gebhart/patrepeval huggingface dataset:
Abstract 1758: Targeting EphB4 with a novel antibody in acute leukemia (2014)

Abstract Introduction: EphB4, a receptor tyrosine kinase, binds to ephrinB2, a cell surface ligand, resulting in bidirectional signaling through both receptor and ligand. EphB4 stimulates cell proliferation and migration through the phosphatidylinositol 3-kinase (PI3K) and Akt signaling pathway. MAb131 is a novel anti-EphB4 monoclonal antibody that induces degradation of EphB4 through receptor endocytosis. We investigated the use of MAb131 as a therapeutic agent for acute leukemia. Methods: Peripheral blood or bone marrow specimens from patients with acute myeloid leukemia (AML) and acute lymphoblastic leukemia (ALL) were obtained after informed consent. EphB4 and ephrinB2 expression in cells were profiled using flow cytometry. Cell lines and patient samples were treated with MAb131 at 0, 10 and 100ug/ml concentrations. Blocking experiment was performed with 200ug/ml sEphB4-HSA in combination with 10ug/ml MAb131. Downregulation of EphB4 was evaluated by flow cytometry. Phosphorylated AKT (pAKT) levels were measured by Western blot. Cell viability was measured by trypan blue exclusion. Results: EphB4 was highly expressed on the cell surface in the majority of leukemia cell lines of both myeloid (K562, Molm14, U937) and lymphoid (REH, RS4;11, Jurkat) origin; only one leukemia cell line evaluated, KG-1, did not express EphB4. In contrast, none of the lymphoma cell lines (BJAB, Ramos, Namwala) expressed EphB4. Of 9 AML patient samples evaluated, 4 expressed high levels of EphB4, and 5 expressed low levels of EphB4. Of 7 ALL patient samples evaluated, 2 expressed high levels of EphB4, 3 had low expression and 2 did not express EphB4. None of the cells showed robust expression of ephrinB2. Treatment of ALL and AML cell lines with MAb131 induced downregulation of EphB4, decreased levels of pAKT, and &amp;gt;90% cell death after 72h. Primary AML and ALL samples also showed downregulation of surface EphB4 and increased cell death with MAb131 treatment. A decoy receptor comprised of the soluble extracellular domain of EphB4 fused to albumin (sEphB4-HSA) was used to block MAb131 binding to EphB4 and confirm specificity of MAb131 activity. Conclusion: We present the first report that EphB4 signaling is active in acute leukemia and can be targeted therapeutically. MAb131, a novel anti-EphB4 antibody, has potent anti-leukemic activity as a single agent in vitro and is likely to sensitize leukemia to cytotoxic chemotherapy through downregulation of AKT signaling. Based on these results, clinical studies exploring the efficacy of EphB4/ephrinB2 antagonists in patients with acute leukemia should be pursued. Citation Format: Miriam Y. Kim, Aparna Jorapur, Amy R. McManus, Ren Liu, Valery Krasnoperov, Kranthi Naga, Parkash S. Gill, Akil Merchant. Targeting EphB4 with a novel antibody in acute leukemia. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 1758. doi:10.1158/1538-7445.AM2014-1758
Unraveling the activity of glycosyltransferases and other PTM enzymes with bioluminescent biochemical and cell based assays (2019)

