gebhart/patrepeval huggingface dataset:
Preclinical evaluation in nonhuman primates of murine monoclonal anti-idiotype antibody that mimics the disialoganglioside GD2. (1997)

The antiganglioside GD2 monoclonal antibody 14G2a (Ab1) served as an immunogen to generate the anti-idiotype (anti-Id) 1A7 (IgG1,kappa), which mimics GD2 both antigenically and biologically. Anti-Id 1A7 induced anti-GD2 antibodies in mice and rabbits. In this preclinical study, a pair of cynomolgus monkeys, immunized with 1A7 that had been mixed with QS-21 adjuvant, produced anti-anti-Id antibodies (Ab3), which reacted with the GD2-positive melanoma cell line M21/P6 cells but not with GD2-negative LS174-T cells. The Ab3 shared Ids with mAb 14G2a (Ab1), as demonstrated by their ability to inhibit binding of 1A7 to this Ab1. The Ab3 bound specifically to purified GD2 antigen and competed with the Ab1 14G2a in binding to a GD2-positive melanoma cell line or to purified GD2, suggesting that Ab1 and Ab3 may bind to the same epitope and may behave as an Ab1-like antibody (Ab1'). The isotype of the GD2-specific antibodies was mostly IgG in nature. The specificity of the antibodies for GD2 was further confirmed by dot blot analysis. These antisera also specifically lysed GD2-positive target cells in an antibody-dependent cellular cytotoxicity assay. The induction of anti-GD2 responses in monkeys did not cause any apparent side effects, despite the fact that GD2 antigen is expressed by many normal tissues of these animals. Taken together, these results suggest that anti-Id 1A7 can induce GD2-specific antibodies in nonhuman primates and can thus serve as a potential network antigen for triggering active anti-GD2 antibodies in patients with GD2-positive neuroectodermal tumors.
Development and Validation of an Immuno-PET Tracer as a Companion Diagnostic Agent for Antibody-Drug Conjugate Therapy to Target the CA6 Epitope (2015)

Three antibody fragments were produced and examined as potential companion diagnostic agents. (64)Cu-DOTA-B-Fab is a stable and effective immuno-PET tracer for CA6 imaging in vivo.
Constitutive Gi2-dependent Activation of Adenylyl Cyclase Type II by the 5-HT1A Receptor (1999)

The 5-HT1A receptor is implicated in depression and anxiety. This receptor couples to G(i) proteins to inhibit adenylyl cyclase (AC) activity but can stimulate AC in tissues (e.g. hippocampus) that express ACII. The role of ACII in receptor-mediated stimulation of cAMP formation was examined in HEK-293 cells transfected with the 5-HT1A receptor, which mediated inhibition of basal and G(s)-induced cAMP formation in the absence of ACII. In cells cotransfected with 5-HT1A receptor and ACII plasmids, 5-HT1A agonists induced a 1. 5-fold increase in cAMP level. Cotransfection of 5-HT1A receptor, ACII, and Galpha(i2), but not Galpha(i1), Galpha(i3), or Galpha(o), resulted in an agonist-independent 6-fold increase in the basal cAMP level, suggesting that G(i2) preferentially coupled the receptor to ACII. The 5-HT1B receptor also constitutively activated ACII. Constitutive activity of the 5-HT1A receptor was blocked by pertussis toxin and the Gbetagamma antagonist, betaCT, suggesting an important role for Gbetagamma-mediated activation of ACII. The Thr-149 --> Ala mutation in the second intracellular domain of the 5-HT1A receptor disrupted Gbetagamma-selective activation of ACII. Spontaneous 5-HT1A receptor activity was partially attenuated by 5-HT1A receptor partial agonists with anxiolytic activity (e.g. buspirone and flesinoxan) but was not altered by full agonists or antagonists. Thus, anxiolytic activity may involve inhibition of spontaneous 5-HT1A receptor activity.
Free-standing carbon nanotube films for extreme ultraviolet pellicle application (2018)

