gebhart/patrepeval huggingface dataset:
&lt;italic&gt;In vitro&lt;/italic&gt; selection of high-affinity DNA aptamers for streptavidin (2009)

In this study, we developed a systematic evolution of ligands by exponential enrichment (SELEX) method using a combination of magnetic beads immobilization and flow cytometric measurement. As an example, the selection of streptavidin-specific aptamers was performed. In this protocol, the conventional SELEX procedure was optimized, first using magnetic beads for target immobilization to facilitate highly efficient separation of the binding single-stranded DNA (ssDNA) aptamers from the unbound ssDNAs, and second using flow cytometry and fluorescein labeling to monitor the enrichment. The sensitivity of flow cytometry was adequate for ssDNA quantification during the SELEX procedures. The streptavidin-specific aptamers obtained in this work can be used as tools for characterization of the occupancy of streptavidin-modified surfaces with biotinylated target molecules. The method described in the study is also generally applicable to target molecules other than streptavidin.
Microstructural design studies for locally dissipative acoustic metamaterials (2014)

Stress wave attenuation performance of locally dissipative acoustic metamaterials with various damped oscillator microstructures is studied using mechanical lattice models. The presence of damping is represented by a complex effective mass. Analytical solutions and numerical verifications of transmissibility are obtained for Kelvin-Voigt-type (KVO), Maxwell-type, and Zener-type (ZO) oscillators with viscous damping. Although peak attenuation at resonance is diminished, dissipative microstructures can provide broad spectrum attenuation without increasing mass ratio, obviating the bandgap width limitation of locally resonant microstructures. KVO gives the best broad spectrum performance akin to a low-pass filter for excitation frequencies above a cut-off value for a prescribed transmissibility criterion. For ZO, by tailoring the damping and stiffness, the frequency range of appreciable attenuation can at least span the bandgap widths of two limiting locally resonant cases. Static and frequency-dependent measures of optimal damping that maximize the attenuation characteristics are proposed. A transitional value for the excitation frequency is identified within the locally resonant bandgap, above which there always exists an optimal amount of damping that renders the attenuation for the dissipative metamaterial greater than that for the locally resonant case. Further microstructures with hysteretic damping depict a frequency-independent scaling in the effective mass and attenuation factor, but the bandgap width remains nearly the same as that for the corresponding viscously damped microstructures. This study demonstrates that dissipative microstructures, which are to some extent unavoidable in practical designs, when tuned, provide a means to substantially enhance the attenuation bandwidth of locally resonant acoustic metamaterials while also enabling the removal of the energy sequestered by the oscillators from the system.
Development of parallel cutting simulation with adaptive octree model in virtual machine tool (2012)

For real-time machining simulation, cutting geometry needs to be computed with high efficiency. The cutting geometry is extracted through material removal simulation. Adaptive octree model is widely applied for material removal simulation. To increase the efficiency of material removal simulation using adaptive octree, an algorithm of parallel computation is proposed in this paper. The parallel material removal simulation is integrated with milling force evaluation in virtual machine tool.
Convenient and Selective Preparation of Mono-alkoxyphenylsilanes from Phenylsilane and Alcohols (2006)

Abstract The selective dehydrogenative coupling of phenylsilane and alcohols, including primary, secondary, and tertiary alcohols, was smoothly catalyzed by bis(hexafluoroacetylacetonato)copper(II) complex to afford the corresponding mono-alkoxysilanes in good-to-high yield after distillation.
Burkholderia cocovenenans (van Damme et al. 1960) Gillis et al. 1995 and Burkholderia vandii Urakami et al. 1994 are junior synonyms of Burkholderia gladioli (Severini 1913) Yabuuchi et al. 1993 and Burkholderia plantarii (Azegami et al. 1987) Urakami et al. 1994, respectively (1999)

Reference strains of Burkholderia cocovenenans and Burkholderia vandii were compared with strains of other Burkholderia species using SDS-PAGE of whole-cell proteins, DNA-DNA hybridization and extensive biochemical characterization. Burkholderia gladioli and B. cocovenenans were indistinguishable in the chemotaxonomic and biochemical analyses. Burkholderia plantarii and B. vandii had indistinguishable whole-cell protein patterns but the B. vandii type strain differed from B. plantarii strains in several biochemical tests. The DNA-DNA binding levels (higher than 70%) indicated that (i) B. gladioli and B. cocovenenans, and (ii) B. plantarii and B. vandii each represent a single species. It is concluded that B. cocovenenans and B. vandii are junior synonyms of B. gladioli and B. plantarii, respectively.
Quantitative Measurements of Multilayer Physical Adsorption on Heterogeneous Surfaces from Nonlinear Light Scattering (1997)

