gebhart/patrepeval huggingface dataset:
Characterization of Human Glioblastoma Cell Lines in vitro and their Xenografts in Nude Mice by DNA Fingerprinting (1990)

Human gliomas were grown as permanent tissue cultures and xenografts in nude mice. DNA fingerprint patterns from two human gliomas were established using two different hypervariable multilocus probes [( GTG]5 and 33.15). In general the cell lines investigated showed an overall stability in the DNA fingerprint pattern. However, differences in the DNA fingerprint patterns were shown to occur depending upon the above mentioned parameters.
Virologic Differences Do Not Fully Explain the Diversification of Swine Influenza Viruses in the United States (2016)

There appear to be no differences in the abilities of classical swine and TRIG swine viruses to exclude a second virus, suggesting that under the right circumstances both viruses have similar opportunities to reassort. The increased percentage of TRIG polymerase gene segments in reassortant H3 viruses indicates that these viruses may be more compatible with gene segments from other viruses; however, this needs to be investigated further. Nevertheless, the classical swine virus also showed the ability to reassort, suggesting that factors other than reassortment capacity alone are responsible for the different epidemiologies of TRIG and classical swine viruses. The post-TRIG diversity was likely driven by increased intensive farming practices rather than virologic properties. Our results indicate that host ecology can be a significant factor in viral evolution.
FLOW STRUCTURES AND SUSPENDED SEDIMENT TRANSPORT AROUND SUBMERGED SPUR-DIKES (2012)

In this study, coherent flow structures and mechanisms of suspended sediment transport around submerged spur-dikes were investigated by performing a flume experiment with Particle Image Velocimetry (PIV) technique for particles of neutral buoyancy and relatively heavy materials. Large Eddy Simulation (LES) and Direct Numerical Calculation (DNS) of particle motion were additionally applied in order to interprete the results by the PIV experiment. The experimental results show that correlation coefficients of the PIV analysis for heavy particles decrease when vorticity around the cross-stream axis increase around a shear layer between over-flows on dikes and stagnant regions in-between dikes. It is numerically explained that the heavy particles were preferentially transported by downward motions which were provided by separation eddies with cross-stream axis from top of dikes.
Near surface velocities at Ekofisk from Scholte and refracted wave analysis (2014)

Summary Life of Field Seismic (LoFS) permanent seabed seismic system has been installed and operating at the Ekofisk field since 2008. High quality active source seismic and passive seismic data have been recorded in the field and effectively used for management of the reservoir and overburden. In this paper we demonstrate how horizontally propagating surface waves from active source seismic data allow us to estimate near surface seismic velocities and associated anisotropy. We also show how the observed time dependent velocity changes are empirically associated with strain and stress changes from production induced subsidence. We base our analysis on Scholte waves, which are dispersive surface waves that propagate horizontally under the seabed, and critically refracted compressional (CRC) waves, which are P-waves that propagate horizontally along the seabed starting with the critical offset. The results indicate that the average seismic velocity is related to the expected principal stress magnitude, and seismic anisotropy is related to stress change preferential directions
MiniLDV - Concept Study for a Small-Size Low-Cost Laser Doppler Velocimeter (2022)

Main idea of this concept study MiniLDV is a small-size and low-cost Laser-Doppler Velocimeter. The sensor<br> system will be based on laser diodes, photo diodes, and special multifunctional integrated optical circuits with<br> embedded frequency shift functionality. Basis of MiniLDV will be a back scattering set-up with four beams,<br> i.e. measurement possibility for two velocity components. The system is planned to be very small and with<br> low weight. First simulations for size an energy density of the measuring volume are presented.
Holographic diffraction of complex beams and gratings: theory and simulation (2023)