To enable high volume manufacturing with extreme ultraviolet (EUV) lithography, a pellicle membrane is needed to protect the reticle from particles at EUV source powers beyond 250 W. Identifying a membrane with high EUV transmission, mechanical integrity, thermal stability, and chemical resistance to the scanner environment is extremely challenging; yet, these properties are required to realize next-generation EUV pellicle solutions. Free-standing carbon nanotube (CNT) film as an alternative next-generation core pellicle material is proposed. We demonstrate that free-standing CNT films possess very high EUV transmission (up to 99%) and good transmission uniformity (∼0.4 % half range), mechanical stability (maximum deflection ∼0.08 mm at 2 Pa), thermal stability (no transmission change under greater than 250 W equivalent EUV power in vacuum), and scalability to a full pellicle size (∼15 × 12 cm2). The capability of the CNT membrane to withstand high EUV power in the presence of H2 for a limited time is demonstrated. Other CNT membrane properties are presented that are important for the pellicle application: low EUV scattering, low EUV reflectivity, and sufficient transmission to enable through-pellicle inspection with DUV light or electrons. The ability of the CNT film to stop particles is tested. The influence of hydrogen at higher EUV powers and prolonged exposures on the lifetime of the CNT pellicle remains the current research focus. Approaches for coating the free-standing CNT films for protection are discussed.
High performance discrete Fourier transforms on graphics processors (2008)

We present novel algorithms for computing discrete Fourier transforms with high performance on GPUs. We present hierarchical, mixed radix FFT algorithms for both power-of-two and non-power-of-two sizes. Our hierarchical FFT algorithms efficiently exploit shared memory on GPUs using a Stockham formulation. We reduce the memory transpose overheads in hierarchical algorithms by combining the transposes into a block-based multi-FFT algorithm. For non-power-of-two sizes, we use a combination of mixed radix FFTs of small primes and Bluestein's algorithm. We use modular arithmetic in Bluestein's algorithm to improve the accuracy. We implemented our algorithms using the NVIDIA CUDA API and compared their performance with NVIDIA's CUFFT library and an optimized CPU-implementation (Intel's MKL) on a high-end quad-core CPU. On an NVIDIA GPU, we obtained performance of up to 300 GFlops, with typical performance improvements of 2-4times over CUFFT and 8-40times improvement over MKL for large sizes.
Transmission-Line Identities for a Class of Interconnected Coupled-Line Sections with Application to Adjustable Microstrip and Stripline Tuners (1980)

Transmission-line identities are developed for a class of interconnected coupled-line sections. The identities, which may be used in several applications, are employed to synthesize adjustable microstrip and stripline tuners consisting of parallel, coupled or uncoupled strips with movable bridging wires. The tuners, which are analogous to waveguide and coaxial-line multistub tuners, can be used, in principle, to match any impedance falling within the Smith Chart. An experiment on a 12-GHz adjustable microstrip tuner is described, and the results are found to agree favorably with the theory.
DNA Methylation Analysis Triggered by Bulge Specific Immuno-Recognition (2012)

We report the sequence-selective discrimination of the cytosine methylation status in DNA with anti methylcytosine antibody for the first time. This was realized by employing an affinity measurement involving the target methylcytosine in a bulge region and anti methylcytosine antibody, following hybridization with a bulge-inducing DNA to ensure that only the target methylcytosine is located in the bulge. The affinity of the antibody for methylcytosine in the bulge was 79% of that in a single strand of DNA; however, the affinity for nontarget methylcytosine in a double strand of DNA decreased greatly. This is because the antibody cannot bind with an inwardly turned methylcytosine in the duplex region owing to the large antibody size. In contrast, the methylcytosine in the bulge is recognized by the antibody because it is available to rotate freely owing to the single bond between deoxyribose and phosphate in a DNA chain. By employing the difference between the affinity in the bulge and that in the duplex, we could determine selectively whether or not the target cytosine was methylated in an O(6)-methylguanine DNA methyltransferase (MGMT) promoter sequence with a single base level. The proposed bulge-specific assay technique can be combined with a widely used absorbance measurement method that employs the color change in tetramethyl benzidine induced by horseradish peroxidase-labeled secondary antibody. The sequence-selective discrimination of the methylation status could also be obtained with various types of interfering genomic DNA contamination without any conventional bisulfite treatment, polymerase chain reaction, (PCR) or electrophoresis.
Live‐Cell Studies of p300/CBP Histone Acetyltransferase Activity and Inhibition (2012)