We present measurements of equilibrium multilayer physical adsorption on porous, heterogeneous ice films using nonlinear light scattering. The dependence of scattering intensity on surface coverage is modeled using the adsorption theory of Brunauer, Emmett, and Teller, and an extension based on the Bragg-Williams formalism. We show that a complete equation of state for an adsorbed species can be experimentally determined within this simple framework.
Social and Economic Inequality and Asian Americans in the United States (2002)

ABSTRACT Describing social and economic inequality within the Asian American community is difficult. Depending on how “Asian American” is defined, there are twenty to thirty cultures, countries of origin, and a wide range of identities and circumstances that influence economic and social well-being. It is almost presumptuous to attempt to categorize such a diverse collection of identities as one group. At the same time, Asians and Pacific Islanders have been an increasing population group in the U.S. over the past thirty years. A common conception of them now is that of the “model minority”; i.e., as a minority group which has through hard work rather than political confrontation achieved the American Dream. Simple economic and educational comparisons suggest that Asian Americans have done quite well. Yet those comparisons are misleading. When controlling for educational status, Asian Americans have lower incomes than their White counterparts. Asian Americans, especially recent immigrants, also have higher poverty rates, whether for individuals, families, or children, than Whites. Overall, the impact of race continues to be significant for the well-being of this minority group, putting them at a disadvantage in American society.
Synthesis of general topology multiple coupled resonator filters by optimization (2002)

A synthesis procedure, using optimization, for multiple coupled resonator filters having general topology and general response is described. The error function for the optimization is based on the values of the characteristic function at its zeros and poles. The optimization is performed directly on the element values of the coupling matrix. Convergence of the optimization is extremely fast and nearly independent of the starting coupling matrix. Examples of the design of practical filters with symmetric or asymmetric responses and topology are presented.
Detection of impact damage of stiffened composite panels using embedded small-diameter optical fibers (2004)

It is well known that barely visible damage is often induced in composite structures subjected to out-of-plane impact, and the mechanical properties of the composites degrade markedly. The stiffened composite panels which are the representative structural elements of airplanes are characterized by impact damage different from that of coupon-level specimens. Therefore, the objective of this study is to apply small-diameter optical fiber sensors to stiffened composite panels for the detection of impact damage. In this study, both multi-mode optical fibers and fiber Bragg grating (FBG) sensors are used for detecting impact load and impact damage in stiffened composite panels. The fibers have polyimide coating with 40 µm cladding diameter which has no serious effect on the mechanical properties of composites. Impact tests are performed using stiffened composite panels with embedded optical fibers. The characteristics of impact damage are investigated. The impact load, the strain and the optical responses of the optical fibers are measured as a function of time. And we discuss the relationships among the optical responses, the impact load and the impact damage.
Artificial intelligence in education : AI-ED in the wired and wireless future (2001)

This text presents the proceedings from the 10th International Conference on Artificial Intelligence in Education, one from a series of conferences designed to report on the state of research in the field of intelligent system theory and technology for educational application. This field is interdisciplinary and brings together researchers from the domains of computer science, psychology, linguistics, sociology and philosophy (to name a few). Researchers contributed papers that explore the emerging roles of mobile computing and distributed technologies in intelligent educational applications and look at artificial intelligence in a wired and wireless future.
Targeted advertising for online social networks (2009)

Generating targeted advertisements for online social networks is a problem of growing interest. Monetizing activity in online social networks has been the topic of heated discussion lately. The undiscriminating tastes and spending power of a majority of its members makes this medium for self-expression and opinion sharing a very lucrative venue for advertising. The recent $240 million investment by Microsoft in Facebook clearly reaffirms the opportunity in targeted advertising for online social networks. Content-targeted advertisement programs such as Google AdSense and Yahoo Contextual Match work by automatically spotting keywords in web pages and displaying ads based on the keywords. The displayed ads are also refereed as Contextual Advertisements. These ads are generally represented by a URL along with a textual description that is also used to match the ad with the target page. This model works relatively well on the Web but its applicability to social networks is being met with some important challenges. User activity on venues such as forums, marketplaces and groups on social networking sites are excellent targets for monetization. We present an algorithm based on keyword clustering to generate targeted ads.
4-D seismic reservoir simulation in a South Timbalier 295 turbidite reservoir (1998)

This case history describes a combination of time-lapse (or 4-D) seismic with 3-D elastic seismic modeling, reservoir characterization, and fluid-flow simulation to better understand drainage patters of oil, gas, and water into wells and to identify bypassed pay.
Enantioselective Gold Catalysis: Opportunities Provided by Monodentate Phosphoramidite Ligands with an Acyclic TADDOL Backbone (2010)

