gebhart/patrepeval huggingface dataset:
Antibodies against the carboxyl-terminal 5-kDa peptide of the alpha subunit of transducin crossreact with the 40-kDa but not the 39-kDa guanine nucleotide binding protein from brain. (1985)

We tested 18 antisera showing reactivity against the alpha subunit of transducin, the guanine nucleotide binding protein from rod outer segment, for crossreactivity against the 40- and 39-kDa guanine nucleotide binding proteins purified from bovine brain. A single antiserum, CW6, showed crossreactivity, and this was predominantly against the 40-kDa protein. Immunoblots of the tryptic fragments of transducin alpha subunit with multiple antisera raised against that subunit showed that only CW6 recognizes a COOH-terminal 5-kDa peptide that includes the site of pertussis toxin ADP-ribosylation. Antibodies against the 5-kDa peptide, affinity-purified from CW6, specifically react with the 40-kDa brain protein on immunoblots. The results show that the 39- and 40-kDa guanine nucleotide binding proteins from brain differ immunochemically and that the COOH-terminal 5-kDa peptide of transducin alpha subunit is homologous to a region in the 40-kDa brain protein. We speculate that this homologous region may be in a domain that confers specificity for receptor interactions of guanine nucleotide binding proteins.
Humanized Cobra Venom Factor: Experimental Therapeutics for Targeted Complement Activation and Complement Depletion (2007)

Cobra Venom Factor (CVF) is the complement-activating protein in cobra venom. CVF is a structural and functional analog of complement component C3. In serum, CVF forms a physicochemically stable and control-resistant C3/C5 convertase that continuously activates C3 and C5, ultimately leading to depletion of serum complement. As CVF can be safely administered to vertebrate animals, it has become an important tool for complement depletion to study the biological functions of complement and its role in the pathogenesis of disease. CVF has also been used for targeted complement activation by chemically coupling it to monoclonal antibodies. Complement depletion is an attractive concept for pharmacological intervention in diseases where complement activation is part of the pathogenetic mechanism. Toward that end, the structural homology of CVF and C3 has been exploited by creating hybrid proteins in which short portions of C3 sequence have been exchanged with corresponding portions of CVF that introduce the desired ability of forming a stable convertase into human C3. These human C3 derivatives are "humanized CVF" proteins that represent an attractive biopharmaceutical for therapeutic complement depletion.
Enabling unrestricted automated synthesis of portable hardware accelerators for virtual machines (2005)

The performance of virtual machines (e.g., Java Virtual Machines---JVMs) can be significantly improved when critical code sections (e.g., Java bytecode methods) are migrated from software to reconfigurable hardware. In contrast to the compile-once-run-anywhere concept of virtual machines, reconfigurable applications lack portability and transparent SW/HW interfacing: applicability of accelerated hardware solutions is often limited to a single platform. In this work, we apply a virtualisation layer that provides portable and seamless integration of hardware and software components to a Java Virtual Machine platform, making it capable of accelerating any Java bytecode method by using platform-independent hardware accelerators. The virtualisation layer not only improves portability of accelerated Java bytecode applications, but also supports runtime optimisations and enables unrestricted automated synthesis of arbitrary Java bytecode to hardware. To show the advantages and measure the limited overheads of our approach, we run several accelerated applications (handwritten and synthesised) on a real embedded platform. We also show our synthesis flow and discuss its advanced features fostered by the virtualisation layer.
Kinetics of Pyruvate Decarboxylase Deactivation by Benzaldehyde (2003)

Based on experimental data, a kinetic model for the deactivation of partially purified pyruvate decarboxylase (PDC) by benzaldehyde (0–200 mM) in MOPS buffer (2.5 M) has been developed. An initial lag period prior to deactivation was found to occur. With first order dependencies of PDC deactivation on exposure time and on benzaldehyde concentration, a reaction time deactivation constant of 2.64×10−3 h−1 and a benzaldehyde deactivation coefficient of 1.98×10−4 mM−1 h−1 were determined for benzaldehyde concentrations up to 200 mM. The PDC deactivation kinetic equations established in this study are an essential component in an overall model being developed to describe the enzymatic biotransformation of benzaldehyde and pyruvate to produce the pharmaceutical intermediate (R)-phenylacetylcarbinol (R-PAC).
Conformai and tunable optical dielectric metasurfaces based on flexible stretchable substrates (2016)