Histone acetyltransferase enzymes (HATs) are important therapeutic targets, but there are few cell-based assays available for evaluating the pharmacodynamics of HAT inhibitors. Here we present the application of a FRET-based reporter, Histac, in live-cell studies of p300/CBP HAT inhibition, by both genetic and pharmacologic disruption. shRNA knockdown of p300/CBP led to increased Histac FRET, thus suggesting a role for p300/CBP in the acetylation of the histone H4 tail. Additionally, we describe a new p300/CBP HAT inhibitor, C107, and show that it can also increase cellular Histac FRET. Taken together, these studies provide a live-cell strategy for identifying and evaluating p300/CBP inhibitors.
A 200 MHz CMOS Driver with Output Impedance Automatic Control (1991)

A fast CMOS digital output driver is presented; the circuit can work at a rate of 200 Mbit/sec with an eye pattern opened more than 80%. The output impedance of the driver can track the characteristic resistance of the line with an accuracy better than 10% and the whole power consumption is less than 30 mW.
Deletion of Marek's Disease Virus Large Subunit of Ribonucleotide Reductase Impairs Virus Growth In Vitro and In Vivo (2013)

Marek's disease virus (MDV), a highly cell-associated lymphotropic alphaherpesvirus, is the causative agent of a neoplastic disease in domestic chickens called Marek's disease (MD). In the unique long (UL) region of the MDV genome, open reading frames UL39 and UL40 encode the large and small subunits of the ribonucleotide reductase (RR) enzyme, named RR1 and RR2, respectively. MDV RR is distinguishable from that present in chicken and duck cells by monoclonal antibody T81. Using recombinant DNA technology we have generated a mutant MDV (Md5deltaRR1) in which RR1 was deleted. PCR amplification of the RR gene in Md5deltaRR1-infected duck embryo fibroblasts (DEF) confirmed the deletion of the 2.4 kb RR1 gene with a resultant amplicon of a 640-bp fragment. Restriction enzyme digests with SalI confirmed a UL39 deletion and the absence of gross rearrangement. The biologic characteristics of Md5deltaRR1 virus were studied in vitro and in vivo. The Md5deltaRR1 replicated in DEF, but significantly slower than parental Md5-BAC, suggesting that RR is important but not essential for replication in fibroblasts. In vivo studies, however, showed that the RR1 deletion virus was impaired for its ability to replicate in chickens. Inoculation of specific-pathogen-free (SPF) chickens with Md5deltaRR1 showed the mutant virus is nonpathogenic and does not induce MD in birds. A revertant virus, Md5deltaRR1/R, was generated with the restored phenotype of the parental Md5-BAC in vivo, indicating that RR is essential for replication of the virus in chickens. Protection studies in SPF chickens indicated that the Md5deltaRR1 virus is not a candidate vaccine against MD.
SAR Study of 1-Aryl-4-(phenylarylmethyl)piperazines as Ligands for Both Dopamine D2 and Serotonin 5-HT1A Receptors Showing Varying Degrees of (Ant)agonism. Selection of a Potential Atypical Antipsychotic (2006)

The syntheses of several 1-aryl-4-(arylpyridylmethyl)piperazines (4) and their affinities for dopamine D(2) and serotonin 5-HT(1A) receptors are described. The compounds were evaluated both in vitro and in vivo, resulting in the identification of the drug candidate SLV313 (4e) with equipotent and full D(2) receptor antagonism and 5-HT(1A) receptor agonism. Minor structural modifications in SLV313 revealed the possibility of designing compounds possessing varying degrees of partial agonism on one or both target receptors.
Ex vivo peripheral nerve detection of rats by spontaneous Raman spectroscopy (2015)

