gebhart/patrepeval huggingface dataset:
Cloning and analysis of a recombinant antigen containing an epitope specific for human T-cell lymphotropic virus type II (1992)

An immunodominant HTLV-I-specific epitope in the HTLV-I envelope glycoprotein (GP) 46 has been described. To determine if the analogous region of HTLV-II contains a similarly immunogenic and specific epitope, the polymerase chain reaction (PCR) was used to amplify HTLV-II DNA fragments encoding various portions of the putative epitope. The synthesized DNAs were cloned into lambda-phage gt11 and screened for production of immunoreactive fusion protein using sera from HTLV-II- or HTLV-I-infected individuals. Antisera from HTLV-II-infected individuals identified three of four recombinant clones when tested in a plaque immunoassay. Fusion protein from one of the clones, GH2-K15, was purified and analyzed by Western blot against a panel of HTLV-I and HTLV-II antisera. Twenty-one of 22 HTLV-II-infected sera were reactive with the GH2-K15 epitope. Sera from HTLV-I-infected and HTLV-I-uninfected individuals did not cross-react with GH2-K15. Western blot analysis of recombinant proteins encoding portions of the HTLV-II sequences in the Gh2-K15 antigen localized the HTLV-II-specific epitope to a 17-amino acid sequence. Recombinant antigens containing this epitope should be useful for type-specific serologic diagnosis of HTLV-II infection.
Direct Analysis of Aerosolized Chemical Warfare Simulants Captured on a Modified Glass-Based Substrate by “Paper-Spray” Ionization (2017)

Paper spray ionization mass spectrometry offers a rapid alternative platform requiring no sample preparation. Aerosolized chemical warfare agent (CWA) simulants trimethyl phosphate, dimethyl methylphosphonate, and diisopropyl methylphosphonate were captured by passing air through a glass fiber filter disk within a disposable paper spray cartridge. CWA simulants were aerosolized at varying concentrations using an in-house built aerosol chamber. A custom 3D-printed holder was designed and built to facilitate the aerosol capture onto the paper spray cartridges. The air flow through each of the collection devices was maintained equally to ensure the same volume of air sampled across methods. Each approach yielded linear calibration curves with R2 values between 0.98–0.99 for each compound and similar limits of detection in terms of disbursed aerosol concentration. While the glass fiber filter disk has a higher capture efficiency (≈40%), the paper spray method produces analogous results even with a lower captu...
Design of an Adaptive Optics Scanning Laser Ophthalmoscope (2005)

This chapter contains sections titled: Introduction Light Delivery Raster Scanning Adaptive Optics in the SLO Optical Layout for the AOSLO Image Acquisition Software Interface for the AOSLO Calibration and Testing AO Performance Results Imaging Results Discussions on Improving Performance of the AOSLO
Adaptable infrared surface plasmon resonance spectroscopy accessory (2012)

A second generation prototype enabling surface plasmon resonance spectroscopic measurements in the infrared (IR) range is described. The new design (v2) uses the optical train (optics and detector) within conventional FT-IR spectrometers by confining dimensions of the accessory to space available within the sample compartment of the spectrometer. The v2 accessory builds upon knowledge gained from a previous version that was based on a modified commercial variable angle spectroscopic accessory and addresses observed limitations of the original design-improved temporal stability and measurement acquisition speed, crucial to biomolecular binding studies, as well as optical flexibility, a requirement for investigations of novel plasmon-supporting materials. Different aspects of the accessory, including temporal stability, mechanical resilience, and sensitivity to changes in refractive index of a sample were evaluated and presented in this contribution.
Extraction of Astaxanthin Plgment from Crawfish Waste Using a Soy Oil Process (1982)