Post translational modifications (PTMs) are central to all aspects of biological regulation. PTMs amplify the diverse functions of the proteome by covalently adding functional groups to proteins. These modifications include phosphorylation, methylation, glycosylation, and ubiquitination, and influence many aspects of normal cell biology and pathogenesis. Examples of post translational modification enzymes include but are not limited to, kinases/phosphatases, methyltransferases/demethylases, and glycosyltransferases/glucanases. Under normal physiological conditions, the regulation of PTM enzymes is tightly regulated. However, under pathological conditions, these enzyme activities can be dysregulated, and the disruption of the intracellular networks they govern leads to an array of diseases including cancer and inflammation. Consequently, PTM enzymes have become important targets for drug discovery creating a need for development of activity detection assays. Current assays to analyze cellular or biochemical PTM enzyme activities can be tedious, non‐homogeneous, and not easily adaptable to HTS. They can also suffer from generation of false hits due to compound interference or require special instruments for detection. To overcome these shortcomings, we developed an array of biochemical and cellular bioluminescent assays to detect these enzyme activities. This presentation will showcase how cellular mechanisms driven by PTM in general and phosphorylation and glcnacylation in particular can be addressed by analyzing these enzyme's cellular activity using the NanoLuc Binary Technology (NanoBiT), a two‐subunit complementation system based on NanoLuc luciferase. We will also discuss how the bioluminescent nucleotide assays that detect UDP, GDP, UMP and CMP as means to measure glycosyltransferase activities can streamline studies on GT specificity of transfer of different sugars to different acceptors. We will show their use in screening for specific inhibitors as well as in studies of their modes of action. Development of these bioluminescent detection assays will enable the investigation of key signaling pathways and the study of many PTM enzymes in general and GTs in particular, which may have significant impact on diverse areas of glycobiology research. This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal .
Design methodology for modular tools Yann QueudevilleTodor IvanovUwe VroomenAndreas Buhrig-Polaczek • Stefanie ElgetiMarkus ProbstMarek BehrChristian Windeck • Walter MichaeliChristopher NussbaumChristian Hinke (2011)

Serving individual customer needs at reason- able prices can be a profitable target market in high-wage countries. The dilemma between scale and scope-oriented production is one major research topic within the Cluster of Excellence ''Integrative Production Technology for High- Wage Countries'' at the RWTH Aachen University. One main objective of this project is to bridge the existing gap between individual manufacturing and mass production. Modularization is a widely accepted approach in tool-based manufacturing processes. In this paper, we propose a flexible design methodology for modular tools and dies. The methodology will assist the design engineer in setting up a series of modularized tools in a conceptually closed manner. The described methodology covers modularization in a broad sense, i.e. it includes hardware modularization as well as modularization of the construction process. The methodology consists of three phases: initiation, analysis and design phase.
Continuous‐time model predictive control of a permanent magnet synchronous motor drive with disturbance decoupling (2017)

The design and the experimental validation of a continuous‐time model predictive control (CTMPC) for a permanent magnet synchronous motor (PMSM) drive with disturbance decoupling is discussed. The CTMPC approach uses Taylor series expansion to derive a closed‐form solution to the problem of model predictive control even though the system behaviour is described by a non‐linear model. This type of controller requires an exact knowledge of the system model to guarantee an accurate prediction of the system behaviour, while the PMSM is usually subjected to model uncertainties and external disturbances such as the load torque. Moreover, in the proposed approach, the predicted speed tracking error is directly used to determine the required voltage command without the need for a cascaded control scheme. As a result, the load torque is seen as unmatched disturbance which makes exact disturbance decoupling more challenging. To overcome such a problem, a non‐linear disturbance observer is designed and combined with the CTMPC method to enhance the prediction accuracy under parameter variation and unknown load torque. The feasibility of the proposed approach is experimentally investigated, and good transient and steady‐state performances are obtained.
Ivory optomechanical tools for controlling random vibration effects (2007)

Vibration effects can be a maj or limiter in the performance of optical instruments used for guidance, control, surveillance and observation. The author has recently developed software that takes the physical prescription data for the optical system, calculates the influence coefficients between all the elements in the system and the system's image and then prepares a NASTRAN finite element model ofthe optical imaging behavior. This model can be added to the elastic model ofthe optical instrument and NASTRAN can then calculate all the motions ofthe image on the detector. This paper describes the use of the Ivory Optomechanical Modeling Tools in analyzing optical instruments in vibration environments and uses a recent FUR project as a practical example oftheir utility.
Army family physician satisfaction. (1995)

Army family physicians are more satisfied with being family physicians than they are with being military officers. They are, however, satisfied with both professions. The Army, as an organization, may want to explore how its system of rewards interplay with rank and amount of time in patient care to make them predictive of satisfaction.
A Monopulse Rotman Lens Phased Array for Enhanced Angular Resolution (2007)

