gebhart/patrepeval huggingface dataset:
Cloning and identification of the infectious salmon anaemia virus haemagglutinin (2001)

Infectious salmon anaemia virus (ISAV) is an orthomyxo-like virus that causes serious disease in Atlantic salmon (Salmo salar). Like the orthomyxoviruses, ISAV has been shown to possess haemagglutinin (HA) activity. This study presents the cloning, expression and identification of the ISAV HA gene, which was isolated from a cDNA library by immunoscreening. The HA gene contained an ISAV-specific conserved nucleotide motif in the 5' region and a 1167 bp open reading frame encoding a protein with a predicted molecular mass of 42.4 kDa. The HA gene was expressed in a baculovirus system. A monoclonal antibody (MAb) shown previously to be directed against the ISAV HA reacted with insect cells infected with recombinant baculovirus. Salmon erythrocytes also adsorbed to these cells and adsorption was inhibited by the addition of either the ISAV-specific MAb or a polyclonal rabbit serum prepared against purified virus, confirming the virus specificity of the reaction. Immunoblot analyses indicated that ISAV HA, in contrast to influenza virus HA, is not posttranslationally cleaved. Sequence comparisons of the HA gene from five Norwegian, one Scottish and one Canadian isolate revealed a highly polymorphic region that may be useful in epidemiological studies.
2A2-B11 Development of a Human-sized Multifingered Hand with Detachable Wrist (2009)

In this paper, we proposed a human-sized multifingered robot hand with detachable mechanism at the wrist. The fingers are driven by wires and are controlled by actuators embedded in the arm part. The robot hand can be split into the hand part and the arm part. The driving force from the arm part is transmitted to the hand part by gear mechanism at the wrist. The developed robot hand is the size of 200(length) x 78(width) x 24.6[mm](thickness) and can exert 10[N] at the fingertip. The performance of the robot hand is shown by a motion control experiment.
Clear Air Turbulence: Detection by Infrared Observations of Water Vapor (1977)

"Forward-looking" infrared measurements of water vapor from the C-141A Kuiper Airborne Observatory of the National Aeronautics and Space Administration Ames Research Center show large, distinctly identifiable, signal anomalies from 4 to 10 minutes in advance of subsequent encounters with clear air turbulence (CAT). These anomalies are characteristically different from the signals not followed by CAT encounters. Results of airborne field trials in which the infrared radiometer was used indicate that, out of 51 situations, 80 percent were CAT alerts followed by CAT encounters, 12 percent were "false alarms" (CAT alerts not followed by CAT encounters), and 8 percent were CAT encounters not preceded by an infrared signal anomaly or CAT alert.
Use of Fully Biodegradable Panels to Reduce Derelict Pot Threats to Marine Fauna (2012)

Fishing pots (i.e., traps) are designed to catch fish or crustaceans and are used globally. Lost pots are a concern for a variety of fisheries, and there are reports that 10-70% of deployed pots are lost annually. Derelict fishing pots can be a source of mortality for target and bycatch species for several years. Because continual removal of derelict gear can be impractical over large spatial extents, modifications are needed to disarm gear once it is lost. We tested a fully biodegradable panel with a cull or escape ring designed for placement on the sides of a crab pot that completely degrades into environmentally neutral constituents after approximately 1 year. This panel is relatively inexpensive, easy to install, and can be used in multiple fisheries. We used the blue crab (Callinectes sapidus) fishery as a test case because it is a large pot fishery and blue crab pots are similar to traps used in other pot fisheries. We had commercial fishers deploy pots with panels alongside standard pots in Chesapeake Bay (U.S.A.) to assess potential effects of our experimental pots on blue crab catch. We compared the number, biomass, and size of crabs captured between standard and experimental pots and evaluated differences in catch over a crabbing season (March-November) at five locations. There was no evidence that biodegradable panels adversely affected catch. In all locations and time periods, legal catches were comparable in abundance, biomass, and size between experimental and standard pots. Properly designed biodegradable panels appear to be a viable solution to mitigate adverse effects of derelict pots.
A low-voltage CMOS LNA with multiple magnetic feedback for WLAN applications (2006)

