gebhart/patrepeval huggingface dataset:
Epidermal growth factor receptor. Characterization of a monoclonal antibody specific for the receptor of A431 cells. (1983)

A monoclonal antibody to the epidermal growth factor (EGF) receptor of A431 cells was obtained after fusion of immunized BALB/c mouse spleen cells with NS-1 myeloma cells. Specific binding of the antibody to the plasma membrane of A431 cells was demonstrated by indirect immunofluorescence and electron microscopy. The antibody did not react with human KB cells, normal rat kidney cells, or Swiss 3T3 cells. The antibody is an IgG3K; it specifically immunoprecipitated a Mr approximately 170,000 protein from radiolabeled A431 cell extracts. This protein is phosphorylated in a EGF-dependent manner in intact A431 cells and in Triton X-100-solubilized plasma membranes. The specificity of the interaction of the antibody with the Mr = 170,000 protein was confirmed by electrophoretic transfer of A431 cell proteins to nitrocellulose followed by incubation with the antibody and 125I-protein A. When 125I-EGF was covalently cross-linked to its receptor, the 125I-EGF-receptor complex was specifically precipitated by the antibody. The monoclonal antibody did not inhibit the binding of 125I-EGF to its receptor in intact A431 cells and also failed to stimulate the phosphorylation of the Triton X-100-solubilized EGF receptor. The results indicate that the antibody and EGF bind to different sites on the EGF receptor. The antibody will be useful for isolating the EGF receptor in an unactivated form.
Function and Regulation of Tumor Necrosis Factor Receptor Type 2 (2004)

TNF is a major proinflammatory cytokine, which exerts its effects through two different receptors known as TNF-R1 and TNF-R2. Whereas TNF-R1 induced signaling pathways have been very well characterized during the past years, TNF-R2 has been much less well studied. Nevertheless, the function of TNF-R2 should not be underestimated, the more because this receptor shows a much more restricted but inducible expression. Several inflammatory diseases and cancers show upregulated levels of soluble TNF-R2 or are associated with TNF-R2 polymorphisms, implicating an important role for TNF-R2 as a therapeutic target. Here we will review the mechanisms that regulate TNF-R2 expression, as well as discuss TNF-R2 induced signal transduction and cross-talk with TNF-R1.
Variation of Wavefront Aberration of Eye Over Days (2004)

Purpose: Our objective is to determine the magnitude of the wave aberration variations over time, especially the high order, and whether this variation is sufficiently large to negate the usefulness of static cancellation (non–adaptive optic) methods to achieve improved vision. Methods: Five (5) male subjects, age from 33 to 45, participated in the study. All measurements were performed using a new grating–based wavefront sensor (Ophthonix, Inc., San Diego, CA). The data were collected over a 5–day period. For all subjects, the right eyes were measured with non–dilated pupil and data were analyzed at 4 mm diameter zone. There were two sessions each day, one in the morning, one in the afternoon, for a total of 10 sessions for each subject. Subject’s vision was first auto–refracted using the wavefront sensor and a corrective lens is inserted in the line of sight. Subjects were instructed to maintain fixation at a wall picture throughout the measurement. Results: The mean of the individual total RMS wave front errors of 5 subjects ranges from 0.25 microns to 5.16 microns (SD from 0 to 0.17 microns). The mean magnitude of the high order RMS component varies from 0.07 to 0.25 microns (SD from 0 to 0.03 μm). One–way ANOVA test indicates that for each subject there is no significant difference in wave aberrations among measurements in the morning, afternoon, or in different days (total RMS: F = 0.002 and = 1; high order RMS: F = 0.041 and = 1; spherical equivalent: F = 0.002 and = 1). Conclusions: The low order RMS wavefront error fluctuates more than the high order. However, both the low and high order fluctuations are sufficiently small, and static cancellation of high order aberrations can be effective
Ryanodine receptors are targeted by anti-apoptotic Bcl-XL involving its BH4 domain and Lys87 from its BH3 domain (2015)