Volume holographic optical elements (HOEs) are of great interest for dense information storage and optical processing such as wavelength division multiplexing (WDM) and angle multiplexing. There are numerous theoretical frameworks that attempt to model and test diffraction from a holographic grating, among the most prominent of which is Kogelnik’s coupled-wave theory, which applies to thick holograms. However, diffraction from grating geometries resulting from interference among more than two wave-vectors is difficult to model mathematically. In particular, gratings formed from converging or diverging beams present curved profiles that vary with the position inside the material. One approach to analyze these types of holographic gratings is to use a finite element method (FEM) to search for a steady-state solution for the wave equation of a beam propagating through, and diffracting from, the grating. Such a method will necessarily be computationally intensive given that the simulation will require a resolution smaller than the reading wavelength but will encompass a large volume, as is required for a thick hologram. Current technology has enabled this approach to be a viable alternative to traditional modeling. Here, we present the results of an FEM analysis using the COMSOL Multiphysics 6.0 computer program to simulate the diffraction of holographic gratings with non-trivial profiles. The results enable us to more accurately design volume HOEs with non-planar profiles such as lenses, WDM, etc., to achieve better Bragg selectivity and overall higher performance.
Evaluation of a Developed MRI-Guided Focused Ultrasound System in 7 T Small Animal MRI and Proof-of-Concept in a Prostate Cancer Xenograft Model to Improve Radiation Therapy (2023)

Focused ultrasound (FUS) can be used to physiologically change or destroy tissue in a non-invasive way. A few commercial systems have clinical approval for the thermal ablation of solid tumors for the treatment of neurological diseases and palliative pain management of bone metastases. However, the thermal effects of FUS are known to lead to various biological effects, such as inhibition of repair of DNA damage, reduction in tumor hypoxia, and induction of apoptosis. Here, we studied radiosensitization as a combination therapy of FUS and RT in a xenograft mouse model using newly developed MRI-compatible FUS equipment. Xenograft tumor-bearing mice were produced by subcutaneous injection of the human prostate cancer cell line PC-3. Animals were treated with FUS in 7 T MRI at 4.8 W/cm<sup>2</sup> to reach ~45 °C and held for 30 min. The temperature was controlled via fiber optics and proton resonance frequency shift (PRF) MR thermometry in parallel. In the combination group, animals were treated with FUS followed by X-ray at a single dose of 10 Gy. The effects of FUS and RT were assessed via hematoxylin-eosin (H&E) staining. Tumor proliferation was detected by the immunohistochemistry of Ki67 and apoptosis was measured by a TUNEL assay. At 40 days follow-up, the impact of RT on cancer cells was significantly improved by FUS as demonstrated by a reduction in cell nucleoli from 189 to 237 compared to RT alone. Inhibition of tumor growth by 4.6 times was observed in vivo in the FUS + RT group (85.3%) in contrast to the tumor volume of 393% in the untreated control. Our results demonstrated the feasibility of combined MRI-guided FUS and RT for the treatment of prostate cancer in a xenograft mouse model and may provide a chance for less invasive cancer therapy through radiosensitization.
Synthesis, Characterization, and Morphology of Model Graft Copolymers with Trifunctional Branch Points (1996)

Well-defined graft copolymers with polyisoprene backbones and polystyrene branches, having trifunctional branch points, of the type S2IS2 (H-shaped) and (SI)I(SI) (π-shaped) were synthesized by anionic polymerization high-vacuum techniques. The synthetic strategy involves the preparation of the outer parts of the molecules, carrying one reactive Si−Cl bond, followed by coupling with difunctional living poly(isoprenyllithium) chains. In this way, the number and placement of the branches can be precisely controlled. Molecular characterization of the fractionated samples by size exclusion chromatography with UV and RI detection, membrane osmometry, low-angle laser light scattering, and 1H-NMR spectroscopy confirmed that the materials exhibit narrow molecular weight distributions and low compositional heterogeneity. The strongly microphase-separated morphologies of these two samples were characterized using TEM and SAXS. The π architecture with a PS volume fraction of 0.21 was found to form body-centered cubic spheres, while the H architecture with a PI volume fraction of 0.64 was found to form a lamellar morphology. The observed morphology for these architectures was rationalized by formally dividing the π and H architectures into component simple (single) graft block copolymers which were mapped onto Milner's morphology diagram for simple graft copolymers.
ChemInform Abstract: DIVERSE MECHANISMS OF CARBON‐HYDROGEN BOND FORMATION THROUGH BINUCLEAR REDUCTIVE ELIMINATION REACTIONS (1982)