A CMOS low-noise-amplifier (LNA) topology that utilizes multiple monolithic transformer magnetic feedback is presented. The proposed topology permits negative and positive feedback to be applied constructively, in order to simultaneously neutralize the gate-drain overlap capacitance of the amplifying transistor and achieve high gain at high frequencies when driving an on-chip capacitance. It also allows for a stable design with adequate gain and large reverse isolation without noise figure (NF) degradation. Simulation results indicate voltage conversion gain of 17 dB, NF of 1.6 dB and third-order input intercept point (IIP3) of 13 dBm. The design is being implemented in a 0.13 mum CMOS technology
A highly stable CMOS Self-Compensated Oscillator (SCO) based on an LC tank temperature Null concept (2011)

A highly stable all silicon Self-Compensated Oscillator (SCO) reference source is presented. Self compensation across temperature is achieved using a newly discovered phenomenon in LC-tanks named the Temperature Null (TNULL) which has been described and briefly analyzed. A quadrature oscillator architecture has been used to implement the SCO in a 0.18μm CMOS technology. The SCO has on-chip infrastructure facilitating low cost trimming and frequency calibration at room temperature. Excellent frequency stability of ±50ppm has been measured across temperature (0 - 70°C), 3.0 - 3.6V supply and 1 - 15pF load. The SCO has a programmable frequency range of 1 - 133MHz, consumes 7.1mA at 25MHz and has an RMS period jitter of 2ps at 125MHz.
A solution to the service agent transport problem (2015)

We introduce a new problem in the area of scheduling and route planning operations called the service agent transport problem (SATP). Within the SATP, autonomous service agents must perform tasks at a number of locations. The agents are free to move between locations, however, the agents may also be transported throughout the region by a limited number of faster-moving transport agents. The goal of the SATP is to plan a schedule of service agent and transport agent actions such that all locations are serviced in the shortest amount of time. We pose the problem using a mixed-integer linear programming optimization framework, and compare several complexity reduction heuristics to the full optimization.
Robust control for parallel operated L-Inverters with uncertainty and disturbance estimator (2016)

In conventional droop control, accurate proportional load sharing could not be achieved among parallel operated inverters due to the mismatch of output impedance and system disturbances. In this paper, an uncertainty and disturbance estimator (UDE)-based robust droop control strategy is proposed for accurate proportional load sharing, particularly reactive power sharing, among parallel operated L-inverters. The reactive power dynamics is derived from power delivery equation passed by a low-pass filter, while the reactive power reference is designed with the feedback of load voltage. The reactive power control is developed based on UDE-based method. The model nonlinearity and uncertainty (e.g., power angle), and system operation disturbances (e.g., change of output impedance, and load change), can be estimated and compensated by this UDE-based robust droop control. Experimental validation is provided to show the effectiveness of the proposed method.
Low temperature rhombohedral single crystal SiGe epitaxy on c-plane sapphire (2016)

Current best practice in epitaxial growth of rhombohedral SiGe onto (0001) sapphire (A<sub>l2</sub>O<sub>3</sub>) substrate surfaces requires extreme conditions to grow a single crystal SiGe film. Previous models described the sapphire surface reconstruction as the overriding factor in rhombohedral epitaxy, requiring a high temperature Al-terminated surface for high quality films. Temperatures in the 850-1100°C range were thought to be necessary to get SiGe to form coherent atomic matching between the (111) SiGe plane and the (0001) sapphire surface. Such fabrication conditions are difficult and uneconomical, hindering widespread application. This work proposes an alternative model that considers the bulk sapphire structure and determines how the SiGe film nucleates and grows. Accounting for thermal expansion effects, calculations using this new model show that both pure Ge and SiGe can form single crystal films in the 450-550°C temperature range. Experimental results confirm these predictions, where x-ray diffraction and atomic force microscopy show the films fabricated at low temperature rival the high temperature films in crystallographic and surface quality. Finally, an explanation is provided for why films of comparable high quality can be produced in either temperature range.
Abstract 4097: Integrative analysis of epigenetic and transcriptional alterations in head and neck squamous cell carcinomas (2012)