The tail makes the difference: Removing the isopropylidene acetal unit from well-known TADDOL ligands improved the performance of the derived phosphoramidite ligands in asymmetric gold catalysis (see scheme; Ts=4-toluenesulfonyl). X-ray crystallography showed that the binding pocket has an effective threefold symmetry, with through-space interactions between the arene rings of the ligand and the gold center.
Gamete quality and broodstock management in temperate fish (2013)

Abstract The ability to fully control sexual maturation and spawning and to produce large numbers of high quality seeds ‘on demand’ (i.e. all year long) is a primary requirement for the successful development of aquaculture. This relies on optimal broodstock management practices based on extensive knowledge of the nutritional and environmental requirements of fish in captivity. However, for many established, emerging and new farmed fish species, such knowledge is limited or not available yet. The level of domestication also plays an essential role as stocks with improved traits in farming conditions are selected. Importantly, reliable indicators of egg quality are still lacking and hatcheries still rely on wild harvested broodstocks in many farmed fish species. These key challenges must be addressed urgently to ensure the sustainable development of the E uropean fish farming sector. This review gives an overview of methods to assess egg/sperm quality and many of the most important factors affecting gamete production and quality, including broodstock nutrition, environmental and spawning induction protocols, genetic management, gamete preservation and new reproductive strategies.
Laser-Induced Magnetic Nanostructures with Tunable Topological Properties (2013)

We report the creation and real-space observation of magnetic structures with well-defined topological properties and a lateral size as low as about 150 nm. They are generated in a thin ferrimagnetic film by ultrashort single optical laser pulses. Thanks to their topological properties, such structures can be classified as Skyrmions of a particular type that does not require an externally applied magnetic field for stabilization. Besides Skyrmions, we are able to generate magnetic features with topological characteristics that can be tuned by changing the laser fluence. The stability of such features is accounted for by an analytical model based on the interplay between the exchange and the magnetic dipole-dipole interactions.
The mechanism of the reaction of chymotrypsin with <i>p</i>-nitrophenyl acetate (1956)

5. Release of these materials from mycelium treated with fatty acid was greatest at acid pH values, but change of pH had no significant effect upon the release by detergents.
An artificial neural network (ANN)-based lung-tumor motion predictor for intrafractional MR tumor tracking (2012)

A new ANN-based lung-tumor motion predictor is developed for MRI-based intrafractional tumor tracking. The prediction accuracy of our predictor is evaluated using a realistic simulated MR imaging rate and system delays. For 120-520 ms system delays, mean RMSE values of 0.5-0.9 mm (ranges 0.0-2.8 mm from 29 patients) are achieved. Further, the advantage of patient specific ANN structure and IW in lung-tumor motion prediction is demonstrated by a 30%-60% decrease in mean RMSE values.
Trafficking of Porin-Deficient <i>Salmonella typhimurium</i> Mutants inside HeLa Cells: <i>ompR</i> and <i>envZ</i> Mutants Are Defective for the Formation of <i>Salmonella</i> -Induced Filaments (1998)

Outer membrane porin genes of Salmonella typhimurium, including ompC, ompF, and tppB, are regulated by the products of ompB, a two-component regulatory locus encoding OmpR and EnvZ. S. typhimurium ompR mutants are attenuated in mice, but to date no one has studied the intracellular trafficking of S. typhimurium porin-deficient mutants. In this study, isogenic transposon mutants of S. typhimurium with insertions in ompR, envZ, ompF, ompC, ompD, osmZ, and tppB were compared with wild-type SL1344 for trafficking in the human epithelial cell line HeLa. We found that ompR and envZ mutants were reduced or completely inhibited for the formation of Salmonella-induced filaments (Sifs). This result was confirmed with an ompB deletion mutant. Sifs are tubular structures containing lysosomal glycoprotein which are induced specifically by intracellular Salmonella. Genetic analysis showed that the ompR mutation could be complemented in trans by cloned ompR to restore its ability to induce Sifs. In contrast, mutations in the known ompR-regulated genes ompF, ompC, and tppB (as well as the ompR-independent porin gene, ompD) had no effect on Sif formation relative to that of wild-type SL1344, thus indicating that OmpR does not exert its role on these genes to induce Sif formation. The omp mutants studied were able to invade and replicate in HeLa cells at levels comparable to those in wild-type SL1344. We conclude that OmpR and EnvZ appear to regulate Sif formation triggered by intracellular S. typhimurium.
Scientists in wonderland: A report on visualization applications in the CAVE virtual reality environment (1993)

