gebhart/patrepeval huggingface dataset:
Exploring single-molecule interactions through 3D optical trapping and tracking: From thermal noise to protein refolding (2006)

The focus of this thesis is the development and application of a novel technique for investigating the structure and dynamics of weak interactions between and within single-molecules. This approach is designed to explore unusual features in bi-directional transitions near equilibrium. The basic idea is to infer molecular events by observing changes in the threedimensional Brownian fluctuations of a functionalized microsphere held weakly near a reactive substrate. Experimentally, I have developed a unique optical tweezers system that combines an interference technique for accurate 3D tracking (∼1 nm vertically, and ∼2–3 nm laterally) with a continuous autofocus system which stabilizes the trap height to within 1-2 nm over hours. A number of different physical and biological systems were investigated with this instrument. Data interpretation was assisted by a multi-scale Brownian Dynamics simulation that I have developed. I have explored the 3D signatures of different molecular tethers, distinguishing between single and multiple attachments, as well as between stiff and soft linkages. As well, I have developed a technique for measuring the force-dependent compliance of molecular tethers from thermal noise fluctuations and demonstrated this with a short ssDNA oligomer. Another practical approach that I have developed for extracting information from fluctuation measurements is Inverse Brownian Dynamics, which yields the underlying potential of mean force and position dependent diffusion coefficient from the Brownian motion of a particle. I have also developed a new force calibration method that takes into account video motion blur, and that uses this information to measure bead dynamics. Perhaps most significantly, I have made the first direct observations of the refolding of spectrin repeats under mechanical force, and investigated the force-dependent kinetics of this transition.
Polymerase and RNA Studies on Milk Virions From Women of the Parsi Community<xref ref-type="fn" rid="FN1">1</xref> (1972)

Several milk samples From women of the Parsi community were examined for reverse transcriptase. They were processed by methods similar to those used for isolating B-type particles from mouse milk and collecting the material sedimenting between densities of 1.16 g/cm3 and 1.19 g/cm3 in a sucrose-density gradient. On examination, 4 of 12 samples had DNA-polymerizing activity. The reaction product after phenol extraction revealed the presence of nascent DNA attached to RNA sedimenting in the 30S-45S region.
Polyethylene glycol versus dual sugar assay for gastrointestinal permeability analysis: is it time to choose? (2012)

Hourly urinary excretion and diagnostic accuracy of PEG and sugar probes show high concordance for detection of indomethacin-induced increases in gastrointestinal permeability. This comparative study improves our knowledge of permeability analysis in man by providing a clear overview of both tests and demonstrates equivalent performance in the current setting.
Functionalization of Single-Walled Carbon Nanotubes with Well-Defined Polymers by Radical Coupling (2005)

Polystyrene and poly[(tert-butyl acrylate)-b-styrene] with well-defined molecular weights and polydispersities were prepared by nitroxide-mediated free-radical polymerization. The homopolymers and block copolymers were used to functionalize shortened single-walled carbon nanotubes (SWNTs) through a radical coupling reaction involving polymer-centered radicals generated at 125 °C via loss of the stable free-radical nitroxide capping agent. The resulting polymer−SWNT composites were fully characterized and were found to be highly soluble in a variety of organic solvents. This solubility could also be altered through chemical modification of the appended polymers. The tert-butyl groups of appended poly[(tert-butyl acrylate)-b-styrene] could be removed to produce poly[(acrylic acid)-b-styrene]-functionalized carbon nanotubes. The resulting composite was found to form aggregates in a mixture of chloroform/methanol (v/v: 1/1) as determined by dynamic light scattering.
Acid-catalyzed and Thermal Cleavage Reactions of Di-tertiary-1,3-diols<sup>1</sup> (1952)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAcid-catalyzed and Thermal Cleavage Reactions of Di-tertiary-1,3-diols1James English Jr. and Frederick V. Brutcher Jr.Cite this: J. Am. Chem. Soc. 1952, 74, 17, 4279–4282Publication Date (Print):September 1, 1952Publication History Published online1 May 2002Published inissue 1 September 1952https://pubs.acs.org/doi/10.1021/ja01137a012https://doi.org/10.1021/ja01137a012research-articleACS PublicationsRequest reuse permissionsArticle Views183Altmetric-Citations25LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Geometry of multi-layer freeform structures for architecture (2007)

The geometric challenges in the architectural design of freeform shapes come mainly from the physical realization of beams and nodes. We approach them via the concept of parallel meshes, and present methods of computation and optimization. We discuss planar faces, beams of controlled height, node geometry, and multilayer constructions. Beams of constant height are achieved with the new type of edge offset meshes. Mesh parallelism is also the main ingredient in a novel discrete theory of curvatures. These methods are applied to the construction of quadrilateral, pentagonal and hexagonal meshes, discrete minimal surfaces, discrete constant mean curvature surfaces, and their geometric transforms. We show how to design geometrically optimal shapes, and how to find a meaningful meshing and beam layout for existing shapes.
Preparation of <i>n</i>‐butyl‐2‐(2′‐triphenylmethyltetrazol‐5‐yl)phenylborinic acid (1995)