Abstract Objective: Head and Neck Squamous Cell Carcinoma (HNSCC) is the sixth most common cancer worldwide with a 50% patient survival rate 5 years post-diagnosis despite current therapeutic strategies. A direct comprehensive genome wide integrated analysis of epigenetic and transcriptional alteration in primary HNSCC has not been performed before. Such data would greatly enrich our knowledge about HNSCC biology and would be beneficial for the development of the individual targeted therapy. Experimental Design: 44 primary HNSCC and 25 normal mucosal samples were used in the Affymetrix GeneChip Human Exon 1.0 array and for the Illumina Infinium Human Methylation 27 array. To analyze the data we employed a novel screening approach based on Cancer Outlier Profile Analysis (COPA). With use of this approach we determined 81 significant differentially expressed and 37 significant differentially methylated genes with both oncogenic and tumor suppressing properties. Results: Out of total 118 candidate genes we picked 36 candidate tumor suppressing genes with strong correlation between hypermethylation and decrease of expression in tumor samples, such as BANK1, ADFP, MAPK4, ZNF71 and others. 20 genes out of total 36 were validated by bisulfite sequencing in a separate cohort of 32 primary HNSCC tumor and 16 normal mucosal tissues. Out of the total 20 genes, 13 demonstrated at least 40% difference in methylation, most notably for BANK1 81% of tumors were more methylated as compared to normals. 7 of these newly discovered genes out of the 36 belong to Zinc Finger Proteins (ZNF) group and they have never been reported as tumor suppressors in HNSCC before. Bisulfite sequencing and quantitative real time PCR (qRT-PCR) analysis of ZNFs revealed that they are strongly hypermethylated and underexpressed in HNSCC tumor samples. Conclusions: Our new screening approach allowed identification of 36 candidate tumor suppressor genes aberrantly methylated and transcriptionally suppressed in HNSCC. Validation of gene expression and methylation allowed the detection of ZNF genes whose downregulation may play a significant role in HNSCC tumor development. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4097. doi:1538-7445.AM2012-4097
Micromachined electrodes for high density neural stimulation systems (2003)

High-resolution retinal prosthetic systems require high-density stimulation electrodes to restore the vision of blind patients suffering from retinitis pigmentosa and macular degeneration. Micromachining the surface of electrodes to obtain high aspect ratio features can tremendously increase the effective area of the electrode. A unique process has been developed to obtain high aspect ratio structures by plating on the sidewall of recently developed and insufficiently rinsed resist. A quadrupling of the effective area of the electrode surface has been achieved with modest micromachining and should translate into a similar improvement in visual resolution.
Mycobacterium tuberculosis Prokaryotic Ubiquitin-like Protein-deconjugating Enzyme Is an Unusual Aspartate Amidase (2012)

Deamidase of Pup (Dop), the prokaryotic ubiquitin-like protein (Pup)-deconjugating enzyme, is critical for the full virulence of Mycobacterium tuberculosis and is unique to bacteria, providing an ideal target for the development of selective chemotherapies. We used a combination of genetics and chemical biology to characterize the mechanism of depupylation. We identified an aspartate as a potential nucleophile in the active site of Dop, suggesting a novel protease activity to target for inhibitor development.
PyzoFlex (2012)

Ferroelectric material supports both pyro- and piezoelectric effects that can be used for sensing pressures on large, bended surfaces. We present PyzoFlex, a pressure-sensing input device that is based on a ferroelectric material. It is constructed with a sandwich structure of four layers that can be printed easily on any material. We use this material in combination with a high-resolution Anoto-sensing foil to support both hand and pen input tracking. The foil is bendable, energy-efficient, and it can be produced in a printing process. Even a hovering mode is feasible due to its pyroelectric effect. In this paper, we introduce this novel input technology and discuss its benefits and limitations.
Microfabricated passive vapor preconcentrator/injector designed for microscale gas chromatography (2012)