Nerve-sparing surgery is increasingly being applied to avoid functional deficits of the limbs and organs following surgery. Peripheral nerves that should be preserved are, however, sometimes misidentified due to similarity of shape and color to non-nerve tissues. To avoid misidentification of peripheral nerves, development of an in situ nerve detection method is desired. In this study, we report the label-free detection of ex vivo peripheral nerves of Wistar rats by using Raman spectroscopy. We obtained Raman spectra of peripheral nerves (myelinated and unmyelinated nerves) and their adjacent tissues of Wistar rats without any treatment such as fixation and/or staining. For the identification of tissue species and further analysis of spectral features, we proposed a principal component regression-based discriminant analysis with representative Raman spectra of peripheral nerves and their adjacent tissues. Our prediction model selectively detected myelinated nerves and unmyelinated nerves of Wistar rats with respective sensitivities of 95.5% and 88.3% and specificities of 99.4% and 93.5%. Furthermore, important spectral features for the identification of tissue species were revealed by detailed analysis of principal components of representative Raman spectra of tissues. Our proposed approach may provide a unique and powerful tool for peripheral nerve detection for nerve-sparing surgery in the future.
Privacy and Fairness in Recommender Systems via Adversarial Training of User Representations (2019)

Latent factor models for recommender systems represent users and items as low dimensional vectors. Privacy risks of such systems have previously been studied mostly in the context of recovery of personal information in the form of usage records from the training data. However, the user representations themselves may be used together with external data to recover private user information such as gender and age. In this paper we show that user vectors calculated by a common recommender system can be exploited in this way. We propose the privacy-adversarial framework to eliminate such leakage of private information, and study the trade-off between recommender performance and leakage both theoretically and empirically using a benchmark dataset. An advantage of the proposed method is that it also helps guarantee fairness of results, since all implicit knowledge of a set of attributes is scrubbed from the representations used by the model, and thus can't enter into the decision making. We discuss further applications of this method towards the generation of deeper and more insightful recommendations.
ICD lead failure detection through high frequency impedance (2014)

Abrasion-induced insulation breach is a common failure mode of silicone-body, transvenous, implantable cardioverter defibrillator leads. It is caused either by external compression or internal motion of conducting cables. The present method of monitoring lead integrity measures low frequency conductor impedance. It cannot detect insulation failures until both the silicone lead body and inner fluoropolymer insulation have been breached completely, exposing conductors directly to blood or tissue. Thus the first clinical presentation may be either failure to deliver a life-saving shock or painful, inappropriate shocks in normal rhythm. We present a new method for identifying lead failure based on high frequency impedance measurements. This method was evaluated in 3D electromagnetic simulation and bench testing to identify insulation defects in the St. Jude Medical Riata® lead, which is prone to insulation breach.
Developing the Surface Chemistry of Transparent Butyl Rubber for Impermeable Stretchable Electronics (2016)

Transparent butyl rubber is a new elastomer that has the potential to revolutionize stretchable electronics due to its intrinsically low gas permeability. Encapsulating organic electronic materials and devices with transparent butyl rubber protects them from problematic degradation due to oxygen and moisture, preventing premature device failure and enabling the fabrication of stretchable organic electronic devices with practical lifetimes. Here, we report a methodology to alter the surface chemistry of transparent butyl rubber to advance this material from acting as a simple device encapsulant to functioning as a substrate primed for direct device fabrication on its surface. We demonstrate a combination of plasma and chemical treatment to deposit a hydrophilic silicate layer on the transparent butyl rubber surface to create a new layered composite that combines Si-OH surface chemistry with the favorable gas-barrier properties of bulk transparent butyl rubber. We demonstrate that these surface Si-OH groups react with organosilanes to form self-assembled monolayers necessary for the deposition of electronic materials, and furthermore demonstrate the fabrication of stretchable gold wires using nanotransfer printing of gold films onto transparent butyl rubber modified with a thiol-terminated self-assembled monolayer. The surface modification of transparent butyl rubber establishes this material as an important new elastomer for stretchable electronics and opens the way to robust, stretchable devices.
A Low Hysteresis NiTiFe Shape Memory Alloy Based Thermal Conduction Switch (2006)

