gebhart/patrepeval huggingface dataset:
Defense against biologic warfare with superantigen toxins. (2002)

The lethal effect of superantigens can be blocked with a peptide antagonist that inhibits their action at the top of the toxicity cascade before activation of T cells occurs. Superantigenic toxin antagonists may serve not only as countermeasures to biologic warfare but may be useful in the treatment of staphylococcal and streptococcal toxic shock, as well as in some cases of septic shock.
Use of reflection tomography to predict pore pressure in overpressured reservoir sands (2003)

PreviousNext No AccessSEG Technical Program Expanded Abstracts 2003Use of reflection tomography to predict pore pressure in overpressured reservoir sandsAuthors: C. M. SayersT. J. H. SmitC. van EdenR. WervelmanB. BachmannT. FittsJ. BinghamK. McLachlanP. HooymanS. NoethD. MandhiriC. M. SayersShell U.K. Exploration and Production Ltd., T. J. H. SmitShell U.K. Exploration and Production Ltd., C. van EdenShell U.K. Exploration and Production Ltd., R. WervelmanShell U.K. Exploration and Production Ltd., B. BachmannShell U.K. Exploration and Production Ltd., T. FittsExxonMobil Upstream Research Company, J. BinghamExxonMobil International Ltd, K. McLachlanExxonMobil International Ltd, P. HooymanSchlumberger, S. NoethSchlumberger, and D. MandhiriSchlumbergerhttps://doi.org/10.1190/1.1817541 SectionsAboutPDF/ePub ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinked InRedditEmail Permalink: https://doi.org/10.1190/1.1817541FiguresReferencesRelatedDetailsCited ByA machine learning methodology for multivariate pore-pressure predictionComputers & GeosciencesPyGeoPressure: Geopressure Prediction in PythonJournal of Open Source Software, Vol. 3, No. 30Modeling Geopressures in a Tight Gas Reservoir, An Argentinean Case14 August 2018Use of prestack depth migration for improving the accuracy of horizontal drilling in unconventional reservoirsThe Leading Edge, Vol. 37, No. 1Pore Pressure and Elastic Moduli Estimation Considerations for a Simplified Geomechanical Model of the Vaca Muerta FormationSergio Cuervo and Ezequiel Lombardo12 September 2017 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 C. M. Sayers, T. J. H. Smit, C. van Eden, R. Wervelman, B. Bachmann, T. Fitts, J. Bingham, K. McLachlan, P. Hooyman, S. Noeth, and D. Mandhiri, (2003), "Use of reflection tomography to predict pore pressure in overpressured reservoir sands," SEG Technical Program Expanded Abstracts : 1362-1365. https://doi.org/10.1190/1.1817541 Plain-Language Summary PDF DownloadLoading ...
Free-Surface Microfluidics/Surface-Enhanced Raman Spectroscopy for Real-Time Trace Vapor Detection of Explosives (2012)

The dominant physical transport processes are analyzed in a free-surface microfluidic and surface-enhanced Raman spectroscopy (SERS) chemical detection system. The analysis describes the characteristic fluid dynamics and mass transport effects occurring in a microfluidic detection system whose analyte absorption and concentration capability is designed to operate on principles inspired by canine olfaction. The detection system provides continuous, real-time monitoring of particular vapor-phase analytes at concentrations of 1 ppb. The system is designed with a large free-surface-to-volume ratio microfluidic channel which allows for polar or hydrophilic airborne analytes to readily be partitioned from the surrounding gas phase into the aqueous phase for detection. The microfluidic stream can concentrate certain molecules by up to 6 orders of magnitude, and SERS can enhance the Raman signal by 9-10 orders of magnitude for molecules residing in the so-called SERS "hot spots", providing extremely high detection sensitivity. The resulting vibrational spectra are sufficiently specific to identify the detected analyte unambiguously. Detection performance was demonstrated using a nominal 1 ppb, 2,4-dinitrotoluene (2,4-DNT) vapor stream entrained within N(2) gas. Applications to homeland security arise from the system's high sensitivity and its ability to provide highly reproducible, continuous chemical detection monitoring with minimal sampling requirements.
Patterned silicon molecular beam epitaxy with submicron lateral resolution (1982)

