gebhart/patrepeval huggingface dataset:
Improved Electrochemiluminescent Label for DNA Probe Assays: Rapid Quantitative Assays of HIV-1 Polymerase Chain Reaction Products (1992)

We describe the characterization and utility of a new electrochemiluminescent (ECL) label for oligonucleotides, utilizing phosphoramidite chemistry. This phosphoramidite of the tris(2,2-bipyridine)ruthenium(II) complex, bis(2,2-bipyridine)(4-[4-(2-cyanoethoxy-N,N-diisopropyl-amino) phosphinoxybutyl]4'-methyl)2,2-bipyridine ruthenium(II) dihexafluorophosphate or Origen phosphoramidite, enables the direct incorporation of the label during automated DNA synthesis. Efficiency of this automated synthesis allows the direct utilization of probes without further purification. Introduction of this labeling group is reproducible, and the ECL signal recovered is not influenced by hybridization. Furthermore, neither hybridization kinetics nor hybrid stability was affected by our label. We also demonstrate the utility of these labels for the development of rapid assays with oligonucleotides direct from automated synthesis. The clinical utility of these labeled oligonucleotides is shown with assays of total nucleic acid, extracted from peripheral blood lymphocytes of patients with acquired immunodeficiency syndrome (AIDS), to detect the human immunodeficiency virus (HIV-1). The results demonstrate the ability of the assay to quantify 30-2000 copies of HIV1 gag genes and to rapidly detect (less than 45 min) HIV-1 gag genes in a nonseparation assay. The application of this assay to clinical samples demonstrates the utility of these assays for rapid and quantitative analysis.
Mammalian cell ganglioside-binding specificities of E. coli enterotoxins LT-IIb and variant LT-IIb(T13I) (2009)

LT-IIb, a type II heat-labile enterotoxin of Escherichia coli, is a potent immunologic adjuvant with high affinity binding for ganglioside GD1a. Earlier study suggested that LT-IIb bound preferentially to the terminal sugar sequence NeuAcalpha2-3Galbeta1-3GalNAc. However, studies in our laboratory suggested a less restrictive binding epitope. LT-IIb(T13I), an LT-IIb variant, engineered by a single isoleucine-threonine substitution, retains biological activity, but with less robust inflammatory effects. We theorized that LT-IIb has a less restrictive binding epitope than previously proposed and that immunologic differences between LT-IIb and LT-IIb (T13I) correlate with subtle ganglioside binding differences. Ganglioside binding epitopes, determined by affinity overlay immunoblotting and enzymatic degradation of ganglioside components of RAW264.7 macrophages, indicated that LT-IIb bound to a broader array of gangliosides than previously recognized. Each possessed NeuAcalpha2-3Galbeta1-3GalNAc, although not necessarily as a terminal sequence. Rather, each had a requisite terminal or penultimate single sialic acid and binding was independent of ceramide composition. RAW264.7 enterotoxin-binding and non-binding ganglioside epitopes were definitively identified as GD1a and GM1a, respectively, by enzymatic degradation and mass spectroscopy. Affinity overlay immunoblots, constructed to the diverse array of known ganglioside structures of murine peritoneal macrophages, established that LT-IIb bound NeuAc- and NeuGc-gangliosides with nearly equal affinity. However, LT-IIb(T13I) exhibited enhanced affinity for NeuGc-gangliosides and more restrictive binding. These studies further elucidate the binding epitope for LT-IIb and suggest that the diminished inflammatory activity of LT-IIb(T13I) is mediated by a subtle shift in ganglioside binding. These studies underscore the high degree of specificity required for ganglioside-protein interactions.
Experimental Apparatus for Assessing the Nonlinear Dynamics of Engine Restart and Shutdown (2018)

An experimental apparatus has been designed and fabricated to assess the nonlinear dynamics of internal combustion engine (ICE) restart and shutdown. The final objective for the apparatus is to validate the application of two-scale command shaping (TSCS) for reduction of unwanted vibrations during ICE restart. The apparatus allows user-specified torque profiles to be applied to a three-cylinder ICE from an electric machine (EM). In turn, the apparatus can measure oscillations in the driveline and chassis, which will ultimately determine the efficacy of TSCS as applied to engine restart. Preliminary results from the apparatus document its ability to measure the unwanted oscillations in the response of the powertrain during ICE restart and shutdown. The apparatus is also expected to provide data, combined with parameter estimation techniques, to determine otherwise uncertain parameters associated with the ICE and EM.
0.7-in. 1280x1024 active-matrix electroluminescent display using a 12-μm pixel structure (1998)