The design, fabrication, and preliminary testing of a micromachined-Si passive vapor preconcentrator/injector (μPPI) are described. Intended for incorporation in a gas chromatographic microsystem (μGC) for analyzing organic vapor mixtures, the μPPI captures vapors from the air at a known rate by means of passive diffusion (i.e., without pumping) and then desorbs the vapor sample thermally by means of an integrated heater and injects it downstream (with pumping). The μPPI chip comprises a 1.8 μL deep reactive-ion-etched (DRIE) Si cavity with a resistively heated membrane floor and a DRIE-Si cap containing >1500 parallel diffusion channels, each 54 × 54 × 200 μm. The cavity is packed with 750 μg of a commercial graphitized carbon adsorbent. Fluidic and heat-transfer modeling was used to guide the design process to ensure power-efficient sample transfer during thermal desorption. Experiments performed with toluene at concentrations of ~1 ppm gave a constant sampling rate of 9.1 mL min(-1) for up to 30 min, which is within 2% of theoretical predictions and corresponds to a linear dynamic mass uptake range of ~1 μg. The cavity membrane could be heated to 250 °C in 0.23 s with 1 W of applied power and, with 50 mL min(-1) of suction flow provided by a downstream pump, yielded >95% desorption/injection efficiency of toluene samples over an 8-fold range of captured mass.
Two-Dimensional Arrays of Poly(<i>N</i>-Isopropylacrylamide) Microspheres:Formation, Characterization and Application (2014)

Abstract In the present short review, loosely packed two-dimensional arrays of hydrogel colloids with quasi-hexagonal order, which are fabricated by self-assembly on solid substrates, are discussed. For this purpose the most prominent hydrogel microgel, composed of poly( N -isopropylacrylamide), is considered. Its extraordinary properties dictate not only the formation of loosely packed 2D colloidal crystals but also pave the road to various applications ranging from optical devices to cell culture substrates.
Mediator-Free Amperometric Determination of Toxic Substances Based on Their Inhibition of Immobilized Horseradish Peroxidase (1996)

We have demonstrated the feasibility of quantitatively detecting selected toxic materials through their inhibitory effect on an enzyme electrode that utilizes colloidal gold-immobilized horseradish peroxidase and does not require a mediator. Quantitative detection of azide, cyanide, thiourea, sulfide, and dichromate is demonstrated. The sensitivity and inhibition kinetics for this immobilized enzyme electrode are found to be different from those observed previously for homogeneous horseradish peroxidase. Possible reasons for this difference are discussed. Due to the availability of a large number of enzymes and their toxic inhibitors, this work based on immobilized enzyme inhibition coupled to an electrode surface significantly broadens the possible applications of biosensors and offers alternative methods for toxic substance determination.
High Velocity Pulsed Wire-Arc Spray (2000)

Abstract Wire arc spraying has traditionally filled metallic coating needs for low end users, while higher quality coatings required the use of higher cost systems. A new high velocity wire arc spray device has been developed through a NASA SBIR project whose high particle velocity capabilities could provide high quality coatings while keeping costs well below those associated with HVOF and plasma spray approaches. In addition, this technique achieves these high velocities in an extremely short acceleration path. This new device employs a pulsed plasma as the accelerative medium for the molten droplets. This pulsed plasma is capable of accelerating the droplets from the tips of the wires up to high velocities and atomizing them to very fine size. This results in a fine microstructure in the deposit. Recent experiments using a Control-Vision system measured velocities for aluminum droplets in the range of 950-1500 m/s and stainless steel droplets in the range of 850 m/s and 925 m/s. These velocities are achieved with an acceleration distance of only 3.2 cm, thus making this process an ideal candidate for coating the interior of automotive cylinder bores and other areas where only a short acceleration region is available.
Synthesis of Novel C2‐Aryl Pyrrolobenzodiazepines (PBDs) as Potential Antitumor Agents. (2002)