Patterned epitaxial silicon films are grown on silicon substrates by molecular beam deposition (MBE) through an oxide masking layer. Epitaxial patterns faithfully reproduce the oxide mask, which is fabricated by conventional photolithographic processes. Resolution is determined solely by the mask, and linewidths below 1 μ are demonstrated. Sample morphology and crystallinity are examined by scanning and transmission electron microscopy, and Nomarski interference contrast microscopy in conjunction with chemical defect etching. These techniques confirm that patterned films are epitaxial and free of observable defects. A chemical liftoff step dissolves the oxide mask and leaves an elevated silicon pattern. Patterned film growth requires no modification to the MBE apparatus.
Coherent optical multicarrier systems (1989)

Optical coherent multicarrier systems with highly selective tunable optical heterodyne receivers can be used for transmission and switching of broadband signals. Some technical solutions for coherent bidirectional subscriber lines, a ten-channel distribution system, and a switching setup with computer-controlled receiver tuning are presented. The laboratory experiments, including carrier-frequency stabilization, multiplexing, and demultiplexing, as well as the fiber components used, are described. The influence of fiber nonlinearities on multicarrier transmission is considered.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Memristor-based adder designs (2018)

This chapter presents various designs of memristor-based adders. IMPLY, hybridCMOS, threshold gate, and MAD approaches are employed to implement ripplecarry, carry-select, conditional-sum, and carry-lookahead adders. Each design is described and analyzed in terms of complexity and delay. Completed schematics are also given.
Solute Capture and Doping of Al in Cu<sub>2</sub>O: Corrosion, Tarnish Resistance, and Cation Release of High-Purity Cu-Al Alloys in Artificial Perspiration (2018)

Frequently-touched surfaces are a common transmission source for hospital and community acquired infections. Cu alloys have shown promise as antimicrobial surfaces, able to kill even antibiotic-resistant bacteria within minutes. However, the most efficacious alloy systems readily tarnish making them unsuitable for hospital applications and tarnish-resistant (e.g., passive) systems often cannot maintain sufficient Cu ion release to maintain antimicrobial function. An ideal alloy would have optimal corrosion, tarnishing, and Cu release tuned through alloying elements. Cu-Al alloys are tarnish-resistant, yet the precise role of Al remains unclear. High-purity binary alloys of Cu-Al were fully immersed in artificial perspiration at open circuit to evaluate soluble cation release, quantity and identity of corrosion products, as well as interrogate the role of Al on the chemical, structural, and electronic defect structure of oxides formed. Al became captured in Cu2O as a substitutional cation defect which in turn caused structural, and electronic modifications. This doped film did not inhibit soluble Cu cation release for antimicrobial function even after 144 h. Al-doped cuprous oxide had fewer electronic charge carriers (holes) due to Al-doping and subsequent increased electronic resistance. These results are promising regarding the aim of generating a tunable tarnish-resistant layer for an antimicrobial Cu-based alloy.
Development of broadly neutralizing antibodies targeting the cytomegalovirus subdominant antigen gH (2022)

Abstract Human cytomegalovirus (HCMV) is a β-herpesvirus that increases morbidity and mortality in immunocompromised individuals including transplant recipients and newborns. New anti-HCMV therapies are an urgent medical need for diverse patient populations. HCMV infection of a broad range of host tissues is dependent on the gH/gL/gO trimer and gH/gL/UL28/UL130/UL131A pentamer complexes on the viral envelope. We sought to develop safe and effective therapeutics against HCMV by generating broadly-neutralizing, human monoclonal antibodies (mAbs) from VelocImmune® mice immunized with gH/gL cDNA. Following high-throughput binding and neutralization screening assays, 11 neutralizing antibodies were identified with unique CDR3 regions and a high-affinity (K D 1.4-65 nM) to the pentamer complex. The antibodies bound to distinct regions within Domains 1 and 2 of gH and effectively neutralized diverse clinical strains in physiologically relevant cell types including epithelial cells, trophoblasts, and monocytes. Importantly, combined adminstration of mAbs with ganciclovir, an FDA approved antiviral, greatly limited virus dissemination. Our work identifies several anti-gH/gL mAbs and sheds light on gH neutralizing epitopes that can guide future vaccine strategies.
Purification and Characterization of a Novel Phosphorylase, Kojibiose Phosphorylase, from Thermoanaerobium brockii. (1999)

