemi, Marco; Sullivan, Shannon; Selvaratnam, Inthuja; Tannenbaum, Cara; Straus, Sharon E

2017-01-01

To review the literature on strategies implemented or identified to prevent or reduce gender bias in peer review of research grants. Studies of any type of qualitative or quantitative design examining interventions to reduce or prevent gender bias during the peer review of health-related research grants were included. Electronic databases including MEDLINE, EMBASE, Education Resources Information Center (ERIC), PsycINFO, Joanna Briggs, the Cochrane Library, Evidence Based Medicine (EBM) Reviews, and the Campbell Library were searched from 2005 to April 2016. A search for grey (i.e., difficult to locate or unpublished) literature was conducted and experts in the field were consulted to identify additional potentially relevant articles. Two individuals screened titles and abstracts, full-text articles, and abstracted data with discrepancies resolved by a third person consistently. After screening 5524 citations and 170 full-text articles, one article evaluating gender-blinding of grant applications using an uncontrolled before-after study design was included. In this study, 891 applications for long-term fellowships in 2006 were included and 47% of the applicants were women. These were scored by 13 peer reviewers (38% were women). The intervention included eliminating references to gender from the applications, letters of recommendations, and interview reports that were sent to the committee members for evaluation. The proportion of successful applications led by women did not change with gender-blinding, although the number of successful applications that were led by men increased slightly. There is limited research on interventions to mitigate gender bias in the peer review of grants. Only one study was identified and no difference in the proportion of women who were successful in receiving grant funding was observed. Our results suggest that interventions to prevent gender bias should be adapted and tested in the context of grant peer review to determine if they will have an impact.

Strategies to Prevent or Reduce Gender Bias in Peer Review of Research Grants: A Rapid Scoping Review

PubMed Central

Tricco, Andrea C.; Thomas, Sonia M.; Antony, Jesmin; Rios, Patricia; Robson, Reid; Pattani, Reena; Ghassemi, Marco; Sullivan, Shannon; Selvaratnam, Inthuja; Tannenbaum, Cara; Straus, Sharon E.

2017-01-01

Objective To review the literature on strategies implemented or identified to prevent or reduce gender bias in peer review of research grants. Methods Studies of any type of qualitative or quantitative design examining interventions to reduce or prevent gender bias during the peer review of health-related research grants were included. Electronic databases including MEDLINE, EMBASE, Education Resources Information Center (ERIC), PsycINFO, Joanna Briggs, the Cochrane Library, Evidence Based Medicine (EBM) Reviews, and the Campbell Library were searched from 2005 to April 2016. A search for grey (i.e., difficult to locate or unpublished) literature was conducted and experts in the field were consulted to identify additional potentially relevant articles. Two individuals screened titles and abstracts, full-text articles, and abstracted data with discrepancies resolved by a third person consistently. Results After screening 5524 citations and 170 full-text articles, one article evaluating gender-blinding of grant applications using an uncontrolled before-after study design was included. In this study, 891 applications for long-term fellowships in 2006 were included and 47% of the applicants were women. These were scored by 13 peer reviewers (38% were women). The intervention included eliminating references to gender from the applications, letters of recommendations, and interview reports that were sent to the committee members for evaluation. The proportion of successful applications led by women did not change with gender-blinding, although the number of successful applications that were led by men increased slightly. Conclusions There is limited research on interventions to mitigate gender bias in the peer review of grants. Only one study was identified and no difference in the proportion of women who were successful in receiving grant funding was observed. Our results suggest that interventions to prevent gender bias should be adapted and tested in the context of grant peer review to determine if they will have an impact. PMID:28061509

Piezo-phototronic sensor

DOEpatents

Wang, Zhong L.; Hu, Youfan; Zhang, Yan

2013-10-15

A device includes a substrate having a first surface. A piezoelectric nanowire is disposed on the first surface of the substrate. The piezoelectric nanowire has a first end and an opposite second end. The piezoelectric nanowire is subjected to an amount of strain. A first Schottky contact is in electrical communication with the first end of the piezoelectric nanowire. A second Schottky contact is in electrical communication with the second end of the piezoelectric nanowire. A bias voltage source is configured to impart a bias voltage between the first Schottky contact and the second Schottky contact. A mechanism is configured to measure current flowing through the piezoelectric nanowire. The amount of strain is selected so that a predetermined current will flow through the piezoelectric nanowire when light of a selected intensity is applied to a first location on the piezoelectric nanowire.

Microwave switching power divider. [antenna feeds

NASA Technical Reports Server (NTRS)

Stockton, R. J.; Johnson, R. W. (Inventor)

1981-01-01

A pair of parallel, spaced-apart circular ground planes define a microwave cavity with multi-port microwave power distributing switching circuitry formed on opposite sides of a thin circular dielectric substrate disposed between the ground planes. The power distributing circuitry includes a conductive disk located at the center of the substrate and connected to a source of microwave energy. A high speed, low insertion loss switching diode and a dc blocking capacitor are connected in series between the outer end of a transmission line and an output port. A high impedance, microwave blocking dc bias choke is connected between each switching diode and a source of switching current. The switching source forward biases the diodes to couple microwave energy from the conductive disk to selected output ports and, to associated antenna elements connected to the output ports to form a synthesized antenna pattern.

Epitaxially grown BaM hexaferrite films having uniaxial axis in the film plane for self-biased devices

PubMed Central

Zhang, Xiaozhi; Meng, Siqin; Song, Dongsheng; Zhang, Yao; Yue, Zhenxing; Harris, Vincent G.

2017-01-01

Barium hexaferrite (BaM) films with in-plane c-axis orientation are promising and technically important materials for self-biased magnetic microwave devices. In this work, highly oriented BaM films with different thickness and an in-plane easy axis (c-axis) of magnetization were grown on a-plane single-crystal sapphire substrates by direct current magnetron sputtering. A procedure involving seed layers, layer-by-layer annealing was adopted to reduce the substrate-induced strains and allow for the growth of thick (~3.44 μm) films. The epitaxial growth of the BaM film on sapphire was revealed by high-resolution transmission electron microscopy with dislocations being observed at the film-substrate interface. The orientation was also verified by X-ray diffraction and more notably, polarized Raman scattering. The magnetic properties and ferromagnetic resonant frequencies were experimentally characterized by a vibrating sample magnetometry and a frequency-swept ferromagnetic resonant flip-chip technique, respectively. The micron-thick BaM films exhibited a large remanence ratio of 0.92 along in-plane easy axis and a small one of 0.09 for the in-plane hard axis loop measurement. The FMR frequency was 50.3 GHz at zero field and reached 57.9 GHz under a magnetic field of 3 kOe, indicating that the epitaxial BaM films with strong self-biased behaviors have good electromagnetic properties in millimeter-wave range. PMID:28276492

Effect of negative bias on TiAlSiN coating deposited on nitrided Zircaloy-4

NASA Astrophysics Data System (ADS)

Jun, Zhou; Zhendong, Feng; Xiangfang, Fan; Yanhong, Liu; Huanlin, Li

2018-01-01

TiAlSiN coatings were deposited on the nitrided Zircaloy-4 by multi-arc ion plating at -100 V, -200 V and -300 V. In this study, the high temperature oxidation behavior of coatings was tested by a box-type resistance furnace in air for 3 h at 800 °C; the macro-morphology of coatings was observed and analyzed by a zoom-stereo microscope; the micro-morphology of coatings was analyzed by a scanning electron microscopy (SEM), and the chemical elements of samples were analyzed by an energy dispersive spectroscopy(EDS); the adhesion strength of the coating to the substrate was measured by an automatic scratch tester; and the phases of coatings were analyzed by an X-ray diffractometer(XRD). Results show that the coating deposited at -100 V shows better high temperature oxidation resistance behavior, at the same time, Al elements contained in the coating is of the highest amount, meanwhile, the adhesion strength of the coating to the substrate is the highest, which is 33N. As the bias increases, high temperature oxidation resistance behavior of the coating weakens first and then increases, the amount of large particles on the surface of the coating increases first and then decreases whereas the density of the coating decreases first and then increases, and adhesion strength of the coating to the substrate increases first and then weakens. The coating's quality is relatively poor when the bias is -200 V.

Epitaxially grown BaM hexaferrite films having uniaxial axis in the film plane for self-biased devices.

PubMed

Zhang, Xiaozhi; Meng, Siqin; Song, Dongsheng; Zhang, Yao; Yue, Zhenxing; Harris, Vincent G

2017-03-09

Barium hexaferrite (BaM) films with in-plane c-axis orientation are promising and technically important materials for self-biased magnetic microwave devices. In this work, highly oriented BaM films with different thickness and an in-plane easy axis (c-axis) of magnetization were grown on a-plane single-crystal sapphire substrates by direct current magnetron sputtering. A procedure involving seed layers, layer-by-layer annealing was adopted to reduce the substrate-induced strains and allow for the growth of thick (~3.44 μm) films. The epitaxial growth of the BaM film on sapphire was revealed by high-resolution transmission electron microscopy with dislocations being observed at the film-substrate interface. The orientation was also verified by X-ray diffraction and more notably, polarized Raman scattering. The magnetic properties and ferromagnetic resonant frequencies were experimentally characterized by a vibrating sample magnetometry and a frequency-swept ferromagnetic resonant flip-chip technique, respectively. The micron-thick BaM films exhibited a large remanence ratio of 0.92 along in-plane easy axis and a small one of 0.09 for the in-plane hard axis loop measurement. The FMR frequency was 50.3 GHz at zero field and reached 57.9 GHz under a magnetic field of 3 kOe, indicating that the epitaxial BaM films with strong self-biased behaviors have good electromagnetic properties in millimeter-wave range.

A Systematic Review of Experimental Paradigms for Exploring Biased Interpretation of Ambiguous Information with Emotional and Neutral Associations

PubMed Central

Schoth, Daniel E.; Liossi, Christina

2017-01-01

Interpretation biases have been extensively explored in a range of populations, including patients with anxiety and depressive disorders where they have been argued to influence the onset and maintenance of such conditions. Other populations in which interpretation biases have been explored include patients with chronic pain, anorexia nervosa, and alcohol dependency among others, although this literature is more limited. In this research, stimuli with threatening/emotional and neutral meanings are presented, with participant responses indicative of ambiguity resolution. A large number of paradigms have been designed and implemented in the exploration of interpretation biases, some varying in minor features only. This article provides a review of experimental paradigms available for exploring interpretation biases, with the aim to stimulate and inform the design of future research exploring cognitive biases across a range of populations. A systematic search of the experimental literature was conducted in Medline, PsychINFO, Web of Science, CINAHL, and Cochrane Library databases. Search terms were information, stimuli, and ambiguous intersected with the terms interpretation and bias*. Forty-five paradigms were found, categorized into those using ambiguous words, ambiguous images, and ambiguous scenarios. The key features, strengths and limitations of the paradigms identified are discussed. PMID:28232813

Hole filling and library optimization: application to commercially available fragment libraries.

PubMed

An, Yuling; Sherman, Woody; Dixon, Steven L

2012-09-15

Compound libraries comprise an integral component of drug discovery in the pharmaceutical and biotechnology industries. While in-house libraries often contain millions of molecules, this number pales in comparison to the accessible space of drug-like molecules. Therefore, care must be taken when adding new compounds to an existing library in order to ensure that unexplored regions in the chemical space are filled efficiently while not needlessly increasing the library size. In this work, we present an automated method to fill holes in an existing library using compounds from an external source and apply it to commercially available fragment libraries. The method, called Canvas HF, uses distances computed from 2D chemical fingerprints and selects compounds that fill vacuous regions while not suffering from the problem of selecting only compounds at the edge of the chemical space. We show that the method is robust with respect to different databases and the number of requested compounds to retrieve. We also present an extension of the method where chemical properties can be considered simultaneously with the selection process to bias the compounds toward a desired property space without imposing hard property cutoffs. We compare the results of Canvas HF to those obtained with a standard sphere exclusion method and with random compound selection and find that Canvas HF performs favorably. Overall, the method presented here offers an efficient and effective hole-filling strategy to augment compound libraries with compounds from external sources. The method does not have any fit parameters and therefore it should be applicable in most hole-filling applications. Copyright © 2012 Elsevier Ltd. All rights reserved.

Design of a glutamine substrate tag enabling protein labelling mediated by Bacillus subtilis transglutaminase.

PubMed

Oteng-Pabi, Samuel K; Clouthier, Christopher M; Keillor, Jeffrey W

2018-01-01

Transglutaminases (TGases) are enzymes that catalyse protein cross-linking through a transamidation reaction between the side chain of a glutamine residue on one protein and the side chain of a lysine residue on another. Generally, TGases show low substrate specificity with respect to their amine substrate, such that a wide variety of primary amines can participate in the modification of specific glutamine residue. Although a number of different TGases have been used to mediate these bioconjugation reactions, the TGase from Bacillus subtilis (bTG) may be particularly suited to this application. It is smaller than most TGases, can be expressed in a soluble active form, and lacks the calcium dependence of its mammalian counterparts. However, little is known regarding this enzyme and its glutamine substrate specificity, limiting the scope of its application. In this work, we designed a FRET-based ligation assay to monitor the bTG-mediated conjugation of the fluorescent proteins Clover and mRuby2. This assay allowed us to screen a library of random heptapeptide glutamine sequences for their reactivity with recombinant bTG in bacterial cells, using fluorescence assisted cell sorting. From this library, several reactive sequences were identified and kinetically characterized, with the most reactive sequence (YAHQAHY) having a kcat/KM value of 19 ± 3 μM-1 min-1. This sequence was then genetically appended onto a test protein as a reactive 'Q-tag' and fluorescently labelled with dansyl-cadaverine, in the first demonstration of protein labelling mediated by bTG.

An enzyme-mediated protein-fragment complementation assay for substrate screening of sortase A.

PubMed

Li, Ning; Yu, Zheng; Ji, Qun; Sun, Jingying; Liu, Xiao; Du, Mingjuan; Zhang, Wei

2017-04-29

Enzyme-mediated protein conjugation has gained great attention recently due to the remarkable site-selectivity and mild reaction condition affected by the nature of enzyme. Among all sorts of enzymes reported, sortase A from Staphylococcus aureus (SaSrtA) is the most popular enzyme due to its selectivity and well-demonstrated applications. Position scanning has been widely applied to understand enzyme substrate specificity, but the low throughput of chemical synthesis of peptide substrates and analytical methods (HPLC, LC-ESI-MS) have been the major hurdle to fully decode enzyme substrate profile. We have developed a simple high-throughput substrate profiling method to reveal novel substrates of SaSrtA 7M, a widely used hyperactive peptide ligase, by modified protein-fragment complementation assay (PCA). A small library targeting the LPATG motif recognized by SaSrtA 7M was generated and screened against proteins carrying N-terminal glycine. Using this method, we have confirmed all currently known substrates of the enzyme, and moreover identified some previously unknown substrates with varying activities. The method provides an easy, fast and highly-sensitive way to determine substrate profile of a peptide ligase in a high-throughput manner. Copyright © 2017 Elsevier Inc. All rights reserved.

Photoconducting positions monitor and imaging detector

DOEpatents

Shu, Deming; Kuzay, Tuncer M.

2000-01-01

A photoconductive, high energy photon beam detector/monitor for detecting x-rays and gamma radiation, having a thin, disk-shaped diamond substrate with a first and second surface, and electrically conductive coatings, or electrodes, of a predetermined configuration or pattern, disposed on the surfaces of the substrate. A voltage source and a current amplifier is connected to the electrodes to provide a voltage bias to the electrodes and to amplify signals from the detector.

AC-coupled GaAs microstrip detectors with a new type of integrated bias resistors

NASA Astrophysics Data System (ADS)

Irsigler, R.; Geppert, R.; Göppert, R.; Hornung, M.; Ludwig, J.; Rogalla, M.; Runge, K.; Schmid, Th.; Söldner-Rembold, A.; Webel, M.; Weber, C.

1998-02-01

Full-size single-sided GaAs microstrip detectors with integrated coupling capacitors and bias resistors have been fabricated on 3″ substrate wafers. PECVD deposited SiO 2 and {SiO 2}/{Si 3N 4} layers were used to provide coupling capacitances of 32.5 and 61.6 pF/cm, respectively. The resistors are made of sputtered CERMET using simple lift of technique. The sheet resistivity of 78 kΩ/□ and the thermal coefficient of resistance of less than 4 × 10 -3/°C satisfy the demands of small area biasing resistors, working on a wide temperature range.

Novel semiconducting boron carbide/pyridine polymers for neutron detection at zero bias

NASA Astrophysics Data System (ADS)

Echeverría, Elena; James, Robinson; Chiluwal, Umesh; Pasquale, Frank L.; Colón Santana, Juan A.; Gapfizi, Richard; Tae, Jae-Do; Driver, M. Sky; Enders, A.; Kelber, Jeffry A.; Dowben, P. A.

2015-01-01

Thin films containing aromatic pyridine moieties bonded to boron, in the partially dehydrogenated boron-rich icosahedra (B10C2HX), prove to be an effective material for neutron detection applications when deposited on n-doped (100) silicon substrates. The characteristic I-V curves for the heterojunction diodes exhibit strong rectification and largely unperturbed normalized reverse bias leakage currents with increasing pyridine content. The neutron capture generated pulses from these heterojunction diodes were obtained at zero bias voltage although without the signatures of complete electron-hole collection. These results suggest that modifications to boron carbide may result in better neutron voltaic materials.

High Efficient THz Emission From Unbiased and Biased Semiconductor Nanowires Fabricated Using Electron Beam Lithography

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

Balci, Soner; Czaplewski, David A.; Jung, Il Woong

Besides having perfect control on structural features, such as vertical alignment and uniform distribution by fabricating the wires via e-beam lithography and etching process, we also investigated the THz emission from these fabricated nanowires when they are applied DC bias voltage. To be able to apply a voltage bias, an interdigitated gold (Au) electrode was patterned on the high-quality InGaAs epilayer grown on InP substrate bymolecular beam epitaxy. Afterwards, perfect vertically aligned and uniformly distributed nanowires were fabricated in between the electrodes of this interdigitated pattern so that we could apply voltage bias to improve the THz emission. As amore » result, we achieved enhancement in the emitted THz radiation by ~four times, about 12 dB increase in power ratio at 0.25 THz with a DC biased electric field compared with unbiased NWs.« less

From the ORFeome concept to highly comprehensive, full-genome screening libraries.

PubMed

Rid, Raphaela; Abdel-Hadi, Omar; Maier, Richard; Wagner, Martin; Hundsberger, Harald; Hintner, Helmut; Bauer, Johann; Onder, Kamil

2013-02-01

Recombination-based cloning techniques have in recent times facilitated the establishment of genome-scale single-gene ORFeome repositories. Their further handling and downstream application in systematic fashion is, however, practically impeded because of logistical plus economic challenges. At this juncture, simultaneously transferring entire gene collections in compiled pool format could represent an advanced compromise between systematic ORFeome (an organism's entire set of protein-encoding open reading frames) projects and traditional random library approaches, but has not yet been considered in great detail. In our endeavor to merge the comprehensiveness of ORFeomes with a basically simple, streamlined, and easily executable single-tube design, we have here produced five different pooled screening-ready libraries for both Staphylococcus aureus and Homo sapiens. By evaluating the parallel transfer efficiencies of differentially sized genes from initial polymerase chain reaction (PCR) product amplification to entry and final destination library construction via quantitative real-time PCR, we found that the complexity of the gene population is fairly stably maintained once an entry resource has been successfully established, and that no apparent size-selection bias loss of large inserts takes place. Recombinational transfer processes are hence robust enough for straightforwardly achieving such pooled screening libraries.

The value and impact of information provided through library services for patient care: developing guidance for best practice.

PubMed

Weightman, Alison; Urquhart, Christine; Spink, Siân; Thomas, Rhian

2009-03-01

Previous impact tool-kits for UK health libraries required updating to reflect recent evidence and changes in library services. The National Knowledge Service funded development of updated guidance. Survey tools were developed based on previous impact studies and a systematic review. The resulting draft questionnaire survey was tested at four sites, and the interview schedule was investigated in a fifth area. A literature search in ASSIA, Google Scholar, INTUTE, LISA, LISTA, SCIRUS, Social Sciences Citation Index (Web of Knowledge), and the major UK University and National Libraries Catalogue (COPAC), identified ways to improve response rates. Other expert advice contributed to the guidance. The resulting guidance contains evidence-based advice and a planning pathway for conducting an impact survey as a service audit. The survey tools (critical incident questionnaire and interview schedule) are available online. The evidence-based advice recommends personalizing the request, assuring confidentiality, and using follow-up reminders. Questionnaires should be brief, and small incentives, such as a lottery draw should be considered. Bias is minimized if the survey is conducted and analysed by independent researchers. The guidance is a starting point for a pragmatic survey to assess the impact of health library services.

Spontaneous perpendicular exchange bias effect in L10-MnGa/FeMn bilayers grown by molecular-beam epitaxy

NASA Astrophysics Data System (ADS)

Zhao, X. P.; Lu, J.; Mao, S. W.; Yu, Z. F.; Wei, D. H.; Zhao, J. H.

2018-01-01

We report on the spontaneous perpendicular exchange bias effect in as-grown L10-MnGa/FeMn bilayers. An FeMn layer with different thicknesses is introduced as an antiferromagnetic layer to couple with single-crystalline ferromagnetic L10-MnGa, which is epitaxially grown on a GaAs (001) substrate by molecular-beam epitaxy. The perpendicular exchange bias shows a strong dependence on both the thickness of the FeMn layer and the measurement temperature. A large spontaneous perpendicular exchange bias up to 8.9 kOe is achieved in L10-MnGa/FeMn bilayers at 5 K without any external magnetic treatment. The corresponding effective interfacial exchange energy Jeff is estimated to be 1.4 mJ/m2. The spontaneous perpendicular exchange bias effect in the (001) textured L10-MnGa/FeMn bilayers paves the way for spintronic devices based on exchange biased perpendicularly magnetized materials.

Retarding field analyzer for ion energy distribution measurements at a radio-frequency biased electrode

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

Gahan, D.; Hopkins, M. B.; Dolinaj, B.

2008-03-15

A retarding field energy analyzer designed to measure ion energy distributions impacting a radio-frequency biased electrode in a plasma discharge is examined. The analyzer is compact so that the need for differential pumping is avoided. The analyzer is designed to sit on the electrode surface, in place of the substrate, and the signal cables are fed out through the reactor side port. This prevents the need for modifications to the rf electrode--as is normally the case for analyzers built into such electrodes. The capabilities of the analyzer are demonstrated through experiments with various electrode bias conditions in an inductively coupledmore » plasma reactor. The electrode is initially grounded and the measured distributions are validated with the Langmuir probe measurements of the plasma potential. Ion energy distributions are then given for various rf bias voltage levels, discharge pressures, rf bias frequencies - 500 kHz to 30 MHz, and rf bias waveforms - sinusoidal, square, and dual frequency.« less

Para-nitrobenzyl esterases with enhanced activity in aqueous and nonaqueous media

DOEpatents

Arnold, F.H.; Moore, J.C.

1999-05-25

A method is disclosed for isolating and identifying modified para-nitrobenzyl esterases which exhibit improved stability and/or esterase hydrolysis activity toward selected substrates and under selected reaction conditions relative to the unmodified para-nitrobenzyl esterase. The method involves preparing a library of modified para-nitrobenzyl esterase nucleic acid segments (genes) which have nucleotide sequences that differ from the nucleic acid segment which encodes for unmodified para-nitrobenzyl esterase. The library of modified para-nitrobenzyl nucleic acid segments is expressed to provide a plurality of modified enzymes. The clones expressing modified enzymes are then screened to identify which enzymes have improved esterase activity by measuring the ability of the enzymes to hydrolyze the selected substrate under the selected reaction conditions. Specific modified para-nitrobenzyl esterases are disclosed which have improved stability and/or ester hydrolysis activity in aqueous or aqueous-organic media relative to the stability and/or ester hydrolysis activity of unmodified naturally occurring para-nitrobenzyl esterase. 43 figs.

Para-nitrobenzyl esterases with enhanced activity in aqueous and nonaqueous media

DOEpatents

Arnold, F.H.; Moore, J.C.

1998-04-21

A method is disclosed for isolating and identifying modified para-nitrobenzyl esterases. These enzymes exhibit improved stability and/or esterase hydrolysis activity toward selected substrates and under selected reaction conditions relative to the unmodified para-nitrobenzyl esterase. The method involves preparing a library of modified para-nitrobenzyl esterase nucleic acid segments (genes) which have nucleotide sequences that differ from the nucleic acid segment which encodes for unmodified para-nitrobenzyl esterase. The library of modified para-nitrobenzyl nucleic acid segments is expressed to provide a plurality of modified enzymes. The clones expressing modified enzymes are then screened to identify which enzymes have improved esterase activity by measuring the ability of the enzymes to hydrolyze the selected substrate under the selected reaction conditions. Specific modified para-nitrobenzyl esterases are disclosed which have improved stability and/or ester hydrolysis activity in aqueous or aqueous-organic media relative to the stability and/or ester hydrolysis activity of unmodified naturally occurring para-nitrobenzyl esterase. 43 figs.

High-throughput screening for combinatorial thin-film library of thermoelectric materials.

PubMed

Watanabe, Masaki; Kita, Takuji; Fukumura, Tomoteru; Ohtomo, Akira; Ueno, Kazunori; Kawasaki, Masashi

2008-01-01

A high-throughput method has been developed to evaluate the Seebeck coefficient and electrical resistivity of combinatorial thin-film libraries of thermoelectric materials from room temperature to 673 K. Thin-film samples several millimeters in size were deposited on an integrated Al2O3 substrate with embedded lead wires and local heaters for measurement of the thermopower under a controlled temperature gradient. An infrared camera was used for real-time observation of the temperature difference Delta T between two electrical contacts on the sample to obtain the Seebeck coefficient. The Seebeck coefficient and electrical resistivity of constantan thin films were shown to be almost identical to standard data for bulk constantan. High-throughput screening was demonstrated for a thermoelectric Mg-Si-Ge combinatorial library.

Screening of chemical compound libraries identified new anti-Toxoplasma gondii agents.

PubMed

Adeyemi, Oluyomi Stephen; Sugi, Tatsuki; Han, Yongmei; Kato, Kentaro

2018-02-01

Toxoplasma gondii is the etiological agent of toxoplasmosis, a common parasitic disease that affects nearly one-third of the human population. The primary infection can be asymptomatic in healthy individuals but may prove fatal in immunocompromised individuals. Available treatment options for toxoplasmosis patients are limited, underscoring the urgent need to identify and develop new therapies. Non-biased screening of libraries of chemical compounds including the repurposing of well-characterized compounds is emerging as viable approach to achieving this goal. In the present investigation, we screened libraries of natural product and FDA-approved compounds to identify those that inhibited T. gondii growth. We identified 32 new compounds that potently inhibit T. gondii growth. Our findings are new and promising, and further strengthen the prospects of drug repurposing as well as the screening of a wide range of chemical compounds as a viable source of alternative anti-parasitic therapeutic agents.

Substrate Specifity Profiling of the Aspergillus fumigatus Proteolytic Secretome Reveals Consensus Motifs with Predominance of Ile/Leu and Phe/Tyr

PubMed Central

Watson, Douglas S.; Feng, Xizhi; Askew, David S.; Jambunathan, Kalyani; Kodukula, Krishna; Galande, Amit K.

2011-01-01

Background The filamentous fungus Aspergillus fumigatus (AF) can cause devastating infections in immunocompromised individuals. Early diagnosis improves patient outcomes but remains challenging because of the limitations of current methods. To augment the clinician's toolkit for rapid diagnosis of AF infections, we are investigating AF secreted proteases as novel diagnostic targets. The AF genome encodes up to 100 secreted proteases, but fewer than 15 of these enzymes have been characterized thus far. Given the large number of proteases in the genome, studies focused on individual enzymes may overlook potential diagnostic biomarkers. Methodology and Principal Findings As an alternative, we employed a combinatorial library of internally quenched fluorogenic probes (IQFPs) to profile the global proteolytic secretome of an AF clinical isolate in vitro. Comparative protease activity profiling revealed 212 substrate sequences that were cleaved by AF secreted proteases but not by normal human serum. A central finding was that isoleucine, leucine, phenylalanine, and tyrosine predominated at each of the three variable positions of the library (44.1%, 59.1%, and 57.0%, respectively) among substrate sequences cleaved by AF secreted proteases. In contrast, fewer than 10% of the residues at each position of cleaved sequences were cationic or anionic. Consensus substrate motifs were cleaved by thermostable serine proteases that retained activity up to 50°C. Precise proteolytic cleavage sites were reliably determined by a simple, rapid mass spectrometry-based method, revealing predominantly non-prime side specificity. A comparison of the secreted protease activities of three AF clinical isolates revealed consistent protease substrate specificity fingerprints. However, secreted proteases of A. flavus, A. nidulans, and A. terreus strains exhibited striking differences in their proteolytic signatures. Conclusions This report provides proof-of-principle for the use of protease substrate specificity profiling to define the proteolytic secretome of Aspergillus fumigatus. Expansion of this technique to protease secretion during infection could lead to development of novel approaches to fungal diagnosis. PMID:21695046

Betty Petersen Memorial Library - NCWCP Publications - NWS

Science.gov Websites

(.PDF file) 254 1982 Smith W. 1-2 Day Comparative BWB and LFM Threat Scores and Bias 1971 - 1982 (.PDF Stackpole J. Tracton M. S. Comparative Evaluation of ECMWF and NMC Spectral Forecasts February - July 1982 file) 269 1983 Smith W. 1-2 Day Comparative BWB and LFM Threat Scores, No Precipitation Threat Scores

Analysis of Mycobacterium avium subsp. paratuberculosis mutant libraries reveals loci-dependent transcription biases and strategies to novel mutant discovery

USDA-ARS?s Scientific Manuscript database

Mycobacterium avium subsp. paratuberculosis (MAP) is the etiologic agent of Johne’s disease in ruminants and it has been implicated as a cause of Crohn’s disease in humans. The generation of comprehensive random mutant banks by transposon mutagenesis is a fundamental wide genomic technology utilized...

Chemical & Biological Point Detection Decontamination

DTIC Science & Technology

2002-04-01

high priority in biological defense. Research on multivalent assays is also ongoing. Biased libraries, generated from immunized animals, or unbiased ...2003 TBD decontamination and modeling and simulation I I The Chem-Bio Point Detection Roadmap The summary level updated and expanded Bio Point... Molecular Imprinted Polymer Sensor, Dendrimer-based Antibody Assays, Pyrolysis-GC-ion mobility spectrometry, and surface enhanced Raman spectroscopy. Data

Cognitive Biases in Military Decision Making

DTIC Science & Technology

2007-06-14

the pet dog would be wise to avoid cats. Juxtapose this with someone who lives in a rainforest and expects rain or someone who lives on a different farm...Library of Congress at the end of 2000? 8. How long, in miles, is the Amazon River? 9. How fast does the earth spin at the equator? 10. How many

Microgap flat panel display

DOEpatents

Wuest, C.R.

1998-12-08

A microgap flat panel display is disclosed which includes a thin gas-filled display tube that utilizes switched X-Y ``pixel`` strips to trigger electron avalanches and activate a phosphor at a given location on a display screen. The panel utilizes the principal of electron multiplication in a gas subjected to a high electric field to provide sufficient electron current to activate standard luminescent phosphors located on an anode. The X-Y conductive strips of a few micron widths may for example, be deposited on opposite sides of a thin insulating substrate, or on one side of the adjacent substrates and function as a cathode. The X-Y strips are separated from the anode by a gap filled with a suitable gas. Electrical bias is selectively switched onto X and Y strips to activate a ``pixel`` in the region where these strips overlap. A small amount of a long-lived radioisotope is used to initiate an electron avalanche in the overlap region when bias is applied. The avalanche travels through the gas filled gap and activates a luminescent phosphor of a selected color. The bias is adjusted to give a proportional electron multiplication to control brightness for given pixel. 6 figs.

Design and Performance of a Pinned Photodiode CMOS Image Sensor Using Reverse Substrate Bias.

PubMed

Stefanov, Konstantin D; Clarke, Andrew S; Ivory, James; Holland, Andrew D

2018-01-03

A new pinned photodiode (PPD) CMOS image sensor with reverse biased p-type substrate has been developed and characterized. The sensor uses traditional PPDs with one additional deep implantation step to suppress the parasitic reverse currents, and can be fully depleted. The first prototypes have been manufactured on an 18 µm thick, 1000 Ω·cm epitaxial silicon wafers using 180 nm PPD image sensor process. Both front-side illuminated (FSI) and back-side illuminated (BSI) devices were manufactured in collaboration with Teledyne e2v. The characterization results from a number of arrays of 10 µm and 5.4 µm PPD pixels, with different shape, the size and the depth of the new implant are in good agreement with device simulations. The new pixels could be reverse-biased without parasitic leakage currents well beyond full depletion, and demonstrate nearly identical optical response to the reference non-modified pixels. The observed excessive charge sharing in some pixel variants is shown to not be a limiting factor in operation. This development promises to realize monolithic PPD CIS with large depleted thickness and correspondingly high quantum efficiency at near-infrared and soft X-ray wavelengths.

Rectified photocurrent in a planar ITO/graphene/ITO photodetector on SiC by local irradiation of ultraviolet light

NASA Astrophysics Data System (ADS)

Yang, Junwei; Guo, Liwei; Huang, Jiao; Mao, Qi; Guo, Yunlong; Jia, Yuping; Peng, Tonghua; Chen, Xiaolong

2017-10-01

A rectified photocurrent behaviour is demonstrated in a simple planar structure of ITO-graphene-ITO formed on a SiC substrate when an ultraviolet (UV) light is locally incident on one of the edges between the graphene and ITO electrode. The photocurrent has similar characteristics as those of a vertical structure graphene/semiconductor junction photodiode, but is clearly different from those found in a planar structure metal-graphene-metal device. Furthermore, the device behaves multi-functionally as a photodiode with sensitive UV photodetection capability (responsivity of 11.7 mA W-1 at 0.3 V) and a self-powered UV photodetector (responsivity of 4.4 mA W-1 at zero bias). Both features are operative in a wide dynamic range and with a fast speed of response in about gigahertz. The linear I-V behaviour with laser power at forward bias and cutoff at reverse bias leads to a conceptual photodiode, which is compatible with modern semiconductor planar device architecture. This paves a potential way to realize ultrafast graphene planar photodiodes for monolithic integration of graphene-based devices on the same SiC substrate.

Design and Performance of a Pinned Photodiode CMOS Image Sensor Using Reverse Substrate Bias †

PubMed Central

Clarke, Andrew S.; Ivory, James; Holland, Andrew D.

2018-01-01

A new pinned photodiode (PPD) CMOS image sensor with reverse biased p-type substrate has been developed and characterized. The sensor uses traditional PPDs with one additional deep implantation step to suppress the parasitic reverse currents, and can be fully depleted. The first prototypes have been manufactured on an 18 µm thick, 1000 Ω·cm epitaxial silicon wafers using 180 nm PPD image sensor process. Both front-side illuminated (FSI) and back-side illuminated (BSI) devices were manufactured in collaboration with Teledyne e2v. The characterization results from a number of arrays of 10 µm and 5.4 µm PPD pixels, with different shape, the size and the depth of the new implant are in good agreement with device simulations. The new pixels could be reverse-biased without parasitic leakage currents well beyond full depletion, and demonstrate nearly identical optical response to the reference non-modified pixels. The observed excessive charge sharing in some pixel variants is shown to not be a limiting factor in operation. This development promises to realize monolithic PPD CIS with large depleted thickness and correspondingly high quantum efficiency at near-infrared and soft X-ray wavelengths. PMID:29301379

Electrical and optical characteristics of heterojunction devices composed of silicon nanowires and mercury selenide nanoparticle films on flexible plastics.

PubMed

Yeo, Minje; Yun, Junggwon; Kim, Sangsig

2013-09-01

A pn heterojunction device based on p-type silicon (Si) nanowires (NWs) prepared by top-down method and n-type mercury selenide (HgSe) nanoparticles (NPs) synthesized by the colloidal method have been fabricated on a flexible plastic substrate. The synthesized HgSe NPs were analyzed through the effective mass approximation. The characteristics of the heterojunction device were examined and studied with the energy band diagram. The device showed typical diode characteristics with a turn-on voltage of 1.5 V and exhibited a high rectification ratio of 10(3) under relatively low forward bias. Under illumination of 633-nm-wavelength light, the device presented photocurrent efficiency of 117.5 and 20.1 nA/W under forward bias and reverse bias conditions, respectively. Moreover, the photocurrent characteristics of the device have been determined by bending of the plastic substrate upward and downward with strain of 0.8%. Even though the photocurrent efficiency has fluctuations during the bending cycles, the values are roughly maintained for 10(4) bending cycles. This result indicates that the fabricated heterojunction device has the potential to be applied as fundamental elements of flexible nanoelectronics.

Method and apparatus for improved high power impulse magnetron sputtering

DOEpatents

Anders, Andre

2013-11-05

A high power impulse magnetron sputtering apparatus and method using a vacuum chamber with a magnetron target and a substrate positioned in the vacuum chamber. A field coil being positioned between the magnetron target and substrate, and a pulsed power supply and/or a coil bias power supply connected to the field coil. The pulsed power supply connected to the field coil, and the pulsed power supply outputting power pulse widths of greater that 100 .mu.s.

Control of the sidewall angle of an absorber stack using the Faraday cage system for the change of pattern printability in EUVL

NASA Astrophysics Data System (ADS)

Jang, Il-Yong; Huh, Sung-Min; Moon, Seong-Yong; Woo, Sang-Gyun; Lee, Jin-Kwan; Moon, Sang Heup; Cho, HanKu

2008-10-01

A patterned TaN substrate, which is candidate for a mask absorber in extreme ultra-violet lithography (EUVL), was etched to have inclined sidewalls by using a Faraday cage system under the condition of a 2-step process that allowed the high etch selectivity of TaN over the resist. The sidewall angle (SWA) of the patterned substrate, which was in the shape of a parallelogram after etching, could be controlled by changing the slope of a substrate holder that was placed in the Faraday cage. The performance of an EUV mask, which contained the TaN absorber of an oblique pattern over the molybdenum/silicon multi-layer, was simulated for different cases of SWA. The results indicated that the optical properties, such as the critical dimension (CD), an offset in the CD bias between horizontal and vertical patterns (H-V bias), and a shift in the image position on the wafer, could be controlled by changing the SWA of the absorber stack. The simulation result showed that the effect of the SWA on the optical properties became more significant at larger thicknesses of the absorber and smaller sizes of the target CD. Nevertheless, the contrast of the aerial images was not significantly decreased because the shadow effect caused by either sidewall of the patterned substrate cancelled with each other.

Low noise and conductively cooled microchannel plates

NASA Technical Reports Server (NTRS)

Feller, W. B.

1990-01-01

Microchannel plate (MCP) dynamic range has recently been enhanced for both very low and very high input flux conditions. Improvements in MCP manufacturing technology reported earlier have led to MCPs with substantially reduced radioisotope levels, giving dramatically lower internal background-counting rates. An update is given on the Galileo low noise MCP. Also, new results in increasing the MCP linear counting range for high input flux densities are presented. By bonding the active face of a very low resistance MCP (less than 1 megaohm) to a substrate providing a conductive path for heat transport, the bias current limit (hence, MCP output count rate limit) can be increased up to two orders of magnitude. Normal pulse-counting MCP operation was observed at bias currents of several mA when a curved-channel MCP (80:1) was bonded to a ceramic multianode substrate; the MCP temperature rise above ambient was less than 40 C.

