gebhart/patrepeval huggingface dataset:
Helicobacter pylori VacA cytotoxin associated with the bacteria increases epithelial permeability independently of its vacuolating activity (1999)

Polarized epithelial monolayers of Madin-Darby canine kidney (MDCK) cells were used to study the pathogenicity of Helicobater pylori, with an emphasis on the effect of VacA. The adherence of H. pylori to MDCK monolayers resulted in a decrease in trans-epithelial resistance (TER) across the cell monolayer. Isogenic vacA mutants did not lower the TER, demonstrating that the effect is strictly linked to the action of the toxin. A similar effect was observed with all VacA-producing strains, including those producing m2 toxins that are inactive in the vacuolating assay. In contrast to that seen with purified toxin, TER decrease was not enhanced by acid pH, which may indicate that the toxin associated to the bacterial surface is possibly in a monomeric state and therefore does not require a pH-induced conformation to be active. These data raise the possibility that one role of VacA in ulcerogenesis may consist of increasing the paracellular permeability of the gastric epithelium.
Data‐driven model based design and analysis of antenna structures (2016)

Data‐driven models, or metamodels, offer an efficient way to mimic the behaviour of computation‐intensive simulators. Subsequently, the usage of such computationally cheap metamodels is indispensable in the design of contemporary antenna structures where computation‐intensive simulations are often performed in a large scale. Although metamodels offer sufficient flexibility and speed, they often suffer from an exponential growth of required training samples as the dimensionality of the problem increases. In order to alleviate this issue, a Gaussian process based approach, known as Gradient‐Enhanced Kriging (GEK) , is proposed in this work to achieve cost‐efficient modelling of antenna structures. The GEK approach incorporates adjoint‐based sensitivity data in addition to function data obtained from electromagnetic simulations. The approach is illustrated using a dielectric resonator and an ultra‐wideband antenna structures. The method demonstrates significant accuracy improvement with the less number of training samples over the Ordinary Kriging (OK) approach which utilises function data only. The discussed technique has been favourably compared with OK in terms of computational cost.
Supplementary Tables from A Modified Nucleoside 6-Thio-2′-Deoxyguanosine Exhibits Antitumor Activity in Gliomas (2023)

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ViBE: A Compressed Video Database Structured for Active Browsing and Search (2004)

In this paper, we describe a unique new paradigm for video database management known as ViBE (video indexing and browsing environment). ViBE is a browseable/searchable paradigm for organizing video data containing a large number of sequences. The system first segments video sequences into shots by using a new feature vector known as the Generalized Trace obtained from the DC-sequence of the compressed data. Each video shot is then represented by a hierarchical structure known as the shot tree. The shots are then classified into pseudo-semantic classes that describe the shot content. Finally, the results are presented to the user in an active browsing environment using a similarity pyramid data structure. The similarity pyramid allows the user to view the video database at various levels of detail. The user can also define semantic classes and reorganize the browsing environment based on relevance feedback. We describe how ViBE performs on a database of MPEG sequences.
Electrical Double Layer-Induced Ion Surface Accumulation for Ultrasensitive Refractive Index Sensing with Nanostructured Porous Silicon Interferometers (2018)

Herein, we provide the first experimental evidence on the use of electrical double layer (EDL)-induced accumulation of charged ions (using both Na<sup>+</sup> and K<sup>+</sup> ions in water as the model) onto a negatively charged nanostructured surface (e.g., thermally growth SiO<sub>2</sub>)-Ion Surface Accumulation, ISA-as a means of improving performance of nanostructured porous silicon (PSi) interferometers for optical refractometric applications. Nanostructured PSi interferometers are very promising optical platforms for refractive index sensing due to PSi huge specific surface (hundreds of m<sup>2</sup> per gram) and low preparation cost (less than $0.01 per 8 in. silicon wafer), though they have shown poor resolution ( R) and detection limit (DL) (on the order of 10<sup>-4</sup>-10<sup>-5</sup> RIU) compared to other plasmonic and photonic platforms ( R and DL on the order of 10<sup>-7</sup>-10<sup>-8</sup> RIU). This can be ascribed to both low sensitivity and high noise floor of PSi interferometers when bulk refractive index variation of the solution infiltrating the nanopores either approaches or is below 10<sup>-4</sup> RIU. Electrical double layer-induced ion surface accumulation (EDL-ISA) on oxidized PSi interferometers allows the interferometer output signal (spectral interferogram) to be impressively amplified at bulk refractive index variation below 10<sup>-4</sup> RIU, increasing, in turn, sensitivity up to 2 orders of magnitude and allowing reliable measurement of refractive index variations to be carried out with both DL and R of 10<sup>-7</sup> RIU. This represents a 250-fold-improvement (at least) with respect to the state-of-the-art literature on PSi refractometers and pushes PSi interferometer performance to that of state-of-the-art ultrasensitive photonics/plasmonics refractive index platforms.
Electron-impurity tunneling in selectively dopedn-typeAlxGa1−xAs/GaAs heterostructures (1985)