We introduce an elastic dielectric metasurface platform for developing ultra-slim arbitrarily shaped multifunctional and tunable optical devices. We demonstrate conformal metasurfaces for decoupling optical function and geometrical form, and elastic metasurface lenses with high tunability.
Abstract 1557: High mobility group box 1 secretion supports tumor progression of human malignant mesothelioma (2012)

Abstract Human malignant mesothelioma (MM) is an aggressive and highly lethal cancer, often associated with exposure to asbestos and erionite. Prognosis is poor, due to late-stage diagnosis and resistance to current conventional therapies. We previously showed that high-mobility group box-1 protein (HMGB1), a damage-associated molecular pattern (DAMP) protein, is involved in the early stages of mesothelial cell transformation. Here we show that HMGB1 establishes an autocrine circuit in MM cells influencing tumor cell proliferation and survival. MM cells express HMGB1 at high levels and secrete HMGB1 into the extracellular space. Accordingly, HMGB1 levels in MM patients’ sera are significantly higher than in those of healthy individuals. In addition, motility, survival and anchorage-independent growth of HMGB1-secreting MM cells were inhibited in vitro by a monoclonal antibody (mAb) against HMGB1, by the recombinant HMGB1 competitive antagonist BoxA and by antibodies against the receptor for advanced glycation end products (RAGE). Inhibition of HMGB1 reduced the growth of MM xenografts in SCID mice and extended survival. Our findings indicate that MM cells become “addicted” to HMGB1 and that targeting HMGB1 can be a promising novel therapeutic approach for MM. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 1557. doi:1538-7445.AM2012-1557
Lithium-ion Battery Thermal Safety by Early Internal Detection, Prediction and Prevention (2019)

Temperature rise in Lithium-ion batteries (LIBs) due to solid electrolyte interfaces breakdown, uncontrollable exothermic reactions in electrodes and Joule heating can result in the catastrophic failures such as thermal runaway, which is calling for reliable real-time electrode temperature monitoring. Here, we present a customized LIB setup developed for early detection of electrode temperature rise during simulated thermal runaway tests incorporating a modern additive manufacturing-supported resistance temperature detector (RTD). An advanced RTD is embedded in a 3D printed polymeric substrate and placed behind the electrode current collector of CR2032 coin cells that can sustain harsh electrochemical operational environments (acidic electrolyte without Redox, short-circuiting, leakage etc.) without participating in electrochemical reactions. The internal RTD measured an average 5.8 °C higher temperature inside the cells than the external RTD with almost 10 times faster detection ability, prohibiting thermal runaway events without interfering in the LIBs' operation. A temperature prediction model is developed to forecast battery surface temperature rise stemming from measured internal and external RTD temperature signatures.
An Antigenic Determinant on Human Centromere Protein B (CENP-B) A vailable for Production of Human-Specific Anticentromere Antibodies in Mouse. (1992)

Centromere protein B (CENP-B) is one of the centromere DNA binding proteins constituting centromere heterochromatin throughout the cell cycles. Some components of mammalian centromeres including CENP-B are target antigens for autoimmune disease patients, often those with scleroderma. Recent isolations of CENP-B genes from human and mouse suggested that CENP-B was highly conserved among mammals. From the previous analysis of the reactivity of patient anticentromere sera, two autoepitopes have been located on the DNA binding domain at the amino-terminal region. The amino acid sequences for both the epitopes are perfectly conserved in the two species, human and mouse. In this study, to identify a human-specific antigenic determinant, the remaining two epitopes were further located in separate carboxyl-terminal regions of human CENP-B. Although the amino acid sequence of one epitope is identical to that of the corresponding region in mouse CENP-B, the other has a less homologous sequence. To confirm that the latter epitope was available for production of human-specific anticentromere antibodies, mice were immunized with the recombinant human CENP-B product. One serum that exclusively stained human centromere structure, but not that of other mammals, was identified in the immunofluorescence microscopic observation. The epitope analysis showed that the less conserved one was recognized by this serum. These results suggested that the corresponding region defines the antigenic determinants for the species specificity.
A torque transducer utilizing a circularly polarized ring (1992)