Adhesion strength of sputtered TiAlN-coated WC insert tool

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

Budi, Esmar; Razali, M. Mohd.; Nizam, A. R. Md.

2013-09-09

The adhesion strength of TiAlN coating that deposited by using DC magnetron sputtering on WC insert tool are studied. TiAlN coating are deposited on Tungsten Carbide (WC) insert tool by varying negatively substrate bias from 79 to 221 volt and nitrogen flow rate from 30 to 72 sccm. The adhesion strength are obtained by using Rockwell indentation test method with a Brale diamond at applied load of 60,100 and 150 kgf. The lateral diameter of indentation is plotted on three different applied loads and the adhesion strength of TiAlN coating was obtained from the curved slopes at 100 and 150more » kgf. The lower curve slop indicated better adhesion strength. The results shows that the adhesion strength of sputterred TiAlN coating tend to increase as the negatively substrate bias and nitrogen flow rate are increased.« less

Low Al-composition p-GaN/Mg-doped Al0.25Ga0.75N/n+-GaN polarization-induced backward tunneling junction grown by metal-organic chemical vapor deposition on sapphire substrate

PubMed Central

Zhang, Kexiong; Liang, Hongwei; Liu, Yang; Shen, Rensheng; Guo, Wenping; Wang, Dongsheng; Xia, Xiaochuan; Tao, Pengcheng; Yang, Chao; Luo, Yingmin; Du, Guotong

2014-01-01

Low Al-composition p-GaN/Mg-doped Al0.25Ga0.75N/n+-GaN polarization-induced backward tunneling junction (PIBTJ) was grown by metal-organic chemical vapor deposition on sapphire substrate. A self-consistent solution of Poisson-Schrödinger equations combined with polarization-induced theory was used to model PIBTJ structure, energy band diagrams and free carrier concentrations distribution. The PIBTJ displays reliable and reproducible backward tunneling with a current density of 3 A/cm2 at the reverse bias of −1 V. The absence of negative differential resistance behavior of PIBTJ at forward bias can mainly be attributed to the hole compensation centers, including C, H and O impurities, accumulated at the p-GaN/Mg-doped AlGaN heterointerface. PMID:25205042

Tunable ferrite-based metamaterial structure and its application to a leaky-wave antenna

NASA Astrophysics Data System (ADS)

Berneti, Elahe Kargar; Ghalibafan, Javad

2018-06-01

In this paper, a new magnetically tunable substrate integrated waveguide (SIW) with composite right/left-handed (CRLH) response is presented. The structure consists of an array of interdigital slots on the upper wall of a SIW line with normally magnetized ferrite substrate. The electromagnetic properties of this structure are studied and the dispersion diagram is considered. The simulated results show that the proposed structure has a separate right- and left-handed leakage frequency region which can be simply controlled by varying the applied ferrite magnetic bias field. As an application, this leakage frequency band is exploited to build a new leaky-wave antenna (LWA) which its radiation pattern can be independently scanned by varying the frequency or the magnetic bias field. As another advantage, there is not any mechanical switch or electrical tuning chip in the proposed leaky-wave antenna.

High-power microstrip RF switch

NASA Technical Reports Server (NTRS)

Choi, S. D.

1971-01-01

A microstrip-type single-pole double-throw (SPDT) switch whose RF and bias portions contain only a metallized alumina substrate and two PIN diodes has been developed. A technique developed to eliminate the dc blocking capacitors needed for biasing the diodes is described. These capacitors are extra components and could lower the reliability significantly. An SPDT switch fabricated on a 5.08 x 5.08 x 0.127-cm (2 x 2 x 0.050-in.) substrate has demonstrated an RF power-handling capability greater than 50 W at S-band. The insertion loss is less than 0.25 db and the input-to-off port isolation is greater than 36 db over a bandwidth larger than 30 MHz. The input voltage standing-wave ratio is lower than 1.07 over the same bandwidth. Theoretical development of the switch characteristics and experimental results, which are in good agreement with theory, are presented.

Low Al-composition p-GaN/Mg-doped Al0.25Ga0.75N/n+-GaN polarization-induced backward tunneling junction grown by metal-organic chemical vapor deposition on sapphire substrate.

PubMed

Zhang, Kexiong; Liang, Hongwei; Liu, Yang; Shen, Rensheng; Guo, Wenping; Wang, Dongsheng; Xia, Xiaochuan; Tao, Pengcheng; Yang, Chao; Luo, Yingmin; Du, Guotong

2014-09-10

Low Al-composition p-GaN/Mg-doped Al0.25Ga0.75N/n(+)-GaN polarization-induced backward tunneling junction (PIBTJ) was grown by metal-organic chemical vapor deposition on sapphire substrate. A self-consistent solution of Poisson-Schrödinger equations combined with polarization-induced theory was used to model PIBTJ structure, energy band diagrams and free carrier concentrations distribution. The PIBTJ displays reliable and reproducible backward tunneling with a current density of 3 A/cm(2) at the reverse bias of -1 V. The absence of negative differential resistance behavior of PIBTJ at forward bias can mainly be attributed to the hole compensation centers, including C, H and O impurities, accumulated at the p-GaN/Mg-doped AlGaN heterointerface.

Construction and characterization of a normalized cDNA library of Nannochloropsis oculata (Eustigmatophyceae)

NASA Astrophysics Data System (ADS)

Yu, Jianzhong; Ma, Xiaolei; Pan, Kehou; Yang, Guanpin; Yu, Wengong

2010-07-01

We constructed and characterized a normalized cDNA library of Nannochloropsis oculata CS-179, and obtained 905 nonredundant sequences (NRSs) ranging from 431-1 756 bp in length. Among them, 496 were very similar to nonredundant ones in the GenBank ( E ≤1.0e-05), and 349 ESTs had significant hits with the clusters of eukaryotic orthologous groups (KOG). Bases G and/or C at the third position of codons of 14 amino acid residues suggested a strong bias in the conserved domain of 362 NRSs (>60%). We also identified the unigenes encoding phosphorus and nitrogen transporters, suggesting that N. oculata could efficiently transport and metabolize phosphorus and nitrogen, and recognized the unigenes that involved in biosynthesis and storage of both fatty acids and polyunsaturated fatty acids (PUFAs), which will facilitate the demonstration of eicosapentaenoic acid (EPA) biosynthesis pathway of N. oculata. In comparison with the original cDNA library, the normalized library significantly increased the efficiencies of random sequencing and rarely expressed genes discovering, and decreased the frequency of abundant gene sequences.

Critical Features of Fragment Libraries for Protein Structure Prediction

PubMed Central

dos Santos, Karina Baptista

2017-01-01

The use of fragment libraries is a popular approach among protein structure prediction methods and has proven to substantially improve the quality of predicted structures. However, some vital aspects of a fragment library that influence the accuracy of modeling a native structure remain to be determined. This study investigates some of these features. Particularly, we analyze the effect of using secondary structure prediction guiding fragments selection, different fragments sizes and the effect of structural clustering of fragments within libraries. To have a clearer view of how these factors affect protein structure prediction, we isolated the process of model building by fragment assembly from some common limitations associated with prediction methods, e.g., imprecise energy functions and optimization algorithms, by employing an exact structure-based objective function under a greedy algorithm. Our results indicate that shorter fragments reproduce the native structure more accurately than the longer. Libraries composed of multiple fragment lengths generate even better structures, where longer fragments show to be more useful at the beginning of the simulations. The use of many different fragment sizes shows little improvement when compared to predictions carried out with libraries that comprise only three different fragment sizes. Models obtained from libraries built using only sequence similarity are, on average, better than those built with a secondary structure prediction bias. However, we found that the use of secondary structure prediction allows greater reduction of the search space, which is invaluable for prediction methods. The results of this study can be critical guidelines for the use of fragment libraries in protein structure prediction. PMID:28085928

Critical Features of Fragment Libraries for Protein Structure Prediction.

PubMed

Trevizani, Raphael; Custódio, Fábio Lima; Dos Santos, Karina Baptista; Dardenne, Laurent Emmanuel

2017-01-01

The use of fragment libraries is a popular approach among protein structure prediction methods and has proven to substantially improve the quality of predicted structures. However, some vital aspects of a fragment library that influence the accuracy of modeling a native structure remain to be determined. This study investigates some of these features. Particularly, we analyze the effect of using secondary structure prediction guiding fragments selection, different fragments sizes and the effect of structural clustering of fragments within libraries. To have a clearer view of how these factors affect protein structure prediction, we isolated the process of model building by fragment assembly from some common limitations associated with prediction methods, e.g., imprecise energy functions and optimization algorithms, by employing an exact structure-based objective function under a greedy algorithm. Our results indicate that shorter fragments reproduce the native structure more accurately than the longer. Libraries composed of multiple fragment lengths generate even better structures, where longer fragments show to be more useful at the beginning of the simulations. The use of many different fragment sizes shows little improvement when compared to predictions carried out with libraries that comprise only three different fragment sizes. Models obtained from libraries built using only sequence similarity are, on average, better than those built with a secondary structure prediction bias. However, we found that the use of secondary structure prediction allows greater reduction of the search space, which is invaluable for prediction methods. The results of this study can be critical guidelines for the use of fragment libraries in protein structure prediction.

Phage display: concept, innovations, applications and future.

PubMed

Pande, Jyoti; Szewczyk, Magdalena M; Grover, Ashok K

2010-01-01

Phage display is the technology that allows expression of exogenous (poly)peptides on the surface of phage particles. The concept is simple in principle: a library of phage particles expressing a wide diversity of peptides is used to select those that bind the desired target. The filamentous phage M13 is the most commonly used vector to create random peptide display libraries. Several methods including recombinant techniques have been developed to increase the diversity of the library. On the other extreme, libraries with various biases can be created for specific purposes. For instance, when the sequence of the peptide that binds the target is known, its affinity and selectivity can be increased by screening libraries created with limited mutagenesis of the peptide. Phage libraries are screened for binding to synthetic or native targets. The initial screening of library by basic biopanning has been extended to column chromatography including negative screening and competition between selected phage clones to identify high affinity ligands with greater target specificity. The rapid isolation of specific ligands by phage display is advantageous in many applications including selection of inhibitors for the active and allosteric sites of the enzymes, receptor agonists and antagonists, and G-protein binding modulatory peptides. Phage display has been used in epitope mapping and analysis of protein-protein interactions. The specific ligands isolated from phage libraries can be used in therapeutic target validation, drug design and vaccine development. Phage display can also be used in conjunction with other methods. The past innovations and those to come promise a bright future for this field. Copyright © 2010 Elsevier Inc. All rights reserved.

A library of programmable DNAzymes that operate in a cellular environment.

PubMed

Kahan-Hanum, Maya; Douek, Yehonatan; Adar, Rivka; Shapiro, Ehud

2013-01-01

DNAzymes were used as inhibitory agents in a variety of experimental disease settings, such as cancer, viral infections and even HIV. Drugs that become active only upon the presence of preprogrammed abnormal environmental conditions may enable selective molecular therapy by targeting abnormal cells without injuring normal cells. Here we show a novel programmable DNAzyme library composed of variety of Boolean logic gates, including YES, AND, NOT, OR, NAND, ANDNOT, XOR, NOR and 3-input-AND gate, that uses both miRNAs and mRNAs as inputs. Each gate is based on the c-jun cleaving Dz13 DNAzyme and active only in the presence of specific input combinations. The library is modular, supports arbitrary inputs and outputs, cascadable, highly specific and robust. We demonstrate the library's potential diagnostic abilities on miRNA and mRNA combinations in cell lysate and its ability to operate in a cellular environment by using beacon-like c-jun mimicking substrate in living mammalian cells.

A library of programmable DNAzymes that operate in a cellular environment

PubMed Central

Kahan-Hanum, Maya; Douek, Yehonatan; Adar, Rivka; Shapiro, Ehud

2013-01-01

DNAzymes were used as inhibitory agents in a variety of experimental disease settings, such as cancer, viral infections and even HIV. Drugs that become active only upon the presence of preprogrammed abnormal environmental conditions may enable selective molecular therapy by targeting abnormal cells without injuring normal cells. Here we show a novel programmable DNAzyme library composed of variety of Boolean logic gates, including YES, AND, NOT, OR, NAND, ANDNOT, XOR, NOR and 3-input-AND gate, that uses both miRNAs and mRNAs as inputs. Each gate is based on the c-jun cleaving Dz13 DNAzyme and active only in the presence of specific input combinations. The library is modular, supports arbitrary inputs and outputs, cascadable, highly specific and robust. We demonstrate the library's potential diagnostic abilities on miRNA and mRNA combinations in cell lysate and its ability to operate in a cellular environment by using beacon-like c-jun mimicking substrate in living mammalian cells. PMID:23525068

Synthesis of a bifunctional cytidine derivative and its conjugation to RNA for in vitro selection of a cytidine deaminase ribozyme

PubMed Central

Rublack, Nico

2014-01-01

Summary Over the past 20 years, the generation of functional RNAs by in vitro selection has become a standard technique. Apart from aptamers for simple binding of defined ligands, also RNAs for catalysis of chemical reactions have been selected. In the latter case, a key step often is the conjugation of one of the two reactants to the library, requiring suitable strategies for terminal or internal RNA functionalization. With the aim of selecting a ribozyme for deamination of cytidine, we have set up a selection scheme involving the attachment of the cytidine acting as deamination substrate to the 3'-terminus of the RNAs in the library, and library immobilization. Here, we report the synthesis of a bifunctional cytidine derivative suitable for conjugation to RNA and linkage of the conjugated library to a streptavidine-coated surface. Successful conjugation of the cytidine derivative to the 3'-terminus of a model RNA is demonstrated. PMID:25246949

Computational Redesign of Acyl-ACP Thioesterase with Improved Selectivity toward Medium-Chain-Length Fatty Acids

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

Grisewood, Matthew J.; Hernández-Lozada, Néstor J.; Thoden, James B.

Enzyme and metabolic engineering offer the potential to develop biocatalysts for converting natural resources to a wide range of chemicals. To broaden the scope of potential products beyond natural metabolites, methods of engineering enzymes to accept alternative substrates and/or perform novel chemistries must be developed. DNA synthesis can create large libraries of enzyme-coding sequences, but most biochemistries lack a simple assay to screen for promising enzyme variants. Our solution to this challenge is structure-guided mutagenesis, in which optimization algorithms select the best sequences from libraries based on specified criteria (i.e., binding selectivity). We demonstrate this approach by identifying medium-chain (C8–C12)more » acyl-ACP thioesterases through structure-guided mutagenesis. Medium-chain fatty acids, which are products of thioesterase-catalyzed hydrolysis, are limited in natural abundance, compared to long-chain fatty acids; the limited supply leads to high costs of C6–C10 oleochemicals such as fatty alcohols, amines, and esters. Here, we applied computational tools to tune substrate binding of the highly active ‘TesA thioesterase in Escherichia coli. We used the IPRO algorithm to design thioesterase variants with enhanced C12 or C8 specificity, while maintaining high activity. After four rounds of structure-guided mutagenesis, we identified 3 variants with enhanced production of dodecanoic acid (C12) and 27 variants with enhanced production of octanoic acid (C8). The top variants reached up to 49% C12 and 50% C8 while exceeding native levels of total free fatty acids. A comparably sized library created by random mutagenesis failed to identify promising mutants. The chain length-preference of ‘TesA and the best mutant were confirmed in vitro using acyl-CoA substrates. Molecular dynamics simulations, confirmed by resolved crystal structures, of ‘TesA variants suggest that hydrophobic forces govern ‘TesA substrate specificity. Finally, we expect the design rules that we uncovered and the thioesterase variants that we identified will be useful to metabolic engineering projects aimed at sustainable production of medium-chain-length oleochemicals.« less

High quality epoxysilane substrate for clinical multiplex serodiagnostic proteomic microarrays

NASA Astrophysics Data System (ADS)

Ewart, Tom; Carmichael, Stuart; Lea, Peter

2005-09-01

Polylysine and aminopropylsilane treated glass comprised the majority of substrates employed in first generation genetic microarray substrates. Second generation single stranded long oligo libraries with amino termini provided for controlled terminal specific attachment, and rationally designed unique sequence libraries with normalized melting temperatures. These libraries benefit from active covalent coupling surfaces such as Epoxysilane. The latter's oxime ring shows versatile reactivity with amino-, thiol- and hydroxyl- groups thus encompassing small molecule, oligo and proteomic microarray applications. Batch-to-batch production uniformity supports entry of the Epoxysilane process into clinical diagnostics. We carried out multiple print runs of 21 clinically relevant bacterial and viral antigens at optimized concentrations, plus human IgG and IgM standards in triplicate on multiple batches of Epoxysilane substrates. A set of 45 patient sera were assayed in a 35 minute protocol using 10 microliters per array in a capillary-fill format (15 minute serum incubation, wash, 15 minute incubation with Cy3-labeled anti-hIgG plus Dy647-labeled anti-hIgM, final wash). The LOD (3 SD above background) was better than 1 microgram/ml for IgG, and standard curves were regular and monotonically increasing over the range 0 to 1000 micrograms/ml. Ninety-five percent of the CVs for the standards were under 10%, and 90% percent of CVs for antigen responses were under 10% across all batches of Epoxysilane and print runs. In addition, where SDs are larger than expected, microarray images may be readily reviewed for quality control purposes and pin misprints quickly identified. In order to determine the influence of stirring on sensitivity and speed of the microarray assay, we printed 10 common ToRCH antigens (H. pylori, T. gondii, Rubella, Rubeola, C. trachomatis, Herpes 1 and 2, CMV, C. jejuni, and EBV) in Epoxysilane-activated slide-wells. Anti-IgG-Cy3 direct binding to printed IgG calibration spots could be detected (3 x LOD) above background at 100 pg/ml (0.13 femtomoles sample content) in a 10 minute incubation. The LOD for detection of serum anti-H. pylori antibody level was 9 ng/ml in the same incubation time.

Computational Redesign of Acyl-ACP Thioesterase with Improved Selectivity toward Medium-Chain-Length Fatty Acids

DOE PAGES

Grisewood, Matthew J.; Hernández-Lozada, Néstor J.; Thoden, James B.; ...

2017-04-20

Enzyme and metabolic engineering offer the potential to develop biocatalysts for converting natural resources to a wide range of chemicals. To broaden the scope of potential products beyond natural metabolites, methods of engineering enzymes to accept alternative substrates and/or perform novel chemistries must be developed. DNA synthesis can create large libraries of enzyme-coding sequences, but most biochemistries lack a simple assay to screen for promising enzyme variants. Our solution to this challenge is structure-guided mutagenesis, in which optimization algorithms select the best sequences from libraries based on specified criteria (i.e., binding selectivity). We demonstrate this approach by identifying medium-chain (C8–C12)more » acyl-ACP thioesterases through structure-guided mutagenesis. Medium-chain fatty acids, which are products of thioesterase-catalyzed hydrolysis, are limited in natural abundance, compared to long-chain fatty acids; the limited supply leads to high costs of C6–C10 oleochemicals such as fatty alcohols, amines, and esters. Here, we applied computational tools to tune substrate binding of the highly active ‘TesA thioesterase in Escherichia coli. We used the IPRO algorithm to design thioesterase variants with enhanced C12 or C8 specificity, while maintaining high activity. After four rounds of structure-guided mutagenesis, we identified 3 variants with enhanced production of dodecanoic acid (C12) and 27 variants with enhanced production of octanoic acid (C8). The top variants reached up to 49% C12 and 50% C8 while exceeding native levels of total free fatty acids. A comparably sized library created by random mutagenesis failed to identify promising mutants. The chain length-preference of ‘TesA and the best mutant were confirmed in vitro using acyl-CoA substrates. Molecular dynamics simulations, confirmed by resolved crystal structures, of ‘TesA variants suggest that hydrophobic forces govern ‘TesA substrate specificity. Finally, we expect the design rules that we uncovered and the thioesterase variants that we identified will be useful to metabolic engineering projects aimed at sustainable production of medium-chain-length oleochemicals.« less

Voltage contrast X-ray photoelectron spectroscopy reveals graphene-substrate interaction in graphene devices fabricated on the C- and Si- faces of SiC

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

Aydogan, Pinar; Suzer, Sefik, E-mail: suzer@fen.bilkent.edu.tr; Arslan, Engin

2015-09-21

We report on an X-ray photoelectron spectroscopy (XPS) study of two graphene based devices that were analyzed by imposing a significant current under +3 V bias. The devices were fabricated as graphene layers(s) on hexagonal SiC substrates, either on the C- or Si-terminated faces. Position dependent potential distributions (IR-drop), as measured by variations in the binding energy of a C1s peak are observed to be sporadic for the C-face graphene sample, but very smooth for the Si-face one, although the latter is less conductive. We attribute these sporadic variations in the C-face device to the incomplete electrical decoupling between the graphenemore » layer(s) with the underlying buffer and/or substrate layers. Variations in the Si2p and O1s peaks of the underlayer(s) shed further light into the electrical interaction between graphene and other layers. Since the potential variations are amplified only under applied bias (voltage-contrast), our methodology gives unique, chemically specific electrical information that is difficult to obtain by other techniques.« less

Evaluation of proteases and protease inhibitors in Heterodera glycines cysts obtained from laboratory and field populations

USDA-ARS?s Scientific Manuscript database

Proteases and proteases inhibitors were evaluated in a number of preparations of Heterodera glycines cysts obtained from glasshouse cultures (GH) and field (LR) populations. Using a FRET-peptide library comprising 512 peptide substrate pools that detect 4 endoprotease types (aspartic, cysteine, meta...

Exploring Nitrilase Sequence Space for Enantioselective Catalysis†

PubMed Central

Robertson, Dan E.; Chaplin, Jennifer A.; DeSantis, Grace; Podar, Mircea; Madden, Mark; Chi, Ellen; Richardson, Toby; Milan, Aileen; Miller, Mark; Weiner, David P.; Wong, Kelvin; McQuaid, Jeff; Farwell, Bob; Preston, Lori A.; Tan, Xuqiu; Snead, Marjory A.; Keller, Martin; Mathur, Eric; Kretz, Patricia L.; Burk, Mark J.; Short, Jay M.

2004-01-01

Nitrilases are important in the biosphere as participants in synthesis and degradation pathways for naturally occurring, as well as xenobiotically derived, nitriles. Because of their inherent enantioselectivity, nitrilases are also attractive as mild, selective catalysts for setting chiral centers in fine chemical synthesis. Unfortunately, <20 nitrilases have been reported in the scientific and patent literature, and because of stability or specificity shortcomings, their utility has been largely unrealized. In this study, 137 unique nitrilases, discovered from screening of >600 biotope-specific environmental DNA (eDNA) libraries, were characterized. Using culture-independent means, phylogenetically diverse genomes were captured from entire biotopes, and their genes were expressed heterologously in a common cloning host. Nitrilase genes were targeted in a selection-based expression assay of clonal populations numbering 106 to 1010 members per eDNA library. A phylogenetic analysis of the novel sequences discovered revealed the presence of at least five major sequence clades within the nitrilase subfamily. Using three nitrile substrates targeted for their potential in chiral pharmaceutical synthesis, the enzymes were characterized for substrate specificity and stereospecificity. A number of important correlations were found between sequence clades and the selective properties of these nitrilases. These enzymes, discovered using a high-throughput, culture-independent method, provide a catalytic toolbox for enantiospecific synthesis of a variety of carboxylic acid derivatives, as well as an intriguing library for evolutionary and structural analyses. PMID:15066841

Exchange bias induced by the fully strained La{sub 2/3}Ca{sub 1/3}MnO{sub 3} dead layers

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

Xie, Q. Y.; College of Electronic Science and Engineering, Nanjing University of Posts and Telecommunications, Nanjing 210046; Wu, X. S., E-mail: xswu@nju.edu.cn

A pure compressively strained La{sub 2/3}Ca{sub 1/3}MnO{sub 3} (LCMO) dead layer grown on (001)-oriented LaAlO{sub 3} substrate can show all the rich phenomenon of large bias field shift, coercive field enhancement, and high blocking temperature. The obtained exchange bias field (∼350 Oe) and the enhanced coercivity of about 1160 Oe at 5 K under 500 Oe cooling field are superior to that have been reported in LCMO-based ferromagnetic/antiferromagnetic superlattices or nanoscale systems. Our results clearly demonstrate that the inhomogeneous magnetic dead layer of LCMO can induce a strong exchange bias effect, which may be exploited as a very simple structure for spin-valve device application.

Measurements of the asymmetric dynamic sheath around a pulse biased sphere immersed in flowing metal plasma

NASA Astrophysics Data System (ADS)

Wu, Hongchen; Anders, André

2008-08-01

A long-probe technique was utilized to record the expansion and retreat of the dynamic sheath around a spherical substrate immersed in pulsed cathode arc metal plasma. Positively biased, long cylindrical probes were placed on the side and downstream of a negatively pulsed biased stainless steel sphere of 1 in. (25.4 mm) diameter. The amplitude and width of the negative high voltage pulses (HVPs) were 2 kV, 5 kV, 10 kV, and 2 µs, 4 µs, 10 µs, respectively. The variation of the probe (electron) current during the HVP is a direct measure for the sheath expansion and retreat. Maximum sheath sizes were determined for the different parameters of the HVP. The expected rarefaction zone behind the biased sphere (wake) due to the fast plasma flow was clearly established and quantified.

Effects of Ion Atomic Number on Single-Event Gate Rupture (SEGR) Susceptibility of Power MOSFETs

NASA Technical Reports Server (NTRS)

Lauenstein, J.-M.; Goldsman, N.; Liu, S.; Titus, J.; Ladbury, R. L.; Kim, H. S.; Phan, A. M.; Zafrani, M.; Sherman, P.

2011-01-01

The relative importance of heavy-ion interaction with the oxide, charge ionized in the epilayer, and charge ionized in the drain substrate, on the bias for SEGR failure is experimentally investigated.

Link between microbial composition and carbon substrate-uptake preferences in a PHA-storing community

PubMed Central

Albuquerque, Maria G E; Carvalho, Gilda; Kragelund, Caroline; Silva, Ana F; Barreto Crespo, Maria T; Reis, Maria A M; Nielsen, Per H

2013-01-01

The microbial community of a fermented molasses-fed sequencing batch reactor (SBR) operated under feast and famine conditions for production of polyhydroxyalkanoates (PHAs) was identified and quantified through a 16 S rRNA gene clone library and fluorescence in situ hybridization (FISH). The microbial enrichment was found to be composed of PHA-storing populations (84% of the microbial community), comprising members of the genera Azoarcus, Thauera and Paracoccus. The dominant PHA-storing populations ensured the high functional stability of the system (characterized by high PHA-storage efficiency, up to 60% PHA content). The fermented molasses contained primarily acetate, propionate, butyrate and valerate. The substrate preferences were determined by microautoradiography-FISH and differences in the substrate-uptake capabilities for the various probe-defined populations were found. The results showed that in the presence of multiple substrates, microbial populations specialized in different substrates were selected, thereby co-existing in the SBR by adapting to different niches. Azoarcus and Thauera, primarily consumed acetate and butyrate, respectively. Paracoccus consumed a broader range of substrates and had a higher cell-specific substrate uptake. The relative species composition and their substrate specialization were reflected in the substrate removal rates of different volatile fatty acids in the SBR reactor. PMID:22810062

Unnatural amino acids increase activity and specificity of synthetic substrates for human and malarial cathepsin C.

PubMed

Poreba, Marcin; Mihelic, Marko; Krai, Priscilla; Rajkovic, Jelena; Krezel, Artur; Pawelczak, Malgorzata; Klemba, Michael; Turk, Dusan; Turk, Boris; Latajka, Rafal; Drag, Marcin

2014-04-01

Mammalian cathepsin C is primarily responsible for the removal of N-terminal dipeptides and activation of several serine proteases in inflammatory or immune cells, while its malarial parasite ortholog dipeptidyl aminopeptidase 1 plays a crucial role in catabolizing the hemoglobin of its host erythrocyte. In this report, we describe the systematic substrate specificity analysis of three cathepsin C orthologs from Homo sapiens (human), Bos taurus (bovine) and Plasmodium falciparum (malaria parasite). Here, we present a new approach with a tailored fluorogenic substrate library designed and synthesized to probe the S1 and S2 pocket preferences of these enzymes with both natural and a broad range of unnatural amino acids. Our approach identified very efficiently hydrolyzed substrates containing unnatural amino acids, which resulted in the design of significantly better substrates than those previously known. Additionally, in this study significant differences in terms of the structures of optimal substrates for human and malarial orthologs are important from the therapeutic point of view. These data can be also used for the design of specific inhibitors or activity-based probes.

Fabrication of Carbon Nanotube Networks on Three-Dimensional Building Blocks and Their Applications

DTIC Science & Technology

2012-10-27

increases the detection efficiency via sorting of analyte. There are some reports for sorting or separating blood cell, colloidal and bacteria by...the substrates for cyclic voltammetry (CV), pulsed bias of ECD was applied at -1.2 V during 90, 120 and 150 sec for 1, 3 and 5 μm pillar substrates...Deposition with Al2O3: The atomic layer deposition (ALD, Cyclic 4000, Genitech) was introduced to deposit the Al2O3 on the surfaces of network

Single molecule sequencing of the M13 virus genome without amplification

PubMed Central

Zhao, Luyang; Deng, Liwei; Li, Gailing; Jin, Huan; Cai, Jinsen; Shang, Huan; Li, Yan; Wu, Haomin; Xu, Weibin; Zeng, Lidong; Zhang, Renli; Zhao, Huan; Wu, Ping; Zhou, Zhiliang; Zheng, Jiao; Ezanno, Pierre; Yang, Andrew X.; Yan, Qin; Deem, Michael W.; He, Jiankui

2017-01-01

Next generation sequencing (NGS) has revolutionized life sciences research. However, GC bias and costly, time-intensive library preparation make NGS an ill fit for increasing sequencing demands in the clinic. A new class of third-generation sequencing platforms has arrived to meet this need, capable of directly measuring DNA and RNA sequences at the single-molecule level without amplification. Here, we use the new GenoCare single-molecule sequencing platform from Direct Genomics to sequence the genome of the M13 virus. Our platform detects single-molecule fluorescence by total internal reflection microscopy, with sequencing-by-synthesis chemistry. We sequenced the genome of M13 to a depth of 316x, with 100% coverage. We determined a consensus sequence accuracy of 100%. In contrast to GC bias inherent to NGS results, we demonstrated that our single-molecule sequencing method yields minimal GC bias. PMID:29253901

Single molecule sequencing of the M13 virus genome without amplification.

PubMed

Zhao, Luyang; Deng, Liwei; Li, Gailing; Jin, Huan; Cai, Jinsen; Shang, Huan; Li, Yan; Wu, Haomin; Xu, Weibin; Zeng, Lidong; Zhang, Renli; Zhao, Huan; Wu, Ping; Zhou, Zhiliang; Zheng, Jiao; Ezanno, Pierre; Yang, Andrew X; Yan, Qin; Deem, Michael W; He, Jiankui

2017-01-01

Next generation sequencing (NGS) has revolutionized life sciences research. However, GC bias and costly, time-intensive library preparation make NGS an ill fit for increasing sequencing demands in the clinic. A new class of third-generation sequencing platforms has arrived to meet this need, capable of directly measuring DNA and RNA sequences at the single-molecule level without amplification. Here, we use the new GenoCare single-molecule sequencing platform from Direct Genomics to sequence the genome of the M13 virus. Our platform detects single-molecule fluorescence by total internal reflection microscopy, with sequencing-by-synthesis chemistry. We sequenced the genome of M13 to a depth of 316x, with 100% coverage. We determined a consensus sequence accuracy of 100%. In contrast to GC bias inherent to NGS results, we demonstrated that our single-molecule sequencing method yields minimal GC bias.

Predictions of ion energy distributions and radical fluxes in radio frequency biased inductively coupled plasma etching reactors

NASA Astrophysics Data System (ADS)

Hoekstra, Robert J.; Kushner, Mark J.

1996-03-01

Inductively coupled plasma (ICP) reactors are being developed for low gas pressure (<10s mTorr) and high plasma density ([e]≳1011 cm-3) microelectronics fabrication. In these reactors, the plasma is generated by the inductively coupled electric field while an additional radio frequency (rf) bias is applied to the substrate. One of the goals of these systems is to independently control the magnitude of the ion flux by the inductively coupled power deposition, and the acceleration of ions into the substrate by the rf bias. In high plasma density reactors the width of the sheath above the wafer may be sufficiently thin that ions are able to traverse it in approximately 1 rf cycle, even at 13.56 MHz. As a consequence, the ion energy distribution (IED) may have a shape typically associated with lower frequency operation in conventional reactive ion etching tools. In this paper, we present results from a computer model for the IED incident on the wafer in ICP etching reactors. We find that in the parameter space of interest, the shape of the IED depends both on the amplitude of the rf bias and on the ICP power. The former quantity determines the average energy of the IED. The latter quantity controls the width of the sheath, the transit time of ions across the sheath and hence the width of the IED. In general, high ICP powers (thinner sheaths) produce wider IEDs.

Male- and female-biased gene expression of olfactory-related genes in the antennae of Asian corn borer, Ostrinia furnacalis (Guenée) (Lepidoptera: Crambidae)

USDA-ARS?s Scientific Manuscript database

The Asian corn borer (ACB), Ostrinia furnacalis (Guenée), is a destructive pest insect of cultivated corn crops, for which antennal-expressed receptors are important to detect olfactory cues for mate attraction and oviposition. Non-normalized male and female O. furnacalis antennal cDNA libraries we...

Effectiveness of training in evidence-based medicine skills for healthcare professionals: a systematic review.

PubMed

Hecht, Lars; Buhse, Susanne; Meyer, Gabriele

2016-04-04

Basic skills in evidence-based medicine (EbM) are indispensable for healthcare professionals to promote consumer-centred, evidence-based treatment. EbM training courses are complex interventions - a fact that has not been methodologically reflected by previous systematic reviews. This review evaluates the effects of EbM training for healthcare professionals as well as the quality of reporting of such training interventions. We searched PubMed, EMBASE, CINAHL, Cochrane Library, ERIC, Campbell Library and PsycINFO up to 9/2014. Randomised controlled trials, controlled clinical trials as well as before-after trials were included. Authors were contacted in order to obtain missing data. Two independent reviewers extracted data and assessed risk of bias. We reviewed 14.507 articles; n = 61 appeared potentially eligible; n = 13 involving 1,120 participants were included. EbM training shows some impact on knowledge and skills, whereas the impact on practical EbM application remains unclear. Risk of bias of included trials raises uncertainty about the effects. Description of complex interventions was poor. EbM training has some positive effects on knowledge and skills of healthcare professionals. Appropriate methods for development, piloting, evaluation, reporting and implementation of the training should be applied.

Palindromic Sequence Artifacts Generated during Next Generation Sequencing Library Preparation from Historic and Ancient DNA

PubMed Central

Star, Bastiaan; Nederbragt, Alexander J.; Hansen, Marianne H. S.; Skage, Morten; Gilfillan, Gregor D.; Bradbury, Ian R.; Pampoulie, Christophe; Stenseth, Nils Chr; Jakobsen, Kjetill S.; Jentoft, Sissel

2014-01-01

Degradation-specific processes and variation in laboratory protocols can bias the DNA sequence composition from samples of ancient or historic origin. Here, we identify a novel artifact in sequences from historic samples of Atlantic cod (Gadus morhua), which forms interrupted palindromes consisting of reverse complementary sequence at the 5′ and 3′-ends of sequencing reads. The palindromic sequences themselves have specific properties – the bases at the 5′-end align well to the reference genome, whereas extensive misalignments exists among the bases at the terminal 3′-end. The terminal 3′ bases are artificial extensions likely caused by the occurrence of hairpin loops in single stranded DNA (ssDNA), which can be ligated and amplified in particular library creation protocols. We propose that such hairpin loops allow the inclusion of erroneous nucleotides, specifically at the 3′-end of DNA strands, with the 5′-end of the same strand providing the template. We also find these palindromes in previously published ancient DNA (aDNA) datasets, albeit at varying and substantially lower frequencies. This artifact can negatively affect the yield of endogenous DNA in these types of samples and introduces sequence bias. PMID:24608104

A strategy for rapid production and screening of yeast artificial chromosome libraries.

PubMed

Strauss, W M; Jaenisch, E; Jaenisch, R

1992-01-01

We describe methods for rapid production and screening of yeast artificial chromosome (YAC) libraries. Utilizing complete restriction digests of mouse genomic DNA for ligations in agarose, a 32,000-clone library was produced and screened in seven weeks. Screening was accomplished by subdividing primary transformation plates into pools of approximately 100 clones which were transferred into a master glycerol stock. These master stocks were used to inoculate liquid cultures to produce culture "pools," and ten pools of 100 clones were then combined to yield superpools of 1,000 clones. Both pool and superpool DNA was screened by polymerase chain reaction (PCR) and positive pools representing 100 clones were then plated on selective medium and screened by in situ hybridization. Screening by the two tiered PCR assay and by in situ hybridization was completed in 4-5 days. Utilizing this methodology we have isolated a 150 kb clone spanning the alpha 1(I) collagen (Col1a1) gene as well as 40 kb clones from the Hox-2 locus. To characterize the representation of the YAC library, the size distribution of genomic Sal I fragments was compared to that of clones picked at random from the library. The results demonstrate significant biasing of the cloned fragment distribution, resulting in a loss of representation for larger fragments.

Quality control of next-generation sequencing library through an integrative digital microfluidic platform.

PubMed

Thaitrong, Numrin; Kim, Hanyoup; Renzi, Ronald F; Bartsch, Michael S; Meagher, Robert J; Patel, Kamlesh D

2012-12-01

We have developed an automated quality control (QC) platform for next-generation sequencing (NGS) library characterization by integrating a droplet-based digital microfluidic (DMF) system with a capillary-based reagent delivery unit and a quantitative CE module. Using an in-plane capillary-DMF interface, a prepared sample droplet was actuated into position between the ground electrode and the inlet of the separation capillary to complete the circuit for an electrokinetic injection. Using a DNA ladder as an internal standard, the CE module with a compact LIF detector was capable of detecting dsDNA in the range of 5-100 pg/μL, suitable for the amount of DNA required by the Illumina Genome Analyzer sequencing platform. This DMF-CE platform consumes tenfold less sample volume than the current Agilent BioAnalyzer QC technique, preserving precious sample while providing necessary sensitivity and accuracy for optimal sequencing performance. The ability of this microfluidic system to validate NGS library preparation was demonstrated by examining the effects of limited-cycle PCR amplification on the size distribution and the yield of Illumina-compatible libraries, demonstrating that as few as ten cycles of PCR bias the size distribution of the library toward undesirable larger fragments. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Exploring Pandora's Box: Potential and Pitfalls of Low Coverage Genome Surveys for Evolutionary Biology

PubMed Central

Leese, Florian; Mayer, Christoph; Agrawal, Shobhit; Dambach, Johannes; Dietz, Lars; Doemel, Jana S.; Goodall-Copstake, William P.; Held, Christoph; Jackson, Jennifer A.; Lampert, Kathrin P.; Linse, Katrin; Macher, Jan N.; Nolzen, Jennifer; Raupach, Michael J.; Rivera, Nicole T.; Schubart, Christoph D.; Striewski, Sebastian; Tollrian, Ralph; Sands, Chester J.