A low cost monopulse phased array is described, which is based upon a Rotman lens and switched line phase shifting network. An amplitude comparison monopulse scheme is implemented, where the phased array is capable of scanning the sum and difference beams throughout a 60deg field of view. The sum beam directivity is better than 12 dB within a 6 GHz bandwidth at Ka band. Over 20 dB difference beam nulls were achieved throughout a 1 GHz bandwidth. The entire phase shifting circuit occupies a size of 62 mm by 62 mm, which is no larger than conventional Rotman lens circuitry.
Transplantation of an Autologous Mesothelial Cell Sheet Prepared from Tunica Vaginalis Prevents Post-Operative Adhesions in a Canine Model (2006)

Post-operative adhesions often cause severe complications such as bowel obstruction and abdominopelvic pain. Previously, we reported that transplantation of a mesothelial cell sheet is effective for preventing adhesion in rat model. We also proposed a new technique for harvesting autologous mesothelial cells from tunica vaginalis without intra-abdominal maneuvers. In this study, we examined whether an autologous mesothelial cell sheet can prevent post-operative peritoneal adhesions in a canine adhesion model. Mesothelial cells were isolated from the tunica vaginalis of male beagles. Isolated cells were cultured on fibrin gel. We named this construct the "mesothelial cell sheet." Animals underwent surgery to induce peritoneal adhesion formation and were then transplanted with the mesothelial cell sheets (sheet group, n = 4), fibrin gel (fibrin group, n = 4), or no materials (sham group, n = 4). Four weeks after the transplantation, we evaluated adhesion formation and scored adhesion levels. The abdominal wall transplanted with the mesothelial cell sheet was covered with mesothelium. The total adhesion score of the sheet group was significantly lower than that of the fibrin group and the sham group. These results indicated that transplantation of an autologous mesothelial cell sheet is effective for preventing post-operative adhesion formation in the canine adhesion model. Our mesothelial cell sheet has the potential to be a powerful adhesion prophylactic material in surgery.
Sensor and actuator placement for zero-shaping in dynamical networks (2016)

Placement of sensors and actuators in a linear network model is pursued, with the aim of achieving desirable invariant-zero characteristics for input-output channels (primarily, minimum phase dynamics). Graph-theoretic analyses of the network model's invariant zeros and phase-response properties are undertaken, and used to develop simple insights into and algorithms for sensor and actuator placement.
Environment-invariant measure of distance between evolutions of an open quantum system (2009)

The problem of quantifying the difference between evolutions of an open quantum system (in particular, between the actual evolution of an open system and the ideal target operation on the corresponding closed system) is important in quantum control, especially in control of quantum information processing. Motivated by this problem, we develop a measure for evaluating the distance between unitary evolution operators of a composite quantum system that consists of a sub-system of interest (e.g., a quantum information processor) and environment. The main characteristic of this measure is the invariance with respect to the effect of the evolution operator on the environment, which follows from an equivalence relation that exists between unitary operators acting on the composite system, when the effect on only the sub-system of interest is considered. The invariance to the environment's transformation makes it possible to quantitatively compare the evolution of an open quantum system and its closed counterpart. The distance measure also determines the fidelity bounds of a general quantum channel (a completely positive and trace-preserving map acting on the sub-system of interest) with respect to a unitary target transformation. This measure is also independent of the initial state of the system and straightforward to numerically calculate. As an example, the measure is used in numerical simulations to evaluate fidelities of optimally controlled quantum gate operations (for one- and two-qubit systems), in the presence of a decohering environment. This example illustrates the utility of this measure for optimal control of quantum operations in the realistic case of open-system dynamics.
Highly Convergent Synthesis of Intensively Blue Emissive Furo[2,3‐c]isoquinolines by a Palladium‐Catalyzed Cyclization Cascade of Unsaturated Ugi Products (2016)

A convergent and diversity-oriented approach to the unusual furo[2,3-c]isoquinoline scaffold is presented. This serendipity-driven approach is characterized by an Ugi multicomponent reaction, which gives the substrate for a palladium-catalyzed insertion-alkynylation-cycloisomerization cascade to provide the furo[2,3-c]isoquinolines in moderate to high yield. Upon UV excitation, all representatives are intensively blue luminescent, as observed by the naked eye, and quantitative fluorescence spectroscopy reveals a considerable effect of the substitution pattern on the quantum yields. The electronic structure is semiquantitatively rationalized by DFT and time-dependent DFT calculations.
Measurement of the radial velocity in a cylindrical through-flow hydrocyclone (2006)