Using a 12 by 12 micrometers pixel cell and 1.0 micrometers deign rules, a 0.7-inch diagonal 1280 by 1024 active matrix electroluminescent (AMEL) display has been designed and demonstrated using a silicon-on-insulator based CMOS technology. The display accepts data at 100 MHz via eight data inputs and provides five bits of gray scale. A total of 24 connections are used for all display functions. Architecture, theory of operation, and detailed specification for this new 2000 line-per-inch display will be discussed. The display is the same size as Planar's previously developed AMEL 640 by 480 arrays, thus providing over tour times the number of pixels in the same footprints as the prior design. The display provides workstation resolution in an extremely compact format and offers the same environmental robustness and optical performance as previously demonstrated in 1000 line-per-inch AMEL displays.
An optically transparent air-coupled capacitive micromachined ultrasonic transducer (CMUT) fabricated using adhesive bonding (2017)

Transparent transducers are desired in the applications where optics and acoustics are combined, such as integrating ultrasound sensing or parametric arrays for directional sound in display, combined optical and acoustical microparticle manipulation, and backward-mode photoacoustic imaging. Some piezoelectric materials, e.g., PVDF, LNO, and PLZT, have been investigated for such applications. Besides, a Fabry-Perot (Etalon) optical ultrasound sensor can be used as a transparent ultrasound receiver. Implementing a transparent transducer in CMUT technology is desired to take advantage of wide bandwidth, ease of fabrication, and broad selection of processing materials. We have demonstrated a CMUT with ITO bottom electrode for improved transparency fabricated using anodic bonding. The main hurdle for the transparency in the visible wavelength range was a 2-μm silicon plate. In this work, we have designed and fabricated a CMUT with a glass plate using adhesive bonding and achieved improved transparency in the full visible wavelength range.
Novel 2-Oxoamide Inhibitors of Human Group IVA Phospholipase A<sub>2</sub> (2002)

A novel class of potent human cytosolic phospholipase A(2) (GIVA PLA(2)) inhibitors was developed. These inhibitors were designed to contain the 2-oxoamide functionality and a free carboxyl group. Among the compounds tested, a long-chain 2-oxoamide containing L-gamma-norleucine was the most potent inhibitor, causing a 50% decrease in GIVA PLA(2) activity at 0.009 mole fraction.
ChemInform Abstract: Enantioselective N‐Heterocyclic Carbene Catalyzed Annulation Reactions with Imidazolidinones. (2014)

Abstract This highly selective carbene catalyzed reaction gives various differently substituted bicyclic lactones through a formal [4 + 2] annulation reaction.
Facile Conversion of Red Phosphorus into Soluble Polyphosphide Anions by Reaction with Potassium Ethoxide (2016)

Abstract Soluble polyphosphide anions were successfully generated in a number of organic solvents by the reaction between shelf‐stable red phosphorus and potassium ethoxide. The species were identified by 31 P NMR spectroscopy in solution and by X‐ray crystal‐structure determination of (Bu 4 N) 2 P 16 in the solid state. The reaction was scaled up to gram quantities by using a flow‐chemistry process.
A watermarking system for adaptive streaming (2014)

Content providers use forensic watermarking, a technique for tracing individuals who illegally redistribute content, as one of the means to fight Internet content redistribution piracy — the top threat for many content providers around the world. As adaptive streaming becomes one of the main mechanisms for delivering premium multimedia content over the Internet, it is essential that watermarking works seamlessly in this environment to remain effective. In this technical paper we describe a solution that uniquely watermarks content for each receiving device using a variety of adaptive streaming applications.
Bayesian fusion of camera metadata cues in semantic scene classification (2004)