The thermophilic anaerobe Thermoanaerobium brockii ATCC 35047 produces a novel phosphorylase, kojibiose phosphorylase, which catalyzes the reversible phosphorolysis of kojibiose to form β-glucose 1-phosphate and D-glucose. The enzyme was purified from a cell-free extract to an electrophoretically homogeneous state by successive column chromatography on DEAE-Toyopearl 650S, CM-Toyopearl 6505, Hydroxyapatite, Ultrogel AcA44, Mono Q, and Butyl-Toyopearl 650 M . The enzyme had a molecular weight of 83, 000 by SDS-polyacrylamide gel electrophoresis and a pl of 4 .3 to 4.4 by gel isoelectrofocusing. The enzyme showed the highest activity at pH 5 .5 and 65°C, and was stable from pH 5.5 to 9.7 and up to 65°C. The enzyme activity was inhibited by Hg2+ and Pb2+0. The Km values for kojibiose, Pi, glucose, and β-glucose 1-phosphate were 0 .77, 0.85, 3.52, and 0.77 mM, respectively.
Lens Material Development for Improved Halogen Headlamp Visibility (2003)

<div class="htmlview paragraph">Automobile headlamps are highly controlled products that must meet various performance standards to be commercialized. The combination of the bulb and lens must emit acceptable color and light output. Commercially available headlamps use different types of bulbs but usually a clear or slightly tinted lens. In the past few years, high performance bulbs have been used. These are known as HID or xenon lamps and are characterized by their bluer color compared to standard halogen bulbs.</div> <div class="htmlview paragraph">This paper explores some of the possibilities that new lens material can offer in terms of design and aesthetics with little or no impact on lighting performance as tested per the Society of Automotive Engineers (SAE) J1383 [<span class="xref">1</span>]. Light stability of these new lens materials is also discussed. In addition, this paper illustrates the possibility of creating a system based on halogen bulbs in which the beam chromaticity appears to be similar to a HID system in all angles of the beam pattern that are not in direct view. The potential benefits of such systems with regard to improved road visibility and glare is also discussed.</div>
Solvent stimulated actuation of polyurethane-based shape memory polymer foams using dimethyl sulfoxide and ethanol (2016)

Solvent exposure has been investigated to trigger actuation of shape memory polymers (SMPs) as an alternative to direct heating. This study aimed to investigate the feasibility of using dimethyl sulfoxide (DMSO) and ethanol (EtOH) to stimulate polyurethane-based SMP foam actuation and the required solvent concentrations in water for rapid actuation of hydrophobic SMP foams. SMP foams exhibited decreased <i>T</i><sub>g</sub> when submerged in DMSO and EtOH when compared to water submersion. Kinetic DMA experiments showed minimal or no relaxation for all SMP foams in water within 30 min, while SMP foams submerged in EtOH exhibited rapid relaxation within 1 min of submersion. SMP foams expanded rapidly in high concentrations of DMSO and EtOH solutions, where complete recovery over 30 min was observed in DMSO concentrations greater than 90% and in EtOH concentrations greater than 20%. This study demonstrates that both DMSO and EtOH are effective at triggering volume recovery of polyurethane-based SMP foams, including in aqueous environments, and provides promise for use of this actuation technique in various applications.
Identification of the αvβ3 Integrin-interacting Motif of βig-h3 and Its Anti-angiogenic Effect (2003)

betaig-h3 is an extracellular matrix protein that mediates adhesion and migration of several cell types through interaction with integrins. In the present study, we tested whether betaig-h3 mediates endothelial cell adhesion and migration, thereby regulating angiogenesis. In this study, we demonstrate that not only betaig-h3 itself but also all four fas-1 domains of betaig-h3 mediate endothelial cell adhesion and migration through interaction with the alphavbeta3 integrin. We found that the alphavbeta3 integrin-interacting motif of the four fas-1 domains of betaig-h3 is the same YH motif that we reported previously to interact with alphavbeta5 integrin. The YH peptide inhibited endothelial cell adhesion and migration in a dose-dependent manner. We demonstrate that the YH peptide has anti-angiogenic activity in vitro and in vivo using an endothelial cell tube formation assay and a Matrigel plug assay, respectively. Our results reveal that betaig-h3 bears alphavbeta3 integrin-interacting motifs that mediate endothelial cell adhesion and migration and, therefore, may regulate angiogenesis.
Supplementary Figure 1 from Inhibition of Soluble Tumor Necrosis Factor Prevents Chemically Induced Carcinogenesis in Mice (2023)