2012-01-01

High throughput sequencing technologies are revolutionizing genetic research. With this “rise of the machines”, genomic sequences can be obtained even for unknown genomes within a short time and for reasonable costs. This has enabled evolutionary biologists studying genetically unexplored species to identify molecular markers or genomic regions of interest (e.g. micro- and minisatellites, mitochondrial and nuclear genes) by sequencing only a fraction of the genome. However, when using such datasets from non-model species, it is possible that DNA from non-target contaminant species such as bacteria, viruses, fungi, or other eukaryotic organisms may complicate the interpretation of the results. In this study we analysed 14 genomic pyrosequencing libraries of aquatic non-model taxa from four major evolutionary lineages. We quantified the amount of suitable micro- and minisatellites, mitochondrial genomes, known nuclear genes and transposable elements and searched for contamination from various sources using bioinformatic approaches. Our results show that in all sequence libraries with estimated coverage of about 0.02–25%, many appropriate micro- and minisatellites, mitochondrial gene sequences and nuclear genes from different KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways could be identified and characterized. These can serve as markers for phylogenetic and population genetic analyses. A central finding of our study is that several genomic libraries suffered from different biases owing to non-target DNA or mobile elements. In particular, viruses, bacteria or eukaryote endosymbionts contributed significantly (up to 10%) to some of the libraries analysed. If not identified as such, genetic markers developed from high-throughput sequencing data for non-model organisms may bias evolutionary studies or fail completely in experimental tests. In conclusion, our study demonstrates the enormous potential of low-coverage genome survey sequences and suggests bioinformatic analysis workflows. The results also advise a more sophisticated filtering for problematic sequences and non-target genome sequences prior to developing markers. PMID:23185309

Towards a library of synthetic galaxy spectra and preliminary results of classification and parametrization of unresolved galaxies for Gaia. II

NASA Astrophysics Data System (ADS)

Tsalmantza, P.; Kontizas, M.; Rocca-Volmerange, B.; Bailer-Jones, C. A. L.; Kontizas, E.; Bellas-Velidis, I.; Livanou, E.; Korakitis, R.; Dapergolas, A.; Vallenari, A.; Fioc, M.

2009-09-01

Aims: This paper is the second in a series, implementing a classification system for Gaia observations of unresolved galaxies. Our goals are to determine spectral classes and estimate intrinsic astrophysical parameters via synthetic templates. Here we describe (1) a new extended library of synthetic galaxy spectra; (2) its comparison with various observations; and (3) first results of classification and parametrization experiments using simulated Gaia spectrophotometry of this library. Methods: Using the PÉGASE.2 code, based on galaxy evolution models that take account of metallicity evolution, extinction correction, and emission lines (with stellar spectra based on the BaSeL library), we improved our first library and extended it to cover the domain of most of the SDSS catalogue. Our classification and regression models were support vector machines (SVMs). Results: We produce an extended library of 28 885 synthetic galaxy spectra at zero redshift covering four general Hubble types of galaxies, over the wavelength range between 250 and 1050 nm at a sampling of 1 nm or less. The library is also produced for 4 random values of redshift in the range of 0-0.2. It is computed on a random grid of four key astrophysical parameters (infall timescale and 3 parameters defining the SFR) and, depending on the galaxy type, on two values of the age of the galaxy. The synthetic library was compared and found to be in good agreement with various observations. The first results from the SVM classifiers and parametrizers are promising, indicating that Hubble types can be reliably predicted and several parameters estimated with low bias and variance.

On the shift of the electroluminescence spectra of In{sub x}Ga{sub 1−x}N/GaN structures with various indium contents and various substrate materials caused by the stark effect and mechanical stresses

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

Veleschuk, V. P., E-mail: vvvit@ukr.nd; Vlasenko, A. I.; Kisselyuk, M. P.

2015-08-15

The shift between the maxima of the electroluminescence spectra of In{sub x}Ga{sub 1−x}N/GaN structures is measured at forward and reverse bias depending on the indium content x in the quantum well and on the substrate material (SiC, AuSn/Si, and Al{sub 2}O{sub 3}). It is established that this shift increases as the indium concentration in the In{sub x}Ga{sub 1−x}N layer and mechanical stresses from the substrate increase.

Self-powered p-NiO/n-ZnO heterojunction ultraviolet photodetectors fabricated on plastic substrates

PubMed Central

Hasan, Md Rezaul; Xie, Ting; Barron, Sara C.; Liu, Guannan; Nguyen, Nhan V.; Motayed, Abhishek; Rao, Mulpuri V.; Debnath, Ratan

2016-01-01

A self-powered ultraviolet (UV) photodetector (PD) based on p-NiO and n-ZnO was fabricated using low-temperature sputtering technique on indium doped tin oxide (ITO) coated plastic polyethylene terephthalate (PET) substrates. The p-n heterojunction showed very fast temporal photoresponse with excellent quantum efficiency of over 63% under UV illumination at an applied reverse bias of 1.2 V. The engineered ultrathin Ti/Au top metal contacts and UV transparent PET/ITO substrates allowed the PDs to be illuminated through either front or back side. Morphology, structural, chemical and optical properties of sputtered NiO and ZnO films were also investigated. PMID:26900532

Molecules for organic electronics studied one by one.

PubMed

Meyer, Jörg; Wadewitz, Anja; Lokamani; Toher, Cormac; Gresser, Roland; Leo, Karl; Riede, Moritz; Moresco, Francesca; Cuniberti, Gianaurelio

2011-08-28

The electronic and geometrical structure of single difluoro-bora-1,3,5,7-tetraphenyl-aza-dipyrromethene (aza-BODIPY) molecules adsorbed on the Au(111) surface is investigated by low temperature scanning tunneling microscopy and spectroscopy in conjunction with ab initio density functional theory simulations of the density of states and of the interaction with the substrate. Our DFT calculations indicate that the aza-bodipy molecule forms a chemical bond with the Au(111) substrate, with distortion of the molecular geometry and significant charge transfer between the molecule and the substrate. Nevertheless, most likely due to the low corrugation of the Au(111) surface, diffusion of the molecule is observed for applied bias in excess of 1 V.

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

Ok, Kyung-Chul; Park, Jin-Seong, E-mail: hkim-2@naver.com, E-mail: jsparklime@hanyang.ac.kr; Ko Park, Sang-Hee

We demonstrated the fabrication of flexible amorphous indium gallium zinc oxide thin-film transistors (TFTs) on high-temperature polyimide (PI) substrates, which were debonded from the carrier glass after TFT fabrication. The application of appropriate buffer layers on the PI substrates affected the TFT performance and stability. The adoption of the SiN{sub x}/AlO{sub x} buffer layers as water and hydrogen diffusion barriers significantly improved the device performance and stability against the thermal annealing and negative bias stress, compared to single SiN{sub x} or SiO{sub x} buffer layers. The substrates could be bent down to a radius of curvature of 15 mm and themore » devices remained normally functional.« less

Dimer motion on a periodic substrate: spontaneous symmetry breaking and absolute negative mobility.

PubMed

Speer, David; Eichhorn, Ralf; Evstigneev, Mykhaylo; Reimann, Peter

2012-06-01

We consider two coupled particles moving along a periodic substrate potential with negligible inertia effects (overdamped limit). Even when the particles are identical and the substrate spatially symmetric, a sinusoidal external driving of appropriate amplitude and frequency may lead to spontaneous symmetry breaking in the form of a permanent directed motion of the dimer. Thermal noise restores ergodicity and thus zero net velocity, but entails arbitrarily fast diffusion of the dimer for sufficiently weak noise. Moreover, upon application of a static bias force, the dimer exhibits a motion opposite to that force (absolute negative mobility). The key requirement for all these effects is a nonconvex interaction potential of the two particles.

Diversity-oriented synthesis of a library of substituted tetrahydropyrones using oxidative carbon-hydrogen bond activation and click chemistry.

PubMed

Zaware, Nilesh; Laporte, Matthew G; Farid, Ramy; Liu, Lei; Wipf, Peter; Floreancig, Paul E

2011-05-02

Eighteen (2RS,6RS)-2-(4-methoxyphenyl)-6-(substituted ethyl)dihydro-2H-pyran-4(3H)ones were synthesized via a DDQ-mediated oxidative carbon-hydrogen bond activation reaction. Fourteen of these tetrahydropyrans were substituted with triazoles readily assembled via azide-alkyne click-chemistry reactions. Examples of a linked benzotriazole and pyrazole motif were also prepared. To complement the structural diversity, the alcohol substrates were obtained from stereoselective reductions of the tetrahydropyrone. This library provides rapid access to structurally diverse non-natural compounds to be screened against a variety of biological targets.

Structure and Biocatalytic Scope of Coclaurine N-Methyltransferase.

PubMed

Bennett, Matthew; Thompson, Mark; Shepherd, Sarah; Dunstan, Mark; Herbert, Abigail; Smith, Duncan; Cronin, Victoria; Menon, Binuraj; Levy, Colin; Micklefield, Jason

2018-05-23

Benzylisoquinoline alkaloids (BIAs) are a structurally diverse family of plant secondary metabolites which have been exploited to develop analgesics, antibiotics, antitumor agents and other therapeutic agents. Biosynthesis of BIAs proceeds via a common pathway from tyrosine to (S)-reticulene at which point the pathway diverges. Coclaurine N-methyltransferase (CNMT) is a key enzyme in the pathway to (S)-reticulene, installing the N-methyl substituent that is essential for the bioactivity of many BIAs. In this paper, we describe the first crystal structure of CNMT which, along with mutagenesis studies, defines the enzymes active site architecture. The specificity of CNMT was also explored with a range of natural and synthetic substrates as well as co-factor analogues. Knowledge from this study could be used to generate improved CNMT variants required to produce BIAs or synthetic derivatives. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Structure and properties of TiSiCN coatings with different bias voltages by arc ion plating

NASA Astrophysics Data System (ADS)

Xie, Xinming; Li, Jinlong; Dong, Minpeng; Zhang, Henghua; Wang, Liping

2018-03-01

TiSiCN coatings were deposited on 316 L steel using the multi-arc ion plating system. All the coatings had the same total thickness of approximately 1.6 µm. The TiSiCN coatings were deposited under the mixture constant flow of N2 and C2H2 but varying bias. Information about structures, composition and properties were characterized by scanning electron microscope, x-ray diffraction, x-ray photoelectron spectroscopy, nanoindentation and ball-on-plate wear tests. The results show that all of the coatings consist of a TiCN nano-crystal phase and an Si3N4 amorphous phase. With an increase in the bias, the film becomes denser and exhibits better tribological behavior and mechanical properties. Moreover, the bonding strength between the coatings and the substrate increased and the resistance to thermal shock intensified when the coatings were made at a higher bias voltage.

Quantitation of next generation sequencing library preparation protocol efficiencies using droplet digital PCR assays - a systematic comparison of DNA library preparation kits for Illumina sequencing.

PubMed

Aigrain, Louise; Gu, Yong; Quail, Michael A

2016-06-13

The emergence of next-generation sequencing (NGS) technologies in the past decade has allowed the democratization of DNA sequencing both in terms of price per sequenced bases and ease to produce DNA libraries. When it comes to preparing DNA sequencing libraries for Illumina, the current market leader, a plethora of kits are available and it can be difficult for the users to determine which kit is the most appropriate and efficient for their applications; the main concerns being not only cost but also minimal bias, yield and time efficiency. We compared 9 commercially available library preparation kits in a systematic manner using the same DNA sample by probing the amount of DNA remaining after each protocol steps using a new droplet digital PCR (ddPCR) assay. This method allows the precise quantification of fragments bearing either adaptors or P5/P7 sequences on both ends just after ligation or PCR enrichment. We also investigated the potential influence of DNA input and DNA fragment size on the final library preparation efficiency. The overall library preparations efficiencies of the libraries show important variations between the different kits with the ones combining several steps into a single one exhibiting some final yields 4 to 7 times higher than the other kits. Detailed ddPCR data also reveal that the adaptor ligation yield itself varies by more than a factor of 10 between kits, certain ligation efficiencies being so low that it could impair the original library complexity and impoverish the sequencing results. When a PCR enrichment step is necessary, lower adaptor-ligated DNA inputs leads to greater amplification yields, hiding the latent disparity between kits. We describe a ddPCR assay that allows us to probe the efficiency of the most critical step in the library preparation, ligation, and to draw conclusion on which kits is more likely to preserve the sample heterogeneity and reduce the need of amplification.

Robust DNA Isolation and High-throughput Sequencing Library Construction for Herbarium Specimens.

PubMed

Saeidi, Saman; McKain, Michael R; Kellogg, Elizabeth A

2018-03-08

Herbaria are an invaluable source of plant material that can be used in a variety of biological studies. The use of herbarium specimens is associated with a number of challenges including sample preservation quality, degraded DNA, and destructive sampling of rare specimens. In order to more effectively use herbarium material in large sequencing projects, a dependable and scalable method of DNA isolation and library preparation is needed. This paper demonstrates a robust, beginning-to-end protocol for DNA isolation and high-throughput library construction from herbarium specimens that does not require modification for individual samples. This protocol is tailored for low quality dried plant material and takes advantage of existing methods by optimizing tissue grinding, modifying library size selection, and introducing an optional reamplification step for low yield libraries. Reamplification of low yield DNA libraries can rescue samples derived from irreplaceable and potentially valuable herbarium specimens, negating the need for additional destructive sampling and without introducing discernible sequencing bias for common phylogenetic applications. The protocol has been tested on hundreds of grass species, but is expected to be adaptable for use in other plant lineages after verification. This protocol can be limited by extremely degraded DNA, where fragments do not exist in the desired size range, and by secondary metabolites present in some plant material that inhibit clean DNA isolation. Overall, this protocol introduces a fast and comprehensive method that allows for DNA isolation and library preparation of 24 samples in less than 13 h, with only 8 h of active hands-on time with minimal modifications.

GaAs photoconductive semiconductor switch

DOEpatents

Loubriel, Guillermo M.; Baca, Albert G.; Zutavern, Fred J.

1998-01-01

A high gain, optically triggered, photoconductive semiconductor switch (PCSS) implemented in GaAs as a reverse-biased pin structure with a passivation layer above the intrinsic GaAs substrate in the gap between the two electrodes of the device. The reverse-biased configuration in combination with the addition of the passivation layer greatly reduces surface current leakage that has been a problem for prior PCSS devices and enables employment of the much less expensive and more reliable DC charging systems instead of the pulsed charging systems that needed to be used with prior PCSS devices.

Thickness dependence of the exchange bias in epitaxial manganite bilayers

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

Kobrinskii, A. L.; Goldman, A. M.; Varela del Arco, Maria

Exchange bias has been studied in a series of La{sub 2/3}Ca{sub 1/3}MnO{sub 3}/La{sub 1/3}Ca{sub 2/3}MnO{sub 3} bilayers grown on (001) SrTiO{sub 3} substrates by ozone-assisted molecular-beam epitaxy. The high crystalline quality of the samples and interfaces has been verified using high-resolution x-ray diffractometry and Z-contrast scanning transmission electron microscopy with electron-energy-loss spectroscopy. The dependence of exchange bias on the thickness of the antiferromagnetic layer has been investigated. A critical value for the onset of the hysteresis loop shift has been determined. An antiferromagnetic anisotropy constant has been obtained by fitting the results to the generalized Meiklejohn-Bean model.

Growth of oxide exchange bias layers

DOEpatents

Chaiken, A.; Michel, R.P.

1998-07-21

An oxide (NiO, CoO, NiCoO) antiferromagnetic exchange bias layer produced by ion beam sputtering of an oxide target in pure argon (Ar) sputtering gas, with no oxygen gas introduced into the system. Antiferromagnetic oxide layers are used, for example, in magnetoresistive readback heads to shift the hysteresis loops of ferromagnetic films away from the zero field axis. For example, NiO exchange bias layers have been fabricated using ion beam sputtering of an NiO target using Ar ions, with the substrate temperature at 200 C, the ion beam voltage at 1000V and the beam current at 20 mA, with a deposition rate of about 0.2 {angstrom}/sec. The resulting NiO film was amorphous. 4 figs.

Highly sensitive optically controlled tunable capacitor and photodetector based on a metal-insulator-semiconductor on silicon-on-insulator substrates

NASA Astrophysics Data System (ADS)

Mikhelashvili, V.; Cristea, D.; Meyler, B.; Yofis, S.; Shneider, Y.; Atiya, G.; Cohen-Hyams, T.; Kauffmann, Y.; Kaplan, W. D.; Eisenstein, G.

2015-01-01

We describe a new type of optically sensitive tunable capacitor with a wide band response ranging from the ultraviolet (245 nm) to the near infrared (880 nm). It is based on a planar Metal-Oxide-Semiconductor (MOS) structure fabricated on an insulator on silicon substrate where the insulator layer comprises a double layer dielectric stack of SiO2-HfO2. Two operating configurations have been examined, a single diode and a pair of back-to-back connected devices, where either one or both diodes are illuminated. The varactors exhibit, in all cases, very large sensitivities to illumination. Near zero bias, the capacitance dependence on illumination intensity is sub linear and otherwise it is nearly linear. In the back-to-back connected configuration, the reverse biased diode acts as a light tunable resistor whose value affects strongly the capacitance of the second, forward biased, diode and vice versa. The proposed device is superior to other optical varactors in its large sensitivity to illumination in a very broad wavelength range (245 nm-880 nm), the strong capacitance dependence on voltage and the superior current photo responsivity. Above and beyond that structure requires a very simple fabrication process which is CMOS compatible.

Forward Current Transport Mechanisms of Ni/Au—InAlN/AlN/GaN Schottky Diodes

NASA Astrophysics Data System (ADS)

Wang, Xiao-Feng; Shao, Zhen-Guang; Chen, Dun-Jun; Lu, Hai; Zhang, Rong; Zheng, You-Dou

2014-05-01

We fabricate two Ni/Au-In0.17Al0.83N/AlN/GaN Schottky diodes on substrates of sapphire and Si, respectively, and investigate their forward-bias current transport mechanisms by temperature-dependent current-voltage measurements. In the temperature range of 300-485 K, the Schottky barrier heights (SBHs) calculated by using the conventional thermionic-emission (TE) model are strongly positively dependent on temperature, which is in contrast to the negative-temperature-dependent characteristic of traditional semiconductor Schottky diodes. By fitting the forward-bias I-V characteristics using different current transport models, we find that the tunneling current model can describe generally the I-V behaviors in the entire measured range of temperature. Under the high forward bias, the traditional TE mechanism also gives a good fit to the measured I-V data, and the actual barrier heights calculated according to the fitting TE curve are 1.434 and 1.413 eV at 300K for InAlN/AlN/GaN Schottky diodes on Si and the sapphire substrate, respectively, and the barrier height shows a slightly negative temperature coefficient. In addition, a formula is given to estimate SBHs of Ni/Au—InAlN/AlN/GaN Schottky diodes taking the Fermi-level pinning effect into account.

Investigating the interplay between substrate stiffness and ligand chemistry in directing mesenchymal stem cell differentiation within 3D macro-porous substrates.

PubMed

Haugh, Matthew G; Vaughan, Ted J; Madl, Christopher M; Raftery, Rosanne M; McNamara, Laoise M; O'Brien, Fergal J; Heilshorn, Sarah C

2018-07-01

Dimensionality can have a profound impact on stiffness-mediated differentiation of mesenchymal stem cells (MSCs). However, while we have begun to understand cellular response when encapsulated within 3D substrates, the behavior of cells within macro-porous substrates is relatively underexplored. The goal of this study was to determine the influence of macro-porous topographies on stiffness-mediated differentiation of MSCs. We developed macro-porous recombinant elastin-like protein (ELP) substrates that allow independent control of mechanical properties and ligand chemistry. We then used computational modeling to probe the impact of pore topography on the mechanical stimulus that cells are exposed to within these substrates, and finally we investigated stiffness induced biases towards adipogenic and osteogenic differentiation of MSCs within macro-porous substrates. Computational modeling revealed that there is significant heterogeneity in the mechanical stimuli that cells are exposed to within porous substrates and that this heterogeneity is predominantly due to the wide range of possible cellular orientations within the pores. Surprisingly, MSCs grown within 3D porous substrates respond to increasing substrate stiffness by up-regulating both osteogenesis and adipogenesis. These results demonstrate that within porous substrates the behavior of MSCs diverges from previously observed responses to substrate stiffness, emphasizing the importance of topography as a determinant of cellular behavior. Copyright © 2018 Elsevier Ltd. All rights reserved.

Entomopathogenic bacteria use multiple mechanisms for bioactive peptide library design

NASA Astrophysics Data System (ADS)

Cai, Xiaofeng; Nowak, Sarah; Wesche, Frank; Bischoff, Iris; Kaiser, Marcel; Fürst, Robert; Bode, Helge. B.

2017-04-01

The production of natural product compound libraries has been observed in nature for different organisms such as bacteria, fungi and plants; however, little is known about the mechanisms generating such chemically diverse libraries. Here we report mechanisms leading to the biosynthesis of the chemically diverse rhabdopeptide/xenortide peptides (RXPs). They are exclusively present in entomopathogenic bacteria of the genera Photorhabdus and Xenorhabdus that live in symbiosis with nematodes delivering them to insect prey, which is killed and utilized for nutrition by both nematodes and bacteria. Chemical diversity of the biologically active RXPs results from a combination of iterative and flexible use of monomodular nonribosomal peptide synthetases including substrate promiscuity, enzyme cross-talk and enzyme stoichiometry as shown by in vivo and in vitro experiments. Together, this highlights several of nature's methods for diversification, or evolution, of natural products and sheds light on the biosynthesis of the bioactive RXPs.

A Single-Domain Llama Antibody Potently Inhibits the Enzymatic Activity of Botulinum Neurotoxin by Binding to the Non-Catalytic [alpha]-Exosite Binding Region

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

Dong, Jianbo; Thompson, Aaron A.; Fan, Yongfeng

2010-08-13

Ingestion or inhalation of botulinum neurotoxin (BoNT) results in botulism, a severe and frequently fatal disease. Current treatments rely on antitoxins, which, while effective, cannot reverse symptoms once BoNT has entered the neuron. For treatments that can reverse intoxication, interest has focused on developing inhibitors of the enzymatic BoNT light chain (BoNT Lc). Such inhibitors typically mimic substrate and bind in or around the substrate cleavage pocket. To explore the full range of binding sites for serotype A light chain (BoNT/A Lc) inhibitors, we created a library of non-immune llama single-domain VHH (camelid heavy-chain variable region derived from heavy-chain-only antibody)more » antibodies displayed on the surface of the yeast Saccharomyces cerevisiae. Library selection on BoNT/A Lc yielded 15 yeast-displayed VHH with equilibrium dissociation constants (K{sub d}) from 230 to 0.03 nM measured by flow cytometry. Eight of 15 VHH inhibited the cleavage of substrate SNAP25 (synaptosome-associated protein of 25,000 Da) by BoNT/A Lc. The most potent VHH (Aa1) had a solution K{sub d} for BoNT/A Lc of 1.47 x 10{sup -10} M and an IC{sub 50} (50% inhibitory concentration) of 4.7 x 10{sup -10} M and was resistant to heat denaturation and reducing conditions. To understand the mechanism by which Aa1 inhibited catalysis, we solved the X-ray crystal structure of the BoNT/A Lc-Aa1 VHH complex at 2.6 {angstrom} resolution. The structure reveals that the Aa1 VHH binds in the {alpha}-exosite of the BoNT/A Lc, far from the active site for catalysis. The study validates the utility of non-immune llama VHH libraries as a source of enzyme inhibitors and identifies the BoNT/A Lc {alpha}-exosite as a target for inhibitor development.« less

The Gaia FGK benchmark stars. High resolution spectral library

NASA Astrophysics Data System (ADS)

Blanco-Cuaresma, S.; Soubiran, C.; Jofré, P.; Heiter, U.

2014-06-01

Context. An increasing number of high-resolution stellar spectra is available today thanks to many past and ongoing spectroscopic surveys. Consequently, numerous methods have been developed to perform an automatic spectral analysis on a massive amount of data. When reviewing published results, biases arise and they need to be addressed and minimized. Aims: We are providing a homogeneous library with a common set of calibration stars (known as the Gaia FGK benchmark stars) that will allow us to assess stellar analysis methods and calibrate spectroscopic surveys. Methods: High-resolution and signal-to-noise spectra were compiled from different instruments. We developed an automatic process to homogenize the observed data and assess the quality of the resulting library. Results: We built a high-quality library that will facilitate the assessment of spectral analyses and the calibration of present and future spectroscopic surveys. The automation of the process minimizes the human subjectivity and ensures reproducibility. Additionally, it allows us to quickly adapt the library to specific needs that can arise from future spectroscopic analyses. Based on NARVAL and HARPS data obtained within the Gaia Data Processing and Analysis Consortium (DPAC) and coordinated by the GBOG (Ground-Based Observations for Gaia) working group, and on data retrieved from the ESO-ADP database.The library of spectra is only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (ftp://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/566/A98

Highly sensitive and adaptable fluorescence-quenched pair discloses the substrate specificity profiles in diverse protease families

PubMed Central

Poreba, Marcin; Szalek, Aleksandra; Rut, Wioletta; Kasperkiewicz, Paulina; Rutkowska-Wlodarczyk, Izabela; Snipas, Scott J.; Itoh, Yoshifumi; Turk, Dusan; Turk, Boris; Overall, Christopher M.; Kaczmarek, Leszek; Salvesen, Guy S.; Drag, Marcin

2017-01-01

Internally quenched fluorescent (IQF) peptide substrates originating from FRET (Förster Resonance Energy Transfer) are powerful tool for examining the activity and specificity of proteases, and a variety of donor/acceptor pairs are extensively used to design individual substrates and combinatorial libraries. We developed a highly sensitive and adaptable donor/acceptor pair that can be used to investigate the substrate specificity of cysteine proteases, serine proteases and metalloproteinases. This novel pair comprises 7-amino-4-carbamoylmethylcoumarin (ACC) as the fluorophore and 2,4-dinitrophenyl-lysine (Lys(DNP)) as the quencher. Using caspase-3, caspase-7, caspase-8, neutrophil elastase, legumain, and two matrix metalloproteinases (MMP2 and MMP9), we demonstrated that substrates containing ACC/Lys(DNP) exhibit 7 to 10 times higher sensitivity than conventional 7-methoxy-coumarin-4-yl acetic acid (MCA)/Lys(DNP) substrates; thus, substantially lower amounts of substrate and enzyme can be used for each assay. We therefore propose that the ACC/Lys(DNP) pair can be considered a novel and sensitive scaffold for designing substrates for any group of endopeptidases. We further demonstrate that IQF substrates containing unnatural amino acids can be used to investigate protease activities/specificities for peptides containing post-translationally modified amino acids. Finally, we used IQF substrates to re-investigate the P1-Asp characteristic of caspases, thus demonstrating that some human caspases can also hydrolyze substrates after glutamic acid. PMID:28230157

Application of Stochastic Labeling with Random-Sequence Barcodes for Simultaneous Quantification and Sequencing of Environmental 16S rRNA Genes.

PubMed

Hoshino, Tatsuhiko; Inagaki, Fumio

2017-01-01

Next-generation sequencing (NGS) is a powerful tool for analyzing environmental DNA and provides the comprehensive molecular view of microbial communities. For obtaining the copy number of particular sequences in the NGS library, however, additional quantitative analysis as quantitative PCR (qPCR) or digital PCR (dPCR) is required. Furthermore, number of sequences in a sequence library does not always reflect the original copy number of a target gene because of biases caused by PCR amplification, making it difficult to convert the proportion of particular sequences in the NGS library to the copy number using the mass of input DNA. To address this issue, we applied stochastic labeling approach with random-tag sequences and developed a NGS-based quantification protocol, which enables simultaneous sequencing and quantification of the targeted DNA. This quantitative sequencing (qSeq) is initiated from single-primer extension (SPE) using a primer with random tag adjacent to the 5' end of target-specific sequence. During SPE, each DNA molecule is stochastically labeled with the random tag. Subsequently, first-round PCR is conducted, specifically targeting the SPE product, followed by second-round PCR to index for NGS. The number of random tags is only determined during the SPE step and is therefore not affected by the two rounds of PCR that may introduce amplification biases. In the case of 16S rRNA genes, after NGS sequencing and taxonomic classification, the absolute number of target phylotypes 16S rRNA gene can be estimated by Poisson statistics by counting random tags incorporated at the end of sequence. To test the feasibility of this approach, the 16S rRNA gene of Sulfolobus tokodaii was subjected to qSeq, which resulted in accurate quantification of 5.0 × 103 to 5.0 × 104 copies of the 16S rRNA gene. Furthermore, qSeq was applied to mock microbial communities and environmental samples, and the results were comparable to those obtained using digital PCR and relative abundance based on a standard sequence library. We demonstrated that the qSeq protocol proposed here is advantageous for providing less-biased absolute copy numbers of each target DNA with NGS sequencing at one time. By this new experiment scheme in microbial ecology, microbial community compositions can be explored in more quantitative manner, thus expanding our knowledge of microbial ecosystems in natural environments.

Selective reporting bias of harm outcomes within studies: findings from a cohort of systematic reviews.

PubMed

Saini, Pooja; Loke, Yoon K; Gamble, Carrol; Altman, Douglas G; Williamson, Paula R; Kirkham, Jamie J

2014-11-21

To determine the extent and nature of selective non-reporting of harm outcomes in clinical studies that were eligible for inclusion in a cohort of systematic reviews. Cohort study of systematic reviews from two databases. Outcome reporting bias in trials for harm outcomes (ORBIT II) in systematic reviews from the Cochrane Library and a separate cohort of systematic reviews of adverse events. 92 systematic reviews of randomised controlled trials and non-randomised studies published in the Cochrane Library between issue 9, 2012 and issue 2, 2013 (Cochrane cohort) and 230 systematic reviews published between 1 January 2007 and 31 December 2011 in other publications, synthesising data on harm outcomes (adverse event cohort). A 13 point classification system for missing outcome data on harm was developed and applied to the studies. 86% (79/92) of reviews in the Cochrane cohort did not include full data from the main harm outcome of interest of each review for all of the eligible studies included within that review; 76% (173/230) for the adverse event cohort. Overall, the single primary harm outcome was inadequately reported in 76% (705/931) of the studies included in the 92 reviews from the Cochrane cohort and not reported in 47% (4159/8837) of the 230 reviews in the adverse event cohort. In a sample of primary studies not reporting on the single primary harm outcome in the review, scrutiny of the study publication revealed that outcome reporting bias was suspected in nearly two thirds (63%, 248/393). The number of reviews suspected of outcome reporting bias as a result of missing or partially reported harm related outcomes from at least one eligible study is high. The declaration of important harms and the quality of the reporting of harm outcomes must be improved in both primary studies and systematic reviews. © Saini et al 2014.

Consequences of Normalizing Transcriptomic and Genomic Libraries of Plant Genomes Using a Duplex-Specific Nuclease and Tetramethylammonium Chloride

PubMed Central

Froenicke, Lutz; Lavelle, Dean; Martineau, Belinda; Perroud, Bertrand; Michelmore, Richard

2013-01-01

Several applications of high throughput genome and transcriptome sequencing would benefit from a reduction of the high-copy-number sequences in the libraries being sequenced and analyzed, particularly when applied to species with large genomes. We adapted and analyzed the consequences of a method that utilizes a thermostable duplex-specific nuclease for reducing the high-copy components in transcriptomic and genomic libraries prior to sequencing. This reduces the time, cost, and computational effort of obtaining informative transcriptomic and genomic sequence data for both fully sequenced and non-sequenced genomes. It also reduces contamination from organellar DNA in preparations of nuclear DNA. Hybridization in the presence of 3 M tetramethylammonium chloride (TMAC), which equalizes the rates of hybridization of GC and AT nucleotide pairs, reduced the bias against sequences with high GC content. Consequences of this method on the reduction of high-copy and enrichment of low-copy sequences are reported for Arabidopsis and lettuce. PMID:23409088

Identifying the preferred RNA motifs and chemotypes that interact by probing millions of combinations.

PubMed

Tran, Tuan; Disney, Matthew D

2012-01-01

RNA is an important therapeutic target but information about RNA-ligand interactions is limited. Here, we report a screening method that probes over 3,000,000 combinations of RNA motif-small molecule interactions to identify the privileged RNA structures and chemical spaces that interact. Specifically, a small molecule library biased for binding RNA was probed for binding to over 70,000 unique RNA motifs in a high throughput solution-based screen. The RNA motifs that specifically bind each small molecule were identified by microarray-based selection. In this library-versus-library or multidimensional combinatorial screening approach, hairpin loops (among a variety of RNA motifs) were the preferred RNA motif space that binds small molecules. Furthermore, it was shown that indole, 2-phenyl indole, 2-phenyl benzimidazole and pyridinium chemotypes allow for specific recognition of RNA motifs. As targeting RNA with small molecules is an extremely challenging area, these studies provide new information on RNA-ligand interactions that has many potential uses.

Identifying the Preferred RNA Motifs and Chemotypes that Interact by Probing Millions of Combinations

PubMed Central

Tran, Tuan; Disney, Matthew D.

2012-01-01

RNA is an important therapeutic target but information about RNA-ligand interactions is limited. Here we report a screening method that probes over 3,000,000 combinations of RNA motif-small molecule interactions to identify the privileged RNA structures and chemical spaces that interact. Specifically, a small molecule library biased for binding RNA was probed for binding to over 70,000 unique RNA motifs in a high throughput solution-based screen. The RNA motifs that specifically bind each small molecule were identified by microarray-based selection. In this library-versus-library or multidimensional combinatorial screening approach, hairpin loops (amongst a variety of RNA motifs) were the preferred RNA motif space that binds small molecules. Furthermore, it was shown that indole, 2-phenyl indole, 2-phenyl benzimidazole, and pyridinium chemotypes allow for specific recognition of RNA motifs. Since targeting RNA with small molecules is an extremely challenging area, these studies provide new information on RNA-ligand interactions that has many potential uses. PMID:23047683

Consequences of normalizing transcriptomic and genomic libraries of plant genomes using a duplex-specific nuclease and tetramethylammonium chloride.

PubMed

Matvienko, Marta; Kozik, Alexander; Froenicke, Lutz; Lavelle, Dean; Martineau, Belinda; Perroud, Bertrand; Michelmore, Richard

2013-01-01

Several applications of high throughput genome and transcriptome sequencing would benefit from a reduction of the high-copy-number sequences in the libraries being sequenced and analyzed, particularly when applied to species with large genomes. We adapted and analyzed the consequences of a method that utilizes a thermostable duplex-specific nuclease for reducing the high-copy components in transcriptomic and genomic libraries prior to sequencing. This reduces the time, cost, and computational effort of obtaining informative transcriptomic and genomic sequence data for both fully sequenced and non-sequenced genomes. It also reduces contamination from organellar DNA in preparations of nuclear DNA. Hybridization in the presence of 3 M tetramethylammonium chloride (TMAC), which equalizes the rates of hybridization of GC and AT nucleotide pairs, reduced the bias against sequences with high GC content. Consequences of this method on the reduction of high-copy and enrichment of low-copy sequences are reported for Arabidopsis and lettuce.

Rational evolution of the unusual Y-type oxyanion hole of Rhodococcus sp. CR53 lipase LipR.

PubMed

Infanzón, Belén; Sotelo, Pablo H; Martínez, Josefina; Diaz, Pilar

2018-01-01

Rhodococcus sp CR-53 lipase LipR was the first characterized member of bacterial lipase family X. Interestingly, LipR displays some similarity with α/β-hydrolases of the C. antartica lipase A (CAL-A)-like superfamily (abH38), bearing a Y-type oxyanion hole, never found before among bacterial lipases. In order to explore this unusual Y-type oxyanion hole, and to improve LipR performance, two modification strategies based on site directed or saturation mutagenesis were addressed. Initially, a small library of mutants was designed to convert LipR Y-type oxyanion hole (YDS) into one closer to those most frequently found in bacteria (GGG(X)). However, activity was completely lost in all mutants obtained, indicating that the Y-type oxyanion hole of LipR is required for activity. A second approach was addressed to modify the two main oxyanion hole residues Tyr 110 and Asp 111 , previously described for CAL-A as the most relevant amino acids involved in stabilization of the enzyme-substrate complex. A saturation mutagenesis library was prepared for each residue (Tyr 110 and Asp 111 ), and activity of the resulting variants was assayed on different chain length substrates. No functional LipR variants could be obtained when Tyr 110 was replaced by any other amino acids, indicating that this is a crucial residue for catalysis. However, among the Asp 111 variants obtained, LipR D111G produced a functional enzyme. Interestingly, this LipR-YGS variant showed less activity than wild type LipR on short- or mid- chain substrates but displayed a 5.6-fold increased activity on long chain length substrates. Analysis of the 3D model and in silico docking studies of this enzyme variant suggest that substitution of Asp by Gly produces a wider entrance tunnel that would allow for a better and tight accommodation of larger substrates, thus justifying the experimental results obtained. Copyright © 2017 Elsevier Inc. All rights reserved.

Optimized approach for Ion Proton RNA sequencing reveals details of RNA splicing and editing features of the transcriptome.

PubMed

Brown, Roger B; Madrid, Nathaniel J; Suzuki, Hideaki; Ness, Scott A

2017-01-01

RNA-sequencing (RNA-seq) has become the standard method for unbiased analysis of gene expression but also provides access to more complex transcriptome features, including alternative RNA splicing, RNA editing, and even detection of fusion transcripts formed through chromosomal translocations. However, differences in library methods can adversely affect the ability to recover these different types of transcriptome data. For example, some methods have bias for one end of transcripts or rely on low-efficiency steps that limit the complexity of the resulting library, making detection of rare transcripts less likely. We tested several commonly used methods of RNA-seq library preparation and found vast differences in the detection of advanced transcriptome features, such as alternatively spliced isoforms and RNA editing sites. By comparing several different protocols available for the Ion Proton sequencer and by utilizing detailed bioinformatics analysis tools, we were able to develop an optimized random primer based RNA-seq technique that is reliable at uncovering rare transcript isoforms and RNA editing features, as well as fusion reads from oncogenic chromosome rearrangements. The combination of optimized libraries and rapid Ion Proton sequencing provides a powerful platform for the transcriptome analysis of research and clinical samples.

Optimization of the genotyping-by-sequencing strategy for population genomic analysis in conifers.

PubMed

Pan, Jin; Wang, Baosheng; Pei, Zhi-Yong; Zhao, Wei; Gao, Jie; Mao, Jian-Feng; Wang, Xiao-Ru

2015-07-01

Flexibility and low cost make genotyping-by-sequencing (GBS) an ideal tool for population genomic studies of nonmodel species. However, to utilize the potential of the method fully, many parameters affecting library quality and single nucleotide polymorphism (SNP) discovery require optimization, especially for conifer genomes with a high repetitive DNA content. In this study, we explored strategies for effective GBS analysis in pine species. We constructed GBS libraries using HpaII, PstI and EcoRI-MseI digestions with different multiplexing levels and examined the effect of restriction enzymes on library complexity and the impact of sequencing depth and size selection of restriction fragments on sequence coverage bias. We tested and compared UNEAK, Stacks and GATK pipelines for the GBS data, and then developed a reference-free SNP calling strategy for haploid pine genomes. Our GBS procedure proved to be effective in SNP discovery, producing 7000-11 000 and 14 751 SNPs within and among three pine species, respectively, from a PstI library. This investigation provides guidance for the design and analysis of GBS experiments, particularly for organisms for which genomic information is lacking. © 2014 John Wiley & Sons Ltd.