ABSTRACT The carotenoid astaxanthin has been extracted from processed crawfish waste using a soy oil process. Analyses have included pigment quantitative analysis, effects of protease enzymes on pigment release, use of ethoxyquin as an antioxidant stabilizer agent, and studies of the ratio of added soybean oil to crawfish waste (v/w) for optimal extraction. Hydrolysis of crawfish waste with a commercial protease, Milezyme® 8X resulted in a 58% increase in astaxanthin release. Maximal pigment extraction and oil recovery was obtained from a 1:1 (v/w) ratio of oil to crawfish waste. The astaxanthin‐enriched oil (60 mg/100g oil), obtained from a 1:10 (v/w) ratio, or 3:10 (v/w) after the second stage of extraction, has application for a variety of pigmentation purposes, notably in aquatic diets for salmonid fishes.
Design and characterization of a laminar flow-through dissolution apparatus: Comparison of hydrodynamic conditions to those of common dissolution techniques (2010)

A flow-through dissolution apparatus was designed and evaluated to screen small quantities of pharmaceutical drug compounds early in development. The apparatus was designed to mount on a microscope slide such that a compacted solid drug was positioned flush along one wall and the fluid flow in the apparatus was laminar flow in a rectangular duct. Stereomicroscopic digital images and Raman spectra of the solid were taken during dissolution and the effluent dissolution medium was collected in fractions to determine the dissolution rate by fluorescence or HPLC/UV. Three compounds, triamterene, ketoprofen, and β-naphthoic acid were investigated in the dissolution flow cell at various hydrodynamic conditions. In conditions where no solvent-mediated conversion was expected, there was a decrease in dissolution rate with time in the flow through cell that was associated with surface smoothing. This phenomenon also occurred in rotating disk experiments. In either case, the magnitude and time course of the decrease in dissolution rate with time is generally different enough to distinguish from the decrease in dissolution rate due to solvent-mediated conversion.
Wireline T1 Logging (2003)

Abstract With the recent introduction of NMR Logging While Drilling tools and down-hole NMR Fluid Analyzers, the more fundamental T1 measurement has made its appearance in the oil patch. In both these applications, the preference of T1 over T2 has been its insensitivity to motion, since T1 measurements effectively eliminate the detrimental effects arising from tool motion or fluid flow. Experience has shown that the acquisition and interpretation of T1 logs recorded in the less hostile wireline environment is quite straightforward, mainly due to the absence of tool motion, while yielding several benefits over T2 logs. T1 is a critical fluid NMR parameter and can play a prominent role in fluid typing applications. Also, T1 data sets are more compact and the acquisition is more efficient. Finally, T1 logging offers the potential of substantially increased logging speeds This paper outlines the current T1 logging practice, and substantiates the advantages of T1 logging using real-life data. Examples included demonstrate the value added by wireline T1 measurements into the overall petrophysical understanding of in-situ reservoir fluids.
Development of a Malaria T‐Cell Vaccine for Blood Stage Immunity (1992)

We have defined a strategy for the development of a T-cell vaccine for blood stage immunity, taking into consideration the central role of T cells and MHC restriction in malaria immune responses. We have used the AMPHI computer algorithm to identify putative T-cell epitopes from conserved regions of 11 Plasmodium falciparum asexual stage proteins. Ten of the eleven proteins are currently candidates for vaccine development. Using this algorithm we selected 22 putative T-cell epitope peptides and 8 control peptides. These peptides were used to test the T-cell responses of three defined populations of Caucasians who have (1) recovered from P. falciparum malaria, (2) been exposed, but never clinically infected, (3) never been exposed or infected. Preliminary analysis of our data shows population differences in T-cell responses to putative T-cell epitope peptides. Ultimately, these studies will help to identify those T epitopes that can be incorporated into a T-cell vaccine for protective immunity.
Synthesizing SRN Models from System Operations with SysML Diagrams for Availability Analysis (2011)

The paper proposes a method to synthesize stochastic reward nets (SRN) models from System Modeling Language (SysML) diagrams to evaluate the impact caused by operations in an operation procedure on availability in a systematic way for the ordinary system designers. The proposed method is implemented on in-house model-based system evaluation framework of NEC, called CASSI, for performance and availability analysis.
Pie-Shaped boron-coated straws with enhanced neutron sensitivity (2016)