Abstract Diverse Mechanisms of Carbon‐Hydrogen Bond Formation Through Binuclear Reductive Elimination Reactions.
Parameterization of Submesoscale Eddy-Rich Flows Using a Stochastic Velocity Model (2006)

Abstract In light of the recent high-resolution radar data of surface velocity, which have revealed submesoscale eddies between the Florida Current and the coast, an objective method of detecting eddies and estimating their parameters such as center coordinates, size, and intensity is suggested. The obtained statistics are used to parametrically represent the birth–death process of eddies filling up the observation area via a model stochastic velocity field known as Çinlar flow. It appears that the suggested approach leads to a reasonable parameterization of this process for potential future use in OGCMs or coastal models.
The role of microRNA miR-34a in the regulation of aryl hydrocarbon receptor interacting protein (2013)

Searchable abstracts of presentations at key conferences in endocrinology ISSN 1470-3947 (print) | ISSN 1479-6848 (online)
Supplementary Tables 6-9 from Isolation of T-Cell Receptors Specifically Reactive with Mutated Tumor-Associated Antigens from Tumor-Infiltrating Lymphocytes Based on CD137 Expression (2023)

&lt;p&gt;These tables contain data representing the screening of TIL for recognition of mutated tandem mini-gene constructs.&lt;/p&gt;
Design, Expression, and Immunogenicity of a Soluble HIV Trimeric Envelope Fragment Adopting a Prefusion gp41 Configuration (2005)

The human immunodeficiency virus-1 (HIV-1) envelope glycoprotein (Env) is comprised of non-covalently associated gp120/gp41 subunits that form trimeric spikes on the virion surface. Upon binding to host cells, Env undergoes a series of structural transitions, leading to gp41 rearrangement necessary for fusion of viral and host membranes. Until now, the prefusion state of gp41 ectodomain (e-gp41) has eluded molecular and structural analysis, and thus assessment of the potential of such an e-gp41 conformer to elicit neutralizing antibodies has not been possible. Considering the importance of gp120 amino (C1) and carboxyl (C5) segments in the association with e-gp41, we hypothesize that these regions are sufficient to maintain e-gp41 in a prefusion state. Based on the available gp120 atomic structure, we designed several truncated gp140 variants by including the C1 and C5 regions of gp120 in a gp41 ectodomain fragment. After iterative cycles of protein design, expression and characterization, we obtained a variant truncated at Lys(665) that stably folds as an elongated trimer under physiologic conditions. Several independent biochemical/biophysical analyses strongly suggest that this mini-Env adopts a prefusion e-gp41 configuration that is strikingly distinct from the postfusion trimer-of-hairpin structure. Interestingly, this prefusion mini-Env, lacking the fragment containing the 2F5/4E10 neutralizing monoclonal antibody binding sites, displays no detectable HIV-neutralizing epitopes when employed as an immunogen in rabbits. The result of this immunogenicity study has important implications for HIV-1 vaccine design efforts. Moreover, this engineered mini-Env protein should facilitate three-dimensional structural studies of the prefusion e-gp41 and serve to guide future attempts at pharmacologic and immunologic intervention of HIV-1.
Strategic Attentive Writer for Learning Macro-Actions (2016)

We present a novel deep recurrent neural network architecture that learns to build implicit plans in an end-to-end manner by purely interacting with an environment in reinforcement learning setting. The network builds an internal plan, which is continuously updated upon observation of the next input from the environment. It can also partition this internal representation into contiguous sub- sequences by learning for how long the plan can be committed to - i.e. followed without re-planing. Combining these properties, the proposed model, dubbed STRategic Attentive Writer (STRAW) can learn high-level, temporally abstracted macro- actions of varying lengths that are solely learnt from data without any prior information. These macro-actions enable both structured exploration and economic computation. We experimentally demonstrate that STRAW delivers strong improvements on several ATARI games by employing temporally extended planning strategies (e.g. Ms. Pacman and Frostbite). It is at the same time a general algorithm that can be applied on any sequence data. To that end, we also show that when trained on text prediction task, STRAW naturally predicts frequent n-grams (instead of macro-actions), demonstrating the generality of the approach.
Demonstration of Chemisorption of Carbon Dioxide in 1,3‐Dialkylimidazolium Acetate Ionic Liquids (2011)

