gebhart/patrepeval huggingface dataset:
NEAMS Workbench Workflows (2021)

Modeling and simulation efforts frequently involve loosely coupled workflows. Automation of workflows, data exchanges, and simulation software execution is a productive and often desired feature or improvement for enhancing consistency of results and productivity of the analyst. It facilitates cross-collaboration of different analysts of multidisciplinary simulation by streamlining data exchange processes across local and high performance computing resources. This report proposes a high-level, extensible workflow module to enable consistent and efficient use of tools integrated into the Nuclear Energy Advanced Modeling and Simulation (NEAMS) Workbench with as little user intervention as possible.
Towards the transformation of onions (Allium cepa) (1995)

Abstract This review outlines the potential for developing a reliable transformation system for onions (Allium cepa). A summary of the onion tissue culture literature is presented along with descriptions of the gene transfer systems available. The most suitable regulatory sequences and selective genes that could be used for onion transformation are described, together with the problems which may be encountered following the integration into the particularly large genome of onion. The review proposes likely routes by which transformation and regeneration may be achieved, and suggests possible characteristics of onions which may be altered using such a technique.
Enhanced delivery of a density-modified therapeutic using ultrasound: Comparing the influence of micro- and nano-scale cavitation nuclei (2017)

New strategies are required to enhance the penetration and tumor-wide distribution of cancer therapeutics, including viruses, antibodies, and oligonucleotides. We have shown previously that increasing the density of a nanoparticle can enhance its ultrasound-mediated transport, particularly when exposed to microstreaming. The current study investigates how the physical characteristics and dynamics of different cavitation nucleation agents affect the cavitation-mediated transport of therapeutics not directly bound to the gas nuclei. SonoVue (Bracco, Milan, Italy) microbubble contrast agent (with 3 μm mean initial bubble diameter) and polymeric gas-entrapping nanoparticles (with 260 nm mean initial bubble diameter) were first compared in terms of inertial cavitation threshold and cavitation persistence. Under the same ultrasound exposure conditions (centre frequencies of either 0.5 MHz or 1.6 MHz, and peak negative pressures from 0.2 MPa to 3.5 MPa) their respective cavitation emissions were found to differ in magnitude, frequency composition and duration. The resultant penetration depths of co-injected gold-coated nanoparticles in a tissue-mimicking phantom were also found to vary, with the polymeric gas-entrapping nanoparticles giving rise to greater penetration distances. This study concludes that both the characteristics of the therapeutic and the cavitation nuclei can significantly influence ultrasound-mediated drug delivery.
Evaluation of light scattering and absorption properties ofin vivorat liver using a single-reflectance fiber probe during preischemia, ischemia–reperfusion, and postmortem (2015)

Diffuse reflectance spectroscopy (DRS) has been extensively used for characterization of biological tissues as a noninvasive optical technique to evaluate the optical properties of tissue. We investigated a method for evaluating the reduced scattering coefficient μ(s)', the absorption coefficient μ(a), the tissue oxygen saturation StO₂, and the reduction of heme aa3 in cytochrome c oxidase CcO of in vivo liver tissue using a single-reflectance fiber probe with two source-collector geometries. We performed in vivo recordings of diffuse reflectance spectra for exposed rat liver during the ischemia-reperfusion induced by the hepatic portal (hepatic artery, portal vein, and bile duct) occlusion. The time courses of μ a at 500, 530, 570, and 584 nm indicated the hemodynamic change in liver tissue as well as StO₂. Significant increase in μ(a)(605)/μ(a)(620) during ischemia and after euthanasia induced by nitrogen breathing was observed, which indicates the reduction of heme aa3, representing a sign of mitochondrial energy failure. The time courses of μ(s)' at 500, 530, 570, and 584 nm were well correlated with those of μ(a), which also reflect the scattering by red blood cells. On the other hand, at 700 and 800 nm, a temporary increase in μ(s)' and an irreversible decrease in μ(s)' were observed during ischemia-reperfusion and after euthanasia induced by nitrogen breathing, respectively. The change in μ(s)' in the near-infrared wavelength region during ischemia is indicative of the morphological changes in the cellular and subcellular structures induced by the ischemia, whereas that after euthanasia implies the hepatocyte vacuolation. The results of the present study indicate the potential application of the current DRS system for evaluating the pathophysiological conditions of in vivo liver tissue.
Stability of Peptide in Microarrays: A Challenge for High-Throughput Screening (2011)