The boron-coated straw (BCS) neutron detection technology has been proposed as an attractive <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> He replacement solution in a series of applications in homeland security, neutron science, and safeguards. In order to improve the neutron detection efficiency of the BCS, while maintaining manufacturability, Proportional Technologies, Inc. is introducing a modified BCS with significant performance benefits. The proposed pie-like shape consists of any desired number of arc segments, and an equal number of septa walls, which are radially oriented, and extending a desired distance towards the center of the geometry. Each septum is essentially a segment of the wall that has been collapsed onto itself, resulting in a rigid surface, coated on both sides. The area coated on the septa is added to the area coated on the arc segments, thus offering a significant benefit in sensitivity. Compared to a round straw of the same diameter, the coated wall area of the proposed shape with 12 septa is 3 times larger, assuming the septa are equal in length to each of the arc segments. We present laboratory measurements with two prototype detectors that demonstrate stable operation, a neutron sensitivity that is nearly 3 times higher than that measured in a simple BCS with no septa walls, and adequate energy resolution to effectively discriminate against gamma rays.
Edge-addressed holograms-a novel approach towards narrow bandwidth filters (1989)

The authors outline a novel approach towards achieving the properties of an extremely thick reflection hologram (>or approximately=500 microns) i.e. high angular and spectral selectivity, from a comparatively thin film of holographic material ( approximately=100 microns). The method involves fabricating a conventional 'thin' transmission hologram and interrogating this via an exposed edge of the film using a focussed Gaussian laser beam. Such holograms offer the potential of extremely narrow spectral bandwidths and their use is suggested as filters in single mode fibre de-multiplexing systems. >
Fast PET EM reconstruction from linograms (2003)

The approximate discrete radon transform (ADRT) is a fast forward projection technique for generating linograms. It uses a succession of nearest-neighbor interpolations in a butterfly algorithm analogous to the one used in fast Fourier transforms to gain a (logN)/N speed advantage. We have used matched forward and backward ADRT projectors to perform maximum likelihood expectation maximization (ML-EM) reconstructions for PET (EM-ADRT). Speed and accuracy were tested in four ways. First, the speed of EM-ADRT reconstruction was found to be similar to the speed of the ordered subsets expectation maximization (OSEM). Second, sinograms of Gaussian blobs were generated and reconstructed with 20 iterations of EM-ADRT. Reconstructed blobs in the EM-ADRT images were no more than 0.03 pixels broader than the parent functions, and were mispositioned by no more than a few hundredths of a pixel. The total counts in regions of interest were within 2% of the correct values. Third, Monte Carlo events for hot and cold spheres in a warm background were separately histogrammed into sinograms and linograms. The sinograms were reconstructed by OSEM, the linograms by EM-ADRT. The two iteratively reconstructed images were of similar quality. All structures in the phantoms were resolved and gray levels were recovered quantitatively. Fourth, clinical images reconstructed with EM-ADRT have a qualitative appearance similar to OSEM images. The EM-ADRT method runs about an order of magnitude faster than ordinary ML-EM on data sets of similar size, and generates accurate reconstructed images. It appears to be accurate in every respect required for clinical 2-D PET, and should be well suited to PET reconstruction based on flat-panel technology.
Stable, Well-Defined Nickel(0) Catalysts for Catalytic C–C and C–N Bond Formation (2018)

The synthesis and catalytic activity of several classes of NHC-Ni(0) pre-catalysts stabilized by electron-withdrawing alkenes are described. Variations in the structure of fumarate and acrylate ligands modulate the reactivity and stability of the NHC-Ni(0) pre-catalysts and lead to practical and versatile catalysts for a variety of transformations. The catalytic activity and efficiency of representative members of this class of catalysts have been evaluated in reductive couplings of aldehydes and alkynes and in <i>N</i>-arylations of aryl chlorides.
Epimerization-free access to C-terminal cysteine peptide acids, carboxamides, secondary amides, and esters<i>via</i>complimentary strategies (2017)

C-Terminal cysteine peptide acids are difficult to access without epimerization of the cysteine α-stereocenter. Diversification of the C-terminus after solid-phase peptide synthesis poses an even greater challenge because of the proclivity of the cysteine α-stereocenter to undergo deprotonation upon activation of the C-terminal carboxylic acid. We present herein two general strategies to access C-terminal cysteine peptide derivatives without detectable epimerization, diketopiperazine formation, or piperidinylalanine side products.
Progressive Parametric Query Optimization (2008)