The authors present the experiences at the Electronic Visualization Laboratory (EVL) in introducing computational scientists to the use of virtual reality as a research tool. They describe the virtual environment, the CAVE. They then describe several applications currently being developed at EVL using the CAVE and conclude with a discussion on possible research paths to follow in making virtual reality an effective tool for visualization.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Saccharomyces Genome Database (SGD) provides biochemical and structural information for budding yeast proteins (2003)

The Saccharomyces Genome Database (SGD: http://genome-www.stanford.edu/Saccharomyces/) has recently developed new resources to provide more complete information about proteins from the budding yeast Saccharomyces cerevisiae. The PDB Homologs page provides structural information from the Protein Data Bank (PDB) about yeast proteins and/or their homologs. SGD has also created a resource that utilizes the eMOTIF database for motif information about a given protein. A third new resource is the Protein Information page, which contains protein physical and chemical properties, such as molecular weight and hydropathicity scores, predicted from the translated ORF sequence.
Activation of Toll-like Receptors by Microbial Lipoproteins (2001)

In Drosophila, the Toll family of proteins are central to innate defense against microbial pathogens. Conserved throughout evolution, mammalian Toll-like receptors (TLRs) participate in innate immunity. TLRs mediate activation by microbial ligands including lipoproteins, resulting in the activation of IL-12 and nitric oxide synthase. Microbial lipoproteins also induce host cell apoptosis. In this manner, the ability of microbial lipoproteins to activate TLRs can contribute to host defense and immunopathology during infection.
Methods, applications and concepts of metabolite profiling: Secondary metabolism (2007)

Plants manufacture a vast array of secondary metabolites/natural products for protection against biotic or abiotic environmental challenges. These compounds provide increased fitness due to their antimicrobial, anti-herbivory, and/or alleopathic activities. Secondary metabolites also serve fundamental roles as key signaling compounds in mutualistic interactions and plant development. Metabolic profiling and integrated functional genomics are advancing the understanding of these intriguing biosynthetic pathways and the response of these pathways to environmental challenges. This chapter provides an overview of the basic methods, select applications, and future directions of metabolic profiling of secondary metabolism. The emphasis of the application section includes the combination of primary and secondary metabolic profiling. The future directions section describes the need for increased chromatographic and mass resolution, as well as the inevitable need and benefit of spatially and temporally resolved metabolic profiling.
Low-loss flat-top passband arrayed waveguide gratings realised by first-order mode assistance method (2002)

A novel method of flattening the passband of an arrayed waveguide grating with a small excess loss, which employs a new concept that uses the assist of the weak first-order mode, is described. A 16-channel 100 GHz-spacing demultiplexer with a fibre-to-fibre loss of less than 3.6 dB and a flattened excess loss of 1.85 dB is demonstrated. The 1 dB down passband is widened 2.2 times.
Synthesis and Chemical Degradation of Thermostable Polyamide with Imine Bond for Chemical Recycling (2005)

The mono-, di-, and triamino-substituted cyclic phenylazomethine (CPA) and diamino-substituted linear phenylazomethine (OPA) were synthesized in one-step via dehydration of aromatic amine and ketone in the presence of titanium tetrachloride. The linear and branched aromatic polyamides were prepared by the direct polycondensation of the di- or triamine monomers and various dicarboxylic acids in the presence of triphenyl phosphite and pyridine as condensation agents. Thermogravimetric analysis (TGA) revealed that the polymers had a high thermal stability. The temperature for a 10% weight loss determined by TGA was over 500 °C for some of the polymers. The hydrolysis property of the polymers was investigated using UV−vis spectroscopy. The spectra of the polymer solution in the presence of dilute sulfuric acid revealed that a simple and selective acid-catalyzed hydrolysis of azomethine bonds quantitatively occurred in mild conditions without cleavage of the amide bond, and more than 99% of the azomethine bonds were hydrated in less than 10 min at ambient temerature. The hydrolysis rate of the polymer was also determined. In polymer materials, these aromatic polyamides made it possible to relate high thermal stability with the decomposition property for effective chemical recycling.
CsI(Tl) with photodiodes for identifying subsurface radionuclide contamination (2002)

A cylindrical (15/spl times/61 mm) CsI(Tl) scintillation detector with two side-mounted photodiodes has been developed to collect spectral gamma-ray data in subsurface contaminated formations at the US Department of Energy's Hanford Site. It operates inside small-diameter, thick-wall steel pipes pushed into the ground to depths up to 20 m by a cone penetrometer system. The detector provides a rugged, efficient, magnetic-field-insensitive means for identifying gamma-ray-emitting contaminants (mainly /sup 137/Cs and /sup 60/Co). Mounting two 3/spl times/30-mm photodiodes end-to-end on a flat area along the detector's side provides efficient light collection over the length of the detector.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>