<p>Gating strategy for three-color flow cytometry analysis of splenic MDSCs. Splenocytes were simultaneously stained with anti-CD11b-FITC, anti-Gr1-PE and anti-Ly6C-APC antibodies or the corresponding isotype control antibodies and analyzed by flow cytometry as follows. Gate 1: single cells were gated and cell aggregates were excluded. Gate 2: using side-scatter (SSC) and forward-scatter (FSC), granular and non-granular (mononuclear) cells were gated. Gate 3: CD11b+ granular (A) and mononuclear (B) cells were gated. Gate 4: Gr1 and Ly6 expression on CD11b+ granular (A) and mononuclear (B) cells was examined.</p>
Abstract 5665: New alternatives to photodynamic therapy based on light-enabled drug delivery. (2013)

Abstract Conventional photodynamic therapy (PDT) aims to achieve tumor drug targeting by selectively killing cells upon illumination. PDT serves as a non-invasive treatment option for many types of non-metastatic, light-accessible cancers such as those involving the head and neck, lung, bladder, prostate, or esophagus. The various types of PDT all use the same basic strategy for killing cells; photosensitizing molecules are taken up by cancer cells, and, upon illumination, singlet oxygen is generated in the vicinity of the photosensitizer, killing the cell. A new alternative to PDT is photochemical internalization, in which singlet oxygen generated by a photosensitizer disrupts endosomes containing a toxin, releasing it into the cytoplasm and killing the cell. A drawback to both of these approaches is that moderate levels of oxygen are required, yet tumors are often hypoxic environments. Moreover, during PDT treatment, oxygen levels drop even further as the singlet oxygen is consumed; this can compromise treatment effectiveness. We have sought to address these challenges by developing new strategies for light-based treatment of cancer that are oxygen independent. In the first approach, which we call photocaged permeability, we have attached the anticancer drug doxorubicin to a cell impermeable small molecule via a light-cleavable linker. We show using flow cytometry and confocal microscopy that this conjugate is cell impermeable in the dark, yet upon illumination, doxorubicin is released and enters the cells. The IC50 for our conjugate in JH-EsoAd1 cells using non-cytotoxic doses of light is 1.6 μM, identical to that of doxorubicin alone. No cytotoxicity is observed at doses 30-fold higher in the dark. In a second approach, we have attached doxorubicin to folate receptor and PSMA ligands via a light cleavable linker in order to enable dual cancer cell targeting with both light and ligand specificity. The ability of the resulting conjugates to selectively kill cells expressing the requisite receptors with light will be described. Citation Format: M. Michael Dcona, Deboleena Mitra, Rachel W. Goehe, David A. Gewirtz, Deborah A. Lebman, Matthew C.T. Hartman. New alternatives to photodynamic therapy based on light-enabled drug delivery. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 5665. doi:10.1158/1538-7445.AM2013-5665
Novel method and applications for labeling and identifying lymph nodes (2007)

The lymphatic system comprises a series of interconnected lymph nodes that are commonly distributed along branching or linearly oriented anatomic structures. Physicians must evaluate lymph nodes when staging cancer and planning optimal paths for nodal biopsy. This process requires accurately determining the lymph node's position with respect to major anatomical landmarks. In an effort to standardize lung cancer staging, The American Joint Committee on Cancer (AJCC) has classified lymph nodes within the chest into 4 groups and 14 sub groups. We present a method for automatically labeling lymph nodes according to this classification scheme, in order to improve the speed and accuracy of staging and biopsy planning. Lymph nodes within the chest are clustered around the major blood vessels and the airways. Our fully automatic labeling method determines the nodal group and sub-group in chest CT data by use of computed airway and aorta centerlines to produce features relative to a given node location. A classifier then determines the label based upon these features. We evaluate the efficacy of the method on 10 chest CT datasets containing 86 labeled lymph nodes. The results are promising with 100% of the nodes assigned to the correct group and 76% to the correct sub-group. We anticipate that additional features and training data will further improve the results. In addition to labeling, other applications include automated lymph node localization and visualization. Although we focus on chest CT data, the method can be generalized to other regions of the body as well as to different imaging modalities.
Slurry Bubble Column Reactor Optimization (book chapter) (2007)