Commercial applications usually rely on pre-compiled parameterized procedures to interact with a database. Unfortunately, executing a procedure with a set of parameters different from those used at compilation time may be arbitrarily sub-optimal. Parametric query optimization (PQO) attempts to solve this problem by exhaustively determining the optimal plans at each point of the parameter space at compile time. However, PQO is likely not cost-effective if the query is executed infrequently or if it is executed with values only within a subset of the parameter space. In this paper we propose instead to progressively explore the parameter space and build a parametric plan during several executions of the same query. We introduce algorithms that, as parametric plans are populated, are able to frequently bypass the optimizer but still execute optimal or near-optimal plans.
A Transient Single Cylinder Test System for Engine Research and Control Development (2005)

A transient test system was developed for a single cylinder research engine that greatly improves test accuracy by allowing the single cylinder to operate as though it were part of a multi-cylinder engine. The system contains two unique test components: a high bandwidth transient hydrostatic dynamometer, and an intake airflow simulator. The high bandwidth dynamometer is used to produce a speed trajectory for the single cylinder engine that is equivalent to that produced by a multi-cylinder engine. The dynamometer has high torque capacity and low inertia allowing it to simulate the speed ripple of a multi-cylinder engine while the single cylinder engine is firing. Hardware in loop models of the drivetrain and other components can be used to test the engine as though it were part of a complete vehicle, allowing standardized emissions tests to be run. The intake airflow simulator is a specialized intake manifold that uses solenoid air valves and a vacuum pump to draw air from the manifold plenum in a manner that simulates flow to other engine cylinders, which are not present in the single cylinder test configuration. By regulating this flow from the intake manifold, the pressure in the manifold and the flow through the induction system are nearly identical to that of the multi-cylinder application. The intake airflow simulator allows the intake runner wave dynamics to be more representative of the intended multi-cylinder application because the appropriate pressure trajectory is maintained in the intake manifold plenum throughout the engine cycle. The system is ideally suited for engine control development because an actual engine cylinder is used along with a test system capable of generating a wide range of transient test conditions. The ability to perform transient tests with a single cylinder engine may open up new areas of research exploring combustion and flow under transient conditions. The system can also be used for testing the engine under conditions such as cylinder deactivation, fuel cut-off, and engine restart. The improved rotational dynamics and improved intake manifold dynamics of the test system allow the single cylinder engine to be used for control development and emissions testing early in the engine development process. This can reduce development time and cost because it allows hardware problems to be identified before building more expensive multi-cylinder engines.
Unique Tracheal Fluid MicroRNA Signature Predicts Response to FETO in Patients With Congenital Diaphragmatic Hernia (2015)

Human fetal hypoplastic CDH lungs have a specific miR-200/miR-10a signature. Survival after FETO is associated with increased miR-200 family expression. miR-200b overexpression in CDH lungs results in decreased TGF-β/SMAD signaling.
Detection of Hepatitis B Surface Antigen with the Miniature Centrifugal Fast Analyzer (1979)

A modified reversed passive hemagglutination test for the detection of hepatitis B surface antigen HBsAg is described. Sera and reagent cells coated with antibody to HBsAg (anti-HBs) are loaded separately into the rotor of a miniature centrifugal fast analyzer. The rotor is centrifuged briefly to transfer the components into its cuvettes. After mixing, the suspensions are allowed to stand at room temperature for 30 min, following which the rotor is again centrifuged and the absorbance of each cuvette is monitored. Cells suspended in serum containing HBsAg leave the light path more rapidly than cells suspended in sera free of antigen. The magnitude of change in absorbance varies directly with the concentration of the antigen. In 45 sera tested by the conventional V-plate technique, findings were as follows: 21 positive, 19 false positive and 5 negative. The automated procedure unequivocally differentiated the 21 positives; results for the false positive and negative specimens were identical and clearly distinguishable from the positive results. The automated procedure enhances specificity, offers equivalent sensitivity, and results that are quantitative and objective.
Raman-shifted eye-safe aerosol lidar development (2004)