Echte Chemie: Spektroskopische und kristallographische Analysen bestätigen die chemische Reaktion von CO2 mit Carbenen in flüssigen 1,3-Dialkylimidazoliumacetaten sowie die unterstützende Rolle des Acetations in diesen Reaktionen. Wenn CO2 durch [C2mim][OAc] geleitet wurde, konnte die Bildung des entsprechenden Imidazoliumcarboxylats, [C2mim+-COO−], beobachtet werden. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Dry etching of β-SiC in CF4 and CF4+O2 mixtures (1986)

Dry etching of cubic (100)β-SiC single crystal thin films produced via chemical vapor deposition (CVD) has been performed in CF4 and CF4+O2 mixtures, in both the reactive ion etching (RIE) and plasma etching modes. The latter process yielded measurable etch rates, but produced a dark surface layer which appears, from the results of secondary ion mass spectrometry, to be residual SiC. The RIE samples had no residual layer, but Auger electron spectroscopy did reveal a C-rich surface. The optimal RIE conditions were obtained with 10 sccm of pure CF4 at 40 mTorr and a power density of 0.548 W/cm2, giving an etch rate of 23.3 nm/min. Neither the increase of temperature between 293 and 573 K, nor the incremental addition of O2 to CF4 to 50%, produced any strong effect on the etch rates of SiC during RIE. Pictorial evidence of fine line structures produced by RIE of β-SiC films are also presented.
Gold-Loaded Nanoporous Ferric Oxide Nanocubes with Peroxidase-Mimicking Activity for Electrocatalytic and Colorimetric Detection of Autoantibody (2017)

The enzyme-mimicking activity of iron oxide based nanostructures has provided a significant advantage in developing advanced molecular sensors for biomedical and environmental applications. Herein, we introduce the horseradish peroxidase (HRP)-like activity of gold-loaded nanoporous ferric oxide nanocubes (Au-NPFe<sub>2</sub>O<sub>3</sub>NC) for the development of a molecular sensor with enhanced electrocatalytic and colorimetric (naked eye) detection of autoantibodies. The results showed that Au-NPFe<sub>2</sub>O<sub>3</sub>NC exhibits enhanced peroxidase-like activity toward the catalytic oxidation of 3,3',5,5'-tertamethylbenzidine (TMB) in the presence of H<sub>2</sub>O<sub>2</sub> at room temperature (25 °C) and follows the typical Michaelis-Menten kinetics. The autoantibody sensor based on this intrinsic property of Au-NPFe<sub>2</sub>O<sub>3</sub>NC resulted in excellent detection sensitivity [limit of detection (LOD) = 0.08 U/mL] and reproducibility [percent relative standard deviation (% RSD) = <5% for n = 3] for analyzing p53-specific autoantibodies using electrochemical and colorimetric (naked eye) readouts. The clinical applicability of the sensor has been tested in detecting p53-specific autoantibody in plasma obtained from patients with epithelial ovarian cancer high-grade serous subtype (EOCHGS, number of samples = 2) and controls (benign, number of samples = 2). As Au-NPFe<sub>2</sub>O<sub>3</sub>NC possess high peroxidase-like activity for the oxidation of TMB in the presence of H<sub>2</sub>O<sub>2</sub> [TMB is a common chromogenic substrate for HRP in enzyme-linked immunosorbent assays (ELISAs)], we envisage that our assay could find a wide range of application in developing ELISA-based sensing approaches in the fields of medicine (i.e., detection of other biomarkers the same as p53 autoantibody), biotechnology, and environmental sciences.
Abnormal uterine bleeding: advantages of formal classification to patients, clinicians and researchers (2014)