Anti-apoptotic B-cell lymphoma 2 (Bcl-2) family members target several intracellular Ca(2+)-transport systems. Bcl-2, via its N-terminal Bcl-2 homology (BH) 4 domain, inhibits both inositol 1,4,5-trisphosphate receptors (IP3Rs) and ryanodine receptors (RyRs), while Bcl-XL, likely independently of its BH4 domain, sensitizes IP3Rs. It remains elusive whether Bcl-XL can also target and modulate RyRs. Here, Bcl-XL co-immunoprecipitated with RyR3 expressed in HEK293 cells. Mammalian protein-protein interaction trap (MAPPIT) and surface plasmon resonance (SPR) showed that Bcl-XL bound to the central domain of RyR3 via its BH4 domain, although to a lesser extent compared to the BH4 domain of Bcl-2. Consistent with the ability of the BH4 domain of Bcl-XL to bind to RyRs, loading the BH4-Bcl-XL peptide into RyR3-overexpressing HEK293 cells or in rat hippocampal neurons suppressed RyR-mediated Ca(2+) release. In silico superposition of the 3D-structures of Bcl-2 and Bcl-XL indicated that Lys87 of the BH3 domain of Bcl-XL could be important for interacting with RyRs. In contrast to Bcl-XL, the Bcl-XL(K87D) mutant displayed lower binding affinity for RyR3 and a reduced inhibition of RyR-mediated Ca(2+) release. These data suggest that Bcl-XL binds to RyR channels via its BH4 domain, but also its BH3 domain, more specific Lys87, contributes to the interaction.
Active spatial modulation of free electrons by controlling the shape and intensity of plasmonic fields (2021)

We present active spatial shaping of free-electron wavepackets through their interaction with specially-designed interference patterns of surface plasmons and via the nonlinear intensity dependence of the electron-plasmon interaction.
New Photochromic Hybrid Organic–Inorganic Materials Built from Well-Defined Nano-Building Blocks (2002)

Well-defined photochromic hybrid materials have been prepared by embedding spirooxazine dyes into matrices made of {(BuSn)12-O14(OH)6}2+ nano-building blocks assembled with α,ω-carboxymethyl poly(ethylene glycol) macromonomers (see Figure). Processed as 2–3 μm thick films, these materials exhibit fast and direct photochromism.
Cellular Prion Protein Protects from Inflammatory and Neuropathic Pain (2011)

Cellular prion protein (PrPC) inhibits N-Methyl-D-Aspartate (NMDA) receptors. Since NMDA receptors play an important role in the transmission of pain signals in the dorsal horn of spinal cord, we thus wanted to determine if PrPC null mice show a reduced threshold for various pain behaviours.We compared nociceptive thresholds between wild type and PrPC null mice in models of inflammatory and neuropathic pain, in the presence and the absence of a NMDA receptor antagonist. 2-3 months old male PrPC null mice exhibited an MK-801 sensitive decrease in the paw withdrawal threshold in response both mechanical and thermal stimuli. PrPC null mice also exhibited significantly longer licking/biting time during both the first and second phases of formalin-induced inflammation of the paw, which was again prevented by treatment of the mice with MK-801, and responded more strongly to glutamate injection into the paw. Compared to wild type animals, PrPC null mice also exhibited a significantly greater nociceptive response (licking/biting) after intrathecal injection of NMDA. Sciatic nerve ligation resulted in MK-801 sensitive neuropathic pain in wild-type mice, but did not further augment the basal increase in pain behaviour observed in the null mice, suggesting that mice lacking PrPC may already be in a state of tonic central sensitization. Altogether, our data indicate that PrPC exerts a critical role in modulating nociceptive transmission at the spinal cord level, and fit with the concept of NMDA receptor hyperfunction in the absence of PrPC.
Inhibition of the BMP pathway suppresses tumor growth via downregulation of EGFR in MEK/ERK-dependent colorectal cancer (2022)

Abstract The bone morphogenetic protein (BMP) pathway promotes differentiation and induces apoptosis in normal colorectal epithelial cells. However, the effect of the BMP pathway in colorectal cancer (CRC) is controversial; it can either be tumor promoting or tumor suppressing, depending on the study. In this study, we found that CRC cells reside in a BMP-rich environment based on RNA-sequencing database analysis. Suppression of BMP using a specific BMP inhibitor, LDN193189, suppresses the growth of organoids in some CRC cases. CRC organoids treated with LDN193189 exhibited a decrease in epidermal growth factor receptor, which was, at least in part, mediated by protein degradation induced by leucine-rich repeats and immunoglobulin-like domains protein 1 (LRIG1). Among CRC organoid panels from 18 different patients, suppression of organoid growth by BMP inhibition correlated with the induction of LRIG1 gene expression. Notably, knockdown of LRIG1 in organoids diminished the growth-suppressive effect of LDN193189. Furthermore, simultaneous treatment with LDN192189 and trametinib, an FDA-approved MEK inhibitor, resulted in a combination effect in both in vivo and in vitro xenograft tumor treatment in CRC organoids, which are susceptible to growth suppression by LDN193189. Taken together, the simultaneous inhibition of BMP and MEK can be a novel treatment option in CRC cases, and evaluating in vitro growth suppression and LRIG1 induction by BMP inhibition using patient-derived organoids could offer functional biomarkers for predicting potential responders.
SPAD based imaging of Cherenkov light in radiation therapy (2019)