Microarrays are becoming a common tool in biology for screening large numbers of samples. However, the relevance of such an approach depends on the reproducibility of measurements that is directly linked to the stability of the probes grafted on the chip especially when many cycles of regeneration are performed. Indeed, regeneration of microarray chips is of great interest in improving the throughput and reducing the costs. The impact of treatments performed to remove bound ligands in order to reuse the chip depends partially on the grafted probe and on the characteristics of the probe-ligand interaction. Thus DNA microarrays are considered to be stable as oligonucleotides are highly stable molecules and hybridization reaction depends very little on the conformation of the partners; so, multiple regeneration/rehybridization procedures can be carried out without major loss of signal intensity (Benters et al., 2002, Donhauser et al., 2009). Stability of the probes is much more difficult to achieve when proteins are used. Indeed, such molecules are very complex and heterogeneous, thus there are no general rules to account for their behaviour upon different regeneration steps. Moreover, protein-protein interactions are highly susceptible to partner conformation. This is particularly true in the case of antigen (Ag) – antibody (Ab) binding, and several papers mention a loss of signal after the second or third regeneration step (Barton et al., 2008, Yakovleva et al., 2003). Peptide microarrays are a good alternative, as peptides are shorter and their stability less dependant on their tridimensional structure. Thus they are often used for antibody profiling (Cherif et al., 2006, Halperin et al., 2011, Neuman de Vegvar et al., 2003). However, there is no study dealing with the stability of such microarrays during a large samples screening (>20). Furthermore, a conformational change is not the only parameter which can impact on ligand binding. In this chapter, our aim was to analyze the evolution of the signals during samples screening and to determine which parameters are involved in the decay of the chip efficiency: grafting method, saturation step, probe itself or probe-ligand interactions, presence of protease activity in the sample. We use a microarray system based on pyrrole electropolymerization
FGF2 gene transfer restores hippocampal functions in mouse models of Alzheimer's disease and has therapeutic implications for neurocognitive disorders (2011)

The adult hippocampus plays a central role in memory formation, synaptic plasticity, and neurogenesis. The subgranular zone of the dentate gyrus contains neural progenitor cells with self-renewal and multilineage potency. Transgene expression of familial Alzheimer's disease-linked mutants of β-amyloid precursor protein (APP) and presenilin-1 leads to a significant inhibition of neurogenesis, which is potentially linked to age-dependent memory loss. To investigate the effect of neurogenesis on cognitive function in a relevant disease model, FGF2 gene is delivered bilaterally to the hippocampi of APP+presenilin-1 bigenic mice via an adenoassociated virus serotype 2/1 hybrid (AAV2/1-FGF2). Animals injected with AAV2/1-FGF2 at a pre- or postsymptomatic stage show significantly improved spatial learning in the radial arm water maze test. A neuropathological investigation demonstrates that AAV2/1-FGF2 injection enhances the number of doublecortin, BrdU/NeuN, and c-fos-positive cells in the dentate gyrus, and the clearance of fibrillar amyloid-β peptide (Aβ) in the hippocampus. AAV2/1-FGF2 injection also enhances long-term potentiation in another APP mouse model (J20) compared with control AAV2/1-GFP-injected littermates. An in vitro study confirmed the enhanced neurogenesis of mouse neural stem cells by direct AAV2/1-FGF2 infection in an Aβ oligomer-sensitive manner. Further, FGF2 enhances Aβ phagocytosis in primary cultured microglia, and reduces Aβ production from primary cultured neurons after AAV2/1-FGF2 infection. Thus, our data indicate that virus-mediated FGF2 gene delivery has potential as an alternative therapy of Alzheimer's disease and possibly other neurocognitive disorders.
An improved weighted least-squares design for variable fractional delay FIR filters (1999)