Carbon Nanotubes/Nanofibers by Plasma Enhanced Chemical Vapour Deposition

NASA Technical Reports Server (NTRS)

Teo, K. B. K.; Hash, D. B.; Bell, M. S.; Chhowalla, M.; Cruden, B. A.; Amaratunga, G. A. J.; Meyyappan, M.; Milne, W. I.

2005-01-01

Plasma enhanced chemical vapour deposition (PECVD) has been recently used for the production of vertically aligned carbon nanotubedfibers (CN) directly on substrates. These structures are potentially important technologically as electron field emitters (e.g. microguns, microwave amplifiers, displays), nanoelectrodes for sensors, filter media, superhydrophobic surfaces and thermal interface materials for microelectronics. A parametric study on the growth of CN grown by glow discharge dc-PECVD is presented. In this technique, a substrate containing thin film Ni catalyst is exposed to C2H2 and NH3 gases at 700 C. Without plasma, this process is essentially thermal CVD which produces curly spaghetti-like CN as seen in Fig. 1 (a). With the plasma generated by biasing the substrate at -6OOV, we observed that the CN align vertically during growth as shown in Fig. l(b), and that the magnitude of the applied substrate bias affects the degree of alignment. The thickness of the thin film Ni catalyst was found to determine the average diameter and inversely the length of the CN. The yield and density of the CN were controlled by the use of different diffusion barrier materials under the Ni catalyst. Patterned CN growth [Fig. l(c)], with la variation in CN diameter of 4.1% and 6.3% respectively, is achieved by lithographically defining the Ni thin film prior to growth. The shape of the structures could be varied from very straight nanotube-like to conical tip-like nanofibers by increasing the ratio of C2H2 in the gas flow. Due to the plasma decomposition of C2H2, amorphous carbon (a-C) is an undesirable byproduct which could coat the substrate during CN growth. Using a combination of depth profiled Auger electron spectroscopy to study the substrate and in-situ mass spectroscopy to examine gas phase neutrals and ions, the optimal conditions for a-C free growth of CN is determined.

Effect of magnetron sputtering parameters and stress state of W film precursors on WSe2 layer texture by rapid selenization.

PubMed

Li, Hongchao; Gao, Di; Xie, Senlin; Zou, Jianpeng

2016-11-04

Tungsten diselenide (WSe 2 ) film was obtained by rapid selenization of magnetron sputtered tungsten (W) film. To prevent WSe 2 film peeling off from the substrate during selenization, the W film was designed with a double-layer structure. The first layer was deposited at a high sputtering-gas pressure to form a loose structure, which can act as a buffer layer to release stresses caused by WSe 2 growth. The second layer was deposited naturally on the first layer to react with selenium vapour in the next step. The effect of the W film deposition parameters(such as sputtering time, sputtering-gas pressure and substrate bias voltage)on the texture and surface morphology of the WSe 2 film was studied. Shortening the sputtering time, increasing the sputtering-gas pressure or decreasing the substrate bias voltage can help synthesize WSe 2 films with more platelets embedded vertically in the matrix. The stress state of the W film influences the WSe 2 film texture. Based on the stress state of the W film, a model for growth of the WSe 2 films with different textures was proposed. The insertion direction of the van der Waals gap is a key factor for the anisotropic formation of WSe 2 film.

Effect of UV lamp irradiation during oxidation of Zr/Pt/Si structure on electrical properties of Pt/ZrO 2/Pt/Si structure

NASA Astrophysics Data System (ADS)

Bae, Joon Woo; Lim, Jae-Won; Mimura, Kouji; Uchikoshi, Masahito; Miyazaki, Takamichi; Isshiki, Minoru

2010-03-01

Metal-insulator-metal (MIM) capacitors were fabricated using ZrO 2 films and the effects of structural and native defects of the ZrO 2 films on the electrical and dielectric properties were investigated. For preparing ZrO 2 films, Zr films were deposited on Pt/Si substrates by ion beam deposition (IBD) system with/without substrate bias voltages and oxidized at 200 °C for 60 min under 0.1 MPa O 2 atmosphere with/without UV light irradiation ( λ = 193 nm, Deep UV lamp). The ZrO 2(˜12 nm) films on Pt(˜100 nm)/Si were characterized by X-ray diffraction pattern (XRD), field emission scanning electron microscopy (FE-SEM) and high-resolution transmission electron microscopy (HRTEM), capacitance-voltage ( C- V) and current-voltage ( I- V) measurements were carried out on MIM structures. ZrO 2 films, fabricated by oxidizing the Zr film deposited with substrate bias voltage under UV light irradiation, show the highest capacitance (784 pF) and the lowest leakage current density. The active oxygen species formed by UV irradiation are considered to play an important role in the reduction of the leakage current density, because they can reduce the density of oxygen vacancies.

Van der Waals heterojunction diode composed of WS2 flake placed on p-type Si substrate

NASA Astrophysics Data System (ADS)

Aftab, Sikandar; Farooq Khan, M.; Min, Kyung-Ah; Nazir, Ghazanfar; Afzal, Amir Muhammad; Dastgeer, Ghulam; Akhtar, Imtisal; Seo, Yongho; Hong, Suklyun; Eom, Jonghwa

2018-01-01

P-N junctions represent the fundamental building blocks of most semiconductors for optoelectronic functions. This work demonstrates a technique for forming a WS2/Si van der Waals junction based on mechanical exfoliation. Multilayered WS2 nanoflakes were exfoliated on the surface of bulk p-type Si substrates using a polydimethylsiloxane stamp. We found that the fabricated WS2/Si p-n junctions exhibited rectifying characteristics. We studied the effect of annealing processes on the performance of the WS2/Si van der Waals p-n junction and demonstrated that annealing improved its electrical characteristics. However, devices with vacuum annealing have an enhanced forward-bias current compared to those annealed in a gaseous environment. We also studied the top-gate-tunable rectification characteristics across the p-n junction interface in experiments as well as density functional theory calculations. Under various temperatures, Zener breakdown occurred at low reverse-bias voltages, and its breakdown voltage exhibited a negative coefficient of temperature. Another breakdown voltage was observed, which increased with temperature, suggesting a positive coefficient of temperature. Therefore, such a breakdown can be assigned to avalanche breakdown. This work demonstrates a promising application of two-dimensional materials placed directly on conventional bulk Si substrates.

Effect of magnetron sputtering parameters and stress state of W film precursors on WSe2 layer texture by rapid selenization

PubMed Central

Li, Hongchao; Gao, Di; Xie, Senlin; Zou, Jianpeng

2016-01-01

Tungsten diselenide (WSe2) film was obtained by rapid selenization of magnetron sputtered tungsten (W) film. To prevent WSe2 film peeling off from the substrate during selenization, the W film was designed with a double-layer structure. The first layer was deposited at a high sputtering-gas pressure to form a loose structure, which can act as a buffer layer to release stresses caused by WSe2 growth. The second layer was deposited naturally on the first layer to react with selenium vapour in the next step. The effect of the W film deposition parameters(such as sputtering time, sputtering-gas pressure and substrate bias voltage)on the texture and surface morphology of the WSe2 film was studied. Shortening the sputtering time, increasing the sputtering-gas pressure or decreasing the substrate bias voltage can help synthesize WSe2 films with more platelets embedded vertically in the matrix. The stress state of the W film influences the WSe2 film texture. Based on the stress state of the W film, a model for growth of the WSe2 films with different textures was proposed. The insertion direction of the van der Waals gap is a key factor for the anisotropic formation of WSe2 film. PMID:27812031

A conduction model for contacts to Si-doped AlGaN grown on sapphire and single-crystalline AlN

NASA Astrophysics Data System (ADS)

Haidet, Brian B.; Bryan, Isaac; Reddy, Pramod; Bryan, Zachary; Collazo, Ramón; Sitar, Zlatko

2015-06-01

Ohmic contacts to AlGaN grown on sapphire substrates have been previously demonstrated for various compositions of AlGaN, but contacts to AlGaN grown on native AlN substrates are more difficult to obtain. In this paper, a model is developed that describes current flow through contacts to Si-doped AlGaN. This model treats the current through reverse-biased Schottky barriers as a consequence of two different tunneling-dependent conduction mechanisms in parallel, i.e., Fowler-Nordheim emission and defect-assisted Frenkel-Poole emission. At low bias, the defect-assisted tunneling dominates, but as the potential across the depletion region increases, tunneling begins to occur without the assistance of defects, and the Fowler-Nordheim emission becomes the dominant conduction mechanism. Transfer length method measurements and temperature-dependent current-voltage (I-V) measurements of Ti/Al-based contacts to Si-doped AlGaN grown on sapphire and AlN substrates support this model. Defect-assisted tunneling plays a much larger role in the contacts to AlGaN on sapphire, resulting in nearly linear I-V characteristics. In contrast, contacts to AlGaN on AlN show limited defect-assisted tunneling appear to be only semi-Ohmic.

Raman studied of undoped amorphous carbon thin film deposited by bias assisted-CVD

NASA Astrophysics Data System (ADS)

Ishak, A.; Fadzilah, A. N.; Dayana, K.; Saurdi, I.; Malek, M. F.; Nurbaya, Z.; Shafura, A. K.; Rusop, M.

2018-05-01

The undoped amorphous carbon thin film carbon was deposited at 200°C-350°C by bias assisted-CVD using palm oil as a precursor material. The effect of different substrate deposition temperatures on structural and electrical properties of undoped doped amorphous carbon film was discussed. The structural of undoped amorphous carbon films were correlated with Raman analysis through the evolution of D and G bands, Fourier spectra, and conductivity measurement. The spectral evolution observed showed the increase of upward shift of D and G peaks as substrate deposition temperatures increased. The spectral evolution observed at different substrate deposition temperatures show progressive formation of crystallites. It was predicted that small number of hydrogen is terminated with carbon at surface of thin film as shown by FTIR spectra since palm oil has high number of hydrogen (C67H127O8). These structural changes were further correlated with conductivity and the results obtained are discussed and compared. The conductivity is found in the range of 10-8 Scm-1. The increase of conductivity is correlated by the change of structural properties as correlated with characteristic parameters of Raman spectra including the position of G peak, full width at half maximum of G peak, and ID/IG and FTIR result.

A generic HTS assay for kinase screening: Validation for the isolation of an engineered malate kinase

PubMed Central

Irague, Romain; Topham, Christopher M.; Martineau, Nelly; Baylac, Audrey; Auriol, Clément; Walther, Thomas; François, Jean-Marie; Remaud-Siméon, Magali

2018-01-01

An end-point ADP/NAD+ acid/alkali assay procedure, directly applicable to library screening of any type of ATP-utilising/ADP producing enzyme activity, was implemented. Typically, ADP production is coupled to NAD+ co-enzyme formation by the conventional addition of pyruvate kinase and lactate dehydrogenase. Transformation of enzymatically generated NAD+ into a photometrically active alkali derivative product is then achieved through the successive application of acidic/alkali treatment steps. The assay was successfully miniaturized to search for malate kinase activity in a structurally-guided library of LysC aspartate kinase variants comprising 6,700 clones. The screening procedure enabled the isolation of nine positive variants showing novel kinase activity on (L)-malate, the best mutant, LysC V115A:E119S:E434V exhibited strong substrate selectivity for (L)-malate compared to (L)-aspartate with a (kcat/Km)malate/(kcat/Km)aspartate ratio of 86. Double mutants V115A:E119S, V115A:E119C and E119S:E434V were constructed to further probe the origins of stabilising substrate binding energy gains for (L)-malate due to mutation. The introduction of less sterically hindering side-chains in engineered enzymes carrying E119S and V115A mutations increases the effective volume available for substrate binding in the catalytic pocket. Improved binding of the (L)-malate substrate may be assisted by less hindered movement of the Phe184 aromatic side-chain. Additional favourable long-range electostatic effects on binding arising from the E434V surface mutation are conditionally dependent upon the presence of the V115A mutation close to Phe184 in the active-site. PMID:29462203

The Cognitive Substrate of Subjective Probability

ERIC Educational Resources Information Center

Nilsson, Hakan; Olsson, Henrik; Juslin, Peter

2005-01-01

The prominent cognitive theories of probability judgment were primarily developed to explain cognitive biases rather than to account for the cognitive processes in probability judgment. In this article the authors compare 3 major theories of the processes and representations in probability judgment: the representativeness heuristic, implemented as…

Losing the rose tinted glasses: neural substrates of unbiased belief updating in depression

PubMed Central

Garrett, Neil; Sharot, Tali; Faulkner, Paul; Korn, Christoph W.; Roiser, Jonathan P.; Dolan, Raymond J.

2014-01-01

Recent evidence suggests that a state of good mental health is associated with biased processing of information that supports a positively skewed view of the future. Depression, on the other hand, is associated with unbiased processing of such information. Here, we use brain imaging in conjunction with a belief update task administered to clinically depressed patients and healthy controls to characterize brain activity that supports unbiased belief updating in clinically depressed individuals. Our results reveal that unbiased belief updating in depression is mediated by strong neural coding of estimation errors in response to both good news (in left inferior frontal gyrus and bilateral superior frontal gyrus) and bad news (in right inferior parietal lobule and right inferior frontal gyrus) regarding the future. In contrast, intact mental health was linked to a relatively attenuated neural coding of bad news about the future. These findings identify a neural substrate mediating the breakdown of biased updating in major depression disorder, which may be essential for mental health. PMID:25221492

Avalanche solar blind photodetectors based on single crystalline Mg0.47Zn0.53O thin film on Ga:ZnO substrate

NASA Astrophysics Data System (ADS)

Chen, Hao; Zhang, Jingtao; Chen, Zuxin; Liu, Huiqiang; Ma, Xinzhou; Li, Qiuguo; Chu, Guang; Chu, Sheng

2018-05-01

Single crystalline wurtzite Mg0.47Zn0.53O films were grown on Ga:ZnO substrates by pulse laser deposition. The band gap of the films was measured to be 4.43 eV. Vertical devices were fabricated for solar blind photodetection, realizing a high responsivity of 2 A W‑1 at 278 nm and  ‑5 V bias as well as a rejection ratio (R 278 nm/R 350 nm) of over 6  ×  103. A cut-off wavelength of 286 nm and a response time of 77 ms were also achieved. Besides, the devices showed stable response without degeneration under repeating illumination. The high performance of this photodetector was analyzed and attributed to the avalanche effect from high quality Mg0.47Zn0.53O/Ga:ZnO heterojunction at reverse bias. The avalanche gain was calculated to be 14.5 at  ‑10 V.

High-performance Ge p-i-n photodetector on Si substrate

NASA Astrophysics Data System (ADS)

Chen, Li-qun; Huang, Xiang-ying; Li, Min; Huang, Yan-hua; Wang, Yue-yun; Yan, Guang-ming; Li, Cheng

2015-05-01

High-performance and tensile-strained germanium (Ge) p-i-n photodetector is demonstrated on Si substrate. The epitaxial Ge layers were prepared in an ultrahigh vacuum chemical vapor deposition (UHV-CVD) system using low temperature Ge buffer technique. The devices were fabricated by in situ doping and using Si as passivation layer between Ge and metal, which can improve the ohmic contact and realize the high doping. The results show that the dark current of the photodetector with diameter of 24 μm is about 2.5×10-7 μA at the bias voltage of -1 V, and the optical responsivity is 0.1 A/W at wavelength of 1.55 μm. The 3 dB bandwidth (BW) of 4 GHz is obtained for the photodetector with diameter of 24 μm at reverse bias voltage of 1 V. The long diffusion time of minority carrier in n-type Ge and the large contact resistance in metal/Ge contacts both affect the performance of Ge photodetectors.

Mid-infrared tunable metamaterials

DOEpatents

Brener, Igal; Miao, Xiaoyu; Shaner, Eric A.; Passmore, Brandon Scott

2017-07-11

A mid-infrared tunable metamaterial comprises an array of resonators on a semiconductor substrate having a large dependence of dielectric function on carrier concentration and a semiconductor plasma resonance that lies below the operating range, such as indium antimonide. Voltage biasing of the substrate generates a resonance shift in the metamaterial response that is tunable over a broad operating range. The mid-infrared tunable metamaterials have the potential to become the building blocks of chip based active optical devices in mid-infrared ranges, which can be used for many applications, such as thermal imaging, remote sensing, and environmental monitoring.

Mid-infrared tunable metamaterials

DOEpatents

Brener, Igal; Miao, Xiaoyu; Shaner, Eric A; Passmore, Brandon Scott; Jun, Young Chul

2015-04-28

A mid-infrared tunable metamaterial comprises an array of resonators on a semiconductor substrate having a large dependence of dielectric function on carrier concentration and a semiconductor plasma resonance that lies below the operating range, such as indium antimonide. Voltage biasing of the substrate generates a resonance shift in the metamaterial response that is tunable over a broad operating range. The mid-infrared tunable metamaterials have the potential to become the building blocks of chip based active optical devices in mid-infrared ranges, which can be used for many applications, such as thermal imaging, remote sensing, and environmental monitoring.

Substrate Specificity and Possible Heterologous Targets of Phytaspase, a Plant Cell Death Protease*

PubMed Central

Galiullina, Raisa A.; Kasperkiewicz, Paulina; Chichkova, Nina V.; Szalek, Aleksandra; Serebryakova, Marina V.; Poreba, Marcin; Drag, Marcin; Vartapetian, Andrey B.

2015-01-01

Plants lack aspartate-specific cell death proteases homologous to animal caspases. Instead, a subtilisin-like serine-dependent plant protease named phytaspase shown to be involved in the accomplishment of programmed death of plant cells is able to hydrolyze a number of peptide-based caspase substrates. Here, we determined the substrate specificity of rice (Oryza sativa) phytaspase by using the positional scanning substrate combinatorial library approach. Phytaspase was shown to display an absolute specificity of hydrolysis after an aspartic acid residue. The preceding amino acid residues, however, significantly influence the efficiency of hydrolysis. Efficient phytaspase substrates demonstrated a remarkable preference for an aromatic amino acid residue in the P3 position. The deduced optimum phytaspase recognition motif has the sequence IWLD and is strikingly hydrophobic. The established pattern was confirmed through synthesis and kinetic analysis of cleavage of a set of optimized peptide substrates. An amino acid motif similar to the phytaspase cleavage site is shared by the human gastrointestinal peptide hormones gastrin and cholecystokinin. In agreement with the established enzyme specificity, phytaspase was shown to hydrolyze gastrin-1 and cholecystokinin at the predicted sites in vitro, thus destroying the active moieties of the hormones. PMID:26283788

The inhibition of hemicellulosic sugars on cellulose hydrolysis are highly dependant on the cellulase productive binding, processivity, and substrate surface charges.

PubMed

Zhai, Rui; Hu, Jinguang; Saddler, Jack N

2018-06-01

In this study, the influence of major hemicellulosic sugars (mannose and xylose) on cellulose hydrolysis and major enzyme activities were evaluated by using both commercial enzyme cocktail and purified cellulase monocomponents over a "library" of cellulosic substrates. Surprisingly, the results showed that unlike glucose, mannose/xylose did not inhibit individual cellulase activities but significantly decreased their hydrolytic performance on cellulose substrates. When various enzyme-substrate interactions (e.g. adsorption/desorption, productive binding, and processive moving) were evaluated, it appeared that these hemicellulosic sugars significantly reduced the productive binding and processivity of Cel7A, which in turn limited cellulase hydrolytic efficacy. Among a range of major cellulose characteristics (e.g. crystallinity, degree of polymerization, accessibility, and surface charges), the acid group content of the cellulosic substrates seemed to be the main driver that determined the extent of hemicellulosic sugar inhibition. Our results provided new insights for better understanding the sugar inhibition mechanisms of cellulose hydrolysis. Copyright © 2017 Elsevier Ltd. All rights reserved.

Studies of Niobium Thin Film Produced by Energetic Vacuum Deposition

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

Genfa Wu; Anne-Marie Valente; H. Phillips

2004-05-01

An energetic vacuum deposition system has been used to study deposition energy effects on the properties of niobium thin films on copper and sapphire substrates. The absence of working gas avoids the gaseous inclusions commonly seen with sputtering deposition. A biased substrate holder controls the deposition energy. Transition temperature and residual resistivity ratio of the niobium thin films at several deposition energies are obtained together with surface morphology and crystal orientation measurements by AFM inspection, XRD and TEM analysis. The results show that niobium thin films on sapphire substrate exhibit the best cryogenic properties at deposition energy around 123 eV.more » The TEM analysis revealed that epitaxial growth of film was evident when deposition energy reaches 163 eV for sapphire substrate. Similarly, niobium thin film on copper substrate shows that film grows more oriented with higher deposition energy and grain size reaches the scale of the film thickness at the deposition energy around 153 eV.« less

Validation of picogram- and femtogram-input DNA libraries for microscale metagenomics

DOE PAGES

Rinke, Christian; Low, Serene; Woodcroft, Ben J.; ...

2016-09-22

High-throughput sequencing libraries are typically limited by the requirement for nanograms to micrograms of input DNA. This bottleneck impedes the microscale analysis of ecosystems and the exploration of low biomass samples. Current methods for amplifying environmental DNA to bypass this bottleneck introduce considerable bias into metagenomic profiles. For this study, we describe and validate a simple modification of the Illumina Nextera XT DNA library preparation kit which allows creation of shotgun libraries from sub-nanogram amounts of input DNA. Community composition was reproducible down to 100 fg of input DNA based on analysis of a mock community comprising 54 phylogenetically diversemore » Bacteria and Archaea. The main technical issues with the low input libraries were a greater potential for contamination, limited DNA complexity which has a direct effect on assembly and binning, and an associated higher percentage of read duplicates. We recommend a lower limit of 1 pg (~100–1,000 microbial cells) to ensure community composition fidelity, and the inclusion of negative controls to identify reagent-specific contaminants. Applying the approach to marine surface water, pronounced differences were observed between bacterial community profiles of microliter volume samples, which we attribute to biological variation. This result is consistent with expected microscale patchiness in marine communities. We thus envision that our benchmarked, slightly modified low input DNA protocol will be beneficial for microscale and low biomass metagenomics.« less

Validation of picogram- and femtogram-input DNA libraries for microscale metagenomics

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

Rinke, Christian; Low, Serene; Woodcroft, Ben J.

High-throughput sequencing libraries are typically limited by the requirement for nanograms to micrograms of input DNA. This bottleneck impedes the microscale analysis of ecosystems and the exploration of low biomass samples. Current methods for amplifying environmental DNA to bypass this bottleneck introduce considerable bias into metagenomic profiles. For this study, we describe and validate a simple modification of the Illumina Nextera XT DNA library preparation kit which allows creation of shotgun libraries from sub-nanogram amounts of input DNA. Community composition was reproducible down to 100 fg of input DNA based on analysis of a mock community comprising 54 phylogenetically diversemore » Bacteria and Archaea. The main technical issues with the low input libraries were a greater potential for contamination, limited DNA complexity which has a direct effect on assembly and binning, and an associated higher percentage of read duplicates. We recommend a lower limit of 1 pg (~100–1,000 microbial cells) to ensure community composition fidelity, and the inclusion of negative controls to identify reagent-specific contaminants. Applying the approach to marine surface water, pronounced differences were observed between bacterial community profiles of microliter volume samples, which we attribute to biological variation. This result is consistent with expected microscale patchiness in marine communities. We thus envision that our benchmarked, slightly modified low input DNA protocol will be beneficial for microscale and low biomass metagenomics.« less

Validation of picogram- and femtogram-input DNA libraries for microscale metagenomics

PubMed Central

Low, Serene; Raina, Jean-Baptiste; Skarshewski, Adam; Le, Xuyen H.; Butler, Margaret K.; Stocker, Roman; Seymour, Justin; Tyson, Gene W.

2016-01-01

High-throughput sequencing libraries are typically limited by the requirement for nanograms to micrograms of input DNA. This bottleneck impedes the microscale analysis of ecosystems and the exploration of low biomass samples. Current methods for amplifying environmental DNA to bypass this bottleneck introduce considerable bias into metagenomic profiles. Here we describe and validate a simple modification of the Illumina Nextera XT DNA library preparation kit which allows creation of shotgun libraries from sub-nanogram amounts of input DNA. Community composition was reproducible down to 100 fg of input DNA based on analysis of a mock community comprising 54 phylogenetically diverse Bacteria and Archaea. The main technical issues with the low input libraries were a greater potential for contamination, limited DNA complexity which has a direct effect on assembly and binning, and an associated higher percentage of read duplicates. We recommend a lower limit of 1 pg (∼100–1,000 microbial cells) to ensure community composition fidelity, and the inclusion of negative controls to identify reagent-specific contaminants. Applying the approach to marine surface water, pronounced differences were observed between bacterial community profiles of microliter volume samples, which we attribute to biological variation. This result is consistent with expected microscale patchiness in marine communities. We thus envision that our benchmarked, slightly modified low input DNA protocol will be beneficial for microscale and low biomass metagenomics. PMID:27688978

Magneto-electric transition in nickel-gallium arsenide-nickel multiferroic structure

NASA Astrophysics Data System (ADS)

Galichyan, T. A.; Filippov, D. A.; Laletin, V. M.; Firsova, T. O.; Poddubnaya, N. N.

2018-04-01

Experimental studies of the magnetoelectric effect are presented in structures manufactured by electrolytic deposition of nickel on a substrate of gallium arsenide. It is shown that the use of gold-germanium-nickel sublayer, when sprayed on a substrate, significantly improves the adhesion between electrolytically deposited nickel and substrate. Linear and nonlinear magnetoelectric effects on the alternating magnetic field are observed in these structures. Both effects have resonant character and the resonance frequency of the nonlinear effect is twice less than that of the linear effect. In weak fields, the value of the nonlinear magnetoelectric effect is in quadratic dependence on the alternating magnetic field and unlike the linear magnetoelectric effect, it does not depend on the bias field.

Surface treatment of magnetic recording heads

DOEpatents

Komvopoulos, Kyriakos; Brown, Ian G.; Wei, Bo; Anders, Simone; Anders, Andre; Bhatia, C. Singh

1998-01-01

Surface modification of magnetic recording heads using plasma immersion ion implantation and deposition is disclosed. This method may be carried out using a vacuum arc deposition system with a metallic or carbon cathode. By operating a plasma gun in a long-pulse mode and biasing the substrate holder with short pulses of a high negative voltage, direct ion implantation, recoil implantation, and surface deposition are combined to modify the near-surface regions of the head or substrate in processing times which may be less than 5 min. The modified regions are atomically mixed into the substrate. This surface modification improves the surface smoothness and hardness and enhances the tribological characteristics under conditions of contact-start-stop and continuous sliding. These results are obtained while maintaining original tolerances.

Surface treatment of magnetic recording heads

DOEpatents

Komvopoulos, Kyriakos; Brown, Ian G.; Wei, Bo; Anders, Simone; Anders, Andre; Bhatia, Singh C.

1995-01-01

Surface modification of magnetic recording heads using plasma immersion ion implantation and deposition is disclosed. This method may be carried out using a vacuum arc deposition system with a metallic or carbon cathode. By operating a plasma gun in a long-pulse mode and biasing the substrate holder with short pulses of a high negative voltage, direct ion implantation, recoil implantation, and surface deposition are combined to modify the near-surface regions of the head or substrate in processing times which may be less than 5 min. The modified regions are atomically mixed into the substrate. This surface modification improves the surface smoothness and hardness and enhances the tribological characteristics under conditions of contact-start-stop and continuous sliding. These results are obtained while maintaining original tolerances.

Surface treatment of magnetic recording heads

DOEpatents

Komvopoulos, K.; Brown, I.G.; Wei, B.; Anders, S.; Anders, A.; Bhatia, C.S.

1998-11-17

Surface modification of magnetic recording heads using plasma immersion ion implantation and deposition is disclosed. This method may be carried out using a vacuum arc deposition system with a metallic or carbon cathode. By operating a plasma gun in a long-pulse mode and biasing the substrate holder with short pulses of a high negative voltage, direct ion implantation, recoil implantation, and surface deposition are combined to modify the near-surface regions of the head or substrate in processing times which may be less than 5 min. The modified regions are atomically mixed into the substrate. This surface modification improves the surface smoothness and hardness and enhances the tribological characteristics under conditions of contact-start-stop and continuous sliding. These results are obtained while maintaining original tolerances. 22 figs.

Surface treatment of magnetic recording heads

DOEpatents

Komvopoulos, K.; Brown, I.G.; Wei, B.; Anders, S.; Anders, A.; Bhatia, S.C.

1995-12-19

Surface modification of magnetic recording heads using plasma immersion ion implantation and deposition is disclosed. This method may be carried out using a vacuum arc deposition system with a metallic or carbon cathode. By operating a plasma gun in a long-pulse mode and biasing the substrate holder with short pulses of a high negative voltage, direct ion implantation, recoil implantation, and surface deposition are combined to modify the near-surface regions of the head or substrate in processing times which may be less than 5 min. The modified regions are atomically mixed into the substrate. This surface modification improves the surface smoothness and hardness and enhances the tribological characteristics under conditions of contact-start-stop and continuous sliding. These results are obtained while maintaining original tolerances. 15 figs.

Bias current dependence of resistivity in Co0.4Fe0.4B0.2 ultrathin film prepared by RF magnetron sputtering

NASA Astrophysics Data System (ADS)

Mandal, Snehal; Mazumdar, Dipak; Das, I.

2018-04-01

Ultrathin film of Co0.4Fe0.4B0.2 was prepared on p-type Si (100) substrate by RF magnetron sputtering. X-Ray Reflectivity and Atomic Force Microscopy measurements were performed to estimate the thickness and surface roughness of the film. Electrical transport measurements were performed by four-probe method in a current-in-plane (CIP) geometry. Presence of non-linearity in the current-voltage (I-V) characteristics was observed at higher current range. The electrical resistivity was found to change by several orders of magnitude (105) by changing the bias current from nano-ampere (nA) to milli-ampere (mA) range. This bias current dependence of the resistivity has been explained by different transport mechanisms.

Broadband and high modulation-depth THz modulator using low bias controlled VO2-integrated metasurface.

PubMed

Zhou, Gaochao; Dai, Penghui; Wu, Jingbo; Jin, Biaobing; Wen, Qiye; Zhu, Guanghao; Shen, Ze; Zhang, Caihong; Kang, Lin; Xu, Weiwei; Chen, Jian; Wu, Peiheng

2017-07-24

An active vanadium dioxide integrated metasurface offering broadband transmitted terahertz wave modulation with large modulation-depth under electrical control is demonstrated. The device consists of metal bias-lines arranged with grid-structure patterned vanadium dioxide (VO 2 ) film on sapphire substrate. Amplitude transmission is continuously tuned from more than 78% to 28% or lower in the frequency range from 0.3 THz to 1.0 THz, by means of electrical bias at temperature of 68 °C. The physical mechanism underlying the device's electrical tunability is investigated and found to be attributed to the ohmic heating. The developed device possessing over 87% modulation depth with 0.7 THz frequency band is expected to have many potential applications in THz regime such as tunable THz attenuator.

Exchange bias and bistable magneto-resistance states in amorphous TbFeCo thin films

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

Li, Xiaopu, E-mail: xl6ba@virginia.edu; Ma, Chung T.; Poon, S. Joseph, E-mail: sjp9x@virginia.edu

2016-01-04

Amorphous TbFeCo thin films sputter deposited at room temperature on thermally oxidized Si substrate are found to exhibit strong perpendicular magnetic anisotropy. Atom probe tomography, scanning transmission electron microscopy, and energy dispersive X-ray spectroscopy mapping have revealed two nanoscale amorphous phases with different Tb atomic percentages distributed within the amorphous film. Exchange bias accompanied by bistable magneto-resistance states has been uncovered near room temperature by magnetization and magneto-transport measurements. The exchange anisotropy originates from the exchange interaction between the ferrimagnetic and ferromagnetic components corresponding to the two amorphous phases. This study provides a platform for exchange bias and magneto-resistance switchingmore » using single-layer amorphous ferrimagnetic thin films that require no epitaxial growth.« less

Positional bias in variant calls against draft reference assemblies.

PubMed

Briskine, Roman V; Shimizu, Kentaro K

2017-03-28

Whole genome resequencing projects may implement variant calling using draft reference genomes assembled de novo from short-read libraries. Despite lower quality of such assemblies, they allowed researchers to extend a wide range of population genetic and genome-wide association analyses to non-model species. As the variant calling pipelines are complex and involve many software packages, it is important to understand inherent biases and limitations at each step of the analysis. In this article, we report a positional bias present in variant calling performed against draft reference assemblies constructed from de Bruijn or string overlap graphs. We assessed how frequently variants appeared at each position counted from ends of a contig or scaffold sequence, and discovered unexpectedly high number of variants at the positions related to the length of either k-mers or reads used for the assembly. We detected the bias in both publicly available draft assemblies from Assemblathon 2 competition as well as in the assemblies we generated from our simulated short-read data. Simulations confirmed that the bias causing variants are predominantly false positives induced by reads from spatially distant repeated sequences. The bias is particularly strong in contig assemblies. Scaffolding does not eliminate the bias but tends to mitigate it because of the changes in variants' relative positions and alterations in read alignments. The bias can be effectively reduced by filtering out the variants that reside in repetitive elements. Draft genome sequences generated by several popular assemblers appear to be susceptible to the positional bias potentially affecting many resequencing projects in non-model species. The bias is inherent to the assembly algorithms and arises from their particular handling of repeated sequences. It is recommended to reduce the bias by filtering especially if higher-quality genome assembly cannot be achieved. Our findings can help other researchers to improve the quality of their variant data sets and reduce artefactual findings in downstream analyses.

Information encoded in non-native states drives substrate-chaperone pairing.

PubMed

Mapa, Koyeli; Tiwari, Satyam; Kumar, Vignesh; Jayaraj, Gopal Gunanathan; Maiti, Souvik

2012-09-05

Many proteins refold in vitro through kinetic folding intermediates that are believed to be by-products of native-state centric evolution. These intermediates are postulated to play only minor roles, if any, in vivo because they lack any information related to translation-associated vectorial folding. We demonstrate that refolding intermediate of a test protein, generated in vitro, is able to find its cognate chaperone, from the whole complement of Escherichia coli soluble chaperones. Cognate chaperone-binding uniquely alters the conformation of non-native substrate. Importantly, precise chaperone targeting of substrates are maintained as long as physiological molar ratios of chaperones remain unaltered. Using a library of different chaperone substrates, we demonstrate that kinetically trapped refolding intermediates contain sufficient structural features for precise targeting to cognate chaperones. We posit that evolution favors sequences that, in addition to coding for a functional native state, encode folding intermediates with higher affinity for cognate chaperones than noncognate ones. Copyright © 2012 Elsevier Ltd. All rights reserved.

A specific colorimetric assay for measuring transglutaminase 1 and factor XIII activities.

PubMed

Hitomi, Kiyotaka; Kitamura, Miyako; Alea, Mileidys Perez; Ceylan, Ismail; Thomas, Vincent; El Alaoui, Saïd

2009-11-15

Transglutaminase (TGase) is an enzyme that catalyzes both isopeptide cross-linking and incorporation of primary amines into proteins. Eight TGases have been identified in humans, and each of these TGases has a unique tissue distribution and physiological significance. Although several assays for TGase enzymatic activity have been reported, it has been difficult to establish an assay for discriminating each of these different TGase activities. Using a random peptide library, we recently identified the preferred substrate sequences for three major TGases: TGase 1, TGase 2, and factor XIII. In this study, we use these substrates in specific tests for measuring the activities of TGase 1 and factor XIII.

Photoelectrochemically driven self-assembly method

DOEpatents

Nielson, Gregory N.; Okandan, Murat

2017-01-17

Various technologies described herein pertain to assembling electronic devices into a microsystem. The electronic devices are disposed in a solution. Light can be applied to the electronic devices in the solution. The electronic devices can generate currents responsive to the light applied to the electronic devices in the solution, and the currents can cause electrochemical reactions that functionalize regions on surfaces of the electronic devices. Additionally or alternatively, the light applied to the electronic devices in the solution can cause the electronic devices to generate electric fields, which can orient the electronic devices and/or induce movement of the electronic devices with respect to a receiving substrate. Further, electrodes on a receiving substrate can be biased to attract and form connections with the electronic devices having the functionalized regions on the surfaces. The microsystem can include the receiving substrate and the electronic devices connected to the receiving substrate.

Growth of epitaxial Pb(Zr,Ti)O3 films by pulsed laser deposition

NASA Astrophysics Data System (ADS)

Lee, J.; Safari, A.; Pfeffer, R. L.

1992-10-01

Lead zirconate titanate (PZT) thin films with a composition near the morphotropic phase boundary have been grown on MgO (100) and Y1Ba2Cu3Ox (YBCO) coated MgO substrates. Substrate temperature and oxygen pressure were varied to achieve ferroelectric films with a perovskite structure. Films grown on MgO had the perovskite structure with an epitaxial relationship with the MgO substrate. On the other hand, films grown on the YBCO/MgO substrate had an oriented structure to the surface normal with a misorientation in the plane parallel to the surface. The measured dielectric constant and loss tangent at 1 kHz were 670 and 0.05, respectively. The remnant polarization and coercive field were 42 μC/cm2 and 53 kV/cm. A large internal bias field (12 kV/cm) was observed in the as-deposited state of the undoped PZT films.

Cleavage-site specificity of prolyl endopeptidase FAP investigated with a full-length protein substrate.

PubMed

Huang, Chih-Hsiang; Suen, Ching-Shu; Lin, Ching-Ting; Chien, Chia-Hui; Lee, Hsin-Ying; Chung, Kuei-Min; Tsai, Ting-Yueh; Jiaang, Weir-Tong; Hwang, Ming-Jing; Chen, Xin

2011-06-01

Fibroblast activation protein (FAP) is a prolyl-cleaving endopeptidase proposed as an anti-cancer drug target. It is necessary to define its cleavage-site specificity to facilitate the identification of its in vivo substrates and to understand its biological functions. We found that the previously identified substrate of FAP, α(2)-anti-plasmin, is not a robust substrate in vitro. Instead, an intracellular protein, SPRY2, is cleavable by FAP and more suitable for investigation of its substrate specificity in the context of the full-length globular protein. FAP prefers uncharged residues, including small or bulky hydrophobic amino acids, but not charged amino acids, especially acidic residue at P1', P3 and P4 sites. Molecular modelling analysis shows that the substrate-binding site of FAP is surrounded by multiple tyrosine residues and some negatively charged residues, which may exert least preference for substrates with acidic residues. This provides an explanation why FAP cannot cleave interleukins, which have a glutamate at either P4 or P2', despite their P3-P2-P1 sites being identical to SPRY2 or α-AP. Our study provided new information on FAP cleavage-site specificity, which differs from the data obtained by profiling with a peptide library or with the denatured protein, gelatin, as the substrate. Furthermore, our study suggests that negatively charged residues should be avoided when designing FAP inhibitors.

Gas-phase cationic benzoylation of ambient aromatic substrates studied with the decay technique

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

Occhiucci, G.; Cacace, F.; Speranza, M.