A novel type of magnetoelastic torque transducer is described. It consists of two elements: a circumferentially magnetized magnetostrictive ring, rigidly attached to a shaft carrying the torque to be measured, and a Hall effect or similar magnetic field intensity sensor mounted in proximity to the ring. Stresses in the ring, associated with the torque being transmitted, alter the effective anisotropy orientation from circular to more or less steeply helical. Discontinuity of the axial component of magnetization at the ring ends creates a magnetic field in the space around the ring. A simple analysis predicts both a linear range in the relationship between field intensity and torque and a polarity which depends on the sense of the torque. The electrical output of the field sensor is thus a linear analog of the torque. Experimental transducers exhibit these expected features as well as a small, notably negative, hysteresis. The stability of the circular magnetization is both theoretically supportable and experimentally verified.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Dissecting Functions of <i>KATANIN</i> and <i>WRINKLED1</i> in Cotton Fiber Development by Virus-Induced Gene Silencing    (2012)

Most of the world's natural fiber comes from cotton (Gossypium spp.), which is an important crop worldwide. Characterizing genes that regulate cotton yield and fiber quality is expected to benefit the sustainable production of natural fiber. Although a huge number of expressed sequence tag sequences are now available in the public database, large-scale gene function analysis has been hampered by the low-efficiency process of generating transgenic cotton plants. Tobacco rattle virus (TRV) has recently been reported to trigger virus-induced gene silencing (VIGS) in cotton leaves. Here, we extended the utility of this method by showing that TRV-VIGS can operate in reproductive organs as well. We used this method to investigate the function of KATANIN and WRINKLED1 in cotton plant development. Cotton plants with suppressed KATANIN expression produced shorter fibers and elevated weight ratio of seed oil to endosperm. By contrast, silencing of WRINKLED1 expression resulted in increased fiber length but reduced oil seed content, suggesting the possibility to increase fiber length by repartitioning carbon flow. Our results provide evidence that the TRV-VIGS system can be used for rapid functional analysis of genes involved in cotton fiber development.
PO-0755 <i>in Vivo</i>Mir-200b As A Potential Therapy For Congenital Diaphragmatic Hernia (2014)

<h3></h3> Congenital diaphragmatic hernia (CDH) is associated with lung hypoplasia and pulmonary hypertension (PH) leading to a high morbidity and mortality. MicroRNAs, affect gene expression and miR-200b is involved in epithelial-mesenchymal transition in cancer and is downregulated in rat nitrofen lungs. We hypothesised that miR-200b regulates lung branching. Therefore, we aimed to evaluate whether <i><i>in vivo</i></i> administration of miR-200b influences lung development and branching morphogenesis. Timed-pregnant dams were treated with nitrofen (CDH group) or olive oil (control group) on E9 and received a tail vein injection of miR-200b mimics (5 mg/kg) or saline, respectively. At E21.5 and P0, we dissected the lungs and evaluated the presence or absence of CDH. We estimated the lung hypoplasia and we did histological studies to determine radial alveolar count (RAC) and medial arterial thickness. Nitrofen lungs treated with miR-200 b mimics, <i><i>in vivo</i></i> display improved development and larger size. These embryos were also bigger than the embryos of the nitrofen group plus saline. Their size was similar to control embryos. After RAC analysis revealed that nitrofen treated lungs have larger alveolar spaces than nitrofen lungs. In terms of arteries we did not observe any differences. Administration of miR-200b <i><i>in vivo</i></i> decreases lung hypoplasia and increases the size of the lungs as well as alveolar airspaces. These data show promissing results for miR-200b as a potential therapeutic target in CDH patients. - This work was supported by grants from the MICH, MMSF, Molly Towell, GFT surgeons and Thorlakson Foundation.
Error in estimates of tissue material properties from shear wave dispersion ultrasound vibrometry (2009)