Shape memory alloys possess the ability to return to a preset shape by undergoing a solid state phase transformation at a particular temperature. This work reports on the development and testing of a low temperature thermal conduction switch that incorporates a NiTiFe shape memory element for actuation. The switch was developed to provide a variable conductive pathway between liquid methane and liquid oxygen dewars in order to passively regulate the temperature of methane. The shape memory element in the switch undergoes a rhombohedral or R-phase transformation that is associated with a small hysteresis (typically 1-2 degrees C) and offers the advantage of precision control over a set temperature range. For the NiTiFe alloy used, its thermomechanical processing, subsequent characterization using dilatometry, differential scanning calorimetry and implementation in the conduction switch configuration are addressed. © 2006 American Institute of Physics.
<title>Experimental investigation of beryllium-based multilayer coatings for extreme ultraviolet lithography</title> (1999)

The performance of beryllium-based multilayer coatings designed to reflect light of wavelengths near 11 nm, at normal incidence, is presented. These multilayer coatings are of special interest for extreme ultraviolet lithography (EUVL). The beryllium-based multilayers investigated were Mo/Be, Ru/Be and a new material combination Mo<SUB>2</SUB>C/Be. The highest reflectivity achieved so far is 70% at 11.3 nm with 70 bilayers of Mo/Be. However, even though high reflectivity is very important, there are other parameters to satisfy the requirements for an EUVL production tool. Multilayer stress, thermal stability, radiation stability and long term reflectance stability are of equal or greater importance. An experimental characterization of several coatings was carried out to determine the reflectivity, stress, microstructure, and long term stability of these coatings. Theoretically calculated reflectivities are compared with experimental results for different material pairs; differences between experimental and theoretical reflectivities and bandwidths are addressed.
High-Density Microarray-Mediated Gene Expression Profiling of <i>Escherichia coli</i> (2001)

A nearly complete collection of 4,290 Escherichia coli open reading frames was amplified and arrayed in high density on glass slides. To exploit this reagent, conditions for RNA isolation from E. coli cells, cDNA production with attendant fluorescent dye incorporation, DNA-DNA hybridization, and hybrid quantitation have been established. A brief isopropyl-beta-D-thiogalactopyranoside (IPTG) treatment elevated lacZ, lacY, and lacA transcript content about 30-fold; in contrast, most other transcript titers remained unchanged. Distinct RNA expression patterns between E. coli cultures in the exponential and transitional phases of growth were catalogued, as were differences associated with culturing in minimal and rich media. The relative abundance of each transcript was estimated by using hybridization of a genomic DNA-derived, fluorescently labeled probe as a correction factor. This inventory provided a quantitative view of the steady-state level of each mRNA species. Genes the expression of which was detected by this method were enumerated, and results were compared with the current understanding of E. coli physiology.
<title>In vivo optical coherence tomography and topography of the fundus of the human eye</title> (1995)

The dual beam scanning partial coherence interferometry technique, which was recently developed to measure the fundus profile of the human eye in vivo, is used for tomographic and topographic imaging and for the measurement of different retinal structures, e.g., the contour of the papilla and thickness profiles of retina and retinal nerve fiber layer. In case of well defined, sharp boundaries between two layers of different refractive indices, the absolute position of these retinal structures can be determined with a precision (standard deviation) of 5 micrometers . Compared to first results with this instrument, the measurement time for horizontal and vertical scans was reduced by a factor of 10. At present, the measuring time of a vertical scan over 10 degree(s) in steps of 0.5 degree(s) takes at least 20 seconds without and 80 seconds with signal averaging of 4 longitudinal scans over 1.5 mm distance. Further improvements to 5 - 20 seconds are discussed. The longitudinal resolution of this instrument is approximately 15 micrometers (full-width-half-maximum), depending on the coherence length of the light source; this is about 5 times better than previous measurements. Topographic and tomographic scans across the optic disk reveal an increase of thickness of the retinal nerve fiber layer at the inferior and superior rim of the disk, which are in good agreement with results published in the literature.
ANTISENSE PROPERTIES OF 2′-<i>O</i>-DIMETHYLAMINOOXYETHYL (2′-<i>O</i>-DMAOE) OLIGONUCLEOTIDES (2001)

Antisense oligonucleotides with 2'-O-(2-[N,N-dimethyl)aminooxy]ethyl) or (2'-O-DMAOE) modification were synthesized and evaluated for nuclease resistance and pharmacology both in vitro and in vivo. This modification exhibits very high nuclease resistance and efficacy in various biological (ICAM-1, C-raf and PKC-alpha) targets.