Abstract Understanding the mechanism of formation of an impurity in the key step of the synthesis of Losartan ( 1 ) helped devise a procedure to synthesize the title compound in high yield.
Wheat Protein Composition and Properties of Wheat Glutenin in Relation to Breadmaking Functionality (2002)

The unique breadmaking properties of wheat are generally ascribed to the visco-elastic properties of its gluten proteins. While monomeric gluten proteins (gliadin) show viscous behavior, polymeric gluten proteins (glutenin) are elastic. The unique elasticity of glutenin results to a large extent from its polymeric nature. Glutenin is a highly heterogeneous mixture of polymers consisting of a number of different high- and low-molecular-weight glutenin subunits linked by disulfide bonds. Although glutenin obviously is the major polymeric protein in wheat, other polymeric proteins occur as well. Their importance in breadmaking may be underestimated. Nevertheless, variations in both quantity and quality of glutenin strongly determine variations in breadmaking performance. Structural features of different classes of glutenin subunits are described. Variations in glutenin quality may result from variations in its (1) structure, (2) size distribution, and (3) subunit composition. Some hypotheses on glutenin structure and current insights into the role of glutenin size distribution are evaluated. Finally, different ways in which variation in glutenin composition may directly or indirectly (by affecting glutenin structure and/or size distribution) influence glutenin quality are discussed.
Attenuation correction in cardiac SPECT without a transmission measurement. (1995)

This simple method corrects for nonuniform attenuation in males; studies are underway to adapt the method to determine breast contour in females and to determine the value of the method in clinical practice.
X-Ray Luminescence and X-Ray Fluorescence Computed Tomography: New Molecular Imaging Modalities (2014)

X-ray luminescence and X-ray fluorescence computed tomography (CT) are two emerging technologies in X-ray imaging that provide functional and molecular imaging capability. Both emission-type tomographic imaging modalities use external X-rays to stimulate secondary emissions, either light or secondary X-rays, which are then acquired for tomographic reconstruction. These modalities surpass the limits of sensitivity in current X-ray imaging and have the potential of enabling X-ray imaging to extract molecular imaging information. These new modalities also promise to break through the spatial resolution limits of other in vivo molecular imaging modalities. This paper reviews the development of X-ray luminescence and X-ray fluorescence CT and their relative merits. The discussion includes current problems and future research directions and the role of these modalities in future molecular imaging applications.
Chronic hepatitis in chimpanzee carriers of hepatitis B virus: morphologic, immunologic, and viral DNA studies. (1980)

Years after infection with hepatitis B virus, chimpanzees may have manifestations of the carrier state as described in man. In addition to serologic evidence for persistent viral infection, percutaneous liver biopsy specimens showed hepatitis B virus surface antigen in the cytoplasm and hepatitis B virus core antigen in the nucleus. Four carrier animals had portal inflammatory reaction as seen in human chronic persistent hepatitis. Viral DNA was demonstrated in nucleic acid extracts of liver biopsy specimens by molecular hybridization to cloned plasmic pA01 containing hepatitis B virus DNA sequences. Although a viral molecule of length greater than the putative virus was identified, it did not appear to represent integration of viral DNA into the host genome. The chimpanzee model may serve as a means to study the mechanism of hepatitis B viral persistence and progression to chronic liver disease.
An ESCA study of the termination of the passivation of elemental metals (1978)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAn ESCA study of the termination of the passivation of elemental metalsTery L. BarrCite this: J. Phys. Chem. 1978, 82, 16, 1801–1810Publication Date (Print):August 1, 1978Publication History Published online1 May 2002Published inissue 1 August 1978https://pubs.acs.org/doi/10.1021/j100505a006https://doi.org/10.1021/j100505a006research-articleACS PublicationsRequest reuse permissionsArticle Views2849Altmetric-Citations783LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access options Get e-Alerts
Off-specular reflection from flat interfaces (1994)

The reflection of x ray or neutron from a flat interface with density or compositional fluctuations was studied. An integral equation relating the reflection intensities to the interfacial fluctuations was derived in the Fraunhofer limit. At the specular condition this integral equation, although derived for the off-specular intensities, has an expression identical to a well-established one for the specular component. This integral equation was applied to a flat surface onto which gold spheres of uniform size were randomly adhered. The out-of-plane components for both the real wave and the time reversed wave were approximated by the solution from the specular component. Based on the calculated off-specular intensities near the specular region, an approximation scheme was proposed to estimate the in-plane correlation length.
Aspergillus flavus aflatoxin occurrence and expression of aflatoxin biosynthesis genes in soil (2008)