Shear wave velocity measurements are used in elasticity imaging to find the shear elasticity and viscosity of tissue. A technique called shear wave dispersion ultrasound vibrometry (SDUV) has been introduced to use the dispersive nature of shear wave velocity to locally estimate the material properties of tissue. Shear waves are created using a multifrequency ultrasound radiation force, and the propagating shear waves are measured a few millimeters away from the excitation point. The shear wave velocity is measured using a repetitive pulse-echo method and Kalman filtering to find the phase of the harmonic shear wave at 2 different locations. A viscoelastic Voigt model and the shear wave velocity measurements at different frequencies are used to find the shear elasticity (mu(1)) and viscosity (mu(2)) of the tissue. The purpose of this paper is to report the accuracy of the SDUV method over a range of different values of mu(1) and mu(2). A motion detection model of a vibrating scattering medium was used to analyze measurement errors of vibration phase in a scattering medium. To assess the accuracy of the SDUV method, we modeled the effects of phase errors on estimates of shear wave velocity and material properties while varying parameters such as shear stiffness and viscosity, shear wave amplitude, the distance between shear wave measurements (delta r), signal-to-noise ratio (SNR) of the ultrasound pulse-echo method, and the frequency range of the measurements. We performed an experiment in a section of porcine muscle to evaluate variation of the aforementioned parameters on the estimated shear wave velocity and material property measurements and to validate the error prediction model. The model showed that errors in the shear wave velocity and material property estimates were minimized by maximizing shear wave amplitude, pulse-echo SNR, delta r, and the bandwidth used for shear wave measurements. The experimental model showed optimum performance could be obtained for delta r = 3 - 6 mm, SNR =35 dB, with a frequency range of 100 to 600 Hz, and with a shear wave amplitude on the order of a few microns down to 0.5 microm. The model provides a basis to explore different parameters related to implementation of the SDUV method. The experiment confirmed conclusions made by the model, and the results can be used for optimization of SDUV.
A fiducial detection algorithm for real-time image guided IMRT based on simultaneous MV and kV imaging (2008)

The advantage of highly conformal dose techniques such as 3DCRT and IMRT is limited by intrafraction organ motion. A new approach to gain near real-time 3D positions of internally implanted fiducial markers is to analyze simultaneous onboard kV beam and treatment MV beam images (from fluoroscopic or electronic portal image devices). Before we can use this real-time image guidance for clinical 3DCRT and IMRT treatments, four outstanding issues need to be addressed. (1) How will fiducial motion blur the image and hinder tracking fiducials? kV and MV images are acquired while the tumor is moving at various speeds. We find that a fiducial can be successfully detected at a maximum linear speed of 1.6 cm/s. (2) How does MV beam scattering affect kV imaging? We investigate this by varying MV field size and kV source to imager distance, and find that common treatment MV beams do not hinder fiducial detection in simultaneous kV images. (3) How can one detect fiducials on images from 3DCRT and IMRT treatment beams when the MV fields are modified by a multileaf collimator (MLC)? The presented analysis is capable of segmenting a MV field from the blocking MLC and detecting visible fiducials. This enables the calculation of nearly real-time 3D positions of markers during a real treatment. (4) Is the analysis fast enough to track fiducials in nearly real time? Multiple methods are adopted to predict marker positions and reduce search regions. The average detection time per frame for three markers in a 1024 x 768 image was reduced to 0.1 s or less. Solving these four issues paves the way to tracking moving fiducial markers throughout a 3DCRT or IMRT treatment. Altogether, these four studies demonstrate that our algorithm can track fiducials in real time, on degraded kV images (MV scatter), in rapidly moving tumors (fiducial blurring), and even provide useful information in the case when some fiducials are blocked from view by the MLC. This technique can provide a gating signal or be used for intra-fractional tumor tracking on a Linac equipped with a kV imaging system. Any motion exceeding a preset threshold can warn the therapist to suspend a treatment session and reposition the patient.
Abstract 2243: Targeting the MUC1-C oncoprotein synergistically enhances cytotoxicity of breast carcinoma cells in combination with PI3K inhibitors (2012)