1986-03-05

The gas-phase benzoylation of typical ambient aromatic substrates PhY (Y = OH, OMe, and NH/sub 2/) has been investigated by a combination of the decay technique and of FT ICR mass spectrometry. Labeled phenylium ions, C/sub 6/X/sub 5//sup +/ (X = H and T), from the decay of multiply tritiated benzene, C/sub 6/X/sub 6/, have been allowed to react with excess CO-containing traces of PhY (Y = OH, OMe, and NH/sub 2/), in the pressure range from 90 to 650 torr. Radio GLC and HPLC of the tritiated products demonstrate two competitive reaction channels, i.e., phenylation and benzoylation of themore » aromatic substrates. The results indicate a sharp kinetic bias of the gaseous phenylium ions for the aromatic substrates, measured by an apparent k/sub CO//k/sub PhY/ ratio of 0.12 (Y = OH), 0.13 (Y = OMe), and 0.04 (Y = NH/sub 2/) in the systems at nearly atmospheric pressure. Gas-phase benzoylation displays a high intramolecular selectivity, occurring exclusively at the n-type center of PhOH and PhNH/sub 2/. In the case of PhOMe, appreciable ring benzoylation is observed, characterized by a remarkably high (up to 30:1) bias for the para position. The mechanistic features of the gas-phase benzoylation and phenylation processes, deduced from the decay and the ICR experiments, are discussed and compared with those of related aromatic acylation and alkylation reactions occurring in the dilute gas state. 30 references, 2 tables.« less

GaAs photoconductive semiconductor switch

DOEpatents

Loubriel, G.M.; Baca, A.G.; Zutavern, F.J.

1998-09-08

A high gain, optically triggered, photoconductive semiconductor switch (PCSS) implemented in GaAs as a reverse-biased pin structure with a passivation layer above the intrinsic GaAs substrate in the gap between the two electrodes of the device is disclosed. The reverse-biased configuration in combination with the addition of the passivation layer greatly reduces surface current leakage that has been a problem for prior PCSS devices and enables employment of the much less expensive and more reliable DC charging systems instead of the pulsed charging systems that needed to be used with prior PCSS devices. 5 figs.

Some device implications of voltage controlled magnetic anisotropy in Co/Gd2O3 thin films through REDOX chemistry

NASA Astrophysics Data System (ADS)

Hao, Guanhua; Noviasky, Nicholas; Cao, Shi; Sabirianov, Ildar; Yin, Yuewei; Ilie, Carolina C.; Kirianov, Eugene; Sharma, Nishtha; Sokolov, Andrei; Marshall, Andrew; Xu, Xiaoshan; Dowben, Peter A.

2018-04-01

The effect of intermediate interfacial oxidation on the in-plane magnetization of multilayer stack Pt/Co/Gd2O3, on a p-type silicon substrate, has been investigated by magneto-optical Kerr effect (MOKE) measurements, the anomalous Hall effect, and magnetoresistance measurements. While voltage controlled perpendicular magnetic anisotropy of a metal/oxide heterostructure is known, this heterostructure displays an inverse relationship between voltage and coercivity. The anomalous Hall effect demonstrates a significant change in hysteresis, with the applied bias sign. There is a higher perpendicular magnetic anisotropy with positive bias exposure.

Benchmarking methods and data sets for ligand enrichment assessment in virtual screening.

PubMed

Xia, Jie; Tilahun, Ermias Lemma; Reid, Terry-Elinor; Zhang, Liangren; Wang, Xiang Simon

2015-01-01

Retrospective small-scale virtual screening (VS) based on benchmarking data sets has been widely used to estimate ligand enrichments of VS approaches in the prospective (i.e. real-world) efforts. However, the intrinsic differences of benchmarking sets to the real screening chemical libraries can cause biased assessment. Herein, we summarize the history of benchmarking methods as well as data sets and highlight three main types of biases found in benchmarking sets, i.e. "analogue bias", "artificial enrichment" and "false negative". In addition, we introduce our recent algorithm to build maximum-unbiased benchmarking sets applicable to both ligand-based and structure-based VS approaches, and its implementations to three important human histone deacetylases (HDACs) isoforms, i.e. HDAC1, HDAC6 and HDAC8. The leave-one-out cross-validation (LOO CV) demonstrates that the benchmarking sets built by our algorithm are maximum-unbiased as measured by property matching, ROC curves and AUCs. Copyright © 2014 Elsevier Inc. All rights reserved.

Vertical III-nitride thin-film power diode

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

Wierer, Jr., Jonathan; Fischer, Arthur J.; Allerman, Andrew A.

2017-03-14

A vertical III-nitride thin-film power diode can hold off high voltages (kV's) when operated under reverse bias. The III-nitride device layers can be grown on a wider bandgap template layer and growth substrate, which can be removed by laser lift-off of the epitaxial device layers grown thereon.

Irradiation of MOS-FET devices to provide desired logic functions

NASA Technical Reports Server (NTRS)

Danchenko, V.; Schaefer, D. H.

1972-01-01

Gamma, X-ray, electron, or other radiation is used to shift threshold potentials of MOS devices on logic circuits. Before irradiation MOS gates to be shifted are biased positive and other gates are grounded to substrate. Threshold lasts 10 years. Thermal annealing brings circuit back to original configuration.

Focused library with a core structure extracted from natural products and modified: application to phosphatase inhibitors and several biochemical findings.

PubMed

Hirai, Go; Sodeoka, Mikiko

2015-05-19

Synthesis of a focused library is an important strategy to create novel modulators of specific classes of proteins. Compounds in a focused library are composed of a common core structure and different diversity structures. In this Account, we describe our design and synthesis of libraries focused on selective inhibitors of protein phosphatases (PPases). We considered that core structures having structural and electronic features similar to those of PPase substrates, phosphate esters, would be a reasonable choice. Therefore, we extracted core structures from natural products already identified as PPase inhibitors. Since many PPases share similar active-site structures, such phosphate-mimicking core structures should interact with many enzymes in the same family, and therefore the choice of diversity structures is pivotal both to increase the binding affinity and to achieve specificity for individual enzymes. Here we present case studies of application of focused libraries to obtain PPase inhibitors, covering the overall process from selection of core structures to identification and evaluation of candidates in the focused libraries. To synthesize a library focused on protein serine-threonine phosphatases (PPs), we chose norcantharidin as a core structure, because norcantharidin dicarboxylate shows a broad inhibition profile toward several PPs. From the resulting focused library, we identified a highly selective PP2B inhibitor, NCA-01. On the other hand, to find inhibitors of dual-specificity protein phosphatases (DSPs), we chose 3-acyltetronic acid extracted from natural product RK-682 as a core structure, because its structure resembles the transition state in the dephosphorylation reaction of DSPs. However, a highly selective inhibitor was not found in the resulting focused library. Furthermore, an inherent drawback of compounds having the highly acidic 3-acyltetronic acid as a core structure is very weak potency in cellulo, probably due to poor cell membrane permeability. Therefore, we next modified the core structure from acidic to neutral by transformation to the enamine derivative and constructed a second-generation focused library (RE derivatives). The resulting compounds showed dramatically improved cell membrane permeability and inhibitory selectivity and included VHR (vaccinia VH1-related)-selective RE12 and CDC25A/B (cell division cycle 25A/B)-selective RE44. These inhibitors act on target enzymes in cellulo and do not generate reactive oxygen species, which is a potential problem with quinoid-type inhibitors of CDC25s. The cellular activity of RE12 was further improved by replacement of the side chain to afford RE176, which showed more potent antiproliferative activity than RE12 against HeLa cells. The dramatic change of inhibitory selectivity obtained by core structure modification from 3-acyltetronic acid to its enamine derivative was associated with a change in the mode of action. Namely, RE derivatives were found to be noncompetitive inhibitors with respect to a small-molecular substrate of CDC25A/B, whereas RK-682 was a competitive inhibitor of VHR. We identified the binding site of RE derivatives on the CDC25A as a pocket adjacent to the active site; this appears to be a promising target site for development of further novel inhibitors of CDC25s.

Annotating Enzymes of Uncertain Function: The Deacylation of d-Amino Acids by Members of the Amidohydrolase Superfamily

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

Cummings, J.; Fedorov, A; Xu, C

The catalytic activities of three members of the amidohydrolase superfamily were discovered using amino acid substrate libraries. Bb3285 from Bordetella bronchiseptica, Gox1177 from Gluconobacter oxidans, and Sco4986 from Streptomyces coelicolor are currently annotated as d-aminoacylases or N-acetyl-d-glutamate deacetylases. These three enzymes are 22-34% identical to one another in amino acid sequence. Substrate libraries containing nearly all combinations of N-formyl-d-Xaa, N-acetyl-d-Xaa, N-succinyl-d-Xaa, and l-Xaa-d-Xaa were used to establish the substrate profiles for these enzymes. It was demonstrated that Bb3285 is restricted to the hydrolysis of N-acyl-substituted derivatives of d-glutamate. The best substrates for this enzyme are N-formyl-d-glutamate (k{sub cat}/K{sub m} =more » 5.8 x 10{sup 6} M{sup -1} s{sup -1}), N-acetyl-d-glutamate (k{sub cat}/K{sub m} = 5.2 x 10{sup 6} M{sup -1} s{sup -1}), and l-methionine-d-glutamate (k{sub cat}/K{sub m} = 3.4 x 10{sup 5} M{sup -1} s{sup -1}). Gox1177 and Sco4986 preferentially hydrolyze N-acyl-substituted derivatives of hydrophobic d-amino acids. The best substrates for Gox1177 are N-acetyl-d-leucine (k{sub cat}/K{sub m} = 3.2 x 104 M{sup -1} s-1), N-acetyl-d-tryptophan (kcat/Km = 4.1 x 104 M-1 s-1), and l-tyrosine-d-leucine (kcat/Km = 1.5 x 104 M-1 s-1). A fourth protein, Bb2785 from B. bronchiseptica, did not have d-aminoacylase activity. The best substrates for Sco4986 are N-acetyl-d-phenylalanine and N-acetyl-d-tryptophan. The three-dimensional structures of Bb3285 in the presence of the product acetate or a potent mimic of the tetrahedral intermediate were determined by X-ray diffraction methods. The side chain of the d-glutamate moiety of the inhibitor is ion-paired to Arg-295, while the {alpha}-carboxylate is ion-paired with Lys-250 and Arg-376. These results have revealed the chemical and structural determinants for substrate specificity in this protein. Bioinformatic analyses of an additional {approx}250 sequences identified as members of this group suggest that there are no simple motifs that allow prediction of substrate specificity for most of these unknowns, highlighting the challenges for computational annotation of some groups of homologous proteins.« less

A Xylenol Orange-Based Screening Assay for the Substrate Specificity of Flavin-Dependent para-Phenol Oxidases.

PubMed

Ewing, Tom A; van Noord, Aster; Paul, Caroline E; van Berkel, Willem J H

2018-01-14

Vanillyl alcohol oxidase (VAO) and eugenol oxidase (EUGO) are flavin-dependent enzymes that catalyse the oxidation of para -substituted phenols. This makes them potentially interesting biocatalysts for the conversion of lignin-derived aromatic monomers to value-added compounds. To facilitate their biocatalytic exploitation, it is important to develop methods by which variants of the enzymes can be rapidly screened for increased activity towards substrates of interest. Here, we present the development of a screening assay for the substrate specificity of para -phenol oxidases based on the detection of hydrogen peroxide using the ferric-xylenol orange complex method. The assay was used to screen the activity of VAO and EUGO towards a set of twenty-four potential substrates. This led to the identification of 4-cyclopentylphenol as a new substrate of VAO and EUGO and 4-cyclohexylphenol as a new substrate of VAO. Screening of a small library of VAO and EUGO active-site variants for alterations in their substrate specificity led to the identification of a VAO variant (T457Q) with increased activity towards vanillyl alcohol (4-hydroxy-3-methoxybenzyl alcohol) and a EUGO variant (V436I) with increased activity towards chavicol (4-allylphenol) and 4-cyclopentylphenol. This assay provides a quick and efficient method to screen the substrate specificity of para -phenol oxidases, facilitating the enzyme engineering of known para- phenol oxidases and the evaluation of the substrate specificity of novel para -phenol oxidases.

Autocrine selection of a GLP-1R G-protein biased agonist with potent antidiabetic effects.

PubMed

Zhang, Hongkai; Sturchler, Emmanuel; Zhu, Jiang; Nieto, Ainhoa; Cistrone, Philip A; Xie, Jia; He, LinLing; Yea, Kyungmoo; Jones, Teresa; Turn, Rachel; Di Stefano, Peter S; Griffin, Patrick R; Dawson, Philip E; McDonald, Patricia H; Lerner, Richard A

2015-12-01

Glucagon-like peptide-1 (GLP-1) receptor (GLP-1R) agonists have emerged as treatment options for type 2 diabetes mellitus (T2DM). GLP-1R signals through G-protein-dependent, and G-protein-independent pathways by engaging the scaffold protein β-arrestin; preferential signalling of ligands through one or the other of these branches is known as 'ligand bias'. Here we report the discovery of the potent and selective GLP-1R G-protein-biased agonist, P5. We identified P5 in a high-throughput autocrine-based screening of large combinatorial peptide libraries, and show that P5 promotes G-protein signalling comparable to GLP-1 and Exendin-4, but exhibited a significantly reduced β-arrestin response. Preclinical studies using different mouse models of T2DM demonstrate that P5 is a weak insulin secretagogue. Nevertheless, chronic treatment of diabetic mice with P5 increased adipogenesis, reduced adipose tissue inflammation as well as hepatic steatosis and was more effective at correcting hyperglycaemia and lowering haemoglobin A1c levels than Exendin-4, suggesting that GLP-1R G-protein-biased agonists may provide a novel therapeutic approach to T2DM.

GaAs-based optoelectronic neurons

NASA Technical Reports Server (NTRS)

Lin, Steven H. (Inventor); Kim, Jae H. (Inventor); Psaltis, Demetri (Inventor)

1993-01-01

An integrated, optoelectronic, variable thresholding neuron implemented monolithically in GaAs integrated circuit and exhibiting high differential optical gain and low power consumption is presented. Two alternative embodiments each comprise an LED monolithically integrated with a detector and two transistors. One of the transistors is responsive to a bias voltage applied to its gate for varying the threshold of the neuron. One embodiment is implemented as an LED monolithically integrated with a double heterojunction bipolar phototransistor (detector) and two metal semiconductor field effect transistors (MESFET's) on a single GaAs substrate and another embodiment is implemented as an LED monolithically integrated with three MESFET's (one of which is an optical FET detector) on a single GaAs substrate. The first noted embodiment exhibits a differential optical gain of 6 and an optical switching energy of 10 pJ. The second embodiment has a differential optical gain of 80 and an optical switching energy of 38 pJ. Power consumption is 2.4 and 1.8 mW, respectively. Input 'light' power needed to turn on the LED is 2 micro-W and 54 nW, respectively. In both embodiments the detector is in series with a biasing MESFET and saturates the other MESFET upon detecting light above a threshold level. The saturated MESFET turns on the LED. Voltage applied to the biasing MESFET gate controls the threshold.

Creation of novel structured carbon nanotubes using different-polarity ion plasmas

NASA Astrophysics Data System (ADS)

Hatakeyama, Rikizo; Hirata, Takamichi; Jeong, Goo-Hwan

2004-02-01

In order to develop novel functional carbon-based nanomaterials, an original approach using plasma technology has been performed. When positive or negative bias voltages are applied to a substrate that is covered with single-walled carbon nanotubes (SWNTs) and immersed in alkali-fullerene plasmas, accelerated negative fullerene or positive alkali-metal ions are irradiated on the SWNTs through plasma sheaths in front of the substrate. Field emission gun transmission electron microscopy (FEG-TEM) images clearly show that drastic structural modifications such as severe bending of SWNT bundles and tube tip termination take place after the ion irradiation. Energy dispersive x-ray spectrometry confirms the existence of the elements Na, K and Cs in the samples after alkali-metal irradiation. In particular, Cs encapsulation inside the SWNTs is directly observed, the configuration of which is demonstrated to comprise three varieties by FEG-TEM and scanning TEM. In the case of C_{60}^{ - } irradiation by positive bias application, on the other hand, SWNTs encapsulating fullerene molecules are clearly observed. Furthermore, the fullerene encapsulation yield within the SWNTs linearly increases with an enhancement of the plasma density used. Finally, a sequential bias application with polarity change gives the possibility of formation of a nanojunction structure composed of Cs rows and C60 chains. It is worth emphasizing that our results open a new possibility for novel structured material synthesis using plasma technology.

Characterisation of a novel reverse-biased PPD CMOS image sensor

NASA Astrophysics Data System (ADS)

Stefanov, K. D.; Clarke, A. S.; Ivory, J.; Holland, A. D.

2017-11-01

A new pinned photodiode (PPD) CMOS image sensor (CIS) has been developed and characterised. The sensor can be fully depleted by means of reverse bias applied to the substrate, and the principle of operation is applicable to very thick sensitive volumes. Additional n-type implants under the pixel p-wells, called Deep Depletion Extension (DDE), have been added in order to eliminate the large parasitic substrate current that would otherwise be present in a normal device. The first prototype has been manufactured on a 18 μm thick, 1000 Ω .cm epitaxial silicon wafers using 180 nm PPD image sensor process at TowerJazz Semiconductor. The chip contains arrays of 10 μm and 5.4 μm pixels, with variations of the shape, size and the depth of the DDE implant. Back-side illuminated (BSI) devices were manufactured in collaboration with Teledyne e2v, and characterised together with the front-side illuminated (FSI) variants. The presented results show that the devices could be reverse-biased without parasitic leakage currents, in good agreement with simulations. The new 10 μm pixels in both BSI and FSI variants exhibit nearly identical photo response to the reference non-modified pixels, as characterised with the photon transfer curve. Different techniques were used to measure the depletion depth in FSI and BSI chips, and the results are consistent with the expected full depletion.

Effects of a chirped bias voltage on ion energy distributions in inductively coupled plasma reactors

NASA Astrophysics Data System (ADS)

Lanham, Steven J.; Kushner, Mark J.

2017-08-01

The metrics for controlling reactive fluxes to wafers for microelectronics processing are becoming more stringent as feature sizes continue to shrink. Recent strategies for controlling ion energy distributions to the wafer involve using several different frequencies and/or pulsed powers. Although effective, these strategies are often costly or present challenges in impedance matching. With the advent of matching schemes for wide band amplifiers, other strategies to customize ion energy distributions become available. In this paper, we discuss results from a computational investigation of biasing substrates using chirped frequencies in high density, electronegative inductively coupled plasmas. Depending on the frequency range and chirp duration, the resulting ion energy distributions exhibit components sampled from the entire frequency range. However, the chirping process also produces transient shifts in the self-generated dc bias due to the reapportionment of displacement and conduction with frequency to balance the current in the system. The dynamics of the dc bias can also be leveraged towards customizing ion energy distributions.

Expressing gambling-related cognitive biases in motor behaviour: rolling dice to win prizes.

PubMed

Lim, Matthew S M; Bowden-Jones, Henrietta; Rogers, Robert D

2014-09-01

Cognitive perspectives on gambling propose that biased thinking plays a significant role in sustaining gambling participation and, in vulnerable individuals, gambling problems. One prominent set of cognitive biases include illusions of control involving beliefs that it is possible to influence random gaming events. Sociologists have reported that (some) gamblers believe that it is possible to throw dice in different ways to achieve gaming outcomes (e.g., 'dice-setting' in craps). However, experimental demonstrations of these phenomena are lacking. Here, we asked regular gamblers to roll a computer-simulated, but fair, 6 sided die for monetary prizes. Gamblers allowed the die to roll for longer when attempting to win higher value bets, and when attempting to hit high winning numbers. This behaviour was exaggerated in gamblers motivated to keep gambling following the experience of almost-winning in gambling games. These results suggest that gambling cognitive biases find expression in the motor behaviour of rolling dice for monetary prizes, possibly reflecting embodied substrates.

Metagenomics of an Alkaline Hot Spring in Galicia (Spain): Microbial Diversity Analysis and Screening for Novel Lipolytic Enzymes.

PubMed

López-López, Olalla; Knapik, Kamila; Cerdán, Maria-Esperanza; González-Siso, María-Isabel

2015-01-01

A fosmid library was constructed with the metagenomic DNA from the water of the Lobios hot spring (76°C, pH = 8.2) located in Ourense (Spain). Metagenomic sequencing of the fosmid library allowed the assembly of 9722 contigs ranging in size from 500 to 56,677 bp and spanning ~18 Mbp. 23,207 ORFs (Open Reading Frames) were predicted from the assembly. Biodiversity was explored by taxonomic classification and it revealed that bacteria were predominant, while the archaea were less abundant. The six most abundant bacterial phyla were Deinococcus-Thermus, Proteobacteria, Firmicutes, Acidobacteria, Aquificae, and Chloroflexi. Within the archaeal superkingdom, the phylum Thaumarchaeota was predominant with the dominant species "Candidatus Caldiarchaeum subterraneum." Functional classification revealed the genes associated to one-carbon metabolism as the most abundant. Both taxonomic and functional classifications showed a mixture of different microbial metabolic patterns: aerobic and anaerobic, chemoorganotrophic and chemolithotrophic, autotrophic and heterotrophic. Remarkably, the presence of genes encoding enzymes with potential biotechnological interest, such as xylanases, galactosidases, proteases, and lipases, was also revealed in the metagenomic library. Functional screening of this library was subsequently done looking for genes encoding lipolytic enzymes. Six genes conferring lipolytic activity were identified and one was cloned and characterized. This gene was named LOB4Est and it was expressed in a yeast mesophilic host. LOB4Est codes for a novel esterase of family VIII, with sequence similarity to β-lactamases, but with unusual wide substrate specificity. When the enzyme was purified from the mesophilic host it showed half-life of 1 h and 43 min at 50°C, and maximal activity at 40°C and pH 7.5 with p-nitrophenyl-laurate as substrate. Interestingly, the enzyme retained more than 80% of maximal activity in a broad range of pH from 6.5 to 8.

Deep Sequencing of Random Mutant Libraries Reveals the Active Site of the Narrow Specificity CphA Metallo-β-Lactamase is Fragile to Mutations.

PubMed

Sun, Zhizeng; Mehta, Shrenik C; Adamski, Carolyn J; Gibbs, Richard A; Palzkill, Timothy

2016-09-12

CphA is a Zn(2+)-dependent metallo-β-lactamase that efficiently hydrolyzes only carbapenem antibiotics. To understand the sequence requirements for CphA function, single codon random mutant libraries were constructed for residues in and near the active site and mutants were selected for E. coli growth on increasing concentrations of imipenem, a carbapenem antibiotic. At high concentrations of imipenem that select for phenotypically wild-type mutants, the active-site residues exhibit stringent sequence requirements in that nearly all residues in positions that contact zinc, the substrate, or the catalytic water do not tolerate amino acid substitutions. In addition, at high imipenem concentrations a number of residues that do not directly contact zinc or substrate are also essential and do not tolerate substitutions. Biochemical analysis confirmed that amino acid substitutions at essential positions decreased the stability or catalytic activity of the CphA enzyme. Therefore, the CphA active - site is fragile to substitutions, suggesting active-site residues are optimized for imipenem hydrolysis. These results also suggest that resistance to inhibitors targeted to the CphA active site would be slow to develop because of the strong sequence constraints on function.

Targeting the epigenome: Screening bioactive compounds that regulate histone deacetylase activity

PubMed Central

Godoy, Luis D.; Lucas, Julianna E.; Bender, Abigail J.; Romanick, Samantha S.; Ferguson, Bradley S.

2017-01-01

Scope Nutrigenomics is a rapidly expanding field that elucidates the link between diet-genome interactions. Recent evidence demonstrates that regulation of the epigenome, and in particular inhibition of HDACs, impact pathogenetic mechanisms involved in chronic disease. Few studies, to date, have screened libraries of bioactive compounds that act as epigenetic modifiers. This study screened a library of 131 natural compounds to determine bioactive compounds that inhibit Zn-dependent HDAC activity. Methods and results Using class-specific HDAC substrates, we screened 131 natural compounds for HDAC activity in bovine cardiac tissue. From this screen, we identified 18 bioactive compound HDAC inhibitors. Using our class-specific HDAC substrates, we next screened these 18 bioactive compounds against recombinant HDAC proteins. Consistent with inhibition of HDAC activity, these compounds were capable of inhibiting activity of individual HDAC isoforms. Lastly, we report that treatment of H9c2 cardiac myoblasts with bioactive HDAC inhibitors was sufficient to increase lysine acetylation as assessed via immunoblot. Conclusion This study provided the first step in identifying multiple bioactive compound HDAC inhibitors. Taken together, this report sets the stage for future exploration of these bioactive compounds as epigenetic regulators to potentially ameliorate chronic disease. PMID:27981795

Discovery and characterizaton of a novel lipase with transesterification activity from hot spring metagenomic library.

PubMed

Yan, Wei; Li, Furong; Wang, Li; Zhu, Yaxin; Dong, Zhiyang; Bai, Linhan

2017-03-01

A new gene encoding a lipase (designated as Lip-1 ) was identified from a metagenomic bacterial artificial chromosome(BAC) library prepared from a concentrated water sample collected from a hot spring field in Niujie, Eryuan of Yunnan province in China. The open reading frame of this gene encoded 622 amino acid residues. It was cloned, fused with the oleosin gene and over expressed in Escherichia coli to prepare immobilized lipase artificial oil body AOB-sole-lip-1. The monomeric Sole-lip-1 fusion protein presented a molecular mass of 102.4 kDa. Enzyme assays using olive oil and methanol as the substrates in petroleum ether confirmed its transesterification activity. Hexadecanoic acid methyl ester, 8,11-Octadecadienoic acid methyl ester, 8-Octadecenoic acid methyl ester, and Octadecanoic acid methyl ester were detected. It showed favorable transesterification activity with optimal temperature 45 °C. Besides, the maximal biodiesel yield was obtained when the petroleum ether system as the organic solvent and the substrate methanol in 350 mmol/L (at a molar ratio of methanol of 10.5:1) and the water content was 1%. In light of these advantages, this lipase presents a promising resource for biodiesel production.

Targeting the epigenome: Screening bioactive compounds that regulate histone deacetylase activity.

PubMed

Godoy, Luis D; Lucas, Julianna E; Bender, Abigail J; Romanick, Samantha S; Ferguson, Bradley S

2017-04-01

Nutrigenomics is a rapidly expanding field that elucidates the link between diet-genome interactions. Recent evidence demonstrates that regulation of the epigenome, and in particular inhibition of histone deacetylases (HDACs), impact pathogenetic mechanisms involved in chronic disease. Few studies, to date, have screened libraries of bioactive compounds that act as epigenetic modifiers. This study screened a library of 131 natural compounds to determine bioactive compounds that inhibit Zn-dependent HDAC activity. Using class-specific HDAC substrates, we screened 131 natural compounds for HDAC activity in bovine cardiac tissue. From this screen, we identified 18 bioactive compound HDAC inhibitors. Using our class-specific HDAC substrates, we next screened these 18 bioactive compounds against recombinant HDAC proteins. Consistent with inhibition of HDAC activity, these compounds were capable of inhibiting activity of individual HDAC isoforms. Lastly, we report that treatment of H9c2 cardiac myoblasts with bioactive HDAC inhibitors was sufficient to increase lysine acetylation as assessed via immunoblot. This study provided the first step in identifying multiple bioactive compound HDAC inhibitors. Taken together, this report sets the stage for future exploration of these bioactive compounds as epigenetic regulators to potentially ameliorate chronic disease. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Membrane distributed-reflector laser integrated with SiOx-based spot-size converter on Si substrate.

PubMed

Nishi, Hidetaka; Fujii, Takuro; Takeda, Koji; Hasebe, Koichi; Kakitsuka, Takaaki; Tsuchizawa, Tai; Yamamoto, Tsuyoshi; Yamada, Koji; Matsuo, Shinji

2016-08-08

We demonstrate monolithic integration of a 50-μm-long-cavity membrane distributed-reflector laser with a spot-size converter, consisting of a tapered InP wire waveguide and an SiOx waveguide, on SiO₂/Si substrate. The device exhibits 9.4-GHz/mA^0.5 modulation efficiency with a 2.2-dB fiber coupling loss. We demonstrate 25.8-Gbit/s direct modulation with a bias current of 2.5 mA, resulting in a low energy cost of 132 fJ/bit.

Manipulation of Superparamagnetic Beads on Patterned Exchange-Bias Layer Systems for Biosensing Applications.

PubMed

Ehresmann, Arno; Koch, Iris; Holzinger, Dennis

2015-11-13

A technology platform based on a remotely controlled and stepwise transport of an array arrangement of superparamagnetic beads (SPB) for efficient molecular uptake, delivery and accumulation in the context of highly specific and sensitive analyte molecule detection for the application in lab-on-a-chip devices is presented. The near-surface transport of SPBs is realized via the dynamic transformation of the SPBs' magnetic potential energy landscape above a magnetically stripe patterned Exchange-Bias (EB) thin film layer systems due to the application of sub-mT external magnetic field pulses. In this concept, the SPB velocity is dramatically influenced by the magnitude and gradient of the magnetic field landscape (MFL) above the magnetically stripe patterned EB substrate, the SPB to substrate distance, the magnetic properties of both the SPBs and the EB layer system, respectively, as well as by the properties of the external magnetic field pulses and the surrounding fluid. The focus of this review is laid on the specific MFL design in EB layer systems via light-ion bombardment induced magnetic patterning (IBMP). A numerical approach is introduced for the theoretical description of the MFL in comparison to experimental characterization via scanning Hall probe microscopy. The SPB transport mechanism will be outlined in terms of the dynamic interplay between the EB substrate's MFL and the pulse scheme of the external magnetic field.

Gold Nanoparticles on Functionalized Silicon Substrate under Coulomb Blockade Regime: An Experimental and Theoretical Investigation.

PubMed

Pluchery, Olivier; Caillard, Louis; Dollfus, Philippe; Chabal, Yves J

2018-01-18

Single charge electronics offer a way for disruptive technology in nanoelectronics. Coulomb blockade is a realistic way for controlling the electric current through a device with the accuracy of one electron. In such devices the current exhibits a step-like increase upon bias which reflects the discrete nature of the fundamental charge. We have assembled a double tunnel junction on an oxide-free silicon substrate that exhibits Coulomb staircase characteristics using gold nanoparticles (AuNPs) as Coulomb islands. The first tunnel junction is an insulating layer made of a grafted organic monolayer (GOM) developed for this purpose. The GOM also serves for attaching AuNPs covalently. The second tunnel junction is made by the tip of an STM. We show that this device exhibits reproducible Coulomb blockade I-V curves at 40 K in vacuum. We also show that depending on the doping of the silicon substrate, the whole Coulomb staircase can be adjusted. We have developed a simulation approach based on the orthodox theory that was completed by calculating the bias dependent tunnel barriers and by including an accurate calculation of the band bending. This model accounts for the experimental data and the doping dependence of Coulomb oscillations. This study opens new perspectives toward designing new kind of single electron transistors (SET) based on this dependence of the Coulomb staircase with the charge carrier concentration.

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

Bakoglidis, Konstantinos D., E-mail: konba@ifm.liu.se; Schmidt, Susann; Garbrecht, Magnus

The potential of different magnetron sputtering techniques for the synthesis of low friction and wear resistant amorphous carbon nitride (a-CN{sub x}) thin films onto temperature-sensitive AISI52100 bearing steel, but also Si(001) substrates was studied. Hence, a substrate temperature of 150 °C was chosen for the film synthesis. The a-CN{sub x} films were deposited using mid-frequency magnetron sputtering (MFMS) with an MF bias voltage, high power impulse magnetron sputtering (HiPIMS) with a synchronized HiPIMS bias voltage, and direct current magnetron sputtering (DCMS) with a DC bias voltage. The films were deposited using a N{sub 2}/Ar flow ratio of 0.16 at the totalmore » pressure of 400 mPa. The negative bias voltage, V{sub s}, was varied from 20 to 120 V in each of the three deposition modes. The microstructure of the films was characterized by high-resolution transmission electron microscopy and selected area electron diffraction, while the film morphology was investigated by scanning electron microscopy. All films possessed an amorphous microstructure, while the film morphology changed with the bias voltage. Layers grown applying the lowest substrate bias of 20 V exhibited pronounced intercolumnar porosity, independent of the sputter technique. Voids closed and dense films are formed at V{sub s} ≥ 60 V, V{sub s} ≥ 100 V, and V{sub s} = 120 V for MFMS, DCMS, and HiPIMS, respectively. X-ray photoelectron spectroscopy revealed that the nitrogen-to-carbon ratio, N/C, of the films ranged between 0.2 and 0.24. Elastic recoil detection analysis showed that Ar content varied between 0 and 0.8 at. % and increased as a function of V{sub s} for all deposition techniques. All films exhibited compressive residual stress, σ, which depends on the growth method; HiPIMS produces the least stressed films with values ranging between −0.4 and −1.2 GPa for all V{sub s}, while CN{sub x} films deposited by MFMS showed residual stresses up to −4.2 GPa. Nanoindentation showed a significant increase in film hardness and reduced elastic modulus with increasing V{sub s} for all techniques. The harder films were produced by MFMS with hardness as high as 25 GPa. Low friction coefficients, between 0.05 and 0.06, were recorded for all films. Furthermore, CN{sub x} films produced by MFMS and DCMS at V{sub s} = 100 and 120 V presented a high wear resistance with wear coefficients of k ≤ 2.3 × 10{sup −5} mm{sup 3}/Nm. While all CN{sub x} films exhibit low friction, wear depends strongly on the structural and mechanical characteristics of the films. The MFMS mode is best suited for the production of hard CN{sub x} films, although high compressive stresses challenge the application on steel substrates. Films grown in HiPIMS mode provide adequate adhesion due to low residual stress values, at the expense of lower film hardness. Thus, a relatively wide mechanical property envelope is presented for CN{sub x} films, which is relevant for the optimization of CN{sub x} film properties intended to be applied as low friction and wear resistant coatings.« less

A combination of LongSAGE with Solexa sequencing is well suited to explore the depth and the complexity of transcriptome

PubMed Central

Hanriot, Lucie; Keime, Céline; Gay, Nadine; Faure, Claudine; Dossat, Carole; Wincker, Patrick; Scoté-Blachon, Céline; Peyron, Christelle; Gandrillon, Olivier

2008-01-01

Background "Open" transcriptome analysis methods allow to study gene expression without a priori knowledge of the transcript sequences. As of now, SAGE (Serial Analysis of Gene Expression), LongSAGE and MPSS (Massively Parallel Signature Sequencing) are the mostly used methods for "open" transcriptome analysis. Both LongSAGE and MPSS rely on the isolation of 21 pb tag sequences from each transcript. In contrast to LongSAGE, the high throughput sequencing method used in MPSS enables the rapid sequencing of very large libraries containing several millions of tags, allowing deep transcriptome analysis. However, a bias in the complexity of the transcriptome representation obtained by MPSS was recently uncovered. Results In order to make a deep analysis of mouse hypothalamus transcriptome avoiding the limitation introduced by MPSS, we combined LongSAGE with the Solexa sequencing technology and obtained a library of more than 11 millions of tags. We then compared it to a LongSAGE library of mouse hypothalamus sequenced with the Sanger method. Conclusion We found that Solexa sequencing technology combined with LongSAGE is perfectly suited for deep transcriptome analysis. In contrast to MPSS, it gives a complex representation of transcriptome as reliable as a LongSAGE library sequenced by the Sanger method. PMID:18796152

AXM mutagenesis: an efficient means for the production of libraries for directed evolution of proteins.

PubMed

Holland, Erika G; Buhr, Diane L; Acca, Felicity E; Alderman, Dawn; Bovat, Kristin; Busygina, Valeria; Kay, Brian K; Weiner, Michael P; Kiss, Margaret M

2013-08-30

Affinity maturation is an important part of the recombinant antibody development process. There are several well-established approaches for generating libraries of mutated antibody genes for affinity maturation, but these approaches are generally too laborious or expensive to allow high-throughput, parallel processing of multiple antibodies. Here, we describe a scalable approach that enables the generation of libraries with greater than 10(8) clones from a single Escherichia coli transformation. In our method, a mutated DNA fragment is produced using PCR conditions that promote nucleotide misincorporation into newly synthesized DNA. In the PCR reaction, one of the primers contains at least three phosphorothioate linkages at its 5' end, and treatment of the PCR product with a 5' to 3' exonuclease is used to preferentially remove the strand synthesized with the non-modified primer, resulting in a single-stranded DNA fragment. This fragment then serves as a megaprimer to prime DNA synthesis on a uracilated, circular, single-stranded template in a Kunkel-like mutagenesis reaction that biases nucleotide base-changes between the megaprimer and uracilated DNA sequence in favor of the in vitro synthesized megaprimer. This method eliminates the inefficient subcloning steps that are normally required for the construction of affinity maturation libraries from randomly mutagenized antibody genes. Copyright © 2013. Published by Elsevier B.V.

Development of RF sputtered chromium oxide coating for wear application

NASA Technical Reports Server (NTRS)

Bhushan, B.

1979-01-01

The radio frequency sputtering technique was used to deposite a hard refractory, chromium oxide coating on an Inconel X-750 foil 0.1 mm thick. Optimized sputtering parameters for a smooth and adherent coating were found to be as follows: target-to-substrate spacing, 41.3 mm; argon pressure, 5-10 mTorr; total power to the sputtering module, 400 W (voltage at the target, 1600 V), and a water-cooled substrate. The coating on the annealed foil was more adherent than that on the heat-treated foil. Substrate biasing during the sputter deposition of Cr2O3 adversely affected adherence by removing naturally occurring interfacial oxide layers. The deposited coatings were amorphous and oxygen deficient. Since amorphous materials are extremely hard, the structure was considered to be desirable.

Enhancement of Ti-containing hydrogenated carbon (Tisbnd C:H) films by high-power plasma-sputtering

NASA Astrophysics Data System (ADS)

Gwo, Jyh; Chu, Chun-Lin; Tsai, Ming-Jui; Lee, Shyong

2012-02-01

Ti-containing amorphous hydrogenated carbon (Tisbnd C:H) thin films were deposited on stainless steel SS304 substrates by high-power pulsed magnetron sputtering (HPPMS) in an atmosphere of mixed Ar and C2H2 gases using titanium metal as the cathodic material. The multilayer structure of the deposited film had a Tisbnd TiCsbnd DLC gradient to improve adhesion and reduce residual stress. This study investigates the effects of substrate bias and target-to-substrate distance on the mechanical properties of Tisbnd C:H films. Film properties, including composition, morphology, microstructure, mechanical, and tribology, were examined by glow discharge spectroscopy (GDS), scanning electron microscopy (SEM), X-ray diffraction (XRD), Raman spectroscopy, and a nanoindenter and a pin-on-disk tribometer. Experiments revealed impressive results.

Intermodulation distortion and linearity performance assessment of 50-nm gate length L-DUMGAC MOSFET for RFIC design

NASA Astrophysics Data System (ADS)

Chaujar, Rishu; Kaur, Ravneet; Saxena, Manoj; Gupta, Mridula; Gupta, R. S.

2008-08-01

The distortion and linearity behaviour of MOSFETs is imperative for low-noise applications and RFICs design. In this paper, an extensive study on the RF-distortion and linearity behaviour of Laterally Amalgamated DUal Material GAte Concave (L-DUMGAC) MOSFET is performed and the influence of technology variations such as gate length, negative junction depth (NJD), substrate bias, drain bias and gate material workfunction is explored using ATLAS device simulator. Simulation results reveal that L-DUMGAC MOSFET significantly enhances the linearity and intermodulation distortion performance in terms of figure of merit (FOM) metrics: V, V, IIP3, IMD3 and higher order transconductance coefficients: gm1, gm2, gm3, proving its efficacy for RFIC design. The work, thus, optimize the device's bias point for RFICs with higher efficiency and better linearity performance.