The carcinogen aflatoxin B1 (AFB1) produced by Aspergillus flavus is a major food safety concern in crops. However, information on AFB1 occurrence in soil and crop residue is scarce. A series of experiments investigated the occurrence of AFB1 in soil and corn residues and ascertained the ecology of A. flavus in a Dundee silt loam soil. Samples of untilled soil (0-2 cm) and residues were collected in March 2007 from plots previously planted with a corn isoline containing the Bacillus thuringiensis (Bt) endotoxin gene or the parental non-Bt isoline. AFB1 levels were significantly different in various corn residues. The highest AFB1 levels were observed in cobs containing grain, with 145 and 275 ng.g-1 in Bt and non-Bt, respectively (P > or = F = 0.001). Aflatoxin levels averaged 3.3 and 9.6 ng.g-1 in leaves and (or) stalks and cobs without grain, respectively. All soils had AFB1 ranging from 0.6 to 5.5 ng.g-1 with similar levels in plots from Bt and non-Bt corn. Based on cultural methods, soil contained from log10 3.1 to 4.5 A. flavus cfu.g-1 with about 60% of isolates producing aflatoxin. Laboratory experiments demonstrated that AFB1 is rapidly degraded in soil at 28 degrees C (half-life < or = 5 days). The potential of the soil A. flavus to produce aflatoxins was confirmed by molecular methods. Transcription of 5 aflatoxin biosynthesis genes, including aflD, aflG, aflP, aflR, and aflS, were detected by reverse transcription - polymerase chain reaction analysis in soil. Although AFB1 appears to be transient in soils, it is clear that AFB1 is produced in surface soil in the presence of corn residues, as indicated by A. flavus cfu levels, AFB1 detection, and expression of aflatoxin biosynthetic genes.
Involvement of ras p21 in neurotrophin-induced response of sensory, but not sympathetic neurons. (1993)

Little is known about the signal transduction mechanisms involved in the response to neurotrophins and other neurotrophic factors in neurons, beyond the activation of the tyrosine kinase activity of the neurotrophin receptors belonging to the trk family. We have previously shown that the introduction of the oncogene product ras p21 into the cytoplasm of chick embryonic neurons can reproduce the survival and neurite-outgrowth promoting effects of the neurotrophins nerve growth factor (NGF) and brain-derived neurotrophic factor (BDNF), and of ciliary neurotrophic factor (CNTF). To assess the potential signal-transducing role of endogenous ras p21, we introduced function-blocking anti-ras antibodies or their Fab fragments into cultured chick embryonic neurons. The BDNF-induced neurite outgrowth in E12 nodose ganglion neurons was reduced to below control levels, and the NGF-induced survival of E9 dorsal root ganglion (DRG) neurons was inhibited in a specific and dose-dependent fashion. Both effects could be reversed by saturating the epitope-binding sites with biologically inactive ras p21 before microinjection. Surprisingly, ras p21 did not promote the survival of NGF-dependent E12 chick sympathetic neurons, and the NGF-induced survival in these cells was not inhibited by the Fab-fragments. The survival effect of CNTF on ras-responsive ciliary neurons could not be blocked by anti-ras Fab fragments. These results indicate an involvement of ras p21 in the signal transduction of neurotrophic factors in sensory, but not sympathetic or ciliary neurons, pointing to the existence of different signaling pathways not only in CNTF-responsive, but also in neurotrophin-responsive neuronal populations.
Probabilistic Forecasts of Wind Speed: Ensemble Model Output Statistics by using Heteroscedastic Censored Regression (2009)

Summary As wind energy penetration continues to grow, there is a critical need for probabilistic forecasts of wind resources. In addition, there are many other societally relevant uses for forecasts of wind speed, ranging from aviation to ship routing and recreational boating. Over the past two decades, ensembles of dynamical weather prediction models have been developed, in which multiple estimates of the current state of the atmosphere are used to generate a collection of deterministic forecasts. However, even state of the art ensemble systems are uncalibrated and biased. Here we propose a novel way of statistically post-processing dynamical ensembles for wind speed by using heteroscedastic censored (tobit) regression, where location and spread derive from the ensemble. The resulting ensemble model output statistics method is applied to 48-h-ahead forecasts of maximum wind speed over the North American Pacific Northwest by using the University of Washington mesoscale ensemble. The statistically post-processed density forecasts turn out to be calibrated and sharp, and result in a substantial improvement over the unprocessed ensemble or climatological reference forecasts.
Participación electoral en América Latina: un análisis comparado desde la simultaneidad de las elecciones, 2000-2018 (2019)