During radiotherapy, X-ray beams induce Cherenkov light emission in tissue as part of the dose delivery. This light can be used for dosimetry, in order to track and image the dose as it happens. The Cherenkov light levels are in the range of 10<sup>−6</sup> to 10<sup>−9</sup> W∕cm<sup>2</sup>, which makes it challenging to detect in a clinical environment. However, because the radiation is pulsed in 4 microsecond bursts, time-gated acquisition of the signal allows for robust detection, even in the presence of ambient room lighting. Thus, imaging sensors for this application must be highly sensitive and must be able to time gate faster than a microsecond. In this study, the use of a solid-state detector composed of 64&times;32 single photon avalanche diodes (SPADs) was examined. The advantages of this technology were intra-chip amplification, high dynamic range, superior X-ray noise rejection and fast temporal gating of the acquisition. The results show that the SPAD camera was sensitive enough to detect Cherenkov radiation despite the 3% fill factor. 2D oversampling (&times;25) was also used to increase final image resolution to 320&times;160. In this work we demonstrate the SPAD camera performance in imaging Cherenkov emission from a tissue optical phantom and one patient undergoing radiotherapy. The results show that the SPAD camera was sensitive enough to detect Cherenkov radiation emitted from patient’s surface with signal-to-noise ratio of 14 after 6s acquisition. The SPAD camera sensors could be a viable alternative for Cherenkov imaging, as compared to current imaging methods that are mostly focused around image intensifier-based cameras and so have a range of non-linearities and instabilities which could be solved by an all solid-state camera sensor.
Layered zeolite materials and methods related thereto (2023)

A novel oxide material (MIN-I) comprising YO.sub.2; and X.sub.2O.sub.3, wherein Y is a tetravalent element and X is a trivalent element, wherein X/Y=O or Y/X=30 to 100 is provided. Surprisingly, MIN-I can be reversibly deswollen. MIN-I can further be combined with a polymer to produce a nanocomposite, depolymerized to produce predominantly fully exfoliated layers (MIN-2), and pillared to produce a pillared oxide material (MIN-3), analogous to MCM-36. The materials are useful in a wide range of applications, such as catalysts, thin films, membranes, and coatings.
Application of Conductive Carbon Nanotube Fibers and Composites: Gas Sensor (2013)

Abstract : Sensing based on carbon nanotube (CNT) materials has been as area of interest since the material's discovery by Iijima in 1991 (Nature 1991, 354, 56?58), and an active area of research once CNT availability began to increase via the innovations of Smalley and others (Chem Phys Lett 1995, 243, 49?54). The work presented in this report was conducted at Rice University under contract W911NF-11-1-0249. Here, it is shown that the use of high weight percentage CNT medium density polyethylene (MDPE) composites has suitability towards the sensing of nerve agent stimulants such as dimethyl methylphosphonate (DMMP). The results indicate a possible binary composite approach to sensing, using two variants of CNT. As this work progresses, optimization of the CNT towards sensing DMMP through functionalization is suggested, as is improvement to the experimental apparatus to add functionality, such as controlled and active flow, at a fixed temperature relevant to the application.
Simulation studies of a β-SiC-on-insulator Pockels phase modulator (1999)

We have designed waveguide modulators using (beta) -SiC-on- insulator waveguides and the Pockels effect. A 2D semiconductor device simulator was used to determine the electric field configuration in a double-Schottky diode structure. This allowed us to evaluate the local modulation of the refractive index as a function of applied external bias and to determine the effective index modulation of the guided mode. The optical simulations were performed using the Spectral Index and the Effective Index methods. Different 2D geometries are analyzed and the material parameters needed for fabricating such a device are determined. Application to Mach- Zehnder intensity modulators is described. Such devices have potential for high-speed Si-based photonic devices compatible with silicon technology.
AgInS2quantum dots for the detection of trinitrotoluene (2016)