The interaction of the two-dimensional electron gas at the semiconductor interface of a selectively doped n-type ${\mathrm{Al}}_{\mathrm{x}}$${\mathrm{Ga}}_{1\mathrm{\ensuremath{-}}\mathrm{x}}$As/GaAs heterostructure grown by molecular-beam epitaxy with empty impurity levels in the ${\mathrm{Al}}_{\mathrm{x}}$${\mathrm{Ga}}_{1\mathrm{\ensuremath{-}}\mathrm{x}}$As layer is investigated both experimentally and theoretically. The electron subband energy levels in the triangular potential well of the heterostructure are calculated by a new method and are in excellent agreement with other approaches. The calculation of the electron-impurity tunneling process is based on a square-well potential shape to obtain solutions in an analytic and not in a numerical form. For experimental investigations we used time-resolved Hall effect and conductivity measurements combined with excitation by monochromatic illumination of the sample. The decay of the carrier concentration after illumination is monitored for more than 3 days at temperatures ranging from 20 to 150 K and is conclusively found to be nonexponential. Extrapolation of the decay to the dark concentration yields a total lifetime of photoconductivity of more than ${10}^{12}$ s at T&lt;eq77 K. The optical threshold energies of 0.95${\mathrm{eqE}}_{\mathrm{do}\mathrm{eq}1.10}$ eV for persistent photoconductivity coincides with the values for transient photoconductivity. This result demonstrates that both parts of the photoconductivity are caused by the same deep Si donor in the ${\mathrm{Al}}_{\mathrm{x}}$${\mathrm{Ga}}_{1\mathrm{\ensuremath{-}}\mathrm{x}}$As layer. The relative contributions to persistent photoconductivity of electron excitation from the deep Si donor in the ${\mathrm{Al}}_{\mathrm{x}}$${\mathrm{Ga}}_{1\mathrm{\ensuremath{-}}\mathrm{x}}$As layer as well as electron-hole generation in the GaAs layer are determined for a specific alloy composition of ${\mathrm{Al}}_{\mathrm{x}}$${\mathrm{Ga}}_{1\mathrm{\ensuremath{-}}\mathrm{x}}$As. Electron-hole generation in the GaAs layer contributes only a minor part to the observed persistent photoconductivity of the heterostructure for alloy compositions xeq0.3.
Phase I study of OPB‐51602, an oral inhibitor of signal transducer and activator of transcription 3, in patients with relapsed/refractory hematological malignancies (2015)

We carried out a multicenter dose-escalation phase I study of oral OPB-51602, a signal transducer and activator of transcription 3 phosphorylation inhibitor, in patients with relapsed or refractory hematological malignancies to evaluate the safety, maximum tolerated dose (MTD), pharmacokinetics, and preliminary antitumor activity. Twenty patients were treated with OPB-51602 at doses of 1, 2, 3, 4, and 6 mg in the "3 + 3" dose escalation design. The most common treatment-related adverse events included nausea (55%), peripheral sensory neuropathy (45%), and diarrhea (40%). The most frequently observed grade 3 or 4 drug-related adverse events were neutropenia (20%), leukopenia (15%), lymphopenia (10%), and thrombocytopenia (10%). The MTD was 6 mg, with dose-limiting toxicities of grade 3 lactic acidosis and increased blood lactic acid levels observed in one of three patients and grade 1-2 peripheral neuropathy in three of three patients. The recommended dose was determined to be 4 mg. OPB-51602 was rapidly absorbed, and exposure tended to increase in a dose-dependent manner. Accumulation of OPB-51602 was seen with 4 weeks of multiple treatments. No clear therapeutic response was observed. Durable stable disease was observed in two patients with acute myeloid leukemia and one with myeloma. In conclusion, the MTD of OPB-51602 was 6 mg. OPB-51602 was safe and well tolerated in a dose range of 1-4 mg. However, long-term administration at higher doses was difficult with the daily dosing schedule, and no response was seen. Therefore, further clinical development of OPB-51602 for hematological malignancies with a daily dosing schedule was terminated.
RD-Optimization for MPEG-2 to H.264 Transcoding (2006)