Semantic scene classification based only on low-level vision cues has had limited success on unconstrained image sets. On the other hand, camera metadata related to capture conditions provides cues independent of the captured scene content that can be used to improve classification performance. We consider two problems: indoor-outdoor classification and sunset detection. Analysis of camera metadata statistics for images of each class revealed that metadata fields, such as exposure time, flash fired, and subject distance, is most discriminative for both indoor-outdoor and sunset classification. A Bayesian network is employed to fuse content-based and metadata cues in the probability domain and degrades gracefully, even when specific metadata inputs are missing (a practical concern). Finally, we provide extensive experimental results on the two problems, using content-based and metadata cues to demonstrate the efficacy of the proposed integrated scene classification scheme.
Safety and biodistribution of sulfated archaeal glycolipid archaeosomes as vaccine adjuvants (2018)

Archaeosomes are liposomes comprised of ether lipids derived from various archaea. Unlike conventional ester-linked liposomes, archaeosomes exhibit high pH and thermal stability. As adjuvants, archaeosomes can induce robust, long-lasting humoral and cell-mediated immune responses and enhance protection in murine models of infectious disease and cancer. Archaeosomes constituted with total polar lipids (TPL) of various archaea are relatively complex, comprising >10 different lipid compounds. Archaeosomes can be constituted with semi-synthetic glycerolipids built on ether-linked isoprenoid phytanyl cores with varied synthetic glycol- and amino-head groups. However, such semi-synthetic archaeosomes involve many synthetic steps to arrive at the final desired glycolipid composition. We have developed a novel archaeosome formulation comprising a sulfated saccharide group covalently linked to the free sn-1 hydroxyl backbone of an archaeal core lipid (sulfated S-lactosylarchaeol, SLA) mixed with uncharged glycolipid (lactosylarchaeol, LA). This new class of adjuvants can be easily synthesized and retains strong immunostimulatory activity for induction of cell-mediated immunity following systemic immunization. Herein, we demonstrate the safety of SLA/LA archaeosomes following intramuscular injection to mice and evaluate the immunogenicity, in vivo distribution and cellular uptake of antigen (ovalbumin) encapsulated into SLA/LA archaeosomes. Overall, we have found that semi-synthetic sulfated glycolipid archaeosomes are a safe and effective novel class of adjuvants capable of inducing strong antigen-specific immune responses in mice and protection against subsequent B16 melanoma tumor challenge. A key step in their mechanism of action appears to be the recruitment of immune cells to the injection site and the subsequent trafficking of antigen to local draining lymph nodes.
Automated cardiac pose computation from reconstructed myocardial SPECT images (2011)

A method to automatically compute cardiac pose from 3D reconstructed cardiac SPECT images is presented. Cardiac region of interest (ROI) is generated from input volume as the first step. Left ventricle is then segmented from the ROI and myocardial pruning algorithm is applied to remove unnecessary myocardial mass at the top and the bottom. Pruned myocardial binary mask is subjected to a myocardial clusterification-based skeletonization process. Skeleton of the myocardium is cleaned using a novel distance transform and binning-based histogram cleaning algorithm. Blood pool enclosed within the myocardial walls is iteratively segmented to compute the center of mass (COM) of the left ventricle. An ellipsoid fitting algorithm along with the COM is then employed on the myocardial skeleton to determine the cardiac angles. The method achieves a success rate of 94.4% when evaluated on 643 reconstructed volumes from 331 patients.
Infrared satellite rainfall monitoring: relationships between cloud towers, rainfall intensity, and lightning (2014)

Infrared satellite precipitation estimation algorithms rely on relationships between cloud top properties and rainfall. This study is unique in comparing instantaneous (rather than average) precipitation distributions and lightning strikes to satellite-detected cloud tower attributes. Roughly 2/3 of cloud towers represented areas of strong updrafts rising out of the surrounding cloud mass. Half of the precipitation occurred in the cloud mass outside these towers, matching the probability of finding precipitation in progress when a tower is first detected. Nearly the same pattern occurs for lightning but with lower fractions. Typically, the distribution of instantaneous rainfall rates had the same shape inside and outside the towers, and did not change with tower top temperature or area; yet the frequency of occurrence increased as towers became colder and smaller. This suggests that the location of precipitation events inside a storm does not affect instantaneous rainfall rates, only the frequency of occurrence in time and/or space.
Picosecond pulsed diode ring-laser gyroscope (1991)