AgInS<sub>2</sub> (AIS) quantum dots (QDs) were synthesized via a thermal decomposition reaction with dodecylamine as the ligand to help stabilize the QDs. This reaction procedure is relatively easy to implement, scalable to large batches (up to hundreds of milligrams of QDs are produced), and a convenient method for the synthesis of chalcogenide QDs. Metal powders of AgNO<sub>3</sub> and In(NO<sub>3</sub>)<sub>3</sub>, were used as the metal precursors while diethyldithiocarbamate was used as the sulfur source. The AIS QDs were characterized via transmission electron microscopy, atomic force microscopy, and energy dispersive x-ray spectroscopy. As an application for these less toxic nanomaterials, we demonstrate the selective detection of Trinitrotoluene (TNT) at concentrations as low as 6 micromolar (μM) and without the functionalization of a ligand that is specifically designed to interact with TNT molecules. We also demonstrate a simple approach to patterning the AIS QDs onto filter paper, for the detection of TNT molecules by eye. Collectively, the ease of the synthesis of the less toxic AIS QDs, and the ability to detect TNT molecules by eye suggest an attractive route to highly sensitive and portable substrates for environmental monitoring, chemical warfare agent detection, and other applications.
Effects of a Calcimimetic Compound and Naturally Activating Mutations on the Human Ca2+Receptor and on Ca2+Receptor/Metabotropic Glutamate Chimeric Receptors (2000)

Naturally occurring mutations identified in subjects with autosomal dominant hypocalcemia (ADH) and the calcimimetic compound, R-568, have both been reported to increase Ca2+ sensitivity of the Ca2+ receptor (CaR). To gain insight into their mechanism of action, we studied interactions between four different ADH mutations located in the amino-terminal extracellular domain (ECD) and R-568. We found that R-568 increased the sensitivity of three of the ADH mutant receptors, but the Leu125Pro mutant appeared to be maximally left-shifted in that neither R-568 addition nor combining other ADH mutations with Leu125Pro gave increases in sensitivity comparable to those seen with the three other ADH mutations studied. We also made use of truncation and deletion mutants of the CaR and CaR/metabotropic glutamate receptor type 1 (mGluR1) chimeras to study both the site of action of R-568 and the effect of the Leu125Pro activating mutation. R-568 was effective in receptor constructs containing the seven transmembrane domain (7TM) of the CaR, but not in those containing the mGluR1 7TM. R-568, moreover, imparted Ca2+ responsiveness to CaR constructs lacking all or part of the CaR ECD. The Leu125Pro mutation in contrast conferred no or minimal increase in Ca2+ responsiveness to CaR constructs lacking part of the CaR ECD but showed a striking increase in basal activity in the context of chimeras containing an mGluR1 7TM. Our results localize the site of action of NPS-568 specifically to the CaR 7TM. Our results with the Leu125Pro mutant, furthermore, suggest that the mGluR1 7TM domain may be more permissive for activation than the 7TM domain of the CaR.
Representation of deformable motion for compression of dynamic cardiac image data (2012)

We present a new approach for efficient estimation and storage of tissue deformation in dynamic medical image data like 3-D+t computed tomography reconstructions of human heart acquisitions. Tissue deformation between two points in time can be described by means of a displacement vector field indicating for each voxel of a slice, from which position in the previous slice at a fixed position in the third dimension it has moved to this position. Our deformation model represents the motion in a compact manner using a down-sampled potential function of the displacement vector field. This function is obtained by a Gauss-Newton minimization of the estimation error image, i. e., the difference between the current and the deformed previous slice. For lossless or lossy compression of volume slices, the potential function and the error image can afterwards be coded separately. By assuming deformations instead of translational motion, a subsequent coding algorithm using this method will achieve better compression ratios for medical volume data than with conventional block-based motion compensation known from video coding. Due to the smooth prediction without block artifacts, particularly whole-image transforms like wavelet decomposition as well as intra-slice prediction methods can benefit from this approach. We show that with discrete cosine as well as with Karhunen-Lo`eve transform the method can achieve a better energy compaction of the error image than block-based motion compensation while reaching approximately the same prediction error energy.
Letter to Editor (2013)

issue of Journal of Clinical Biochemistry and Nutrition, by Tomoki Aomatsu et al. entitled "Neutralization of complement component C5 ameliorates the development of dextran sulfate sodium (DSS)-colitis in mice". (1)The authors have evaluated the pathophysiological role of the complement system in a mice colitis model.To study the role of complement, they have used Eculizumab, an antibody directed towards the human complement protein C5.We have two strong issues against this study, both regarding the use of the C5-neutralizing antibody, Eculizumab.
Cooperative spatial scheduling in distributed MIMO MAC with interference/concurrency awareness (2012)