In this paper, we introduce and evaluate a low complexity macroblock partition mode decision algorithm for inter-frame prediction in MPEG-2 to H.264 transcoder. The proposed tools are used to compute an optimal MB coding mode decision with significantly reduced computational complexity. Specifically, we achieve the computational savings by using the following MB information coming from MPEG-2: the MB coding modes, the coded block pattern (CBPC) in MPEG-2, and the mean and variance of the 16 4times4 sub blocks of the MPEG-2 residual MBs. We use data mining algorithms to develop a decision tree for H.264 coding mode decisions. The decision trees are built using RD optimized mode decisions and result in highly efficient mode decisions. The proposed transcoder is 35% faster than the RD optimized H.264 reference transcoder without a significant PSNR degradation. The proposed transcoder performs over 3 dB better than the SAE cost based H.264 transcoding
Multipole Ion Trap as Cluster-Ion Source (2007)

We have developed a new type of ion trap, an external multipole static attraction ion trap (EMSIT) for use as a cluster-ion source. The EMSIT consists of 36 linear pole electrodes of nearly equal length arranged in a 6×6 square lattice and a cylindrical cage electrode surrounding the pole edges. An ion-trapping field is generated between the multipole and the cage electrode by applying ac and dc voltages to the pole electrodes. Simulation results indicated that the EMSIT can confine the ions with a wide range of mass values in the ion-trapping field and act as a mass-selective ion source using the central four poles as an ion extraction guide. In fact, we observed that Xe+ ions were confined in the EMSIT for more than 1 s in the presence of He buffer gas of 5.0×10-2 Pa. Hydrogenated Si cluster ions, SinHx+ (n=2–6), were grown from SiH4 gas and extracted with mass selection, indicating that the EMSIT acts as a cluster-ion source.
An hybrid CPU-GPU framework for quantitative follow-up of abdominal aortic aneurysm volume by CT angiography (2010)

We developed a hybrid CPU-GPU framework enabling semi-automated segmentation of abdominal aortic aneurysm (AAA) on Computed Tomography Angiography (CTA) examinations. AAA maximal diameter (D-max) and volume measurements and their progression between 2 examinations can be generated by this software improving patient followup. In order to improve the workflow efficiency some segmentation tasks were implemented and executed on the graphics processing unit (GPU). A GPU based algorithm is used to automatically segment the lumen of the aneurysm within short computing time. In a second step, the user interacted with the software to validate the boundaries of the intra-luminal thrombus (ILT) on GPU-based curved image reformation. Automatic computation of D-max and volume were performed on the 3D AAA model. Clinical validation was conducted on 34 patients having 2 consecutive MDCT examinations within a minimum interval of 6 months. The AAA segmentation was performed twice by a experienced radiologist (reference standard) and once by 3 unsupervised technologists on all 68 MDCT. The ICC for intra-observer reproducibility was 0.992 (&ge;0.987) for D-max and 0.998 (&ge;0.994) for volume measurement. The ICC for inter-observer reproducibility was 0.985 (0.977-0.90) for D-max and 0.998 (0.996- 0.999) for volume measurement. Semi-automated AAA segmentation for volume follow-up was more than twice as sensitive than D-max follow-up, while providing an equivalent reproducibility.
Increased gene copy numbers at chromosome 20q are frequent in both squamous cell carcinomas and adenocarcinomas of the cervix (2006)

Genome-wide microarray-based comparative genomic hybridization (array CGH) was used to identify common chromosomal alterations involved in cervical carcinogenesis as a first step towards the discovery of novel biomarkers. The genomic profiles of nine squamous cell carcinomas (SCCs) and seven adenocarcinomas (AdCAs), as well as four human papillomavirus (HPV)-immortalized keratinocyte cell lines, were assessed. On a genome-wide scale, SCCs showed significantly more gains than AdCAs. More specifically, there was a striking and highly significant difference between the two histological types for gain at 3q12.1-28, which was predominantly observed in SCC. Other frequent alterations included gains of 1q21.1-31.1 and 20q11.21-13.33, and losses of 11q22.3-25 and 13q14.3-21.33. Subsequent FISH analysis for hTR, located at 3q26, confirmed the presence of 3q gain in SCCs and HPV-immortalized cell lines. Fine mapping of chromosome 20q using multiplex ligation-dependent probe amplification (MLPA) showed copy number increases for a number of genes located at 20q11-q12, including DNMT3B and TOP1. For DNMT3B, this correlated with elevated mRNA expression in 79% of cases. In conclusion, the assessment of frequent genomic alterations resulted in the identification of potential novel biomarkers, which may ultimately enable a better risk stratification of high-risk (hr)-HPV-positive women.
Vaccination of Humans (2006)