Influence of bias voltage on structural and optical properties of TiN{sub x} thin films

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

Singh, Omveer, E-mail: poonia.omveer@gmail.com; Dahiya, Raj P.; Deenbandhu Chhotu Ram University of Science and Technology, Murthal – 131039

In the present work, Ti thin films were deposited on Si substrate using DC sputtering technique. Indigenous hot cathode arc discharge plasma system was used for nitriding over these samples, where the plasma parameters and work piece can be controlled independently. A mixture of H{sub 2} and N{sub 2} gases (in the ratio of 80:20) was supplied into the plasma chamber. The effect of bias voltage on the crystal structure, morphology and optical properties was investigated by employing various physical techniques such as X-ray Diffraction, Atomic Force Microscopy and UV-Vis spectrometry. It was found that bias voltage affects largely themore » crystal structure and band gap which in turn is responsible for the modifications in optical properties of the deposited films.« less

Orthogonal Luciferase-Luciferin Pairs for Bioluminescence Imaging.

PubMed

Jones, Krysten A; Porterfield, William B; Rathbun, Colin M; McCutcheon, David C; Paley, Miranda A; Prescher, Jennifer A

2017-02-15

Bioluminescence imaging with luciferase-luciferin pairs is widely used in biomedical research. Several luciferases have been identified in nature, and many have been adapted for tracking cells in whole animals. Unfortunately, the optimal luciferases for imaging in vivo utilize the same substrate and therefore cannot easily differentiate multiple cell types in a single subject. To develop a broader set of distinguishable probes, we crafted custom luciferins that can be selectively processed by engineered luciferases. Libraries of mutant enzymes were iteratively screened with sterically modified luciferins, and orthogonal enzyme-substrate "hits" were identified. These tools produced light when complementary enzyme-substrate partners interacted both in vitro and in cultured cell models. Based on their selectivity, these designer pairs will bolster multicomponent imaging and enable the direct interrogation of cell networks not currently possible with existing tools. Our screening platform is also general and will expedite the identification of more unique luciferases and luciferins, further expanding the bioluminescence toolkit.

Substrate Specificity of MarP, a Periplasmic Protease Required for Resistance to Acid and Oxidative Stress in Mycobacterium tuberculosis*

PubMed Central

Small, Jennifer L.; O'Donoghue, Anthony J.; Boritsch, Eva C.; Tsodikov, Oleg V.; Knudsen, Giselle M.; Vandal, Omar; Craik, Charles S.; Ehrt, Sabine

2013-01-01

The transmembrane serine protease MarP is important for pH homeostasis in Mycobacterium tuberculosis (Mtb). Previous structural studies revealed that MarP contains a chymotrypsin fold and a disulfide bond that stabilizes the protease active site in the substrate-bound conformation. Here, we determined that MarP is located in the Mtb periplasm and showed that this localization is essential for function. Using the recombinant protease domain of MarP, we identified its substrate specificity using two independent assays: positional-scanning synthetic combinatorial library profiling and multiplex substrate profiling by mass spectrometry. These methods revealed that MarP prefers bulky residues at P4, tryptophan or leucine at P2, arginine or hydrophobic residues at P1, and alanine or asparagine at P1′. Guided by these data, we designed fluorogenic peptide substrates and characterized the kinetic properties of MarP. Finally, we tested the impact of mutating MarP cysteine residues on the peptidolytic activity of recombinant MarP and its ability to complement phenotypes of Mtb ΔMarP. Taken together, our studies provide insight into the enzymatic properties of MarP, its substrate preference, and the importance of its transmembrane helices and disulfide bond. PMID:23504313

Synthetic, switchable enzymes

PubMed Central

Norris, Vic; Krylov, Sergey N.; Agarwal, Pratul K.; White, Glenn J.

2017-01-01

The construction of switchable, radiation-controlled, aptameric enzymes alias swenzymes is, in principle, feasible. We propose a strategy to make such catalysts from two (or more) aptamers each selected to bind specifically to one of the substrates in, for example, a two-substrate reaction. Construction of a combinatorial library of candidate swenzymes entails selecting a set of a million aptamers that bind one substrate and a second set of a million aptamers that bind the second substrate; the aptamers in these sets are then linked pairwise by a linker so bringing together the substrates. In the presence of the substrates, some linked aptamer pairs catalyze the reaction when exposed to external energy in the form of a specific frequency of low intensity, non-ionizing electromagnetic or acoustic radiation. Such swenzymes are detected via a separate, product-capturing, aptamer that changes conformation on capturing the product; this altered conformation allows it (1) to bind to every potential swenzyme in its vicinity (thereby giving a higher probability of capture to the swenzymes that generate the product) and (2) to bind to a sequence on a magnetic bead (thereby permitting purification of the swenzyme plus product-capturing aptamer by precipitation). Attempts to implement the swenzyme strategy may help elucidate fundamental problems in enzyme catalysis. PMID:28448969

Synthetic, Switchable Enzymes.

PubMed

Norris, Vic; Krylov, Sergey N; Agarwal, Pratul K; White, Glenn J

2017-01-01

The construction of switchable, radiation-controlled, aptameric enzymes - "swenzymes" - is, in principle, feasible. We propose a strategy to make such catalysts from 2 (or more) aptamers each selected to bind specifically to one of the substrates in, for example, a 2-substrate reaction. Construction of a combinatorial library of candidate swenzymes entails selecting a set of a million aptamers that bind one substrate and a second set of a million aptamers that bind the second substrate; the aptamers in these sets are then linked pairwise by a linker, thus bringing together the substrates. In the presence of the substrates, some linked aptamer pairs catalyze the reaction when exposed to external energy in the form of a specific frequency of low-intensity, nonionizing electromagnetic or acoustic radiation. Such swenzymes are detected via a separate product-capturing aptamer that changes conformation on capturing the product; this altered conformation allows it (1) to bind to every potential swenzyme in its vicinity (thereby giving a higher probability of capture to the swenzymes that generate the product) and (2) to bind to a sequence on a magnetic bead (thereby permitting purification of the swenzyme plus product-capturing aptamer by precipitation). Attempts to implement the swenzyme strategy may help elucidate fundamental problems in enzyme catalysis. © 2017 S. Karger AG, Basel.

Functional characterization of the Mycobacterium tuberculosis zinc metallopeptidase Zmp1 and identification of potential substrates.

PubMed

Petrera, Agnese; Amstutz, Beat; Gioia, Magda; Hähnlein, Janine; Baici, Antonio; Selchow, Petra; Ferraris, Davide M; Rizzi, Menico; Sbardella, Diego; Marini, Stefano; Coletta, Massimo; Sander, Peter

2012-07-01

Zinc metallopeptidases of bacterial pathogens are widely distributed virulence factors and represent promising pharmacological targets. In this work, we have characterized Zmp1, a zinc metallopeptidase identified as a virulence factor of Mycobacterium tuberculosis and belonging to the neprilysin (NEP; M13) family, whose X-ray structure has been recently solved. Interestingly, this enzyme shows an optimum activity toward a fluorogenic substrate at moderately acidic pH values (i.e., 6.3), which corresponds to those reported for the Mtb phagosome where this enzyme should exert its pathological activity. Substrate specificity of Zmp1 was investigated by screening a peptide library. Several sequences derived from biologically relevant proteins were identified as possible substrates, including the neuropeptides bradykinin, neurotensin, and neuropeptide FF. Further, subsequences of other small bioactive peptides were found among most frequently cleaved sites, e.g., apelin-13 and substance P. We determined the specific cleavage site within neuropeptides by mass spectrometry, observing that hydrophobic amino acids, mainly phenylalanine and isoleucine, are overrepresented at position P1'. In addition, the enzymatic mechanism of Zmp1 toward these neuropeptides has been characterized, displaying some differences with respect to the synthetic fluorogenic substrate and indicating that the enzyme adapts its enzymatic action to different substrates.

Substrate Specificity and Possible Heterologous Targets of Phytaspase, a Plant Cell Death Protease.

PubMed

Galiullina, Raisa A; Kasperkiewicz, Paulina; Chichkova, Nina V; Szalek, Aleksandra; Serebryakova, Marina V; Poreba, Marcin; Drag, Marcin; Vartapetian, Andrey B

2015-10-09

Plants lack aspartate-specific cell death proteases homologous to animal caspases. Instead, a subtilisin-like serine-dependent plant protease named phytaspase shown to be involved in the accomplishment of programmed death of plant cells is able to hydrolyze a number of peptide-based caspase substrates. Here, we determined the substrate specificity of rice (Oryza sativa) phytaspase by using the positional scanning substrate combinatorial library approach. Phytaspase was shown to display an absolute specificity of hydrolysis after an aspartic acid residue. The preceding amino acid residues, however, significantly influence the efficiency of hydrolysis. Efficient phytaspase substrates demonstrated a remarkable preference for an aromatic amino acid residue in the P3 position. The deduced optimum phytaspase recognition motif has the sequence IWLD and is strikingly hydrophobic. The established pattern was confirmed through synthesis and kinetic analysis of cleavage of a set of optimized peptide substrates. An amino acid motif similar to the phytaspase cleavage site is shared by the human gastrointestinal peptide hormones gastrin and cholecystokinin. In agreement with the established enzyme specificity, phytaspase was shown to hydrolyze gastrin-1 and cholecystokinin at the predicted sites in vitro, thus destroying the active moieties of the hormones. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

COMT Val(108/158)Met polymorphism effects on emotional brain function and negativity bias.

PubMed

Williams, Leanne M; Gatt, Justine M; Grieve, Stuart M; Dobson-Stone, Carol; Paul, Robert H; Gordon, Evian; Schofield, Peter R

2010-11-15

Biases toward processing negative versus positive information vary as a function of level of awareness, and are modulated by monoamines. Excessive biases are associated with individual differences in mood and emotional stability, and emotional disorder. Here, we examined the impact of the catechol-O-methyltransferase (COMT) Val(108/158)Met polymorphism, involved in dopamine and norepinephrine catabolism, on both emotional brain function and self-reported negativity bias. COMT genotyping and self-reported level of negativity bias were completed for 46 healthy participants taking part in the Brain Resource International Database. Functional MRI was undertaken during perception of facial expressions of fear and happiness presented under unmasked (consciously identified) and masked (to prevent conscious detection) conditions. Structural MR images were also acquired. A greater number of COMT Met alleles predicted increased activation in brainstem, amygdala, basal ganglia and medial prefrontal regions for conscious fear, but decreased activation for conscious happiness. This pattern was also apparent for brainstem activation for the masked condition. Effects were most apparent for females. These differences could not be explained by gray matter variations. The Met-related profile of activation, particularly prefrontally, predicted greater negativity bias associated with risk for emotional disorder. The findings suggest that the COMT Met allele modulates neural substrates of negative versus positive emotion processing. This effect may contribute to negativity biases, which confer susceptibility for emotional disorders. Copyright 2010 Elsevier Inc. All rights reserved.

Tunable negative differential resistance in planar graphene superlattice resonant tunneling diode

NASA Astrophysics Data System (ADS)

Sattari-Esfahlan, S. M.; Fouladi-Oskuei, J.; Shojaei, S.

2017-04-01

Here, we study the negative differential resistance (NDR) of Dirac electrons in biased planar graphene superlattice (PGSL) and investigate the transport characteristics by adopted transfer matrix method within Landauer-Buttiker formalism. Our model device is based on one-dimensional Kronig-Penney type electrostatic potential in monolayer graphene deposited on a substrate, where the bias voltage is applied by two electrodes in the left and right. At Low bias voltages, we found that NDR appears due to breaking of minibands to Wannier-Stark ladders (WSLs). At the critical bias voltage, delocalization appeared by WS states leads to tunneling peak current in current-voltage (I-V) characteristics. With increasing bias voltage, crossing of rungs from various WSL results in multi-peak NDR. The results demonstrate that the structure parameters like barrier/well thickness and barrier height have remarkable effect on I-V characteristics of PGSL. In addition, Dirac gap enhances peak to valley (PVR) value due to suppressing Klein tunneling. Our results show that the tunable PVR in PGSL resonant tunneling diode can be achievable by structure parameters engineering. NDR at ultra-low bias voltages, such as 100 mV, with giant PVR of 20 is obtained. In our device, the multiple same NDR peaks with ultra-low bias voltage provide promising prospect for multi-valued memories and the low power nanoelectronic tunneling devices.

Conformational state interactions provide clues to the pharmacochaperone potential of serotonin transporter partial substrates

PubMed Central

Bhat, Shreyas; Hasenhuetl, Peter S.; Kasture, Ameya; El-Kasaby, Ali; Baumann, Michael H.; Blough, Bruce E.; Sucic, Sonja; Sandtner, Walter; Freissmuth, Michael

2017-01-01

Point mutations in SLC6 transporters cause misfolding, which can be remedied by pharmacochaperones. The serotonin transporter (SERT/SLC6A4) has a rich pharmacology including inhibitors, releasers (amphetamines, which promote the exchange mode), and more recently, discovered partial substrates. We hypothesized that partial substrates trapped the transporter in one or several states of the transport cycle. This conformational trapping may also be conducive to folding. We selected naphthylpropane-2-amines of the phenethylamine library (PAL) including the partial substrate PAL1045 and its congeners PAL287 and PAL1046. We analyzed their impact on the transport cycle of SERT by biochemical approaches and by electrophysiological recordings; substrate-induced peak currents and steady-state currents monitored the translocation of substrate and co-substrate Na+ across the lipid bilayer and the transport cycle, respectively. These experiments showed that PAL1045 and its congeners bound with different affinities (ranging from nm to μm) to various conformational intermediates of SERT during the transport cycle. Consistent with the working hypothesis, PAL1045 was the most efficacious compound in restoring surface expression and transport activity to the folding-deficient mutant SERT-601PG602-AA. These experiments provide a proof-of-principle for a rational search for pharmacochaperones, which may be useful to restore function to clinically relevant folding-deficient transporter mutants. PMID:28842491

Tagmentation on Microbeads: Restore Long-Range DNA Sequence Information Using Next Generation Sequencing with Library Prepared by Surface-Immobilized Transposomes.

PubMed

Chen, He; Yao, Jiacheng; Fu, Yusi; Pang, Yuhong; Wang, Jianbin; Huang, Yanyi

2018-04-11

The next generation sequencing (NGS) technologies have been rapidly evolved and applied to various research fields, but they often suffer from losing long-range information due to short library size and read length. Here, we develop a simple, cost-efficient, and versatile NGS library preparation method, called tagmentation on microbeads (TOM). This method is capable of recovering long-range information through tagmentation mediated by microbead-immobilized transposomes. Using transposomes with DNA barcodes to identically label adjacent sequences during tagmentation, we can restore inter-read connection of each fragment from original DNA molecule by fragment-barcode linkage after sequencing. In our proof-of-principle experiment, more than 4.5% of the reads are linked with their adjacent reads, and the longest linkage is over 1112 bp. We demonstrate TOM with eight barcodes, but the number of barcodes can be scaled up by an ultrahigh complexity construction. We also show this method has low amplification bias and effectively fits the applications to identify copy number variations.

The role of the (111) texture on the exchange bias and interlayer coupling effects observed in sputtered NiFe/IrMn/Co trilayers

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

Castro, I. L.; Nascimento, V. P.; Passamani, E. C.

2013-05-28

Magnetic properties of sputtered NiFe/IrMn/Co trilayers grown on different seed layers (Cu or Ta) deposited on Si (100) substrates were investigated by magnetometry and ferromagnetic resonance measurements. Exchange bias effect and magnetic spring behavior have been studied by changing the IrMn thickness. As shown by X-ray diffraction, Ta and Cu seed layers provoke different degrees of (111) fcc-texture that directly affect the exchange bias and indirectly modify the exchange spring coupling behavior. Increasing the IrMn thickness, it was observed that the coupling angle between the Co and NiFe ferromagnetic layers increases for the Cu seed system, but it reduces formore » the Ta case. The results were explained considering (i) different anisotropies of the Co and IrMn layers induced by the different degree of the (111) texture and (ii) the distinct exchange bias set at the NiFe/IrMn and IrMn/Co interfaces in both systems. The NiFe and Co interlayer coupling angle is strongly correlated with both exchange bias and exchange magnetic spring phenomena. It was also shown that the highest exchange bias field occurs when an unstressed L1{sub 2} IrMn structure is stabilized.« less

Semi-transparent all-oxide ultraviolet light-emitting diodes based on ZnO/NiO-core/shell nanowires

NASA Astrophysics Data System (ADS)

Shi, Zhi-Feng; Xu, Ting-Ting; Wu, Di; Zhang, Yuan-Tao; Zhang, Bao-Lin; Tian, Yong-Tao; Li, Xin-Jian; Du, Guo-Tong

2016-05-01

Semi-transparent all-oxide light-emitting diodes based on ZnO/NiO-core/shell nanowire structures were prepared on double-polished c-Al2O3 substrates. The entire heterojunction diode showed an average transparency of ~65% in the ultraviolet and visible regions. Under forward bias, the diode displayed an intense ultraviolet emission at ~382 nm, and its electroluminescence performance was remarkable in terms of a low emission onset, acceptable operating stability, and the ability to optically excite emissive semiconductor nanoparticle chromophores.Semi-transparent all-oxide light-emitting diodes based on ZnO/NiO-core/shell nanowire structures were prepared on double-polished c-Al2O3 substrates. The entire heterojunction diode showed an average transparency of ~65% in the ultraviolet and visible regions. Under forward bias, the diode displayed an intense ultraviolet emission at ~382 nm, and its electroluminescence performance was remarkable in terms of a low emission onset, acceptable operating stability, and the ability to optically excite emissive semiconductor nanoparticle chromophores. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr07236k

Ab initio study of the mechanism of bottom-up synthesis of graphene nanoribbons

NASA Astrophysics Data System (ADS)

Xiao, Zhongcan; Ma, Chuanxu; Zhang, Honghai; Liang, Liangbo; Huang, Jingsong; Lu, Wenchang; Hong, Kunlun; Li, An-Ping; Bernholc, Jerry

Graphene nanoribbons (GNRs) can be fabricated with atomic precision by using molecular precursors deposited on a metal substrate, and potentially form the basis for future molecular-scale electronics. The precursor molecules are first annealed to form a polymer, and further annealing at a higher temperature leads to the formation of a GNR. We systematically study the reaction pathways of this cyclodehydrogenation process, using density functional theory and the nudged elastic band method. We find that the Au substrate reduces the reaction barriers for key steps in the cyclodehydrogenation process: cyclization, hydrogen migration and desorption. Furthermore, our calculations explain recent experiments showing that an STM-tip can induce local polymer-to-GNR transition, which can be used to fabricate atomically precise heterojunctions: at a negative bias, the STM tip injects excess holes into the polymer HOMO state, lowering the energy barrier in agreement with Woodward-Hoffmann rules. At a positive bias, when excess electrons are injected into the LUMO state, the energy barrier is not significantly lowered and the transition is not observed.

Energy dissipation mechanism revealed by spatially resolved Raman thermometry of graphene/hexagonal boron nitride heterostructure devices

NASA Astrophysics Data System (ADS)

Kim, Daehee; Kim, Hanul; Yun, Wan Soo; Watanabe, Kenji; Taniguchi, Takashi; Rho, Heesuk; Bae, Myung-Ho

2018-04-01

Understanding the energy transport by charge carriers and phonons in two-dimensional (2D) van der Waals heterostructures is essential for the development of future energy-efficient 2D nanoelectronics. Here, we performed in situ spatially resolved Raman thermometry on an electrically biased graphene channel and its hBN substrate to study the energy dissipation mechanism in graphene/hBN heterostructures. By comparing the temperature profile along the biased graphene channel with that along the hBN substrate, we found that the thermal boundary resistance between the graphene and hBN was in the range of (1-2) ~ × 10-7 m2 K W-1 from ~100 °C to the onset of graphene break-down at ~600 °C in air. Consideration of an electro-thermal transport model together with the Raman thermometry conducted in air showed that a doping effect occurred under a strong electric field played a crucial role in the energy dissipation of the graphene/hBN device up to T ~ 600 °C.

Extensive peptide and natural protein substrate screens reveal that mouse caspase-11 has much narrower substrate specificity than caspase-1

PubMed Central

Ramirez, Monica L. Gonzalez; Poreba, Marcin; Snipas, Scott J.; Groborz, Katarzyna; Drag, Marcin; Salvesen, Guy S.

2018-01-01

Inflammatory cell death, or pyroptosis, is triggered by pathogenic infections or events. It is executed by caspase-1 (in the canonical pyroptosis pathway) or caspase-11 (noncanonical pathway), each via production of a cell-lytic domain from the pyroptosis effector protein gasdermin D through specific and limited proteolysis. Pyroptosis is accompanied by the release of inflammatory mediators, including the proteolytically processed forms of interleukin-1β (IL-1β) and IL-18. Given the similar inflammatory outcomes of the canonical and noncanonical pyroptosis pathways, we hypothesized that caspase-1 and -11 should have very similar activities and substrate specificities. To test this hypothesis, we purified recombinant murine caspases and analyzed their primary specificities by massive hybrid combinatorial substrate library (HyCoSuL) screens. We correlated the substrate preferences of each caspase with their activities on the recombinant natural substrates IL-1β, IL-18, and gasdermin D. Although we identified highly selective and robust peptidyl substrates for caspase-1, we were unable to do so for caspase-11, because caspase-1 cleaved even the best caspase-11 substrates equally well. Caspase-1 rapidly processed pro-IL-1β and -18, but caspase-11 processed these two pro-ILs extremely poorly. However, both caspase-1 and -11 efficiently produced the cell-lytic domain from the gasdermin D precursor. We hypothesize that caspase-11 may have evolved a specific exosite to selectively engage pyroptosis without directly activating pro-IL-1β or -18. In summary, comparing the activities of caspase-1 and -11 in HyCoSuL screens and with three endogenous protein substrates, we conclude that caspase-11 has highly restricted substrate specificity, preferring gasdermin D over all other substrates examined. PMID:29414788

Sequence-based screening for self-sufficient P450 monooxygenase from a metagenome library.

PubMed

Kim, B S; Kim, S Y; Park, J; Park, W; Hwang, K Y; Yoon, Y J; Oh, W K; Kim, B Y; Ahn, J S

2007-05-01

Cytochrome P450 monooxygenases (CYPs) are useful catalysts for oxidation reactions. Self-sufficient CYPs harbour a reductive domain covalently connected to a P450 domain and are known for their robust catalytic activity with great potential as biocatalysts. In an effort to expand genetic sources of self-sufficient CYPs, we devised a sequence-based screening system to identify them in a soil metagenome. We constructed a soil metagenome library and performed sequence-based screening for self-sufficient CYP genes. A new CYP gene, syk181, was identified from the metagenome library. Phylogenetic analysis revealed that SYK181 formed a distinct phylogenic line with 46% amino-acid-sequence identity to CYP102A1 which has been extensively studied as a fatty acid hydroxylase. The heterologously expressed SYK181 showed significant hydroxylase activity towards naphthalene and phenanthrene as well as towards fatty acids. Sequence-based screening of metagenome libraries is expected to be a useful approach for searching self-sufficient CYP genes. The translated product of syk181 shows self-sufficient hydroxylase activity towards fatty acids and aromatic compounds. SYK181 is the first self-sufficient CYP obtained directly from a metagenome library. The genetic and biochemical information on SYK181 are expected to be helpful for engineering self-sufficient CYPs with broader catalytic activities towards various substrates, which would be useful for bioconversion of natural products and biodegradation of organic chemicals.

Status of two-color and large format HgCdTe FPA technology at Raytheon Vision Systems

NASA Astrophysics Data System (ADS)

Smith, E. P. G.; Bornfreund, R. E.; Kasai, I.; Pham, L. T.; Patten, E. A.; Peterson, J. M.; Roth, J. A.; Nosho, B. Z.; De Lyon, T. J.; Jensen, J. E.; Bangs, J. W.; Johnson, S. M.; Radford, W. A.

2006-02-01

Raytheon Vision Systems (RVS) is developing two-color and large format single color FPAs fabricated from molecular beam epitaxy (MBE) grown HgCdTe triple layer heterojunction (TLHJ) wafers on CdZnTe substrates and double layer heterojunction (DLHJ) wafers on Si substrates, respectively. MBE material growth development has resulted in scaling TLHJ growth on CdZnTe substrates from 10cm2 to 50cm2, long-wavelength infrared (LWIR) DLHJ growth on 4-inch Si substrates and the first demonstration of mid-wavelength infrared (MWIR) DLHJ growth on 6-inch Si substrates with low defect density (<1000cm -2) and excellent uniformity (composition<0.1%, cut-off wavelength Δcenter-edge<0.1μm). Advanced FPA fabrication techniques such as inductively coupled plasma (ICP) etching are being used to achieve high aspect ratio mesa delineation of individual detector elements with benefits to detector performance. Recent two-color detectors with MWIR and LWIR cut-off wavelengths of 5.5μm and 10.5μm, respectively, exhibit significant improvement in 78K LW performance with >70% quantum efficiency, diffusion limited reverse bias dark currents below 300pA and RA products (zero field-of-view, +150mV bias) in excess of 1×103 Ωcm2. Two-color 20μm unit-cell 1280×720 MWIR/LWIR FPAs with pixel response operability approaching 99% have been produced and high quality simultaneous imaging of the spectral bands has been achieved by mating the FPA to a readout integrated circuit (ROIC) with Time Division Multiplexed Integration (TDMI). Large format mega pixel 20μm unit-cell 2048×2048 and 25μm unit-cell 2560×512 FPAs have been demonstrated using DLHJ HgCdTe growth on Si substrates in the short wavelength infrared (SWIR) and MWIR spectral range. Recent imaging of 30μm unit-cell 256×256 LWIR FPAs with 10.0-10.7μm 78K cut-off wavelength and pixel response operability as high as 99.7% show the potential for extending HgCdTe/Si technology to LWIR wavelengths.

X-ray photoelectron spectroscopy study of radiofrequency sputtered chromium bromide, molybdenum disilicide, and molybdenum disulfide coatings and their friction properties

NASA Technical Reports Server (NTRS)

Wheeler, D. R.; Brainard, W. A.

1977-01-01

Radiofrequency sputtered coatings of CRB2, MOSI2, and MOS2 were examined by X-ray photoelectron spectroscopy. The effects of sputtering target history, deposition time, RF power level, and substrate bias on film composition were studied. Friction tests were run on RF sputtered surfaces of 440-C steel to correlate XPS data with lubricating properties. Significant deviations from stoichiometry and high oxide levels for all three compounds were related to target outgassing. The effect of biasing on these two factors depended on the compound. Improved stoichiometry correlated well with good friction and wear properties.

Transcriptome analysis of 20 taxonomically related benzylisoquinoline alkaloid-producing plants.

PubMed

Hagel, Jillian M; Morris, Jeremy S; Lee, Eun-Jeong; Desgagné-Penix, Isabel; Bross, Crystal D; Chang, Limei; Chen, Xue; Farrow, Scott C; Zhang, Ye; Soh, Jung; Sensen, Christoph W; Facchini, Peter J

2015-09-18

Benzylisoquinoline alkaloids (BIAs) represent a diverse class of plant specialized metabolites sharing a common biosynthetic origin beginning with tyrosine. Many BIAs have potent pharmacological activities, and plants accumulating them boast long histories of use in traditional medicine and cultural practices. The decades-long focus on a select number of plant species as model systems has allowed near or full elucidation of major BIA pathways, including those of morphine, sanguinarine and berberine. However, this focus has created a dearth of knowledge surrounding non-model species, which also are known to accumulate a wide-range of BIAs but whose biosynthesis is thus far entirely unexplored. Further, these non-model species represent a rich source of catalyst diversity valuable to plant biochemists and emerging synthetic biology efforts. In order to access the genetic diversity of non-model plants accumulating BIAs, we selected 20 species representing 4 families within the Ranunculales. RNA extracted from each species was processed for analysis by both 1) Roche GS-FLX Titanium and 2) Illumina GA/HiSeq platforms, generating a total of 40 deep-sequencing transcriptome libraries. De novo assembly, annotation and subsequent full-length coding sequence (CDS) predictions indicated greater success for most species using the Illumina-based platform. Assembled data for each transcriptome were deposited into an established web-based BLAST portal ( www.phytometasyn.ca) to allow public access. Homology-based mining of libraries using BIA-biosynthetic enzymes as queries yielded ~850 gene candidates potentially involved in alkaloid biosynthesis. Expression analysis of these candidates was performed using inter-library FPKM normalization methods. These expression data provide a basis for the rational selection of gene candidates, and suggest possible metabolic bottlenecks within BIA metabolism. Phylogenetic analysis was performed for each of 15 different enzyme/protein groupings, highlighting many novel genes with potential involvement in the formation of one or more alkaloid types, including morphinan, aporphine, and phthalideisoquinoline alkaloids. Transcriptome resources were used to design and execute a case study of candidate N-methyltransferases (NMTs) from Glaucium flavum, which revealed predicted and novel enzyme activities. This study establishes an essential resource for the isolation and discovery of 1) functional homologues and 2) entirely novel catalysts within BIA metabolism. Functional analysis of G. flavum NMTs demonstrated the utility of this resource and underscored the importance of empirical determination of proposed enzymatic function. Publically accessible, fully annotated, BLAST-accessible transcriptomes were not previously available for most species included in this report, despite the rich repertoire of bioactive alkaloids found in these plants and their importance to traditional medicine. The results presented herein provide essential sequence information and inform experimental design for the continued elucidation of BIA metabolism.

A microfluidic device for preparing next generation DNA sequencing libraries and for automating other laboratory protocols that require one or more column chromatography steps.

PubMed

Tan, Swee Jin; Phan, Huan; Gerry, Benjamin Michael; Kuhn, Alexandre; Hong, Lewis Zuocheng; Min Ong, Yao; Poon, Polly Suk Yean; Unger, Marc Alexander; Jones, Robert C; Quake, Stephen R; Burkholder, William F

2013-01-01

Library preparation for next-generation DNA sequencing (NGS) remains a key bottleneck in the sequencing process which can be relieved through improved automation and miniaturization. We describe a microfluidic device for automating laboratory protocols that require one or more column chromatography steps and demonstrate its utility for preparing Next Generation sequencing libraries for the Illumina and Ion Torrent platforms. Sixteen different libraries can be generated simultaneously with significantly reduced reagent cost and hands-on time compared to manual library preparation. Using an appropriate column matrix and buffers, size selection can be performed on-chip following end-repair, dA tailing, and linker ligation, so that the libraries eluted from the chip are ready for sequencing. The core architecture of the device ensures uniform, reproducible column packing without user supervision and accommodates multiple routine protocol steps in any sequence, such as reagent mixing and incubation; column packing, loading, washing, elution, and regeneration; capture of eluted material for use as a substrate in a later step of the protocol; and removal of one column matrix so that two or more column matrices with different functional properties can be used in the same protocol. The microfluidic device is mounted on a plastic carrier so that reagents and products can be aliquoted and recovered using standard pipettors and liquid handling robots. The carrier-mounted device is operated using a benchtop controller that seals and operates the device with programmable temperature control, eliminating any requirement for the user to manually attach tubing or connectors. In addition to NGS library preparation, the device and controller are suitable for automating other time-consuming and error-prone laboratory protocols requiring column chromatography steps, such as chromatin immunoprecipitation.

A Microfluidic Device for Preparing Next Generation DNA Sequencing Libraries and for Automating Other Laboratory Protocols That Require One or More Column Chromatography Steps

PubMed Central

Tan, Swee Jin; Phan, Huan; Gerry, Benjamin Michael; Kuhn, Alexandre; Hong, Lewis Zuocheng; Min Ong, Yao; Poon, Polly Suk Yean; Unger, Marc Alexander; Jones, Robert C.; Quake, Stephen R.; Burkholder, William F.

2013-01-01

Library preparation for next-generation DNA sequencing (NGS) remains a key bottleneck in the sequencing process which can be relieved through improved automation and miniaturization. We describe a microfluidic device for automating laboratory protocols that require one or more column chromatography steps and demonstrate its utility for preparing Next Generation sequencing libraries for the Illumina and Ion Torrent platforms. Sixteen different libraries can be generated simultaneously with significantly reduced reagent cost and hands-on time compared to manual library preparation. Using an appropriate column matrix and buffers, size selection can be performed on-chip following end-repair, dA tailing, and linker ligation, so that the libraries eluted from the chip are ready for sequencing. The core architecture of the device ensures uniform, reproducible column packing without user supervision and accommodates multiple routine protocol steps in any sequence, such as reagent mixing and incubation; column packing, loading, washing, elution, and regeneration; capture of eluted material for use as a substrate in a later step of the protocol; and removal of one column matrix so that two or more column matrices with different functional properties can be used in the same protocol. The microfluidic device is mounted on a plastic carrier so that reagents and products can be aliquoted and recovered using standard pipettors and liquid handling robots. The carrier-mounted device is operated using a benchtop controller that seals and operates the device with programmable temperature control, eliminating any requirement for the user to manually attach tubing or connectors. In addition to NGS library preparation, the device and controller are suitable for automating other time-consuming and error-prone laboratory protocols requiring column chromatography steps, such as chromatin immunoprecipitation. PMID:23894273

Bio-inspired synthesis and biological evaluation of a colchicine-related compound library.

PubMed

Nicolaou, K C; Valiulin, Roman A; Pokorski, Jonathan K; Chang, Vicki; Chen, Jason S

2012-06-01

A bio-inspired investigation of the reactions of substrates of type 1 with VOF(3) and PIFA [phenyliodine(III) bis(trifluoroacetate)] led to a collection of colchicine-like compounds 2-5 and related systems. Biological evaluation revealed that some of the synthesized products had significant cytotoxic properties against the colon cancer cell line HT-29. Copyright © 2012 Elsevier Ltd. All rights reserved.

Robust low-bias negative differential resistance in graphene superlattices

NASA Astrophysics Data System (ADS)

Sattari-Esfahlan, S. M.; Fouladi-Oskuei, J.; Shojaei, S.

2017-06-01

In this work, we present a detailed theoretical study on the low bias current-voltage (I-V) characteristic of biased planar graphene superlattice (PGSL), provided by a heterostructured substrate and a series of grounded metallic planes placed over a graphene sheet, which induce a periodically modulated Dirac gap and Fermi velocity barrier, respectively. We investigate the effect of PGSL parameters on the I-V characteristic and the appearance of multipeak negative differential resistance (NDR) in the proposed device within the Landauer-Buttiker formalism and adopted transfer matrix method. Moreover‚ we propose a novel venue to control the NDR in PGSL with Fermi velocity barrier. Different regimes of NDR have been recognized, based on the PGSL parameters and external bias. From this viewpoint‚ we obtain multipeak NDR through miniband aligning in PGSL. The maximum pick to valley ratio (PVR) up to 167 obtained for ~{{\\upsilon}c} , the Fermi velocity correlation (ratio of Fermi velocity in barrier and well region), is 1.9 at bias voltages between 70-130 mV. Our findings have good agreement with experiments and can be considered in designing multi-valued memory‚ functional circuit, low power and high-speed nanoelectronic device applications.

Specificity studies on Kallikrein-related peptidase 7 (KLK7) and effects of osmolytes and glycosaminoglycans on its peptidase activity.

PubMed

Oliveira, Juliana R; Bertolin, Thiago C; Andrade, Douglas; Oliveira, Lilian C G; Kondo, Marcia Y; Santos, Jorge A N; Blaber, Michael; Juliano, Luiz; Severino, Beatrice; Caliendo, Giuseppe; Santagada, Vincenzo; Juliano, Maria A

2015-01-01

KLK7 substrate specificity was evaluated by families of fluorescence resonance energy transfer (FRET) peptides derived from Abz-KLFSSK-Q-EDDnp (Abz=ortho-aminobenzoic acid and Q-EDDnp=glutaminyl-N-[2,4-dinitrophenyl] ethylenediamine), by one bead-one peptide FRET peptide library in PEGA resin, and by the FRET peptide libraries Abz-GXX-Z-XX-Q-EDDnp (Z and X are fixed and random natural amino acids, respectively). KLK7 hydrolyzed preferentially F, Y or M, and its S1' and S2' subsites showed selectivity for hydrophilic amino acids, particularly R and K. This set of specificities was confirmed by the efficient kininogenase activity of KLK7 on Abz-MISLM(↓)KRPPGFSPF(↓)RSSRI-NH2 ((↓)indicates cleavage), hydrolysis of somatostatin and substance P and inhibition by kallistatin. The peptide Abz-NLY(↓)RVE-Q-EDDnp is the best synthetic substrate so far described for KLK7 [kcat/Km=455 (mMs)(-1)] that was designed from the KLK7 substrate specificity analysis. It is noteworthy that the NLYRVE sequence is present in human semaphorin 6B. KLK7 is activated by GAGs, inhibited by neutral salts, and activated by high concentration of kosmotropic salt. Pyroglutamic acid inhibited KLK7 (Ki=33mM) and is present in skin moisturizing factor (124mM). The KLK7 specificity described here and elsewhere reflects its participation in patho-physiological events in skin, the gastrointestinal tract and central nervous system, where KLK7 is significantly expressed. Copyright © 2014. Published by Elsevier B.V.

Biochemical profiling in silico--predicting substrate specificities of large enzyme families.

PubMed

Tyagi, Sadhna; Pleiss, Juergen

2006-06-25

A general high-throughput method for in silico biochemical profiling of enzyme families has been developed based on covalent docking of potential substrates into the binding sites of target enzymes. The method has been tested by systematically docking transition state--analogous intermediates of 12 substrates into the binding sites of 20 alpha/beta hydrolases from 15 homologous families. To evaluate the effect of side chain orientations to the docking results, 137 crystal structures were included in the analysis. A good substrate must fulfil two criteria: it must bind in a productive geometry with four hydrogen bonds between the substrate and the catalytic histidine and the oxyanion hole, and a high affinity of the enzyme-substrate complex as predicted by a high docking score. The modelling results in general reproduce experimental data on substrate specificity and stereoselectivity: the differences in substrate specificity of cholinesterases toward acetyl- and butyrylcholine, the changes of activity of lipases and esterases upon the size of the acid moieties, activity of lipases and esterases toward tertiary alcohols, and the stereopreference of lipases and esterases toward chiral secondary alcohols. Rigidity of the docking procedure was the major reason for false positive and false negative predictions, as the geometry of the complex and docking score may sensitively depend on the orientation of individual side chains. Therefore, appropriate structures have to be identified. In silico biochemical profiling provides a time efficient and cost saving protocol for virtual screening to identify the potential substrates of the members of large enzyme family from a library of molecules.