We have demonstrated a novel solid-state ring-laser gyroscope, which utilizes as the gain media a pair of semi-conductor diodes in an external ring cavity. The use of homogeneously broadened gain media is made possible by actively mode locking the laser. We observe no evidence of frequency locking between the counterpropagating optical pulse trains generated in the cavity to within the limit of our experimental resolution.
Prior image constrained compressed sensing: Implementation and performance evaluation (2011)

Regarding the performance of the minimization methods, the nonlinear CG method with NR line search yields the best convergence speed. Regarding the performance of the PICCS image reconstruction, three main conclusions can be reached. (1) The performance of PICCS is optimal when the weighting parameter of the prior image parameter is selected to be near α = 0.5. (2) The spatial resolution measured for static objects in images reconstructed using PICCS from undersampled datasets is not degraded with respect to the fully-sampled reconstruction for α near its optimal value. (3) The noise texture of PICCS reconstructions is similar to that of the prior image, which was reconstructed using the conventional FBP method.
Band selection for Gabor feature based hyperspectral palmprint recognition (2015)

Hyperspectral imaging has recently been introduced into face and palmprint recognition and is now drawing much attention of researchers in this area. Compared to simple 2D imaging technology, hyperspectral image can bring much more information. Due to its ablity to jointly explore the spatial-spectral domain, 3D Gabor wavelets have been successfully applied for hyperspectral palmprint recognition. In this approach, a set of 52 three-dimensional Gabor wavelets with different frequencies and orientations were designed and convolved with the cube to extract discriminative information in the joint spatial-spectral domain. However, there is also much redundancy among the hyperpecstral data, which makes the feature extraction computationally expensive. In this paper, we propose to use AP (affinity propagation) based clustering approach to select representative band images from available large data. As the number of bands has been greatly reduced, the feature extraction process can be efficiently speed up. Experimental results on the publicly available HK-PolyU hyperspectral palmprint database show that the proposed approach not only improves the efficiency, but also reduces the EER of 3D Gabor feature based method from 4% to 3.26%.
Expedited response compaction for scan power reduction (2011)

Transitions embedded in between consecutive stimulus/response bits toggle scan cells during shift operations. The consequent switching activity in the scan chains further propagate into the combinational logic, resulting in elevated power dissipation levels, and thus, endangering the reliability of the chip being tested. Based on the observation that the content of scan chains during shift operations is irrelevant and unimportant, we propose an expedited response compaction technique in order to reduce power dissipation during scan operations. Parallelized (and expedited) compaction operations help compress the entire capture response onto a single reference chain during the first portion of shift cycles, enabling a simultaneous constant-0 feed to all the remaining chains, in which no scan-out power is dissipated during the subsequent shift cycles. This DfT-based approach is nonintrusive for design flow, requires a very minor investment in area, and in turn delivers significant savings in test power. The proposed solution reduces test power without resorting to x-filling, enabling orthogonal x-filling techniques to be applied in conjunction, while retaining the observed responses intact. Experimental results justify the efficacy of the proposed technique in attaining test power reductions.
Targeted Inhibitors of P‐glycoprotein Overcome Multidrug Resistance in Human Cancer Cell Lines (2015)

Multidrug resistance (MDR), the intrinsic or acquired simultaneous resistance to structurally and chemically unrelated drugs, is arguably the largest barrier to the successful chemotherapeutic treatment of cancer. The best studied mechanism of MDR is due to the overexpression of ABC‐transporter member P‐glycoprotein (P‐gp). All ABC‐transporters utilize ATP hydrolysis to actively export substrates out of the cell, but P‐gp is exceptional in that its substrates are diverse enough to include the majority of clinically relevant chemotherapeutics. Researchers have searched for drugs to inhibit P‐gp for decades and largely failed because the majority interacted with the drug‐binding domain of P‐gp and were themselves transported. Using targeted molecular dynamic simulations and massively parallel drug docking studies, we identified novel compounds that inhibit P‐gp by specifically targeting the ATP binding domain of P‐gp. Biochemical and biophysical studies have confirmed ATP hydrolysis is inhibited by these novel compounds. In the studies reported here, we have evaluated these compounds for their ability to restore drug sensitivity to MDR human cancer cell lines that overexpress P‐gp. Effects on other ABC‐transporters capable of conferring the MDR phenotype are being evaluated and lead compounds are undergoing chemical optimization to develop co‐therapeutics capable of reversing MDR in human cancers. This work is supported by NIH NIGMS [Grant 1R15‐GM094771‐01A1] to PDV and JGW, SMU Research Council, SMU Dean's Research Council, the SMU Center for Drug Discovery, Design and Delivery, and the Communities Foundation of Texas, Dallas.
Cloning in Streptococcus pneumoniae of the gene for DpnII DNA methylase (1984)