Abstract Vaccines have been the most effective tool for preventing and eliminating devastating infectious diseases, and thus improving the quality of life. Their role will be increasingly important in the medicine of the future because biotechnology has now broadened the targets of vaccination to include new infectious diseases, immunotherapy of tumours, chronic infections, autoimmunity and allergies.
An On‐Chip Quad‐Wavelength Pyroelectric Sensor for Spectroscopic Infrared Sensing (2019)

Merging photonic structures and optoelectronic sensors into a single chip may yield a sensor-on-chip spectroscopic device that can measure the spectrum of matter. In this work, an on-chip concurrent multiwavelength infrared (IR) sensor, which consists of a set of narrowband wavelength-selective plasmonic perfect absorbers combined with pyroelectric sensors, where the response of each pyroelectric sensor is boosted only at the resonance of the nanostructured absorber, is proposed and realized. The proposed absorber, which is based on Wood's anomaly absorption from a 2D plasmonic square lattice, shows a narrowband polarization-independent resonance (quality factor - <i>Q</i> of 73) with a nearly perfect absorptivity as high as 0.99 at normal incidence. The fabricated quad-wavelength IR sensors exhibit four different narrowband spectral responses at normal incidence following the predesigned resonances in the mid-wavelength infrared region that corresponds to the atmospheric window. The device can be applied for practical spectroscopic applications such as nondispersive IR sensors, IR chemical imaging devices, pyrometers, and spectroscopic thermography imaging.
Exciting Wide NMR Spectra of Static Solid Samples with Weak Radiofrequency Fields (2016)

Abstract Trains of short pulses in the manner of ‘delays alternating with nutations for tailored excitation’ (DANTE) have been applied to the Pake patterns of protons of water molecules trapped in a static powdered sample of barium chlorate monohydrate. The spin dynamics in the course of such experiments have been investigated by means of numerical simulations and compared with the ideal refocusing that can be achieved under magic-angle spinning (MAS). Solid echoes yield essentially undistorted lineshapes, in contrast to direct excitation without refocusing that leads to severe dispersions of the phases because of inhomogeneous interactions such as homonuclear dipolar couplings and anisotropic chemical shifts. The selectivity of DANTE sequences allows one to access ‘slices’ of the Pake pattern that can be related to particular crystallite orientations. Single-crystal spectra can therefore be extracted from powder spectra. A similar behavior is expected for both dipolar and quadrupolar echoes.
Reactivity variations within Group 4 complexes of 1,4-di-tert-butyl-1,4-diazabuta-1,3-diene: Structures of [(C5H5)TiCl{(t-BuNCH)2}] and [(C5H5)2Zr{(t-BuNCH)2}] (2008)

The reactions of the metallocene dichlorides [(η5-C5H5)2MCl2], M = Ti and Zr, with the 1,4-di-tert-butyl-1,4-diazabuta-1,3-diene radical anion (lithium complex) in diethyl ether reveal a reactivity difference within the series, yielding [(C5H5)TiCl{(t-BuNCH)2}] and [(C5H5)2Zr{(t-BuNCH)2}] through the elimination of Li(C5H5) and/or LiCl, respectively. We report the X-ray crystal structures of these complexes, and discuss their reactivity patterns and solution fluxional properties.
High resolution imaging in sub‐horizontal well using a single well high frequency seismic system (1997)