Stability-Diversity Tradeoffs Impose Fundamental Constraints on Selection of Synthetic Human VH/VL Single-Domain Antibodies from In Vitro Display Libraries

PubMed Central

Henry, Kevin A.; Kim, Dae Young; Kandalaft, Hiba; Lowden, Michael J.; Yang, Qingling; Schrag, Joseph D.; Hussack, Greg; MacKenzie, C. Roger; Tanha, Jamshid

2017-01-01

Human autonomous VH/VL single-domain antibodies (sdAbs) are attractive therapeutic molecules, but often suffer from suboptimal stability, solubility and affinity for cognate antigens. Most commonly, human sdAbs have been isolated from in vitro display libraries constructed via synthetic randomization of rearranged VH/VL domains. Here, we describe the design and characterization of three novel human VH/VL sdAb libraries through a process of: (i) exhaustive biophysical characterization of 20 potential VH/VL sdAb library scaffolds, including assessment of expression yield, aggregation resistance, thermostability and tolerance to complementarity-determining region (CDR) substitutions; (ii) in vitro randomization of the CDRs of three VH/VL sdAb scaffolds, with tailored amino acid representation designed to promote solubility and expressibility; and (iii) systematic benchmarking of the three VH/VL libraries by panning against five model antigens. We isolated ≥1 antigen-specific human sdAb against four of five targets (13 VHs and 7 VLs in total); these were predominantly monomeric, had antigen-binding affinities ranging from 5 nM to 12 µM (average: 2–3 µM), but had highly variable expression yields (range: 0.1–19 mg/L). Despite our efforts to identify the most stable VH/VL scaffolds, selection of antigen-specific binders from these libraries was unpredictable (overall success rate for all library-target screens: ~53%) with a high attrition rate of sdAbs exhibiting false positive binding by ELISA. By analyzing VH/VL sdAb library sequence composition following selection for monomeric antibody expression (binding to protein A/L followed by amplification in bacterial cells), we found that some VH/VL sdAbs had marked growth advantages over others, and that the amino acid composition of the CDRs of this set of sdAbs was dramatically restricted (bias toward Asp and His and away from aromatic and hydrophobic residues). Thus, CDR sequence clearly dramatically impacts the stability of human autonomous VH/VL immunoglobulin domain folds, and sequence-stability tradeoffs must be taken into account during the design of such libraries. PMID:29375542

Synthesis and evaluation of conformationally restricted inhibitors of aspartate semialdehyde dehydrogenase.

PubMed

Evitt, Andrew S; Cox, Russell J

2011-05-01

Inhibitors of the enzyme aspartate semialdehyde dehydrogenase, a key biological target for the generation of a new class of antibiotic compounds, have been developed. To investigate improvements to binding within an inhibitor series, the lowering of the entropic barrier to binding through conformational restriction was investigated. A library of linear and cyclic substrate analogues was generated and computational docking used to aid in structure selection. The cyclic phosphonate inhibitor 18 was thus identified as complimentary to the enzyme active-site. Synthesis and in vitro inhibition assay revealed a K(i) of 3.8 mM against natural substrate, where the linear analogue of 18, compound 15, had previously shown no inhibitory activity. Two further inhibitors, phosphate analogue diastereoisomers 17a and 17b, were synthesised and also found to have low millimolar K(i) values. As a result of the computational docking investigations, a novel substrate binding interaction was discovered: hydrogen bonding between the substrate (phosphate hydroxy-group as the hydrogen bond donor) and the NADPH cofactor (2'-oxygen as the hydrogen bond acceptor).

Asymmetric mutations in the tetrameric R67 dihydrofolate reductase reveal high tolerance to active-site substitutions.

PubMed

Ebert, Maximilian C C J C; Morley, Krista L; Volpato, Jordan P; Schmitzer, Andreea R; Pelletier, Joelle N

2015-04-01

Type II R67 dihydrofolate reductase (DHFR) is a bacterial plasmid-encoded enzyme that is intrinsically resistant to the widely-administered antibiotic trimethoprim. R67 DHFR is genetically and structurally unrelated to E. coli chromosomal DHFR and has an unusual architecture, in that four identical protomers form a single symmetrical active site tunnel that allows only one substrate binding/catalytic event at any given time. As a result, substitution of an active-site residue has as many as four distinct consequences on catalysis, constituting an atypical model of enzyme evolution. Although we previously demonstrated that no single residue of the native active site is indispensable for function, library selection here revealed a strong bias toward maintenance of two native protomers per mutated tetramer. A variety of such "half-native" tetramers were shown to procure native-like catalytic activity, with similar KM values but kcat values 5- to 33-fold lower, illustrating a high tolerance for active-site substitutions. The selected variants showed a reduced thermal stability (Tm ∼12°C lower), which appears to result from looser association of the protomers, but generally showed a marked increase in resilience to heat denaturation, recovering activity to a significantly greater extent than the variant with no active-site substitutions. Our results suggest that the presence of two native protomers in the R67 DHFR tetramer is sufficient to provide native-like catalytic rate and thus ensure cellular proliferation. © 2014 The Protein Society.

Influence of the dynamic lattice strain on the transport behavior of oxide heterojunctions

NASA Astrophysics Data System (ADS)

Wang, J.; Hu, F. X.; Chen, L.; Zhao, Y. Y.; Lu, H. X.; Sun, J. R.; Shen, B. G.

2013-01-01

All-perovskite oxide heterojunctions composed of electron-doped titanate LaxSr1 - xTiO3 (x = 0.1, 0.15) and hole-doped manganite La0.67Ca0.33MnO3 films were fabricated on piezoelectric substrate of (001)-0.7Pb(Mg1/3Nb2/3)O3-0.3PbTiO3 (PMN-PT). Taking advantage of the excellent converse piezoelectric effect of PMN-PT, we investigated the influence of the dynamic lattice strain on transport properties of the heterojunctions by applying external bias electric fields on the PMN-PT substrate. Photovoltaic experiments were carried out to characterize the interfacial barrier of the heterojunction. A linear reduction in the barrier height was observed with the increase of the bias field applied on PMN-PT. The value of the barrier height reduces from ˜1.55 (˜1.30) to 1.02 (1.08) eV as the bias field increases from 0 to 12 kV/cm for the junction of La0.10Sr0.9TiO3/La0.67Ca0.33MnO3 (La0.15Sr0.85TiO3/La0.67Ca0.33MnO3). The observed dependency of barrier height on external field can be ascribed to the increasing release of trapped carriers by strain modulation, which results in a suppression of the depletion layer and increases the opportunity for electron tunneling across the depletion area.

Comprehensive analyses of core-shell InGaN/GaN single nanowire photodiodes

NASA Astrophysics Data System (ADS)

Zhang, H.; Guan, N.; Piazza, V.; Kapoor, A.; Bougerol, C.; Julien, F. H.; Babichev, A. V.; Cavassilas, N.; Bescond, M.; Michelini, F.; Foldyna, M.; Gautier, E.; Durand, C.; Eymery, J.; Tchernycheva, M.

2017-12-01

Single nitride nanowire core/shell n-p photodetectors are fabricated and analyzed. Nanowires consisting of an n-doped GaN stem, a radial InGaN/GaN multiple quantum well system and a p-doped GaN external shell were grown by catalyst-free metal-organic vapour phase epitaxy on sapphire substrates. Single nanowires were dispersed and the core and the shell regions were contacted with a metal and an ITO deposition, respectively, defined using electron beam lithography. The single wire photodiodes present a response in the visible to UV spectral range under zero external bias. The detector operation speed has been analyzed under different bias conditions. Under zero bias, the  -3 dB cut-off frequency is ~200 Hz for small light modulations. The current generation was modeled using non-equilibrium Green function formalism, which evidenced the importance of phonon scattering for carrier extraction from the quantum wells.

Superconducting Metallic Glass Transition-Edge-Sensors

NASA Technical Reports Server (NTRS)

Hays, Charles C. (Inventor)

2013-01-01

A superconducting metallic glass transition-edge sensor (MGTES) and a method for fabricating the MGTES are provided. A single-layer superconducting amorphous metal alloy is deposited on a substrate. The single-layer superconducting amorphous metal alloy is an absorber for the MGTES and is electrically connected to a circuit configured for readout and biasing to sense electromagnetic radiation.

Neural Specialization for Speech in the First Months of Life

ERIC Educational Resources Information Center

Shultz, Sarah; Vouloumanos, Athena; Bennett, Randi H.; Pelphrey, Kevin

2014-01-01

How does the brain's response to speech change over the first months of life? Although behavioral findings indicate that neonates' listening biases are sharpened over the first months of life, with a species-specific preference for speech emerging by 3 months, the neural substrates underlying this developmental change are unknown. We…

Influences of W Content on the Phase Transformation Properties and the Associated Stress Change in Thin Film Substrate Combinations Studied by Fabrication and Characterization of Thin Film V1- xW xO2 Materials Libraries.

PubMed

Wang, Xiao; Rogalla, Detlef; Ludwig, Alfred

2018-04-09

The mechanical stress change of VO 2 film substrate combinations during their reversible phase transformation makes them promising for applications in micro/nanoactuators. V 1- x W x O 2 thin film libraries were fabricated by reactive combinatorial cosputtering to investigate the effects of the addition of W on mechanical and other transformation properties. High-throughput characterization methods were used to systematically determine the composition spread, crystalline structure, surface topography, as well as the temperature-dependent phase transformation properties, that is, the hysteresis curves of the resistance and stress change. The study indicates that as x in V 1- x W x O 2 increases from 0.007 to 0.044 the crystalline structure gradually shifts from the VO 2 (M) phase to the VO 2 (R) phase. The transformation temperature decreases by 15 K/at. % and the resistance change is reduced to 1 order of magnitude, accompanied by a wider transition range and a narrower hysteresis with a minimal value of 1.8 K. A V 1- x W x O 2 library deposited on a Si 3 N 4 /SiO 2 -coated Si cantilever array wafer was used to study simultaneously the temperature-dependent stress change σ( T) of films with different W content through the phase transformation. Compared with σ( T) of ∼700 MPa of a VO 2 film, σ( T) in V 1- x W x O 2 films decreases to ∼250 MPa. Meanwhile, σ( T) becomes less abrupt and occurs over a wider temperature range with decreased transformation temperatures.

Metagenomes of complex microbial consortia derived from different soils as sources for novel genes conferring formation of carbonyls from short-chain polyols on Escherichia coli.

PubMed

Knietsch, Anja; Waschkowitz, Tanja; Bowien, Susanne; Henne, Anke; Daniel, Rolf

2003-01-01

Metagenomic DNA libraries from three different soil samples (meadow, sugar beet field, cropland) were constructed. The three unamplified libraries comprised approximately 1267000 independent clones and harbored approximately 4.05 Gbp of environmental DNA. Approximately 300000 recombinant Escherichia coli strains of each library per test substrate were screened for the production of carbonyls from short-chain (C2 to C4) polyols such as 1,2-ethanediol, 2,3-butanediol, and a mixture of glycerol and 1,2-propanediol on indicator agar. Twenty-four positive E. COLI clones were obtained during the initial screen. Fifteen of them contained recombinant plasmids, designated pAK201-215, which conferred a stable carbonyl-forming phenotype on E. coli Sequencing revealed that the inserts of pAK201-215 encoded 26 complete and 14 incomplete predicted protein-encoding genes. Most of these genes were similar to genes with unknown functions from other microorganisms or unrelated to any other known gene. The further analysis was focused on the 7 plasmids (pAK204, pAK206, pAK208, and pAK210-213) recovered from the positive clones, which exhibited an NAD(H)-dependent alcohol oxidoreductase activity with polyols or the correlating carbonyls as substrates in crude extracts. Three genes (ORF6, ORF24, and ORF25) conferring this activity were identified during subcloning of the inserts of pAK204, pAK211, and pAK212. The sequences of the three deduced gene products revealed no significant similarities to known alcohol oxidoreductases, but contained putative glycine-rich regions, which are characteristic for binding of nicotinamide cofactors. Copyright 2003 S. Karger AG, Basel

Analysing and Navigating Natural Products Space for Generating Small, Diverse, But Representative Chemical Libraries.

PubMed

O'Hagan, Steve; Kell, Douglas B

2018-01-01

Armed with the digital availability of two natural products libraries, amounting to some 195 885 molecular entities, we ask the question of how we can best sample from them to maximize their "representativeness" in smaller and more usable libraries of 96, 384, 1152, and 1920 molecules. The term "representativeness" is intended to include diversity, but for numerical reasons (and the likelihood of being able to perform a QSAR) it is necessary to focus on areas of chemical space that are more highly populated. Encoding chemical structures as fingerprints using the RDKit "patterned" algorithm, we first assess the granularity of the natural products space using a simple clustering algorithm, showing that there are major regions of "denseness" but also a great many very sparsely populated areas. We then apply a "hybrid" hierarchical K-means clustering algorithm to the data to produce more statistically robust clusters from which representative and appropriate numbers of samples may be chosen. There is necessarily again a trade-off between cluster size and cluster number, but within these constraints, libraries containing 384 or 1152 molecules can be found that come from clusters that represent some 18 and 30% of the whole chemical space, with cluster sizes of, respectively, 50 and 27 or above, just about sufficient to perform a QSAR. By using the online availability of molecules via the Molport system (www.molport.com), we are also able to construct (and, for the first time, provide the contents of) a small virtual library of available molecules that provided effective coverage of the chemical space described. Consistent with this, the average molecular similarities of the contents of the libraries developed is considerably smaller than is that of the original libraries. The suggested libraries may have use in molecular or phenotypic screening, including for determining possible transporter substrates. © 2017 The Authors. Biotechnology Journal Published by Wiley-VCH Verlag GmbH & Co. KGaA.

A Critical Review of the Literature on Attentional Bias in Cocaine Use Disorder and Suggestions for Future Research

PubMed Central

Leeman, Robert F.; Robinson, Cendrine D.; Waters, Andrew J.; Sofuoglu, Mehmet

2014-01-01

Cocaine use disorder (CUD) continues to be an important public health problem and novel approaches are needed to improve the effectiveness of treatments for CUD. Recently, there has been increased interest in the role of automatic cognition such as attentional bias (AB) in addictive behaviors and AB has been proposed to be a cognitive marker for addictions. Automatic cognition may be particularly relevant to CUD as there is evidence for particularly robust AB to cocaine cues and strong relationships to craving for cocaine and other illicit drugs. Further, the wide-ranging cognitive deficits (e.g., in response inhibition and working memory) evinced by many cocaine users enhance the potential importance of interventions targeting automatic cognition in this population. In the current paper, we discuss relevant addiction theories, followed by a review of studies that examined AB in CUD. We then consider the neural substrates of attentional bias including human neuroimaging, neurobiological and pharmacological studies. We conclude with a discussion of research gaps and future directions for attentional bias in CUD. PMID:25222545

Boron doped bcc-W films: Achieving excellent mechanical properties and tribological performance by regulating substrate bias voltage

NASA Astrophysics Data System (ADS)

Yang, Lina; Zhang, Kan; Zeng, Yi; Wang, Xin; Du, Suxuan; Tao, Chuanying; Ren, Ping; Cui, Xiaoqiang; Wen, Mao

2017-11-01

Boron doped bcc-W (WBx, x = B/W) films were deposited on Si(100) substrates by magnetron co-sputtering pure W and B targets. Our results reveal that when the absolute value of substrate bias voltage (Vb) increases from floating to 240 V, the value of x monotonously decreases from 0.18 to 0.04, accompanied by a phase transition from a mixture of tetragonal γ-W2B and body-centered cubic α-W(B) phase (-Vb ≤ 60 V) to α-W(B) single phase (-Vb > 60 V). Hardness, depending on Vb, increases first and then drops, where the maximum hardness of 30.8 GPa was obtained at -Vb = 60 V and far higher than pure W and W2B theoretical value. In the mixed phase structure, the grain boundaries strengthening, Hall-Petch effect and solid-solution strengthening induced by B dominate the strengthening mechanism. Astonishingly, the film grown at -Vb = 120 V still possesses twice higher hardness than pure W, wherein unexpectedly low (6.7 at.%) B concentration and only the single α-W(B) phase can be identified. In this case, both Hall-Petch effect and solid-solution strengthening work. Besides, low friction coefficient of ∼0.18 can be obtained for the films with α-W(B) phase, which is competitive to that of reported B-rich transition-metal borides, such as TiB2, CrB and CrB2.

Electrical properties of epitaxial 3C- and 6H-SiC p-n junction diodes produced side-by-side on 6H-SiC substrates

NASA Technical Reports Server (NTRS)

Neudeck, Philip G.; Larkin, David J.; Starr, Jonathan E.; Powell, J. Anthony; Salupo, Carl S.; Matus, Lawrence G.

1994-01-01

3C-SiC (beta-SiC) and 6H-SiC p-n junction diodes have been fabricated in regions of both 3C-SiC and 6H-SiC epitaxial layers which were grown side-by-side on low-tilt-angle 6H-SiC substrates via a chemical vapor deposition (CVD) process. Several runs of diodes exhibiting state-of-the-art electrical characteristics were produced, and performance characteristics were measured and compared as a function of doping, temperature, and polytype. The first 3C-SiC diodes which rectify to reverse voltages in excess of 300 V were characterized, representing a six-fold blocking voltage improvement over experimental 3C-SiC diodes produced by previous techniques. When placed under sufficient forward bias, the 3C-SiC diodes emit significantly bright green-yellow light while the 6H-SiC diodes emit in the blue-violet. The 6H-SiC p-n junction diodes represent the first reported high-quality 6H-SiC devices to be grown by CVD on very low-tilt-angle (less than 0.5 deg off the (0001) silicon face) 6H substrates. The reverse leakage current of a 200 micron diameter circular device at 1100 V reverse bias was less than 20 nA at room temperature, and excellent rectification characteristics were demonstrated at the peak characterization temperature of 400 C.

Somatic hypermutation at A/T-rich oligonucleotide substrates shows different strand polarities in Ung-deficient or -proficient backgrounds.

PubMed

Zivojnovic, Marija; Delbos, Frédéric; Girelli Zubani, Giulia; Julé, Amélie; Alcais, Alexandre; Weill, Jean-Claude; Reynaud, Claude-Agnès; Storck, Sébastien

2014-06-01

A/T mutations at immunoglobulin loci are introduced by DNA polymerase η (Polη) during an Msh2/6-dependent repair process which results in A's being mutated 2-fold more often than T's. This patch synthesis is initiated by a DNA incision event whose origin is still obscure. We report here the analysis of A/T oligonucleotide mutation substrates inserted at the heavy chain locus, including or not including internal C's or G's. Surprisingly, the template composed of only A's and T's was highly mutated over its entire 90-bp length, with a 2-fold decrease in mutation from the 5' to the 3' end and a constant A/T ratio of 4. These results imply that Polη synthesis was initiated from a break in the 5'-flanking region of the substrate and proceeded over its entire length. The A/T bias was strikingly altered in an Ung(-/-) background, which provides the first experimental evidence supporting a concerted action of Ung and Msh2/6 pathways to generate mutations at A/T bases. New analysis of Pms2(-/-) animals provided a complementary picture, revealing an A/T mutation ratio of 4. We therefore propose that Ung and Pms2 may exert a mutual backup function for the DNA incision that promotes synthesis by Polη, each with a distinct strand bias. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Somatic Hypermutation at A/T-Rich Oligonucleotide Substrates Shows Different Strand Polarities in Ung-Deficient or -Proficient Backgrounds

PubMed Central

Zivojnovic, Marija; Delbos, Frédéric; Girelli Zubani, Giulia; Julé, Amélie; Alcais, Alexandre; Storck, Sébastien

2014-01-01

A/T mutations at immunoglobulin loci are introduced by DNA polymerase η (Polη) during an Msh2/6-dependent repair process which results in A's being mutated 2-fold more often than T's. This patch synthesis is initiated by a DNA incision event whose origin is still obscure. We report here the analysis of A/T oligonucleotide mutation substrates inserted at the heavy chain locus, including or not including internal C's or G's. Surprisingly, the template composed of only A's and T's was highly mutated over its entire 90-bp length, with a 2-fold decrease in mutation from the 5′ to the 3′ end and a constant A/T ratio of 4. These results imply that Polη synthesis was initiated from a break in the 5′-flanking region of the substrate and proceeded over its entire length. The A/T bias was strikingly altered in an Ung−/− background, which provides the first experimental evidence supporting a concerted action of Ung and Msh2/6 pathways to generate mutations at A/T bases. New analysis of Pms2−/− animals provided a complementary picture, revealing an A/T mutation ratio of 4. We therefore propose that Ung and Pms2 may exert a mutual backup function for the DNA incision that promotes synthesis by Polη, each with a distinct strand bias. PMID:24710273

The effect of PS porosity on the structure, optical and electrical properties of ZnS/PS

NASA Astrophysics Data System (ADS)

Wang, Cai-Feng; Hu, Bo; Yi, Hou-Hui; Li, Wei-Bing

2014-03-01

ZnS films were deposited on porous silicon (PS) substrates with different porosities by pulsed laser deposition (PLD). The crystalline structure, surface morphology of ZnS films on PS substrates and optical, electrical properties of ZnS/PS composites were studied. The results show that, ZnS films deposited on PS substrates were grown in preferred orientation along β-ZnS (111) direction corresponding to crystalline structure of cubic phase. With the increase of PS porosity, the XRD diffraction peak intensity of ZnS films decreases. Some voids and cracks appear in the films. Compared with as-prepared PS, the PL peak of PS for ZnS/PS has a blueshift. The larger the porosity of PS, the greater the blueshift is. A new green light emission located around 550 nm is observed with increasing PS porosity, which is ascribed to defect-center luminescence of ZnS. The blue, green emission of ZnS combined with the red emission of PS, a broad photoluminescence band (450-750 nm) is formed. ZnS/PS composites exhibited intense white light emission. The I-V characteristics of ZnS/PS heterojunctions showed rectifying behavior. Under forward bias conditions, the current density is large. Under reverse bias conditions, the current density nearly to be zero. The forward current increases with increasing PS porosity. This work lay a foundation for the realization of electroluminescence of ZnS/PS and solid white light emission devices.

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

Kasper, M.; Gramse, G.; Hoffmann, J.

We measured the DC and RF impedance characteristics of micrometric metal-oxide-semiconductor (MOS) capacitors and Schottky diodes using scanning microwave microscopy (SMM). The SMM consisting of an atomic force microscopy (AFM) interfaced with a vector network analyser (VNA) was used to measure the reflection S11 coefficient of the metallic MOS and Schottky contact pads at 18 GHz as a function of the tip bias voltage. By controlling the SMM biasing conditions, the AFM tip was used to bias the Schottky contacts between reverse and forward mode. In reverse bias direction, the Schottky contacts showed mostly a change in the imaginary part ofmore » the admittance while in forward bias direction the change was mostly in the real part of the admittance. Reference MOS capacitors which are next to the Schottky diodes on the same sample were used to calibrate the SMM S11 data and convert it into capacitance values. Calibrated capacitance between 1–10 fF and 1/C{sup 2} spectroscopy curves were acquired on the different Schottky diodes as a function of the DC bias voltage following a linear behavior. Additionally, measurements were done directly with the AFM-tip in contact with the silicon substrate forming a nanoscale Schottky contact. Similar capacitance-voltage curves were obtained but with smaller values (30–300 aF) due to the corresponding smaller AFM-tip diameter. Calibrated capacitance images of both the MOS and Schottky contacts were acquired with nanoscale resolution at different tip-bias voltages.« less

Access channels to the buried active site control substrate specificity in CYP1A P450 enzymes.

PubMed

Urban, Philippe; Truan, Gilles; Pompon, Denis

2015-04-01

A cytochrome P450 active site is buried within the protein molecule and several channels connect the catalytic cavity to the protein surface. Their role in P450 catalysis is still matter of debate. The aim of this study was to understand the possible relations existing between channels and substrate specificity. Time course studies were carried out with a collection of polycyclic substrates of increasing sizes assayed with a library of wild-type and chimeric CYP1A enzymes. This resulted in a matrix of activities sufficiently large to allow statistical analysis. Multivariate statistical tools were used to decipher the correlation between observed activity shifts and sequence segment swaps. The global kinetic behavior of CYP1A enzymes toward polycyclic substrates is significantly different depending on the size of the substrate. Mutations which are close or lining the P450 channels significantly affect this discrimination, whereas mutations distant from the P450 channels do not. Size discrimination is taking place for polycyclic substrates at the entrance of the different P450 access channels. It is thus hypothesized that channels differentiate small from large substrates in CYP1A enzymes, implying that residues located at the surface of the protein may be implied in this differential recognition. Catalysis thus occurs after a two-step recognition process, one at the surface of the protein and the second within the catalytic cavity in enzymes with a buried active site. Copyright © 2014 Elsevier B.V. All rights reserved.

High-throughput characterization of film thickness in thin film materials libraries by digital holographic microscopy.

PubMed

Lai, Yiu Wai; Krause, Michael; Savan, Alan; Thienhaus, Sigurd; Koukourakis, Nektarios; Hofmann, Martin R; Ludwig, Alfred

2011-10-01

A high-throughput characterization technique based on digital holography for mapping film thickness in thin-film materials libraries was developed. Digital holographic microscopy is used for fully automatic measurements of the thickness of patterned films with nanometer resolution. The method has several significant advantages over conventional stylus profilometry: it is contactless and fast, substrate bending is compensated, and the experimental setup is simple. Patterned films prepared by different combinatorial thin-film approaches were characterized to investigate and demonstrate this method. The results show that this technique is valuable for the quick, reliable and high-throughput determination of the film thickness distribution in combinatorial materials research. Importantly, it can also be applied to thin films that have been structured by shadow masking.

Selection of cholera toxin specific IgNAR single-domain antibodies from a naïve shark library.

PubMed

Liu, Jinny L; Anderson, George P; Delehanty, James B; Baumann, Richard; Hayhurst, Andrew; Goldman, Ellen R

2007-03-01

Shark immunoglobulin new antigen receptor (IgNAR, also referred to as NAR) variable domains (Vs) are single-domain antibody (sdAb) fragments containing only two hypervariable loop structures forming 3D topologies for a wide range of antigen recognition and binding. Their small size ( approximately 12kDa) and high solubility, thermostability and binding specificity make IgNARs an exceptional alternative source of engineered antibodies for sensor applications. Here, two new shark NAR V display libraries containing >10(7) unique clones from non-immunized (naïve) adult spiny dogfish (Squalus acanthias) and smooth dogfish (Mustelus canis) sharks were constructed. The most conserved consensus sequences derived from random clone sequence were compared with published nurse shark (Ginglymostoma cirratum) sequences. Cholera toxin (CT) was chosen for panning one of the naïve display libraries due to its severe pathogenicity and commercial availability. Three very similar CT binders were selected and purified soluble monomeric anti-CT sdAbs were characterized using Luminex(100) and traditional ELISA assays. These novel anti-CT sdAbs selected from our newly constructed shark NAR V sdAb library specifically bound to soluble antigen, without cross reacting with other irrelevant antigens. They also showed superior heat stability, exhibiting slow loss of activity over the course of one hour at high temperature (95 degrees C), while conventional antibodies lost all activity in the first 5-10min. The successful isolation of target specific sdAbs from one of our non-biased NAR libraries, demonstrate their ability to provide binders against an unacquainted antigen of interest.

A comparative study of ChIP-seq sequencing library preparation methods.

PubMed

Sundaram, Arvind Y M; Hughes, Timothy; Biondi, Shea; Bolduc, Nathalie; Bowman, Sarah K; Camilli, Andrew; Chew, Yap C; Couture, Catherine; Farmer, Andrew; Jerome, John P; Lazinski, David W; McUsic, Andrew; Peng, Xu; Shazand, Kamran; Xu, Feng; Lyle, Robert; Gilfillan, Gregor D

2016-10-21

ChIP-seq is the primary technique used to investigate genome-wide protein-DNA interactions. As part of this procedure, immunoprecipitated DNA must undergo "library preparation" to enable subsequent high-throughput sequencing. To facilitate the analysis of biopsy samples and rare cell populations, there has been a recent proliferation of methods allowing sequencing library preparation from low-input DNA amounts. However, little information exists on the relative merits, performance, comparability and biases inherent to these procedures. Notably, recently developed single-cell ChIP procedures employing microfluidics must also employ library preparation reagents to allow downstream sequencing. In this study, seven methods designed for low-input DNA/ChIP-seq sample preparation (Accel-NGS® 2S, Bowman-method, HTML-PCR, SeqPlex™, DNA SMART™, TELP and ThruPLEX®) were performed on five replicates of 1 ng and 0.1 ng input H3K4me3 ChIP material, and compared to a "gold standard" reference PCR-free dataset. The performance of each method was examined for the prevalence of unmappable reads, amplification-derived duplicate reads, reproducibility, and for the sensitivity and specificity of peak calling. We identified consistent high performance in a subset of the tested reagents, which should aid researchers in choosing the most appropriate reagents for their studies. Furthermore, we expect this work to drive future advances by identifying and encouraging use of the most promising methods and reagents. The results may also aid judgements on how comparable are existing datasets that have been prepared with different sample library preparation reagents.

Viral morphogenesis is the dominant source of sequence censorship in M13 combinatorial peptide phage display.

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

Rodi, D. J.; Soares, A. S.; Makowski, L.

Novel statistical methods have been developed and used to quantitate and annotate the sequence diversity within combinatorial peptide libraries on the basis of small numbers (1-200) of sequences selected at random from commercially available M13 p3-based phage display libraries. These libraries behave statistically as though they correspond to populations containing roughly 4.0{+-}1.6% of the random dodecapeptides and 7.9{+-}2.6% of the random constrained heptapeptides that are theoretically possible within the phage populations. Analysis of amino acid residue occurrence patterns shows no demonstrable influence on sequence censorship by Escherichia coli tRNA isoacceptor profiles or either overall codon or Class II codon usagemore » patterns, suggesting no metabolic constraints on recombinant p3 synthesis. There is an overall depression in the occurrence of cysteine, arginine and glycine residues and an overabundance of proline, threonine and histidine residues. The majority of position-dependent amino acid sequence bias is clustered at three positions within the inserted peptides of the dodecapeptide library, +1, +3 and +12 downstream from the signal peptidase cleavage site. Conformational tendency measures of the peptides indicate a significant preference for inserts favoring a {beta}-turn conformation. The observed protein sequence limitations can primarily be attributed to genetic codon degeneracy and signal peptidase cleavage preferences. These data suggest that for applications in which maximal sequence diversity is essential, such as epitope mapping or novel receptor identification, combinatorial peptide libraries should be constructed using codon-corrected trinucleotide cassettes within vector-host systems designed to minimize morphogenesis-related censorship.« less

Non-ionic detergents facilitate non-specific binding of M13 bacteriophage to polystyrene surfaces.

PubMed

Hakami, Abdulrahim R; Ball, Jonathan K; Tarr, Alexander W

2015-09-01

Phage-displayed random peptide libraries are widely used for identifying peptide interactions with proteins and other substrates. Selection of peptide ligands involves iterative rounds of affinity enrichment. The binding properties of the selected phage clones are routinely tested using immunoassay after propagation to high titre in a bacterial host and precipitation using polyethylene glycol (PEG) and high salt concentration. These immunoassays can suffer from low sensitivity and high background signals. Polysorbate 20 (Tween(®) 20) is a non-ionic detergent commonly used in immunoassay washing buffers to reduce non-specific binding, and is also used as a blocking reagent. We have observed that Tween 20 enhances non-specific M13 library phage binding in a peptide-independent manner. Other non-ionic detergents were also found to promote significant, dose-dependent non-specific phage binding in ELISA. This effect was not observed for assays using phage concentrated by ultracentrifugation, suggesting that interactions occur between detergents and the PEG-precipitated phage, irrespective of the displayed peptide motif. This artefact may impact on successful affinity selection of peptides from phage-display libraries. We propose alternative methods for screening phage libraries for identifying binding interactions with target ligands. Copyright © 2015 Elsevier B.V. All rights reserved.

An History of the Developments of Fraternization Policies.

DTIC Science & Technology

1998-09-01

several months, as she expediently located over 40 inter-library loan books and articles, some published over 200 years ago. Both ladies put in large...Vaughan, who allowed me to borrow some of their books for lengthy periods of time. I would like to provide extra thanks to my wife, Felicia. Felicia put in...generally use a case study methodology. By nature, the data studied is secondhand , subject to biases by the author of the work and the interpreter of the work

Determining the Location of DNA Modification and Mutation Caused by UVB Light in Skin Cancer

DTIC Science & Technology

2015-09-01

Award Number: W81XWH-12-1-0333 TITLE: Determining the Location of DNA Modification and Mutation Caused by UVB Light in Skin Cancer PRINCIPAL...COVERED 15 Aug 2012 – 14 Aug 2015 4. TITLE AND SUBTITLE 5a. CONTRACT NUMBER W81XWH-12-1-0333 Determining the Location of DNA Modification and Mutation ...sequencing libraries generated for both yeast and human cells show pyrimidine bias on the 5’ end, indicating that we are sequencing the dimers

Effect of atomic layer deposition temperature on current conduction in Al2O3 films formed using H2O oxidant

NASA Astrophysics Data System (ADS)

Hiraiwa, Atsushi; Matsumura, Daisuke; Kawarada, Hiroshi

2016-08-01

To develop high-performance, high-reliability gate insulation and surface passivation technologies for wide-bandgap semiconductor devices, the effect of atomic layer deposition (ALD) temperature on current conduction in Al2O3 films is investigated based on the recently proposed space-charge-controlled field emission model. Leakage current measurement shows that Al2O3 metal-insulator-semiconductor capacitors formed on the Si substrates underperform thermally grown SiO2 capacitors at the same average field. However, using equivalent oxide field as a more practical measure, the Al2O3 capacitors are found to outperform the SiO2 capacitors in the cases where the capacitors are negatively biased and the gate material is adequately selected to reduce virtual dipoles at the gate/Al2O3 interface. The Al2O3 electron affinity increases with the increasing ALD temperature, but the gate-side virtual dipoles are not affected. Therefore, the leakage current of negatively biased Al2O3 capacitors is approximately independent of the ALD temperature because of the compensation of the opposite effects of increased electron affinity and permittivity in Al2O3. By contrast, the substrate-side sheet of charge increases with increasing ALD temperature above 210 °C and hence enhances the current of positively biased Al2O3 capacitors more significantly at high temperatures. Additionally, an anomalous oscillatory shift of the current-voltage characteristics with ALD temperature was observed in positively biased capacitors formed by low-temperature (≤210 °C) ALD. This shift is caused by dipoles at the Al2O3/underlying SiO2 interface. Although they have a minimal positive-bias leakage current, the low-temperature-grown Al2O3 films cause the so-called blisters problem when heated above 400 °C. Therefore, because of the absence of blistering, a 450 °C ALD process is presently the most promising technology for growing high-reliability Al2O3 films.

Avalanche multiplication in AlGaN-based heterostructures for the ultraviolet spectral range

NASA Astrophysics Data System (ADS)

Hahn, L.; Fuchs, F.; Kirste, L.; Driad, R.; Rutz, F.; Passow, T.; Köhler, K.; Rehm, R.; Ambacher, O.

2018-04-01

AlxGa1-xN based avalanche photodiodes grown on sapphire substrate with Al-contents of x = 0.65 and x = 0.60 have been examined under back- and frontside illumination with respect to their avalanche gain properties. The photodetectors suitable for the solar-blind ultraviolet spectral regime show avalanche gain for voltages in excess of 30 V reverse bias in the linear gain mode. Devices with a mesa diameter of 100 μm exhibit stable avalanche gain below the break through threshold voltage, exceeding a multiplication gain of 5500 at 84 V reverse bias. A dark current below 1 pA can be found for reverse voltages up to 60 V.

Tunable blue organic light emitting diode based on aluminum calixarene supramolecular complex

NASA Astrophysics Data System (ADS)

Legnani, C.; Reyes, R.; Cremona, M.; Bagatin, I. A.; Toma, H. E.

2004-07-01

In this letter, the results of supramolecular organic light emitting diodes using a calix[4] arene complex thin film as emitter and electron transporting layer are presented. The devices were grown onto glass substrates coated with indium-tin-oxide layer and aluminum thick (150nm) cathode. By applying a dc voltage between the device electrodes in forward bias condition, a blue light emission in the active area of the device was observed. It was found that the electroluminescent emission peak can be tuned between 470 and 510nm changing the applied voltage bias from 4.3 to 5.4V. The observed tunable emission can be associated with an energy transfer from the calixarene compound.

Rectifying Characteristics and Transport Behavior in a Schottky Junction of CaCu3Ti4O12 and Pt

NASA Astrophysics Data System (ADS)

Chen, Cong; Ning, Ting-Yin; Wang, Can; Zhou, Yue-Liang; Zhang, Dong-Xiang; Wang, Pei; Ming, Hai; Yang, Guo-Zhen

2011-08-01

CaCu3Ti4O12 (CCTO) thin films were fabricated on ITO-covered MgO (100) substrates. The rectification characteristics were observed in the CCTO capacitance structure with Pt top electrodes at temperatures ranging from 150 K to 330 K, which are attributed to the formation of a Schottky junction between n-type semiconducting CCTO and Pt due to the difference of their work functions. At low forward-bias voltage, the current-voltage characteristics of the Schottky junction follow . A strong decrease in ideality factor with the increasing temperature is obtained by linear fitting at the low bias voltage.

Apparatus for coating a surface with a metal utilizing a plasma source

DOEpatents

Brown, I.G.; MacGill, R.A.; Galvin, J.E.

1991-05-07

An apparatus and method are disclosed for coating or layering a surface with a metal utilizing a metal vapor vacuum arc plasma source. The apparatus includes a trigger mechanism for actuating the metal vacuum vapor arc plasma source in a pulsed mode at a predetermined rate. The surface or substrate to be coated or layered is supported in position with the plasma source in a vacuum chamber. The surface is electrically biased for a selected period of time during the pulsed mode of operation of the plasma source. Both the pulsing of the metal vapor vacuum arc plasma source and the electrical biasing of the surface are synchronized for selected periods of time. 10 figures.

Apparatus for coating a surface with a metal utilizing a plasma source

DOEpatents

Brown, Ian G.; MacGill, Robert A.; Galvin, James E.

1991-01-01

An apparatus and method for coating or layering a surface with a metal utilizing a metal vapor vacuum arc plasma source. The apparatus includes a trigger mechanism for actuating the metal vacuum vapor arc plasma source in a pulsed mode at a predetermined rate. The surface or substrate to be coated or layered is supported in position with the plasma source in a vacuum chamber. The surface is electrically biased for a selected period of time during the pulsed mode of operation of the plasma source. Both the pulsing of the metal vapor vacuum arc plasma source and the electrical biasing of the surface are synchronized for selected periods of time.

Key Mutations Alter the Cytochrome P450 BM3 Conformational Landscape and Remove Inherent Substrate Bias*

PubMed Central

Butler, Christopher F.; Peet, Caroline; Mason, Amy E.; Voice, Michael W.; Leys, David; Munro, Andrew W.

2013-01-01

Cytochrome P450 monooxygenases (P450s) have enormous potential in the production of oxychemicals, due to their unparalleled regio- and stereoselectivity. The Bacillus megaterium P450 BM3 enzyme is a key model system, with several mutants (many distant from the active site) reported to alter substrate selectivity. It has the highest reported monooxygenase activity of the P450 enzymes, and this catalytic efficiency has inspired protein engineering to enable its exploitation for biotechnologically relevant oxidations with structurally diverse substrates. However, a structural rationale is lacking to explain how these mutations have such effects in the absence of direct change to the active site architecture. Here, we provide the first crystal structures of BM3 mutants in complex with a human drug substrate, the proton pump inhibitor omeprazole. Supported by solution data, these structures reveal how mutation alters the conformational landscape and decreases the free energy barrier for transition to the substrate-bound state. Our data point to the importance of such “gatekeeper” mutations in enabling major changes in substrate recognition. We further demonstrate that these mutants catalyze the same 5-hydroxylation reaction as performed by human CYP2C19, the major human omeprazole-metabolizing P450 enzyme. PMID:23828198

Performance of Between-Study Heterogeneity Measures in the Cochrane Library.