The gene coding for the pneumococcal DNA adenine methylase that recognizes the sequence 5'-GATC-3' was cloned in a strain of Streptococcus pneumoniae that lacked both restriction endonucleases DpnI and DpnII. The gene was cloned as a 3.7-kilobase fragment of chromosomal DNA from a DpnII-containing strain inserted in both possible orientations in the multicopy plasmid vector pMP5 to give recombinant plasmids pMP8 and pMP10. Recombinant plasmids were selected by their resistance to DpnII cleavage. Cells carrying the recombinant plasmids modified phage in vivo so that it was restricted by DpnI- but not DpnII-containing hosts. They also showed levels of DNA methylase activity five times higher than that in cells of the original DpnII strain. No DpnII activity was observed in the clones; therefore, it was concluded that the insert did not contain an intact DpnII endonuclease gene and that methylation of host DNA did not turn on a latent form of the gene.
Synthesis of zeolites in the absence of organic structure-directing agents: factors governing crystal selection and polymorphism (2013)

Organic structure-directing agents (OSDAs) are commonly avoided in commercial zeolite synthesis because of the economic and environmental disadvantages associated with the synthesis and removal of organics occluded within zeolite micropores. Zeolite crystallization in OSDA-free media is the route by which microporous clays form in nature, and it is also the preferred method of producing zeolites in bulk for a wide range of applications. There are many synthesis parameters that influence zeolite crystallization, among which include the molar fractions of reagents (silica, alumina, and hydroxide ions), water content, temperature, synthesis aging and heating time, the selection of extraframework cations, the choice of silica and alumina sources, and the use of crystal seeds. In this review, we discuss zeolite framework types that form in OSDA-free solutions at these different synthesis conditions in an effort to highlight structure-property relationships while simultaneously emphasizing the areas where further studies are needed to optimize and/or discover new materials. Interestingly, fewer than 15% of the total reported zeolite structures have been prepared in the absence of OSDAs. For many of these structures, fundamental mechanisms governing their formation are not well understood. In addition, OSDA-free syntheses tend to be more susceptible to the formation of crystal polymorphs (or impurities) that can be generated through a series of structural transformations during the course of zeolite growth. Here we examine the driving forces for phase transitions and explore methods to control phase selection and polymorphism. In order to better facilitate comparisons among zeolite synthesis parameters, we have reinstituted the approach of using kinetic phase diagrams to identify conditions of phase stability.
High-voltage compliant, capacitive-load invariant neural stimulation electronics compatible with standard bulk-CMOS integration (2014)

A neural stimulator architecture is described which can drive biphasic, constant-current waveforms through a wide range of electrode impedances with approximately ±11V compliance, while using a low-voltage, modern bulk-CMOS technology. The design, based on an H-bridge topology, utilizes a regulated “discharge” phase during biphasic delivery to account for “capacitive-looking” electrodes, extending the bipolar on-chip headroom of a CMOS stimulator. Stimulus current is supplied by integrated switched-capacitor, dynamic voltage supplies (0-12V), which operate with closed-loop control. The stimulator topology also uses a single, low-voltage current DAC to regulate the entire biphasic current waveform. The voltage supply block has been fabricated in 65nm standard CMOS. Cadence simulations of the proposed biphasic driver, designed for 250μA maximum current, are given for several “high” impedance electrode models. The efficacy of the proposed integrated electronics in potential neural stimulation applications is demonstrated with a board-level prototype, which has been designed and evaluated in-vivo (rat).