Hydrocyclones can be used to fractionate fibres according to their papermaking potential. The obtained fractions typically differ in fibre wall thickness and/or degree of fibre treatment. Despite a multitude of potential application scenarios, the process has so far had little commercial success. This is largely explained by the low fractionation efficiency and unfavourable operating characteristics of the process. The fractionation efficiency of a hydrocyclone is closely related to its flow field. The influence of pulp concentration on the tangential velocity field was therefore studied, by using a self-cleaning pitometer. It was found that the pulp concentration had a strong influence on the tangential velocity. At a feed pulp concentration above 7.5 g/l, the suspension rotated almost as a solid body. As a consequence, the magnitude of radial acceleration and shear stresses decreased dramatically. It is suggested that this is detrimental to the fractionation efficiency. The radial velocity field was measured using an Ultrasonic Velocity Profiler. The measurements showed that the rotational centre of the flow field did not correspond with the geometrical centre of the hydrocyclone. This displacement caused the tangential velocity component of the vortex to contribute substantially to the measurement result of the radial velocity component. Based on the findings in respect to the flow field studies, a novel design for a fibre fractionation hydrocyclone was proposed. The flow field inside this hydrocyclone was compared to that in a conventional hydrocyclone. It was found, that high radial acceleration and shear stresses could be maintained in the novel design even at high fibre concentration. The fractionation efficiency of the novel hydrocyclone was characterised in terms of surface roughness difference between fine and coarse fraction. When operated with refined bleached softwood kraft pulp, the novel hydrocyclone could produce fractions with a substantial surface roughness difference without deteriorating the dewatering characteristics of the fine fraction. A low thickening of the reject is proposed to be the explanation for that. When fractionating TMP, the best efficiency occurred at a concentration of 10 g/l.
Nanosecond time-resolved interferometric study on morphological dynamics of doped poly(methyl methacrylate) film upon laser ablation (1994)

A highly sensitive nanosecond time-resolved interferometry was developed and applied to study dynamics of morphological changes of a thin poly(methyl methacrylate) film doped with biphenyl upon laser ablation. It was confirmed that morphological changes started during a nanosecond excitation laser pulse and then followed by an ejection of ablated polymer fragments. Even below the ablation threshold, a transient expansion of the polymer film, followed by slow contraction, was observed. New features of laser ablation dynamics were clarified.
Lactobacillus fermentumHFY06 reduced CCl4-induced hepatic damage in Kunming mice (2019)

This study was conducted to investigate the preventative effect of <i>Lactobacillus fermentum</i> HFY06 on carbon tetrachloride (CCl<sub>4</sub>)-induced liver injury in Kunming mice. Mice were treated with HFY06, then liver damage was induced using CCl<sub>4</sub>. Evaluation indicators included the activities of aspartate aminotransferase (AST), triglycerides (TG), superoxide dismutase (SOD), glutathione peroxidase (GSH-Px), and malondialdehyde (MDA) in serum; cytokines levels of interleukin-6 (IL-6), tumor necrosis factor-α (TNF-α) and interferon-γ (IFN-γ) in serum; and related gene expressions of nuclear factor-κB (NF-κB), TNF-α, cyclooxygenase-2 (COX-2), copper/zinc superoxide dismutase (Cu/Zn-SOD), manganese superoxide dismutase (Mn-SOD), and catalase (CAT). Liver tissue was stained with hematoxylin and eosin for pathological analysis. Compared with the model group, HFY06 reduced the liver index, increased the serum SOD and GSH-Px activities, and reduced the AST, TG, and MDA activities in the mice. Inflammation-related IL-6, TNF-α and IFN-γ levels were also reduced after treatment with a high dose of HFY06. Pathological observation showed that CCl<sub>4</sub> damaged the mouse livers, which were significantly improved after treatment with silymarin and HFY06. qPCR also confirmed that the high dose of HFY06 (10<sup>9</sup> colony-forming units [CFU] per kg per day) upregulated the mRNA expression of the antioxidant genes, Cu/Zn-SOD, Mn-SOD, and CAT, in the liver tissue and downregulated the mRNA expression of the inflammatory factors, NF-κB, TNF-α and COX-2, but HFY06 was less effective than silymarin. These findings indicate that HFY06 prevented CCl<sub>4</sub>-induced liver damage <i>in vivo</i> but was less effective than silymarin. Thus, HFY06 may have a potential role in treating liver diseases.
Marker enzymes in rat liver vesicles involved in transcellular transport (1989)