Digital filters capable of changing their frequency response characteristics are often referred to as variable digital filters (VDFs) and have been found useful in a number of digital signal processing applications. An important class of VDFs is the class of digital filters with variable fractional delay. This paper describes an enhanced weighted least-squares design for variable-fractional-delay finite-impulse response filters, which offers improved performance of the filters obtained with considerably reduced computational complexity compared to a recently proposed weighted least-squares (WLS) design method. The design enhancement is achieved by deriving a closed-form formula for evaluating the WLS objective function. The formula facilitates accurate and efficient function evaluations as compared to summing up a large number of discrete terms, which would be time consuming and inevitably introduce additional errors into the design.
Tetrahydrocannabinolic Acid Synthase, the Enzyme Controlling Marijuana Psychoactivity, is Secreted into the Storage Cavity of the Glandular Trichomes (2005)

Tetrahydrocannabinolic acid (THCA) synthase is the enzyme responsible for the production of tetrahydrocannabinol (THC), the psychoactive component of marijuana (Cannabis sativa L.). We suggest herein that THCA is biosynthesized in the storage cavity of the glandular trichomes based on the following observations. (i) The exclusive expression of THCA synthase was confirmed in the secretory cells of glandular trichomes by reverse transcription-PCR (RT-PCR) analysis. (ii) THCA synthase activity was detected in the storage cavity content. (iii) Transgenic tobacco expressing THCA synthase fused to green fluorescent protein showed fluorescence in the trichome head corresponding to the storage cavity. These results also showed that secretory cells of the glandular trichomes secrete not only metabolites but also biosynthetic enzyme.
Enhanced Reduced Sulfur Emission from Manures of Beef Cattle Fed Distiller's Byproducts (2010)

Reduced sulfur compounds (H2S and methyl sulfides) are normal products of manure decomposition which are emitted from confined animal feeding operations (CAFO). These compounds not only contribute to nuisance odors, but with recent EPA regulations, H2S emissions in excess of 100 lbs per day must be reported by the livestock operation. Feeding distillers byproducts, which can be very high in sulfur, has recently become very common in large feedlots. Two studies were conducted to evaluate the relative impact of feeding wet distillers grain plus solubles (WDGS), which can be high in sulfur, to beef cattle. In the first study, beef cattle in sixteen small-scale pens were fed varying amounts (0%, 20%, 40%, and 60%) of WDGS. Fresh manure composites were collected four times from each pen during the study, and the relative emissions were measured using a laboratory wind tunnel chamber. The relative emission of reduced sulfur was significantly greater (4 to 22-fold) in the 40% and 60% WDGS manures for all time periods compared to the 0% manure composite. A second follow up study in eight production-scale feedlot pens feeding either 0% or 40% WDGS demonstrated that reduced sulfur emissions were consistently larger (up to 2.6-fold) from the feedlot surface near the feed bunk when cattle were fed the 40% diet. Largest reduced sulfur emissions were detected when the feedlot surface was wet. Spatially, relative emission from the feedlot surface after animals were removed from the pens came principally from the wetter edges of the pen. Taken together, the results indicate that very large CAFO need to consider both the sulfur content and the feeding level of WDGS in order to comply with EPAs reduced sulfur emission guidelines. More intensive manure management of the edges of pens may minimize emissions, but further research is needed to demonstrate whether this management practice is truly effective.
CdIn2S4/g-C3N4 heterojunction photocatalysts: enhanced photocatalytic performance and charge transfer mechanism (2016)

CdIn<sub>2</sub>S<sub>4</sub>/g-C<sub>3</sub>N<sub>4</sub> heterojunction with excellent photocatalytic activities have been synthesized. The enhanced photocatalytic performance might be ascribed to the efficient photoinduced charge transfer derived from the heterojunction structure.
Identification of Mg2+ ions next to nucleotides in cryo-EM maps using electrostatic potential maps (2021)