The PALM-COEIN classification is applicable globally and, as momentum gathers, will ameliorate recurrence of historic problems, and harmonise reporting of clinical and scientific research to facilitate future progress in women's health.
Image formation challenges in the MOSAIC platform (2011)

The DARPA MOSAIC program applies multiscale optical design (shared objective lens and parallel array of microcameras) to the acquisition of high pixel count images. Interestingly, these images present as many challenges as opportunities. The imagery is acquired over many slightly overlapping fields with diverse focal, exposure and temporal parameters. Estimation of a consensus image, display of imagery at human-comprehensible resolutions, automated anomaly detection to guide viewer attention, and power management in a distributed electronic environment are just a few of the novel challenges that arise. This talk describes some of these challenges and presents progress to date.
Sidestream bio-P and mainstream anammox in a BNR process with upstream carbon capture (2023)

Abstract The integration of biological phosphorus removal (bio-P) and shortcut nitrogen removal (SNR) processes is challenging because of the conflicting demands on influent carbon: SNR allows for upstream carbon diversion but this reduction of influent carbon (especially volatile fatty acids (VFA) prevents or limits bio-P The objective of this study was to achieve SNR, either via partial nitritation/anammox (PNA) or partial denitrification/anammox (PdNA), simultaneously with biological phosphorus removal in a process with upstream carbon capture. This study took place in a pilot scale A/B process with a sidestream bio-P reactor and tertiary anammox polishing. Despite low influent rbCOD concentrations from the A-stage effluent, bio-P occurred in the B-stage thanks to the addition of A-stage WAS fermentate to the sidestream reactor. Nitrite accumulation occurred in the B-stage via partial denitrification and partial nitritation (NOB out-selection), depending on operational conditions, and was removed along with ammonia by the tertiary anammox MBBR, with the ability to achieve effluent TIN less than 2 mg/L.
In situ x-ray diffraction study of crystallization kinetics in PbZr1-xTixO3, (PZT, x = 0.0, 0.55, 1.0) (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTIn situ x-ray diffraction study of crystallization kinetics in PbZr1-xTixO3, (PZT, x = 0.0, 0.55, 1.0)Angus P. Wilkinson, James S. Speck, Anthony K. Cheetham, Srinivasan Natarajan, and John Meurig ThomasCite this: Chem. Mater. 1994, 6, 6, 750–754Publication Date (Print):June 1, 1994Publication History Published online1 May 2002Published inissue 1 June 1994https://doi.org/10.1021/cm00042a009Request reuse permissionsArticle Views951Altmetric-Citations123LEARN 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 InReddit PDF (561 KB) Get e-Alertsclose Get e-Alerts
Label-free superior contrast with c-band ultra-violet extinction microscopy (2023)

In 1934, Frits Zernike demonstrated that it is possible to exploit the sample's refractive index to obtain superior contrast images of biological cells. The refractive index contrast of a cell surrounded by media yields a change in the phase and intensity of the transmitted light wave. This change can be due to either scattering or absorption caused by the sample. Most cells are transparent at visible wavelengths, which means the imaginary component of their complex refractive index, also known as extinction coefficient k, is close to zero. Here, we explore the use of c-band ultra-violet (UVC) light for high-contrast high-resolution label-free microscopy, as k is naturally substantially higher in the UVC than at visible wavelengths. Using differential phase contrast illumination and associated processing, we achieve a 7- to 300-fold improvement in contrast compared to visible-wavelength and UVA differential interference contrast microscopy or holotomography, and quantify the extinction coefficient distribution within liver sinusoidal endothelial cells. With a resolution down to 215 nm, we are, for the first time in a far-field label-free method, able to image individual fenestrations within their sieve plates which normally requires electron or fluorescence superresolution microscopy. UVC illumination also matches the excitation peak of intrinsically fluorescent proteins and amino acids and thus allows us to utilize autofluorescence as an independent imaging modality on the same setup.