In order to label the vesicles involved in transcellular transfer (transcytosis) through hepatocytes, polymeric IgA (pIgA) was conjugated to horseradish peroxidase (HRP) and injected into rats. The endosomes containing this ligand at 10 or 20 min after injection were isolated by the diaminobenzidine-induced density-shift procedure and their content in various marker enzymes was measured. The endosomes carrying pIgA-HRP 10 min after injection contained only traces of 5'-nucleotidase and low amounts of alkaline phosphodiesterase I. The estimated marker enzyme content is similar to that observed for the particles containing galactosylated bovine serum albumin conjugated to HRP, a ligand degraded in lysosomes. However, 20 min after injection, the transcytotic endosomes showed a marked enrichment in 5'-nucleotidase and especially in alkaline phosphodiesterase I. The results confirm the heterogeneity of rat liver endosomes and substantiate the concept of distinct endosomal compartments.
Dynamics and frequency of Gag transmitted polymorphisms in Zambia (2012)

Methods Using 143 epidemiologically linked transmission pairs from a Zambian cohort we assessed: (1) the frequency of Gag polymorphisms circulating in the population, (2) if the polymorphisms could be associated with the infected individual’s HLA alleles, (3) the frequency at which polymorphisms are transmitted, and (4) the relevance of the transmitted polymorphisms (TP) to the newly infected individual’s HLA-I alleles.
Non-contact surface temperature mapping of alpha-alumina using a Raman scattering method (2019)

Alumina ceramic is widely used as a thermocouple protector or engineering ceramic in harsh environments due to its high-temperature stability, chemical inertness, and low thermal conductivity. Because alumina is prevalent in high-temperature equipment, it is useful to understand its Raman properties to enable temperature measurement via Raman spectroscopy in these harsh-environment systems. In this paper, we report temperature mapping on the surface of high-temperature alumina ceramics via Raman spectroscopy. The ceramics studied were as cast (unpolished) to approximate use in high-temperature industrial applications. Temperature calibration equations were generated covering the range from room temperature to ~1000°C. The most accurate mathematical temperature relation used the Raman line shift of the most intense Stokes A<sub>1g</sub> peak at 418cm<sup>-1</sup>. The average standard deviation of the Raman temperature measurement was less than 5°C over the entire experimental temperature range. This method will provide accurate non-contact surface temperature measurments in harsh environments where thermal radiation and variable surface emissivity contributes significant error to simpler infrared thermometry.
Electroanalysis Using Macro-, Micro-, and Nanochemical Architectures on Electrode Surfaces. Bulk Surface Modification of Glassy Carbon Microspheres with Gold Nanoparticles and Their Electrical Wiring Using Carbon Nanotubes (2006)

Gold nanoparticles (approximately 30-60 nm in diameter) were deposited onto the surface of glassy carbon microspheres (10-20 microm) through electroless plating to produce bulk (i.e., gram) quantities of nanoparticle surface-modified microspheres. The gold nanoparticle-modified powder was then characterized by means of scanning electron microscopy and cyclic voltammetry. The voltammetric response of a macroelectrode consisting of a film of gold nanoparticle-modified glassy carbon microspheres, bound together and "wired-up" using multiwalled carbon nanotubes (MWCNTs), was investigated. We demonstrate that by intelligently exploiting both nano- and microchemical architectures and wiring up the electroactive centers using MWCNTs in this way, we can obtain macroelectrode voltammetric behavior while only using approximately 1% by mass of the expensive gold material that would be required to construct the equivalent gold film macrodisk electrode. The potential utility of electrodes constructed using chemical architectures such as this was demonstrated by applying them to the analytical determination of arsenic(III) concentration. An optimized limit of detection of 2.5 ppb was obtained.