Abstract The mucin 1 (MUC1) heterodimeric protein is aberrantly overexpressed by most human breast carcinomas and contributes to the malignant phenotype. However, there are no effective agents that directly inhibit the oncogenic MUC1-C subunit and induce death of breast cancer cells. We have synthesized MUC1-C peptide inhibitors that bind to the MUC1-C cytoplasmic domain and block the formation of MUC1-C dimers in breast cancer cells. We have shown that inhibition of MUC1-C arrests growth and induces necrotic death of the breast carcinoma cells. Here we demonstrate that combining the MUC1-C inhibitor GO-203-2C with agents that target PI3K (LY294002, GDC0941) induces highly synergistic cytotoxicity of breast carcinoma cells. Notably, GO-203-2C significantly enhanced the effectiveness of these PI3K inhibitors by contributing to the downregulation of p-AKT and p-S6K. Taken together, these findings provide support for combining PI3K inhibitors and GO-203-2C, an agent now undergoing Phase I evaluation, to improve treatment of patients with breast cancer. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 2243. doi:1538-7445.AM2012-2243
Ultra-narrow bandwith optical thin film interference coating for single wavelength lasers (1990)

This patent describes a method of producing single wavelength operation of {ital an ion} laser. It is of the kind which can oscillate on a number of lines simultaneously, at substantially any input power level.
Room temperature continuous wave operation of a surface-emitting two-dimensional photonic crystal diode laser (2004)

We achieved room temperature continuous wave operation of a surface-emitting two-dimensional photonic crystal diode laser by current injection. This is the first time ever that room temperature continuous wave operation of a photonic crystal diode laser has been realized. This laser features single mode oscillation over a large area, which is impossible for conventional lasers. In this work, we optimized the epitaxial layer composition for better carrier confinement and clarified the relationship between the diameter of the air holes in the photonic crystal and the threshold current of the laser in order to estimate the optimized threshold current.
205 Mechanical Properties of Mg_2Si/Mg Composites via Powder Metallurgy Process (2002)

The mechanical properties of the solid-state synthesized Mg_2Si/Mg composites from the mixed Mg-Si powders have been investigated. Results indicate the macro-hardness (HRE) and the tensile strength of the composites increase with increasing the Si content and decreasing the Si size. The particle size of the synthesized Mg_2Si depends on the initial Si size; the mechanical properties of the Mg_2Si/Mg composite are therefore remarkably improved by using fine Si particles or by decreasing the grain size of Mg matrix grains via bulk mechanical alloying process.
Carbon Nanotube-Based Permeable Membranes: A Platform for Studying Nanofluidics (2004)

A membrane of multiwalled carbon nanotubes embedded in a silicon nitride matrix was fabricated for use in studying fluid mechanics on the nanometer scale. Characterization by fluorescent tracer diffusion and scanning electron microscopy suggests that the membrane is void-free near the silicon substrate on which it rests, implying that the hollow core of the nanotube is the only conduction path for molecular transport. Nitrogen flow measurements of a nanoporous silicon nitride membrane, fabricated by sacrificial removal of carbon, give a flow rate of 0.086 cc/sec. Calculations of water flow across a nanotube membrane give a rate of 2.1x10{sup -6} cc/sec (0.12 {micro}L/min).
Analysis of Second Harmonic Generation Phase Measurement for Determination of Molecular Orientation and Effective Second Order Nonlinear Optical Constant (2001)

Abstract The average direction of molecules and the absolute value of an effective second order nonlinear optical constant (∣d eff 7∣) were simultaneously determined using a new second harmonic generation (SHG) phase measurement with theoretical curve fitting. The theoretical curve fitting process was demonstrated using poled poly (methyl methacrylate) films doped with p-nitroaniline (PNA/PMMA), which were used as a reference and a sample. The second harmonic (SH) interference generated between the two poled PNA/PMMA films was modulated by rotating the phase generator inserted between the two. The fitting process derived d eff itself. The average direction of molecules was shown by the sign of d eff . The obtained value of ∣d eff ∣ was verified by that from a Maker fringe measurement. The obtained average direction of molecules coincided with that determined by a poling geometry.