Cryo electron microscopy (cryo-EM) can produce maps of macromolecules that have resolutions that are sufficiently high that structural details such as chemical modifications, water molecules and bound metal ions can be discerned. However, those accustomed to interpreting the electron-density maps of macromolecules produced by X-ray crystallography need to be careful when assigning features such as these in cryo-EM maps because cations, for example, interact far more strongly with electrons than they do with X-rays. Using simulated electrostatic potential (ESP) maps as a tool led us to re-examine a recent cryo-EM map of the human ribosome, and we realized that some of the ESP peaks originally identified as novel groups covalently bonded to the N7, O6 or O4 atoms of several guanines, adenines or uridines, respectively, in this structure are likely to instead represent Mg<sup>2+</sup> ions coordinated to these atoms, which provide only partial charge compensation compared with Mg<sup>2+</sup> ions located next to phosphate groups. In addition, direct evidence is provided for a variation in the level of 2'-O ribose methylation of nucleotides in the human ribosome. ESP maps can thus help in identifying ions next to nucleotide bases, i.e. at positions that can be difficult to address in cryo-EM maps due to charge effects, which are specifically encountered in cryo-EM. This work is particularly relevant to nucleoprotein complexes and shows that it is important to consider charge effects when interpreting cryo-EM maps, thus opening possibilities for localizing charges in structures that may be relevant for enzymatic mechanisms and drug interactions.
Observation of critical phenomena in a protein-water solution (1989)

We report measurements of the intensity of the scattered light and the turbidity of aqueous solutions of the bovine lens protein, ${\ensuremath{\gamma}}_{\mathrm{II}}$-crystallin, near the critical point for binary liquiid phase separation, in a region of the phase diagram which is metastable with respect to protein-crystal formation. We have determined the magnitudes and critical divergences of the osmotic compressibility, ${\mathrm{\ensuremath{\kappa}}}_{\mathrm{T}}$, and the static correlation range, \ensuremath{\xi}. The corresponding critical exponents are \ensuremath{\gamma}=1.21\ifmmode\pm\else\textpm\fi{}0.05 and \ensuremath{\nu}=0.68\ifmmode\pm\else\textpm\fi{}0.1. .AE
Event registration and Vp/Vs correlation analysis in 4C processing (2003)

PreviousNext No AccessSEG Technical Program Expanded Abstracts 2003Event registration and Vp/Vs correlation analysis in 4C processingAuthors: Richard Van DokPål KristiansenRichard Van DokWesternGeco and Pål KristiansenWesternGecohttps://doi.org/10.1190/1.1885425 SectionsAboutPDF/ePub ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinked InRedditEmail Permalink: https://doi.org/10.1190/1.1885425FiguresReferencesRelatedDetailsCited ByMulticomponent seismic data registration by nonlinear optimizationWenlei Gao and Mauricio D. Sacchi13 November 2017 | GEOPHYSICS, Vol. 83, No. 1Estimating VP/VS ratios using smooth dynamic image warpingStefan Compton and Dave Hale23 September 2014 | GEOPHYSICS, Vol. 79, No. 6Automated time-domain transform of converted waves by prestack double-parameter scanning9 July 2013 | Journal of Geophysics and Engineering, Vol. 10, No. 4Attribute‐driven multi‐component registrationDean Witte, Murray Roth, and Jeff Emanuel14 October 2009Automated C‐wave registration by simulated annealingJianxin Jerry Yuan, Girish Nathan, Alex Calvert, and Robert Bloor15 December 2008 SEG Technical Program Expanded Abstracts 2003ISSN (print):1052-3812 ISSN (online):1949-4645Copyright: 2003 Pages: 2452 publication data© 2003 Copyright © 2003 Society of Exploration GeophysicistsPublisher:Society of Exploration Geophysicists HistoryPublished: 03 Jan 2005 CITATION INFORMATION Richard Van Dok and Pål Kristiansen, (2003), "Event registration and Vp/Vs correlation analysis in 4C processing," SEG Technical Program Expanded Abstracts : 785-788. https://doi.org/10.1190/1.1885425 Plain-Language Summary PDF DownloadLoading ...
Experimental clinical substantiation of application of immobilized forms of sodium hypochlorite in treatment of infected pancreatonecrosis (2017)