PreviousNext No AccessSEG Technical Program Expanded Abstracts 1997High resolution imaging in sub‐horizontal well using a single well high frequency seismic systemAuthors: Sylvain SerbutoviezJean LaurentPatrick MeynierDominique GehantSylvain SerbutoviezInstitut Fraçais du Pétrole, Jean LaurentInstitut Fraçais du Pétrole, Patrick MeynierInstitut Fraçais du Pétrole, and Dominique GehantCompagnie générale de Géophysiquehttps://doi.org/10.1190/1.1885891 SectionsAboutPDF/ePub ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinked InReddit Permalink: https://doi.org/10.1190/1.1885891FiguresReferencesRelatedDetails SEG Technical Program Expanded Abstracts 1997 ISSN (print):1052-3812 ISSN (online):1949-4645 Copyright: 1997 Pages: 2067 publication data© 1997 Copyright © 1997 Society of Exploration GeophysicistsPublisher:Society of Exploration Geophysicists HistoryPublished Online: 10 Feb 2005 CITATION INFORMATION Sylvain Serbutoviez, Jean Laurent, Patrick Meynier, and Dominique Gehant, (1997), "High resolution imaging in sub‐horizontal well using a single well high frequency seismic system," SEG Technical Program Expanded Abstracts : 305-308. https://doi.org/10.1190/1.1885891 Plain-Language Summary PDF DownloadLoading ...
World Weeds: Natural Histories and Distributions. L. Holm, J. Doll, E. Holm, J. Pancho, and J. Herberger J. Wiley, New York. 1,129 p. + xv, 1997. Cloth. ISBN 0471-04701-5, $195. (1997)

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Quantitative analysis of tau pathology in human brain using PET with [C-11]PBB3 (2015)

136 Objectives The characteristic neuropathological changes in Alzheimer disease (AD) are deposition of amyloid senile plaques and neurofibrillary tangles. Recently, we have developed a novel radiotracer [C-11]PBB3 for imaging of tau pathology, and its regional distribution was consistent with the spreading of tau pathology with AD progression. In the present study, [C-11]PBB3 binding was examined in greater detail by compartment model analysis. The accuracy of simplified quantitative methods employing a reference brain region was also evaluated. Methods A dynamic PET scan was performed on 7 normal control subjects and 7 AD patients. The kinetic analyses using the standard two-tissue compartment model with four first-order rate constants or three rate constants assuming irreversible binding were applied. The standardized uptake value ratio (SUVR) was calculated using the cerebellum as a reference region. Results [C-11]PBB3 was rapidly metabolized in plasma. The regional brain time-activity curves could be described by the two-tissue compartment model with four or three rate constants. The k4 values obtained from the two-tissue compartment model with four rate constants were very small (0.003-0.006 min-1 in cerebral cortices for AD patients), indicating that [C-11]PBB3 binding could be considered to be approximately irreversible. Significant correlations were observed between the rate constant k3 indicating specific binding and SUVR. A systemic underestimation of SUVR due to a decrease in K1 was observed by the simulation study. The SUVR were significantly higher in AD patients than in control subjects for cerebral cortical regions except the parahippocampal gyrus. Conclusions The SUVR can be used as a measure of tau deposition with a systemic underestimation due to a decrease in CBF and brain atrophy. The partial volume correction method should be applied to estimate tau deposition in the hippocampal region showing focal brain atrophy in AD patients.
Parameter Estimation of a Permanent Magnet Synchronous Motor using Whale Optimization Algorithm (2018)

To design control algorithm for a permanent magnet synchronous motor, the parameter of PMSM must be estimated accurately. In this paper a well known whale optimization algorithm is used to estimate the parameter of PMSM. To validate the algorithm, a PMSM with known coefficients is considered and the parameter of the model is estimated using WAO.
EVOLUTIONARY DYNAMICS OF HOST-PLANT USE IN A GENUS OF LEAF-MINING MOTHS (2003)

We used nuclear 28S rDNA sequence data to estimate the phylogeny of 77 leaf-mining Phyllonorycter (Gracillariidae) moth species, including all 55 British species, feeding on 44 different plant genera. There was strong support for both the monophyly of Phyllonorycter and the placement of the genus Cameraria as its sister group. Host-plant use was mapped onto the moth phylogeny and investigated statistically in several ways. First, we show that the estimated level of cospeciation between leaf miners and their host plants is not greater than expected by chance, despite the physical intimacy of the association. Nevertheless, the pattern of host-plant use is far from random, with closely related Phyllonorycter species generally feeding on closely related plants. However, although Phyllonorycter species from a given host plant tend to form distinct clades, there is also statistical support for multiple independent colonizations of some host-plant taxa (e.g. the order Rosales and the genus Corylus). Despite numerous host shifts, most Phyllonorycter species feed on trees and the few species that attack shrubs or herbs have mostly acquired these habits independently. There is also limited evidence that host shifts to herbs are more likely from shrubs than from trees. Similarly, most species mine the lower surface of leaves but the few upper-surface miners have each evolved the habit independently. Consequently, these shifts to new adaptive zones have not led to substantial radiations.