Concurrent MIMO access is using MIMO-Beamforming vectors to mitigate interference on existing links and exploit spatial spectral opportunity. A novel distributed MIMO MAC, Net-Eigen MAC, was recently developed to (i) null interference on existing links, and (ii) maximize post-processing SNR within desired link, enjoying better throughput performance over conventional single link MAC or SPACEMAC (NullHoc). One key feature in Net-Eigen MAC, named as interference and concurrency awareness, can be utilized by network modules at MAC or higher layer as a powerful tool for network performance improvement. Inspired by such motivation, this paper will present a cooperative scheduling framework that closely utilizes the following two features in Net-Eigen MAC: (i) interference nulling on existing links; (ii) prioritized spatial concurrency among parallel links. Our design monitors all links' performance status, and accordingly schedules each time frame's prioritized concurrency/hierarchy, which naturally triggers two representative examples for practical applications: (i) max-min scheduling that optimizes fair throughput; and (ii) longest-queue-first scheduling that minimizes dropped packets. Extensive simulations show that our proposed design can help Net-Eigen MAC achieve a better performance than SPACEMAC or single link MAC in terms of throughput, delay, or loss ratio.
Sensor fusion method based on millimeter-wave radar profile and stereo camera disparity histogram (2013)

It is known that millimeter-wave radar has a high range resolution. For separating pedestrians from vehicles at far distance, a sensor is also desired a higher angle resolution. This paper proposed a sensor fusion method which combines the radar power profile with the disparity histogram from stereo camera which has a much high angle resolution. Using the combined new feature, the fusion sensor can achieve a high angle resolution. The evaluation experiments show that pedestrians at the distance of 40m are successfully separated from nearby cars.
Strategies for the Synthesis of Supported Gold Palladium Nanoparticles with Controlled Morphology and Composition (2013)

The discovery that supported gold nanoparticles are exceptionally effective catalysts for redox reactions has led to an explosion of interest in gold nanoparticles. In addition, incorporating a second metal as an alloy with gold can enhance the catalyst performance even more. The addition of small amounts of gold to palladium, in particular, and vice versa significantly enhances the activity of supported gold-palladium nanoparticles as redox catalysts through what researchers believe is an electronic effect. In this Account, we describe and discuss methodologies for the synthesis of supported gold-palladium nanoparticles and their use as heterogeneous catalysts. In general, three key challenges need to be addressed in the synthesis of bimetallic nanoparticles: (i) control of the particle morphology, (ii) control of the particle size distribution, and (iii) control of the nanoparticle composition. We describe three methodologies to address these challenges. First, we discuss the relatively simple method of coimpregnation. Impregnation allows control of particle morphology during alloy formation but does not control the particle compositions or the particle size distribution. Even so, we contend that this method is the best preparation method in the catalyst discovery phase of any project, since it permits the investigation of many different catalyst structures in one experiment, which may aid the identification of new catalysts. A second approach, sol-immobilization, allows enhanced control of the particle size distribution and the particle morphology, but control of the composition of individual nanoparticles is not possible. Finally, a modified impregnation method can allow the control of all three of these crucial parameters. We discuss the effect of the different methodologies on three redox reactions: benzyl alcohol oxidation, toluene oxidation, and the direct synthesis of hydrogen peroxide. We show that the coimpregnation method provides the best reaction selectivity for benzyl alcohol oxidation and the direct synthesis of hydrogen peroxide. However, because of the reaction mechanism, the sol-immobilzation method gives very active and selective catalysts for toluene oxidation. We discuss the possible nature of the preferred active structures of the supported nanoparticles for these reactions. This paper is based on the IACS Heinz Heinemann Award Lecture entitled "Catalysis using gold nanoparticles" which was given in Munich in July 2012.