Abstract For Abstract see ChemInform Abstract in Full Text.
Automatic polyp detection in colonoscopy videos using an ensemble of convolutional neural networks (2015)

Computer-aided polyp detection in colonoscopy videos has been the subject of research for over the past decade. However, despite significant advances, automatic polyp detection is still an unsolved problem. In this paper, we propose a new polyp detection method based on a unique 3-way image presentation and convolutional neural networks. Our method learns a variety of polyp features such as color, texture, shape, and temporal information in multiple scales, enabling a more accurate polyp localization. Given a polyp candidate, a set of convolution neural networks - each specialized in one type of features - are applied in the vicinity of the candidate and then their results are aggregated to either accept or reject the candidate. Our experimental results based on our collection of videos, which to our knowledge is the largest annotated polyp database, shows a remarkable performance improvement over the state-of-the-art, significantly reducing the number of false positives in nearly all operating points. In addition, we propose a new performance curve, demonstrating that our new method significantly decreases polyp detection latency, which is defined as the time from the first appearance of a polyp in the video to the time of its first detection by our method.
Flux quantum sigma-delta analog-to-digital converters for rf signals (1999)

The sigma-delta architecture is the method of choice for analog-to-digital converters (ADCs) for high dynamic range applications. This architecture uses oversampling and precise feedback to generate a shaped spectral distribution of the quantization noise. Subsequent digital filtering suppresses out-of-band quantization noise, yielding a large signal to in-band noise ratio. A unique advantage of superconducting electronics is the availability of the flux quantum to provide quantum mechanically accurate feedback at GHz rates. Josephson digital technology extends sigma-delta ADCs from MHz sampling rates to GHz sampling rates, from kHz signal bandwidths to MHz signal bandwidths, with comparable or better dynamic range when compared to semiconductor implementations. This paper presents circuits for Josephson sigma-delta ADCs, including single-loop and double-loop modulators operating at sampling rates up to 2 GHz, and circuits for quantized feedback. The first demonstration of double-loop noise shaping is also presented.
Conceptual design of sleeve rotor synchronous reluctance motor for traction applications (2016)

Synchronous reluctance machines are very appealing for high speed traction motor design due to their robustness, simple structure, absence of magnets, and simple control. The absence of magnets means that synchronous reluctance (SynRel) machines are not susceptible to price variability and sustainability of rare‐earth materials. Moreover, there are no concerns about demagnetisation or uncontrolled generation mode. However, the challenge of achieving a good constant power to speed ratio is dependent on the mechanical aspects of the design. Conventional SynRel designs perform poorly compared with the permanent magnet machines due to the presence of bridges and/or centre posts in absence of the magnets to help saturate these regions. In this case, the challenge of rotor mechanical retention is addressed with the help of a sleeve on the rotor to reduce the need for bridges and/or centre posts. Design optimisation including the mechanical aspects of the sleeve is presented in this study. The final design with a sleeve will be shown to be superior to a conventional design in terms of power density, rotor losses, saliency and torque ripple.
Large-scale Gadolinium-doped Water Cerenkov Detector for Non-Proliferation (2011)

Fission events from Special Nuclear Material (SNM), such as highly enriched uranium or plutonium, can produce simultaneous emission of multiple neutrons and high energy gamma-rays. The observation of time correlations between any of these particles is a significant indicator of the presence of fissionable material. Cosmogenic processes can also mimic these types of correlated signals. However, if the background is sufficiently low and fully characterized, significant changes in the correlated event rate in the presence of a target of interest constitutes a robust signature of the presence of SNM. Since fission emissions are isotropic, adequate sensitivity to these multiplicities requires a high efficiency detector with a large solid angle with respect to the target. Water Cerenkov detectors are a cost-effective choice when large solid angle coverage is required. In order to characterize the neutron detection performance of large-scale water Cerenkov detectors, we have designed and built a 3.5 kL water Cerenkov-based gamma-ray and neutron detector, and modeled the detector response in Geant4 [1]. We report the position-dependent neutron detection efficiency and energy response of the detector, as well as the basic characteristics of the simulation.