Slurry bubble column reactors (SBCR) are the preferred contactors for the conversion of syngas to fules and chemicals partially due to their superior heat and mass transfer characteristics. The multiphase fluid dynamics in these systems greatly affect the reactor volumetric productivity. Here, we have developed a computational fluid dynamics (CFD) assisted design methodology for searching the optimum particle size for maximum production in a SBCR. Reactor optimization due to heat exchanger configuration was also investigated. We have rearranged the heat exchangers in a SBCR and constructed a CFD model for a baffled reactor. The novel arrangement of the exchangers prevents the unfavorable high catalysts concentration at the lower stage of the reactor. Thus an optimum catalyst concentration is maintained during the course of the production of liquid fuels.
SEGMENTATION-FREE ONLINE ARABIC HANDWRITING RECOGNITION (2011)

Arabic script is naturally cursive and unconstrained and, as a result, an automatic recognition of its handwriting is a challenging problem. The analysis of Arabic script is further complicated in comparison to Latin script due to obligatory dots/stokes that are placed above or below most letters. In this paper, we introduce a new approach that performs online Arabic word recognition on a continuous word-part level, while performing training on the letter level. In addition, we appropriately handle delayed strokes by first detecting them and then integrating them into the word-part body. Our current implementation is based on Hidden Markov Models (HMM) and correctly handles most of the Arabic script recognition difficulties. We have tested our implementation using various dictionaries and multiple writers and have achieved encouraging results for both writer-dependent and writer-independent recognition.
Access control in a world of software diversity (2005)

We describe a new design for authentication and access control. In this design, principals embody a flexible notion of authentication. They are compound principals that reflect the identities of the programs that have executed, even those of login programs. These identities are based on a naming tree. Our access control lists are patterns that recognize principals. We show how this design supports a variety of access control scenarios. 1.
Conversion of a murine monoclonal antibody A13 targeting epidermal growth factor receptor to a human monoclonal antibody by guided selection (2012)

Epidermal growth factor receptor (EGFR) is an attractive target for tumor therapy because it is overexpressed in the majority of solid tumors and the increase in receptor expression levels has been linked with a poor clinical prognosis. Also it is well established that blocking the interaction of EGFR and the growth factors could lead to the arrest of tumor growth and possibly result in tumor cell death. A13 is a murine monoclonal antibody (mAb) that specifically binds to various sets of EGFR-expressing tumor cells and inhibits EGF-induced EGFR phosphorylation. We isolated human immunoglobulin genes by guided selection based on the mAb A13. Four different human single chain Fvs (scFvs) were isolated from from hybrid scFv libraries containing a human VH repertoire with the VL of mAb A13 and a human VL repertoire with the VH of mAb A13. All the 4 scFvs bound to EGFR-expressing A431 cells. One scFv (SC414) with the highest affinity was converted to IgG1 (ER414). The ER414 exhibited ∼17 fold lower affinity compared to the A13 mAb. In addition the ER414 inhibited an EGF-induced tyrosine phosphorylation of EGFR with much lower efficacy compared to the A13 mAb and Cetuximab (Merck KgaA, Germany). We identified that the epitope of A13 mAb is retained in ER414. This approach will provide an efficient way of converting a murine mAb to a human mAb.
Mass probe-assisted ionization method for total analysis of biomolecules with electrospray ionization–mass spectrometry (2006)

In this paper, we review the mass probes used for the derivation of a variety of biomolecules efficiently detected by the electrospray ionization-mass spectrometry and mass probe-assisted ionization method for total analysis and determination by consecutive detection with a single instrument. We describe mass probes for a variety of molecules including proteins, nucleobases, metallic cations, and other small molecules.