En este artículo, se efectúa una exploración de los índices de participación electoral registrados en procesos comiciales legislativos y presidenciales del presente siglo en 18 países de América Latina. Se considera como hipótesis principal que la región continúa mostrando unos datos elevados, aunque estancados, de participación electoral, en que la obligatoriedad del voto no es el único factor que se debe tomar en cuenta para entender las cifras que se desprenden de las últimas convocatorias electorales. En este sentido, se estima que la participación en elecciones presidenciales es superior que en elecciones legislativas; adicionalmente, se cree que la simultaneidad de los comicios beneficia la participación electoral en general y, significativamente, el porcentaje de participación en elecciones legislativas.
Electrical fault protection for a large photovoltaic power plant inverter (1988)

The authors analyze the original protection design and describe changes made to improve fault protection after electrical faults caused fires in the DC wiring of a photovoltaic (PV) power plant. The zone-of-protection was extended, and fault detection and response were improved. The results suggest a need for better coordination between DC and AC fault protection philosophies that are commonly applied independently by designers. Design lessons for PV array fault protection are described to assist electrical designers in eliminating fault vulnerabilities from future PV systems. These take into account the unique electrical characteristics of PV generators, including the dispersed-rather than point-source and the current- rather than voltage-source nature of the PV array.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
<title>Restoration, target recognition, and countermeasure removal using the computed tomographic imaging spectrometer (CTIS)</title> (2002)

Computed Tomographic Imaging Spectrometers are described and shown to be capable of providing real-time flash multispectral imagery. Restoration equations and techniques for optimizing performance are described. Experimental results are shown illustrating system optimization and practical usage of CTIS systems.
An exploratory examination of propensity and performance in new venture internationalization (2002)

This exploratory study investigates causes and consequences of internationalization launched by new ventures.
Double Beam Vacuum Ultraviolet Spectrometer and Logarithmic Ratiometer (1972)

An extremely versatile double beam vacuum uv system for reflection or transmission studies of gases, liquids, and solids has been designed and built. Its features include extreme linearity, a very flat baseline, high duty factor, stationary images on the detectors, equal pathlengths, low temperature capabilities, and analog and digital output.
Naturally processed and concealed HLA-A2.1-restricted epitopes from tumor-associated antigen tyrosinase-related protein-2 (2000)

In this study, a computer-assisted reverse immunology approach was utilized in order to identify potentially antigenic peptides derived from the differentiation antigen TRP-2, a melanosomal protein frequently expressed in melanoma. Among the seven peptides complying with HLA-A2.1-binding motifs, two induced specific CD8(+) cytotoxic T lymphocytes. HLA-A2.1(+) melanoma cells expressing TRP-2 were lysed by clones specific for TRP-2(360-368) (TLDSQVMSL) peptide, thus identifying it as a naturally processed epitope. Other T-cell clones directed against TRP-2(476-484) (VMGTLVALV) were unable to lyse HLA-matched TRP-2(+) cell lines. The role of intracellular proteolytic processing in the generation of this epitope was investigated by transfecting mini-genes encoding the TRP-2(476-484) peptide alone or carrying N- or C-terminal extensions. Specific T-cell clones recognized target cells expressing the cytotoxic T-lymphocyte (CTL)-defined epitope or its C-terminally extended precursor, but failed to recognize cells expressing the N-terminally extended TRP-2(476-484) peptide, suggesting the presence of a negative processing signal (NPS). Regarding C-terminus-flanking regions, mutational analysis indicates that the GLY485 residue plays a key role in the processing of the TRP-2(476-484) epitope. Interestingly, proteasome inhibitors preventing the generation of the MART-1/Melan-A(27-35) immunodominant melanoma tumor-associated antigen (TAA) promoted detectable presentation of TRP-2(476-484) epitope in HLA-A2.1(+) and TRP-2(+) tumor lines, as witnessed by cytokine release by specific T-cell clones.
An approach for close-form solution of multilateration equations (2010)

The approach combines both Chan's algorithm and another close-form algorithm to solve the aircraft multilateration surveillance equations. Results developed are applicable for the surveillance system as a final location solution or as an initial one for the iteration algorithm. However, the ambiguous problem occurs if there are only three TOA measurements. So, the approach will also focus on it and provides an advisable comment to avoid the ambiguity in the receiver stations allocation process for the surveillance system in the airport.
Tunneling Between Superconductors (1963)

Despite our assertion to the contrary, the integral of the last two terms in ( 22) is not zero except at 7" = 0.As a result ( 23) is correct only in this neighborhood and Fig. 1 is wrong.By transforming ( 22) into a sum over the poles of the Fermi function, one obtains