PubMed

Ma, Xiaoyue; Lin, Lifeng; Qu, Zhiyong; Zhu, Motao; Chu, Haitao

2018-05-29

The growth in comparative effectiveness research and evidence-based medicine has increased attention to systematic reviews and meta-analyses. Meta-analysis synthesizes and contrasts evidence from multiple independent studies to improve statistical efficiency and reduce bias. Assessing heterogeneity is critical for performing a meta-analysis and interpreting results. As a widely used heterogeneity measure, the I statistic quantifies the proportion of total variation across studies that is due to real differences in effect size. The presence of outlying studies can seriously exaggerate the I statistic. Two alternative heterogeneity measures, the Ir and Im, have been recently proposed to reduce the impact of outlying studies. To evaluate these measures' performance empirically, we applied them to 20,599 meta-analyses in the Cochrane Library. We found that the Ir and Im have strong agreement with the I, while they are more robust than the I when outlying studies appear.

How to differentiate collective variables in free energy codes: Computer-algebra code generation and automatic differentiation

NASA Astrophysics Data System (ADS)

Giorgino, Toni

2018-07-01

The proper choice of collective variables (CVs) is central to biased-sampling free energy reconstruction methods in molecular dynamics simulations. The PLUMED 2 library, for instance, provides several sophisticated CV choices, implemented in a C++ framework; however, developing new CVs is still time consuming due to the need to provide code for the analytical derivatives of all functions with respect to atomic coordinates. We present two solutions to this problem, namely (a) symbolic differentiation and code generation, and (b) automatic code differentiation, in both cases leveraging open-source libraries (SymPy and Stan Math, respectively). The two approaches are demonstrated and discussed in detail implementing a realistic example CV, the local radius of curvature of a polymer. Users may use the code as a template to streamline the implementation of their own CVs using high-level constructs and automatic gradient computation.

Generation and analysis of the improved human HAL9/10 antibody phage display libraries.

PubMed

Kügler, Jonas; Wilke, Sonja; Meier, Doris; Tomszak, Florian; Frenzel, André; Schirrmann, Thomas; Dübel, Stefan; Garritsen, Henk; Hock, Björn; Toleikis, Lars; Schütte, Mark; Hust, Michael

2015-02-19

Antibody phage display is a proven key technology that allows the generation of human antibodies for diagnostics and therapy. From naive antibody gene libraries - in theory - antibodies against any target can be selected. Here we describe the design, construction and characterization of an optimized antibody phage display library. The naive antibody gene libraries HAL9 and HAL10, with a combined theoretical diversity of 1.5×10(10) independent clones, were constructed from 98 healthy donors using improved phage display vectors. In detail, most common phagemids employed for antibody phage display are using a combined His/Myc tag for detection and purification. We show that changing the tag order to Myc/His improved the production of soluble antibodies, but did not affect antibody phage display. For several published antibody libraries, the selected number of kappa scFvs were lower compared to lambda scFvs, probably due to a lower kappa scFv or Fab expression rate. Deletion of a phenylalanine at the end of the CL linker sequence in our new phagemid design increased scFv production rate and frequency of selected kappa antibodies significantly. The HAL libraries and 834 antibodies selected against 121 targets were analyzed regarding the used germline V-genes, used V-gene combinations and CDR-H3/-L3 length and composition. The amino acid diversity and distribution in the CDR-H3 of the initial library was retrieved in the CDR-H3 of selected antibodies showing that all CDR-H3 amino acids occurring in the human antibody repertoire can be functionally used and is not biased by E. coli expression or phage selection. Further, the data underline the importance of CDR length variations. The highly diverse universal antibody gene libraries HAL9/10 were constructed using an optimized scFv phagemid vector design. Analysis of selected antibodies revealed that the complete amino acid diversity in the CDR-H3 was also found in selected scFvs showing the functionality of the naive CDR-H3 diversity.

Nanoplasmonic-gold-cylinder-array-enhanced terahertz source

NASA Astrophysics Data System (ADS)

Zhiguang, Ao; Jinhai, Sun; He, Cai; Guofeng, Song; Jiakun, Song; Yuzhi, Song; Yun, Xu

2016-12-01

Photoconductive antennas (PCAs) based on nanoplasmonic gratings contact electrodes have been proposed to satisfy the demand for high power, efficiency and responsivity terahertz (THz) sources. Reducing the average photo-generated carrier transport path to the photoconductor contact electrodes was previously considered the dominant mechanism to improve PCAs' power. However, considering the bias in a real device, the electric field between gratings is limited and the role of surface plasmonic resonance (SPR) field enhancement is more important in improving THz radiation. This paper, based on SPR, analyzes the interaction between incident light and substrate in nano cylinder array PCAs and clearly shows that the SPR can enhance the light absorption in the substrate. After the optimization of the structure size, the proposed structure can offer 87% optical transmission into GaAs substrate. Compared with conventional PCAs, the optical transmission into the substrate will increase 5.8 times and the enhancement factor of substrate absorption will reach 13.7 respectively. Project supported by the National Basic Research Program of China (Nos. 2015CB351902, 2015CB932402), the National Key Research Program of China (No. 2011ZX01015-001), and the National Natural Science Foundation of China (No. U143231).

Sensitive electrospray mass spectrometry analysis of one-bead-one-compound peptide libraries labeled by quaternary ammonium salts.

PubMed

Bąchor, Remigiusz; Cydzik, Marzena; Rudowska, Magdalena; Kluczyk, Alicja; Stefanowicz, Piotr; Szewczuk, Zbigniew

2012-08-01

A rapid and straightforward method for high-throughput analysis of single resin beads from one-bead-one-compound combinatorial libraries with high resolution electrospray ionization tandem mass spectrometry (HR ESI-MS/MS) is presented. The application of an efficient method of peptide derivatization by quaternary ammonium salts (QAS) formation increases ionization efficiency and reduces the detection limit, allowing analysis of trace amounts of compounds by ESI-MS. Peptides, synthesized on solid support, contain a new cleavable linker composed of a Peg spacer (9-aza-3,6,12,15-tetraoxa-10-on-heptadecanoic acid), lysine with ɛ-amino group marked by the N,N,N-triethylglycine salt, and methionine, which makes possible the selective cleavage by cyanogen bromide. Even a small portion of peptides derivatized by QAS cleaved from a single resin bead is sufficient for sequencing by HR ESI-MS/MS experiments. The developed strategy was applied to a small training library of α chymotrypsin substrates. The obtained results confirm the applicability of the proposed method in combinatorial chemistry.

Alumina nanoparticle/polymer nanocomposite dielectric for flexible amorphous indium-gallium-zinc oxide thin film transistors on plastic substrate with superior stability

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

Lai, Hsin-Cheng; Pei, Zingway, E-mail: zingway@dragon.nchu.edu.tw; Graduate Institute of Optoelectronic Engineering, National Chung Hsing University, Taichung 40227, Taiwan

In this study, the Al{sub 2}O{sub 3} nanoparticles were incorporated into polymer as a nono-composite dielectric for used in a flexible amorphous Indium-Gallium-Zinc Oxide (a-IGZO) thin-film transistor (TFT) on a polyethylene naphthalate substrate by solution process. The process temperature was well below 100 °C. The a-IGZO TFT exhibit a mobility of 5.13 cm{sup 2}/V s on the flexible substrate. After bending at a radius of 4 mm (strain = 1.56%) for more than 100 times, the performance of this a-IGZO TFT was nearly unchanged. In addition, the electrical characteristics are less altered after positive gate bias stress at 10 V for 1500 s. Thus, this technology ismore » suitable for use in flexible displays.« less

Investigation of high-speed Si photodetectors in standard CMOS technology

NASA Astrophysics Data System (ADS)

Wang, Huaqiang; Guo, Xia

2018-05-01

In this paper, the frequency response characteristics of the photodetector(PD) were studied considering intrinsic and extrinsic effects. Then we designed the interdigitated p-i-n PD on Silicon-on-Insulator (SOI) and epitaxial (EPI) substrates with photosensitive area of 30-μm diameter, fabricated by CMOS process. The 2-μm finger-spacing devices exhibited a 205 MHz bandwidth at a reverse bias of 3 V processed on 2-μm SOI substrates. EPI devices with 1 μm finger spacing exhibited a 131 MHz bandwidth under -3 V. Responsivity of 0.051 A/W and 0.21 A/W were measured at 850 nm on SOI and EPI substrates, respectively. Compared with the bulk silicon PD, the bandwidth is greatly improved. The PD gains the high cost performance ratio, which can be widely used in short distance communication such as visible light communication and free space optical communication.

Multi-functional properties of CaCu3Ti4O12 thin films

NASA Astrophysics Data System (ADS)

Felix, A. A.; Rupp, J. L. M.; Varela, J. A.; Orlandi, M. O.

2012-09-01

In this work, electric transport properties of CaCu3Ti4O12 (CCTO) thin films were investigated for resistive switching, rectifying and gas sensor applications. Single phase CCTO thin films were produced by polymeric precursor method (PPM) on different substrates and their electrical properties were studied. Films produced on LNO/Si substrates have symmetrical non-ohmic current-voltage characteristics, while films deposited on Pt/Si substrates have a highly asymmetrical non-ohmic behavior which is related to a metal-semiconductor junction formed at the CCTO/Pt interface. In addition, results confirm that CCTO has a resistive switching response which is enhanced by Schottky contacts. Sensor response tests revealed that CCTO films are sensitive to oxygen gas and exhibit n-type conductivity. These results demonstrate the versatility of CCTO thin film prepared by the PPM method for gas atmosphere or bias dependent resistance applications.

Modeling genome coverage in single-cell sequencing

PubMed Central

Daley, Timothy; Smith, Andrew D.

2014-01-01

Motivation: Single-cell DNA sequencing is necessary for examining genetic variation at the cellular level, which remains hidden in bulk sequencing experiments. But because they begin with such small amounts of starting material, the amount of information that is obtained from single-cell sequencing experiment is highly sensitive to the choice of protocol employed and variability in library preparation. In particular, the fraction of the genome represented in single-cell sequencing libraries exhibits extreme variability due to quantitative biases in amplification and loss of genetic material. Results: We propose a method to predict the genome coverage of a deep sequencing experiment using information from an initial shallow sequencing experiment mapped to a reference genome. The observed coverage statistics are used in a non-parametric empirical Bayes Poisson model to estimate the gain in coverage from deeper sequencing. This approach allows researchers to know statistical features of deep sequencing experiments without actually sequencing deeply, providing a basis for optimizing and comparing single-cell sequencing protocols or screening libraries. Availability and implementation: The method is available as part of the preseq software package. Source code is available at http://smithlabresearch.org/preseq. Contact: andrewds@usc.edu Supplementary information: Supplementary material is available at Bioinformatics online. PMID:25107873

Digital gene expression analysis with sample multiplexing and PCR duplicate detection: A straightforward protocol.

PubMed

Rozenberg, Andrey; Leese, Florian; Weiss, Linda C; Tollrian, Ralph

2016-01-01

Tag-Seq is a high-throughput approach used for discovering SNPs and characterizing gene expression. In comparison to RNA-Seq, Tag-Seq eases data processing and allows detection of rare mRNA species using only one tag per transcript molecule. However, reduced library complexity raises the issue of PCR duplicates, which distort gene expression levels. Here we present a novel Tag-Seq protocol that uses the least biased methods for RNA library preparation combined with a novel approach for joint PCR template and sample labeling. In our protocol, input RNA is fragmented by hydrolysis, and poly(A)-bearing RNAs are selected and directly ligated to mixed DNA-RNA P5 adapters. The P5 adapters contain i5 barcodes composed of sample-specific (moderately) degenerate base regions (mDBRs), which later allow detection of PCR duplicates. The P7 adapter is attached via reverse transcription with individual i7 barcodes added during the amplification step. The resulting libraries can be sequenced on an Illumina sequencer. After sample demultiplexing and PCR duplicate removal with a free software tool we designed, the data are ready for downstream analysis. Our protocol was tested on RNA samples from predator-induced and control Daphnia microcrustaceans.

Bias-selectable dual-band mid-/long-wavelength infrared photodetectors based on InAs/InAs{sub 1−x}Sb{sub x} type-II superlattices

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

Haddadi, A.; Chevallier, R.; Chen, G.

2015-01-05

A high performance bias-selectable mid-/long-wavelength infrared photodetector based on InAs/InAs{sub 1−x}Sb{sub x} type-II superlattices on GaSb substrate has been demonstrated. The mid- and long-wavelength channels' 50% cut-off wavelengths were ∼5.1 and ∼9.5 μm at 77 K. The mid-wavelength channel exhibited a quantum efficiency of 45% at 100 mV bias voltage under front-side illumination and without any anti-reflection coating. With a dark current density of 1 × 10{sup −7} A/cm{sup 2} under 100 mV applied bias, the mid-wavelength channel exhibited a specific detectivity of 8.2 × 10{sup 12 }cm·√(Hz)/W at 77 K. The long-wavelength channel exhibited a quantum efficiency of 40%, a dark current density of 5.7 × 10{sup −4} A/cm{sup 2} undermore » −150 mV applied bias at 77 K, providing a specific detectivity value of 1.64 × 10{sup 11 }cm·√(Hz)/W.« less

An accurate filter loading correction is essential for assessing personal exposure to black carbon using an Aethalometer.

PubMed

Good, Nicholas; Mölter, Anna; Peel, Jennifer L; Volckens, John

2017-07-01

The AE51 micro-Aethalometer (microAeth) is a popular and useful tool for assessing personal exposure to particulate black carbon (BC). However, few users of the AE51 are aware that its measurements are biased low (by up to 70%) due to the accumulation of BC on the filter substrate over time; previous studies of personal black carbon exposure are likely to have suffered from this bias. Although methods to correct for bias in micro-Aethalometer measurements of particulate black carbon have been proposed, these methods have not been verified in the context of personal exposure assessment. Here, five Aethalometer loading correction equations based on published methods were evaluated. Laboratory-generated aerosols of varying black carbon content (ammonium sulfate, Aquadag and NIST diesel particulate matter) were used to assess the performance of these methods. Filters from a personal exposure assessment study were also analyzed to determine how the correction methods performed for real-world samples. Standard correction equations produced correction factors with root mean square errors of 0.10 to 0.13 and mean bias within ±0.10. An optimized correction equation is also presented, along with sampling recommendations for minimizing bias when assessing personal exposure to BC using the AE51 micro-Aethalometer.

A sensitive assay using a native protein substrate for screening HIV-1 maturation inhibitors targeting the protease cleavage site between the matrix and capsid.

PubMed

Lee, Sook-Kyung; Cheng, Nancy; Hull-Ryde, Emily; Potempa, Marc; Schiffer, Celia A; Janzen, William; Swanstrom, Ronald

2013-07-23

The matrix/capsid processing site in the HIV-1 Gag precursor is likely the most sensitive target to inhibit HIV-1 replication. We have previously shown that modest incomplete processing at the site leads to a complete loss of virion infectivity. In the study presented here, a sensitive assay based on fluorescence polarization that can monitor cleavage at the MA/CA site in the context of the folded protein substrate is described. The substrate, an MA/CA fusion protein, was labeled with the fluorescein-based FlAsH (fluorescein arsenical hairpin) reagent that binds to a tetracysteine motif (CCGPCC) that was introduced within the N-terminal domain of CA. By limiting the size of CA and increasing the size of MA (with an N-terminal GST fusion), we were able to measure significant differences in polarization values as a function of HIV-1 protease cleavage. The sensitivity of the assay was tested in the presence of increasing amounts of an HIV-1 protease inhibitor, which resulted in a gradual decrease in the fluorescence polarization values demonstrating that the assay is sensitive in discerning changes in protease processing. The high-throughput screening assay validation in 384-well plates showed that the assay is reproducible and robust with an average Z' value of 0.79 and average coefficient of variation values of <3%. The robustness and reproducibility of the assay were further validated using the LOPAC(1280) compound library, demonstrating that the assay provides a sensitive high-throughput screening platform that can be used with large compound libraries for identifying novel maturation inhibitors targeting the MA/CA site of the HIV-1 Gag polyprotein.

Design, Fabrication and Testing of Tunable RF Meta-atoms

DTIC Science & Technology

2012-06-14

Simple cantilever beam with actuation pad covered with a thin dielectric layer for short circuit protection...Cantilever actuation simulated with CoventorWare ® to determine the biasing voltage necessary to draw the cantilevers to the actuation pads ...Capacitive tunable meta-atom fabricated on quartz substrate. The meta-atom had to be cut at the metal trace leading to the cantilever actuation pads

Silicon oxide permeation barrier coating of PET bottles and foils

NASA Astrophysics Data System (ADS)

Steves, Simon; Deilmann, Michael; Awakowicz, Peter

2009-10-01

Modern packaging materials such as polyethylene terephthalate (PET) have displaced established materials in many areas of food and beverage packaging. Plastic packing materials offer are various advantages concerning production and handling. PET bottles for instance are non-breakable and lightweight compared to glass and metal containers. However, PET offers poor barrier properties against gas permeation. Therefore, the shelf live of packaged food is reduced. Permeation of gases can be reduced by depositing transparent plasma polymerized silicon oxide (SiOx) barrier coatings. A microwave (2.45 GHz) driven low pressure plasma reactor is developed based on a modified Plasmaline antenna to treat PET foils or bottles. To increase the barrier properties of the coatings furthermore a RF substrate bias (13.56 MHz) is applied. The composition of the coatings is analyzed by means of Fourier transform infrared (FTIR) spectroscopy regarding carbon and hydrogen content. Influence of gas phase composition and substrate bias on chemical composition of the coatings is discussed. A strong relation between barrier properties and film composition is found: good oxygen barriers are observed as carbon content is reduced and films become quartz-like. Regarding oxygen permeation a barrier improvement factor (BIF) of 70 is achieved.

Normal and anomalous transport phenomena in two-dimensional NaCl, MoS2 and honeycomb surfaces

NASA Astrophysics Data System (ADS)

Mbemmo, A. M. Fopossi; Kenmoé, G. Djuidjé; Kofané, T. C.

2018-04-01

Understanding the effects of anisotropy and substrate shape on the stochastic processes is critically needed for the improvement of the quality of the transport information. The effect of biharmonic force on the transport phenomena of a particle in two-dimensional is investigated in the framework of three representative substrate lattices: NaCl, MoS2 and honeycomb. We focus on the particles drift velocity, to characterize the transport properties in the system. Normal and anomalous transport are identified for a particular set of the system parameters such as the biharmonic parameter, the bias force, the phase-lag of two signals, as well as the noise amplitude. According to the direction ψ where the bias force is applied, we determine the biharmonic parameter ɛ for the presence of anomalous transport and show that for the NaCl surface, the anomalous transport is observed for 2 < ɛ < 10. For the MoS2 surface, it appears at monochromatic driven (ɛ = 0) and for 3 < ɛ < 9. In particular for the honeycomb surface anomalous transport is generated for 0 ⩽ ɛ < 6 only when ψ > 30 °.

Nanoscale Control over the Mixing Behavior of Surface-Confined Bicomponent Supramolecular Networks Using an Oriented External Electric Field

PubMed Central

2017-01-01

Strong electric fields are known to influence the properties of molecules as well as materials. Here we show that by changing the orientation of an externally applied electric field, one can locally control the mixing behavior of two molecules physisorbed on a solid surface. Whether the starting two-component network evolves into an ordered two-dimensional (2D) cocrystal, yields an amorphous network where the two components phase separate, or shows preferential adsorption of only one component depends on the solution stoichiometry. The experiments are carried out by changing the orientation of the strong electric field that exists between the tip of a scanning tunneling microscope and a solid substrate. The structure of the two-component network typically changes from open porous at negative substrate bias to relatively compact when the polarity of the applied bias is reversed. The electric-field-induced mixing behavior is reversible, and the supramolecular system exhibits excellent stability and good response efficiency. When molecular guests are adsorbed in the porous networks, the field-induced switching behavior was found to be completely different. Plausible reasons behind the field-induced mixing behavior are discussed. PMID:29112378

Low dark current and high speed ZnO metal–semiconductor–metal photodetector on SiO{sub 2}/Si substrate

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

Çalışkan, Deniz, E-mail: dcaliskan@fen.bilkent.edu.tr; Department of Nanotechnology and Nanomedicine, Hacettepe University, 06800 Beytepe, Ankara; Bütün, Bayram

2014-10-20

ZnO thin films are deposited by radio-frequency magnetron sputtering on thermally grown SiO{sub 2} on Si substrates. Pt/Au contacts are fabricated by standard photolithography and lift-off in order to form a metal-semiconductor-metal (MSM) photodetector. The dark current of the photodetector is measured as 1 pA at 100 V bias, corresponding to 100 pA/cm{sup 2} current density. Spectral photoresponse measurement showed the usual spectral behavior and 0.35 A/W responsivity at a 100 V bias. The rise and fall times for the photocurrent are measured as 22 ps and 8 ns, respectively, which are the lowest values to date. Scanning electron microscope image shows high aspect ratio andmore » dense grains indicating high surface area. Low dark current density and high speed response are attributed to high number of recombination centers due to film morphology, deducing from photoluminescence measurements. These results show that as deposited ZnO thin film MSM photodetectors can be used for the applications needed for low light level detection and fast operation.« less

Structure of the human protein kinase MPSK1 reveals an atypical activation loop architecture.

PubMed

Eswaran, Jeyanthy; Bernad, Antonio; Ligos, Jose M; Guinea, Barbara; Debreczeni, Judit E; Sobott, Frank; Parker, Sirlester A; Najmanovich, Rafael; Turk, Benjamin E; Knapp, Stefan

2008-01-01

The activation segment of protein kinases is structurally highly conserved and central to regulation of kinase activation. Here we report an atypical activation segment architecture in human MPSK1 comprising a beta sheet and a large alpha-helical insertion. Sequence comparisons suggested that similar activation segments exist in all members of the MPSK1 family and in MAST kinases. The consequence of this nonclassical activation segment on substrate recognition was studied using peptide library screens that revealed a preferred substrate sequence of X-X-P/V/I-phi-H/Y-T*-N/G-X-X-X (phi is an aliphatic residue). In addition, we identified the GTPase DRG1 as an MPSK1 interaction partner and specific substrate. The interaction domain in DRG1 was mapped to the N terminus, leading to recruitment and phosphorylation at Thr100 within the GTPase domain. The presented data reveal an atypical kinase structural motif and suggest a role of MPSK1 regulating DRG1, a GTPase involved in regulation of cellular growth.

The active site of O-GlcNAc transferase imposes constraints on substrate sequence

PubMed Central

Rafie, Karim; Blair, David E.; Borodkin, Vladimir S.; Albarbarawi, Osama; van Aalten, Daan M. F.

2016-01-01

O-GlcNAc transferase (OGT) glycosylates a diverse range of intracellular proteins with O-linked N-acetylglucosamine (O-GlcNAc), an essential and dynamic post-translational modification in metazoa. Although this enzyme modifies hundreds of proteins with O-GlcNAc, it is not understood how OGT achieves substrate specificity. In this study, we describe the application of a high-throughput OGT assay on a library of peptides. The sites of O-GlcNAc modification were mapped by ETD-mass spectrometry, and found to correlate with previously detected O-GlcNAc sites. Crystal structures of four acceptor peptides in complex with human OGT suggest that a combination of size and conformational restriction defines sequence specificity in the −3 to +2 subsites. This work reveals that while the N-terminal TPR repeats of hOGT may play a role in substrate recognition, the sequence restriction imposed by the peptide-binding site makes a significant contribution to O-GlcNAc site specificity. PMID:26237509

Identification and characterization of a chitin deacetylase from a metagenomic library of deep-sea sediments of the Arctic Ocean.

PubMed

Liu, Jinlin; Jia, Zhijuan; Li, Sha; Li, Yan; You, Qiang; Zhang, Chunyan; Zheng, Xiaotong; Xiong, Guomei; Zhao, Jin; Qi, Chao; Yang, Jihong

2016-09-15

The chemical and biological compositions of deep-sea sediments are interesting because of the underexplored diversity when it comes to bioprospecting. The special geographical location and climates make Arctic Ocean a unique ocean area containing an abundance of microbial resources. A metagenomic library was constructed based on the deep-sea sediments of Arctic Ocean. Part of insertion fragments of this library were sequenced. A chitin deacetylase gene, cdaYJ, was identified and characterized. A metagenomic library with 2750 clones was obtained and ten clones were sequenced. Results revealed several interesting genes, including a chitin deacetylase coding sequence, cdaYJ. The CdaYJ is homologous to some known chitin deacetylases and contains conserved chitin deacetylase active sites. CdaYJ protein exhibits a long N-terminal and a relative short C-terminal. Phylogenetic analysis revealed that CdaYJ showed highest homology to CDAs from Alphaproteobacteria. The cdaYJ gene was subcloned into the pET-28a vector and the recombinant CdaYJ (rCdaYJ) was expressed in Escherichia coli BL21 (DE3). rCdaYJ showed a molecular weight of 43kDa, and exhibited deacetylation activity by using p-nitroacetanilide as substrate. The optimal pH and temperature of rCdaYJ were tested as pH7.4 and 28°C, respectively. The construction of metagenomic library of the Arctic deep-sea sediments provides us an opportunity to look into the microbial communities and exploiting valuable gene resources. A chitin deacetylase CdaYJ was identified from the library. It showed highest deacetylation activity under slight alkaline and low temperature conditions. CdaYJ might be a candidate chitin deacetylase that possesses industrial and pharmaceutical potentials. Copyright © 2016 Elsevier B.V. All rights reserved.

High-throughput resistivity apparatus for thin-film combinatorial libraries

NASA Astrophysics Data System (ADS)

Hewitt, K. C.; Casey, P. A.; Sanderson, R. J.; White, M. A.; Sun, R.

2005-09-01

An apparatus, capable of measuring the dc resistance versus temperature of a 49-member library prepared by thin-film deposition techniques was designed and tested. The library is deposited by dc magnetron sputtering onto 10.16cm×10.16cm alumina substrates on which are placed aluminum masks consisting of 8mm diam holes cut on a 7×7 grid, the center-to-center spacing being 10.15mm. Electrical contact to the library is made in a standard van der Pauw geometry using 196 spring-loaded, gold-coated pins, four pins for each member of the library. The temperature is controlled using a helium refrigerator in combination with a liquid-nitrogen radiation shield that greatly reduces radiative heating of the sample stage. With the radiation shield, the cold finger is able to sustain a minimum temperature of 7K and the sample stage a minimum temperature of 27K. The temperature (27-291K) dependent dc resistivity of a thin-film silver library of varying thickness (48-639nm) is presented to highlight the capabilities of the apparatus. The thickness dependence of both the resistivity and the temperature coefficient of resistivity are quantitatively consistent with the literature. For thicknesses greater than about 100nm, the room-temperature resistivity (3.4μΩcm) are consistent with Matthiessen's rule for 1%-2% impurity content, and the temperature coefficient of resistivity is consistent with the bulk value. For thicknesses less than 100nm, an increase in resistivity by a factor of 8 is found, which may be due to surface and boundary scattering effects; a corresponding increase in the temperature coefficient of resistivity is consistent with a concomitant decrease in the magnitude of the elastic constants and surface scattering effects.

Transparent anodic TiO2 nanotube arrays on plastic substrates for disposable biosensors and flexible electronics.

PubMed

Farsinezhad, Samira; Mohammadpour, Arash; Dalrymple, Ashley N; Geisinger, Jared; Kar, Piyush; Brett, Michael J; Shankar, Karthik

2013-04-01

Exploitation of anodically formed self-organized TiO2 nanotube arrays in mass-manufactured, disposable biosensors, rollable electrochromic displays and flexible large-area solar cells would greatly benefit from integration with transparent and flexible polymeric substrates. Such integration requires the vacuum deposition of a thin film of titanium on the desired substrate, which is then anodized in suitable media to generate TiO2 nanotube arrays. However the challenges associated with control of Ti film morphology, nanotube array synthesis conditions, and film adhesion and transparency, have necessitated the use of substrate heating during deposition to temperatures of at least 300 degrees C and as high as 500 degrees C to generate highly ordered open-pore nanotube arrays, thus preventing the use of polymeric substrates. We report on a film growth technique that exploits atomic peening to achieve high quality transparent TiO2 nanotube arrays with lengths up to 5.1 microm at room temperature on polyimide substrates without the need for substrate heating or substrate biasing or a Kauffman ion source. The superior optical quality and uniformity of the nanotube arrays was evidenced by the high specular reflectivity and the smooth pattern of periodic interferometric fringes in the transmission spectra of the nanotube arrays, from which the wavelength-dependent effective refractive index was extracted for the air-TiO2 composite medium. A fluorescent immunoassay biosensor constructed using 5.1 microm-long transparent titania nanotube arrays (TTNAs) grown on Kapton substrates detected human cardiac troponin I at a concentration of 0.1 microg ml(-1).

Methods for Developing Evidence Reviews in Short Periods of Time: A Scoping Review

PubMed Central

Abou-Setta, Ahmed M.; Jeyaraman, Maya; Attia, Abdelhamid; Al-Inany, Hesham G.; Ferri, Mauricio; Ansari, Mohammed T.; Garritty, Chantelle M.; Bond, Kenneth; Norris, Susan L.

2016-01-01

Introduction Rapid reviews (RR), using abbreviated systematic review (SR) methods, are becoming more popular among decision-makers. This World Health Organization commissioned study sought to summarize RR methods, identify differences, and highlight potential biases between RR and SR. Methods Review of RR methods (Key Question 1 [KQ1]), meta-epidemiologic studies comparing reliability/ validity of RR and SR methods (KQ2), and their potential associated biases (KQ3). We searched Medline, EMBASE, Cochrane Library, grey literature, and checked reference lists, used personal contacts, and crowdsourcing (e.g. email listservs). Selection and data extraction was conducted by one reviewer (KQ1) or two reviewers independently (KQ2-3). Results Across all KQs, we identified 42,743 citations through the literature searches. KQ1: RR methods from 29 organizations were reviewed. There was no consensus on which aspects of the SR process to abbreviate. KQ2: Studies comparing the conclusions of RR and SR (n = 9) found them to be generally similar. Where major differences were identified, it was attributed to the inclusion of evidence from different sources (e.g. searching different databases or including different study designs). KQ3: Potential biases introduced into the review process were well-identified although not necessarily supported by empirical evidence, and focused mainly on selective outcome reporting and publication biases. Conclusion RR approaches are context and organization specific. Existing comparative evidence has found similar conclusions derived from RR and SR, but there is a lack of evidence comparing the potential of bias in both evidence synthesis approaches. Further research and decision aids are needed to help decision makers and reviewers balance the benefits of providing timely evidence with the potential for biased findings. PMID:27930662

Automated Microbial Metabolism Laboratory

NASA Technical Reports Server (NTRS)

1973-01-01

Development of the automated microbial metabolism laboratory (AMML) concept is reported. The focus of effort of AMML was on the advanced labeled release experiment. Labeled substrates, inhibitors, and temperatures were investigated to establish a comparative biochemical profile. Profiles at three time intervals on soil and pure cultures of bacteria isolated from soil were prepared to establish a complete library. The development of a strategy for the return of a soil sample from Mars is also reported.

Extensive peptide and natural protein substrate screens reveal that mouse caspase-11 has much narrower substrate specificity than caspase-1.

PubMed

Ramirez, Monica L Gonzalez; Poreba, Marcin; Snipas, Scott J; Groborz, Katarzyna; Drag, Marcin; Salvesen, Guy S

2018-05-04

Inflammatory cell death, or pyroptosis, is triggered by pathogenic infections or events. It is executed by caspase-1 (in the canonical pyroptosis pathway) or caspase-11 (noncanonical pathway), each via production of a cell-lytic domain from the pyroptosis effector protein gasdermin D through specific and limited proteolysis. Pyroptosis is accompanied by the release of inflammatory mediators, including the proteolytically processed forms of interleukin-1β (IL-1β) and IL-18. Given the similar inflammatory outcomes of the canonical and noncanonical pyroptosis pathways, we hypothesized that caspase-1 and -11 should have very similar activities and substrate specificities. To test this hypothesis, we purified recombinant murine caspases and analyzed their primary specificities by massive hybrid combinatorial substrate library (HyCoSuL) screens. We correlated the substrate preferences of each caspase with their activities on the recombinant natural substrates IL-1β, IL-18, and gasdermin D. Although we identified highly selective and robust peptidyl substrates for caspase-1, we were unable to do so for caspase-11, because caspase-1 cleaved even the best caspase-11 substrates equally well. Caspase-1 rapidly processed pro-IL-1β and -18, but caspase-11 processed these two pro-ILs extremely poorly. However, both caspase-1 and -11 efficiently produced the cell-lytic domain from the gasdermin D precursor. We hypothesize that caspase-11 may have evolved a specific exosite to selectively engage pyroptosis without directly activating pro-IL-1β or -18. In summary, comparing the activities of caspase-1 and -11 in HyCoSuL screens and with three endogenous protein substrates, we conclude that caspase-11 has highly restricted substrate specificity, preferring gasdermin D over all other substrates examined. © 2018 by The American Society for Biochemistry and Molecular Biology, Inc.

Effects of Inductively Coupled Plasma Hydrogen on Long-Wavelength Infrared HgCdTe Photodiodes

NASA Astrophysics Data System (ADS)

Boieriu, P.; Buurma, C.; Bommena, R.; Blissett, C.; Grein, C.; Sivananthan, S.

2013-12-01

Bulk passivation of semiconductors with hydrogen continues to be investigated for its potential to improve device performance. In this work, hydrogen-only inductively coupled plasma (ICP) was used to incorporate hydrogen into long-wavelength infrared HgCdTe photodiodes grown by molecular-beam epitaxy. Fully fabricated devices exposed to ICP showed statistically significant increases in zero-bias impedance values, improved uniformity, and decreased dark currents. HgCdTe photodiodes on Si substrates passivated with amorphous ZnS exhibited reductions in shunt currents, whereas devices on CdZnTe substrates passivated with polycrystalline CdTe exhibited reduced surface leakage, suggesting that hydrogen passivates defects in bulk HgCdTe and in CdTe.

Formation of definite GaN p-n junction by Mg-ion implantation to n--GaN epitaxial layers grown on a high-quality free-standing GaN substrate

NASA Astrophysics Data System (ADS)

Oikawa, Takuya; Saijo, Yusuke; Kato, Shigeki; Mishima, Tomoyoshi; Nakamura, Tohru

2015-12-01

P-type conversion of n--GaN by Mg-ion implantation was successfully performed using high quality GaN epitaxial layers grown on free-standing low-dislocation-density GaN substrates. These samples showed low-temperature PL spectra quite similar to those observed from Mg-doped MOVPE-grown p-type GaN, consisting of Mg related donor-acceptor pair (DAP) and acceptor bound exciton (ABE) emission. P-n diodes fabricated by the Mg-ion implantation showed clear rectifying I-V characteristics and UV and blue light emissions were observed at forward biased conditions for the first time.

High extinction ratio terahertz wire-grid polarizers with connecting bridges on quartz substrates.

PubMed

Cetnar, John S; Vangala, Shivashankar; Zhang, Weidong; Pfeiffer, Carl; Brown, Elliott R; Guo, Junpeng

2017-03-01

A terahertz (THz) wire-grid polarizer with metallic bridges on a quartz substrate was simulated, fabricated, and tested. The device functions as a wide-band polarizer to incident THz radiation. In addition, the metallic bridges permit the device to function as a transparent electrode when a DC bias is applied to it. Three design variations of the polarizer with bridges and a polarizer without bridges were studied. Results show the devices with bridges have average s-polarization transmittance of less than -3  dB and average extinction ratios of approximately 40 dB across a frequency range of 220-990 GHz and thus are comparable to a polarizer without bridges.

Responsivity drop due to conductance modulation in GaN metal-semiconductor-metal Schottky based UV photodetectors on Si(111)

NASA Astrophysics Data System (ADS)

Ravikiran, L.; Radhakrishnan, K.; Dharmarasu, N.; Agrawal, M.; Wang, Zilong; Bruno, Annalisa; Soci, Cesare; Lihuang, Tng; Kian Siong, Ang

2016-09-01

GaN Schottky metal-semiconductor-metal (MSM) UV photodetectors were fabricated on a 600 nm thick GaN layer, grown on 100 mm Si (111) substrate using an ammonia-MBE growth technique. In this report, the effect of device dimensions, applied bias and input power on the linearity of the GaN Schottky-based MSM photodetectors on Si substrate were investigated. Devices with larger interdigitated spacing, ‘S’ of 9.0 μm between the fingers resulted in good linearity and flat responsivity characteristics as a function of input power with an external quantum efficiency (EQE) of ˜33% at an applied bias of 15 V and an input power of 0.8 W m-2. With the decrease of ‘S’ to 3.0 μm, the EQE was found to increase to ˜97%. However, devices showed non linearity and drop in responsivity from flatness at higher input power. Moreover, the position of dropping from flatter responsivity was found to shift to lower powers with increased bias. The drop in the responsivity was attributed to the modulation of conductance in the MSM due to the trapping of electrons at the dislocations, resulting in the formation of depletion regions around them. In devices with lower ‘S’, both the image force reduction and the enhanced collection efficiency increased the photocurrent as well as the charging of the dislocations. This resulted in the increased depletion regions around the dislocations leading to the modulation of conductance and non-linearity.

Characterizing the Diversity and Biological Relevance of the MLPCN Assay Manifold and Screening Set

PubMed Central

Zhang, Jintao; Lushington, Gerald H.; Huan, Jun

2011-01-01

The NIH Molecular Libraries Initiative (MLI), launched in 2004 with initial goals of identifying chemical probes for characterizing gene function and druggability, has produced PubChem, a chemical genomics knowledgebase for fostering translation of basic research into new therapeutic strategies. This paper assesses progress toward these goals by evaluating MLI target novelty and propensity for undergoing biochemically or therapeutically relevant modulations and the degree of chemical diversity and biogenic bias inherent in the MLI screening set. Our analyses suggest that while MLI target selection has not yet been fully optimized for biochemical diversity, it covers biologically interesting pathway space that complements established drug targets. We find the MLI screening set to be chemically diverse and to have greater biogenic bias than comparable collections of commercially available compounds. Biogenic enhancements such as incorporation of more metabolite-like chemotypes are suggested. PMID:21568288

Imidazopyridine- and purine-thioacetamide derivatives: potent inhibitors of nucleotide pyrophosphatase/phosphodiesterase 1 (NPP1).

PubMed

Chang, Lei; Lee, Sang-Yong; Leonczak, Piotr; Rozenski, Jef; De Jonghe, Steven; Hanck, Theodor; Müller, Christa E; Herdewijn, Piet

2014-12-11

Nucleotide pyrophosphatase/phosphodiesterase 1 (NPP1) belongs to the family of ecto-nucleotidases, which control extracellular nucleotide, nucleoside, and (di)phosphate levels. To study the (patho)physiological roles of NPP1 potent and selective inhibitors with drug-like properties are required. Therefore, a compound library was screened for NPP1 inhibitors using a colorimetric assay with p-nitrophenyl 5'-thymidine monophosphate (p-Nph-5'-TMP) as an artificial substrate. This led to the discovery of 2-(3H-imidazo[4,5-b]pyridin-2-ylthio)-N-(3,4-dimethoxyphenyl)acetamide (5a) as a hit compound with a Ki value of 217 nM. Subsequent structure-activity relationship studies led to the development of purine and imidazo[4,5-b]pyridine analogues with high inhibitory potency (Ki values of 5.00 nM and 29.6 nM, respectively) when assayed with p-Nph-5'-TMP as a substrate. Surprisingly, the compounds were significantly less potent when tested versus ATP as a substrate, with Ki values in the low micromolar range. A prototypic inhibitor was investigated for its mechanism of inhibition and found to be competitive versus both substrates.