OBJECTIVE. The study substantiated the possibility of application of sodium hypochlorite for treatment of infected pancreatonecrosis. MATERIAL AND METHODS. The experimental study was conducted on 288 rats. Clinical research was carried out on 94 patients who were divided into two statistically homogenous groups. «Levomecol» ointment was used in the first group for sanation of omental bursae (lesser sac). The immobilized form of sodium hypochlorite was applied for the second group. RESULTS. Anti-inflammatory activity of immobilized form of sodium hypochlorite exceeded this activity in case of «Levomecol» application in 1,2-1,4 times. Anti-microbial activity was higher in 1,6-1,8 times at different terms of treatment of experimental animals. The proposed method of treatment of infected pancreatonecrosis allowed doctors to decrease the number of postoperative complications in patients on 11,2 % and lethality - on 9,2 %. CONCLUSIONS. It was stated that the application of immobilized forms of sodium hypochlorite for sanation of the omental bursae was pathogenically justified and efficient.
Detecting virus mutations via dynamic matching (2009)

To defeat current commercial antivirus software, the virus developers are employing obfuscation techniques to create mutating viruses. The current antivirus software cannot handle the obfuscated viruses well since its detection methods that are based upon static signatures are not resilient to even slight variations in the code that forms the virus. In this paper, we propose a new type of virus signature, called dynamic signature, and an algorithm for matching dynamic signatures. Our dynamic signature is created based on the runtime behavior of a virus. Therefore, an obfuscated virus can also be detected using a dynamic signature as long as it dynamically behaves like the original virus. We also discuss issues related to deploying our virus detection approach. Our experiments based upon several known mutating viruses show that our method is effective in identifying obfuscated viruses.
Rod-like attapulgite/polyimide nanocomposites with simultaneously improved strength, toughness, thermal stability and related mechanisms (2008)

Rod-like silicates (attapulgite, ATT) with covalently grafted polymer chains chemically identical to the matrix were incorporated into polyimide films, which resulted in prominent improvements in strength and toughness and elevation as high as 51 °C of the thermal decomposition temperature. The dispersion uniformity of ATT nanorods in the polyimide was confirmed by SEM observations and UV-vis spectra. High grafting efficiency of the polymer on the particle surface significantly confines the segmental motion of the polyimide, causing a 33 °C increase in the glass transition temperature and remarkable broadening in the primary transition of nanocomposite films. The decreases in strength and toughness of the samples with high particle contents indicate that there are other factors impacting the mechanical properties of nanocomposites, besides percolated particle networks and attractive interfacial interactions. The plastic deformation observed on the fracture surface of nanocomposites suggests that the introduction of free volume, due to the exclusive volume effect of particles and polymer chains, might play a crucial role especially for those samples with high particle contents. Some fundamental facts based on the free volume effect are proposed to elucidate the possible reasons why the strength and toughness of nanocomposites decrease at high particle contents, which implies that there probably exists a limit upon simultaneously reinforcing and toughening a polymer matrix by means of adding nanoparticles. Similarly, such a limit probably impairs the improvement in thermal stability of nanocomposites at high particle contents, although the segmental confinement effect and porous feature of rod-like silicates have led to pronounced improvements in the thermal stability of the polyimide.
The use of microfibrillated cellulose in fine paper manufacturing – Results from a pilot scale papermaking trial (2014)

In this work the strength enhancing capabilities of microfibrillated cellulose (MFC) in highly filled papers was studied. Both the MFC production and the paper making were done in pilot scale under ...
Prognostic Implication of Creatine Kinase Elevation Following Elective Coronary Artery Interventions (1997)

Creatine kinase elevation following elective PTCA is associated with increased late cardiac mortality. This increase in cardiac mortality is independent of clinical variables, severity of heart disease, coronary artery lesion characteristics, interventional devices, and procedural outcomes. Even patients with lesser degrees of CK elevation are at significantly increased risk for late cardiac death.
Online Learning under Delayed Feedback (2013)

Online learning with delayed feedback has received increasing attention recently due to its several applications in distributed, web-based learning problems. In this paper we provide a systematic study of the topic, and analyze the effect of delay on the regret of online learning algorithms. Somewhat surprisingly, it turns out that delay increases the regret in a multiplicative way in adversarial problems, and in an additive way in stochastic problems. We give meta-algorithms that transform, in a black-box fashion, algorithms developed for the non-delayed case into ones that can handle the presence of delays in the feedback loop. Modifications of the well-known UCB algorithm are also developed for the bandit problem with delayed feedback, with the advantage over the meta-algorithms that they can be implemented with lower complexity.