The authors present the design and first observations of an backscatter lidar at a wavelength of 1543 nm. The transmitter utilizes stimulated Raman scattering in methane to shift the Nd:YAG fundamental to this eye-safe wavelength.
Relationship between tumor gene expression and recurrence in stage II/III colon cancer: Quantitative RT-PCR assay of 757 genes in fixed paraffin-embedded (FPE) tissue (2006)

3518 Background: As an initial step in developing abetter method of assessing prognosis following potentially curative surgery for colon cancer, we performed an exploratory gene identification study. Methods: RNA was extracted from three 10-micron sections of the FPE tumor tissue obtained at the initial diagnosis from 353 patients entered between 1977 and 1984 into the surgery-only or surgery-plus BCG arms of NSABP C-01/C-02. Expression was quantified for 757 cancer-related and reference genes with RT-PCR. Results: Blocks from 270 patients were evaluable after pre-specified exclusions: 128 were stage II and 142 were stage III. All patients had ≥ 5-year follow up. In univariate Cox proportional hazard analyses, 148 genes exhibited a nominally significant (unadjusted p-value <0.05) linear association with recurrence-free interval (RFI) (7 genes p≤0.001, 66 genes 0.001<p<0.01; 75 genes 0.01≤p<0.05). False discovery rate calculations suggest that about 25% of the 148 genes are expected to be false positives. Higher expression was associated with shorter RFI for 118 genes including SERPINB5, DUSP1, AKT3, TIMP1, ANXA2, RHOB (p≤ 0.001) and with longer RFI for 30 genes including BRCA1 (p≤0.001). The relationship between gene expression and RFI was similar for stage II and stage III patients for 143 of the 148 genes found to be significant. The largest cluster of genes is functionally related to extracellular matrix remodeling. The magnitude of the hazard ratios is similar to that observed in the early Oncotype DX studies in breast cancer and should allow clinically useful separation into low/intermediate/high risk groups. Conclusions: Quantitative RT-PCR assay of FPE colon cancer tissue can be used to identify large numbers of genes associated with RFI in patients with stage II and III colon cancer. If these results are confirmed by additional studies in progress, this technique has promise to improve selection of colon cancer patients for adjuvant chemotherapy. Funded in part as a collaborative arrangement under contract between the NSABP Foundation, Inc., and Genomic Health, Inc. [Table: see text]
Novel architectures for squares, and sums of squares, of cross-correlations of bipolar sequences with applications to CDMA (2013)

This paper describes novel architectures for computing squares, and sums of squares, of cross-correlations of bipolar sequences. Both metrics are used in improved channel decoder metrics for CDMA systems, but also appear in other signal processing applications. The key idea is to compute outer products of each code vector with itself, and formulate the metrics so as to avoid explicit computation of cross-correlations. The expensive squaring unit is also eliminated. A detailed complexity analysis is carried out in which we demonstrate the advantages of these architectures. They also offer easier updates when there are incremental changes in the system. We also describe a few variations and special cases including short codes and asynchronous users, and point out further enhancements.
Force sensing micro-forceps for robot assisted retinal surgery (2012)

Membrane peeling is a standard vitreoretinal procedure, where the surgeon delaminates a very thin membrane from retina surface using surgical picks and forceps. This requires extremely delicate manipulation of the retinal tissue. Applying excessive forces during the surgery can cause serious complications leading to vision loss. For successful membrane peeling, most of the applied forces need to be very small, well below the human tactile sensation threshold. In this paper, we present a robotic system that combines a force sensing forceps tool and a cooperatively-controlled surgical robot. This combination allows us to measure the forces directly at the tool tip and use this information for limiting the applied forces on the retina. This may prevent many iatrogenic injuries and allow safer maneuvers during vitreoretinal procedures. We show that our system can successfully eliminate hand-tremor and excessive forces in membrane peeling experiments on the inner shell membrane of a chicken embryo.