gebhart/patrepeval huggingface dataset:
High performance DNA sequencing, and the detection of mutations and polymorphisms, on the Clipper sequencer (1999)

The Visible Genetics Clipper sequencer is a new platform for automated DNA sequencing which employs disposable MicroCel cassettes and 50 microm thick polyacrylamide gels. Two DNA ladders can be analyzed simultaneously in each of 16 lanes on a gel, after labeling with far-red absorbing dyes such as Cy5 and Cy5.5. This allows a simultaneous bidirectional sequencing of four templates. We have evaluated the Clipper sequencer, by cycle-sequencing of an M13 single-stranded DNA standard, and by coupled amplification and sequencing (CLIP) of reverse-transcribed human immunodeficiency virus (HIV-1) RNA standards and clinical patient samples. (i) Limitations of instrument. We have examined basic instrument parameters such as detector stability, background, digital sampling rate, and gain. With proper usage, the optical and electronic subsystems of the Clipper sequencer do not limit the data collection or sequence-determination processes. (ii) Limitations of gel performance. We have also examined the physics of DNA band separation on 50 microm thick MicroCel gels. We routinely obtain well-resolved sequence which can be base-called with 98.5% accuracy to position approximately 450 on an 11 cm gel, and to position approximately 900 on a 25 cm gel. Resolution on 5 and 11 cm gels ultimately is limited by a sharp decrease in spacing between adjacent bands, in the biased reptation separation regime. Fick's (thermal) diffusion appears to be of minor importance on 6 cm or 11 cm gels, but becomes an additional resolution-limiting factor on 25 cm gels. (iii) Limitations of enzymology. Template quality, primer nesting, choice of DNA polymerase, and choice between dye primers and dye terminators are key determinants of the ability to detect mutations and polymorphisms on the Clipper sequencer, as on other DNA sequencers. When CLIP is used with dye-labeled primers and a DNA polymerase of the F667Y, delta(5'--> 3' exo) class, we can routinely detect single-nucleotide mutations and polymorphisms over the 0.35-0.65 heterozygosity range. We present an example of detecting therapeutically relevant mutations in a clinical HIV-1 RNA isolate.
Design of a soft, parallel end-effector applied to robot-guided ultrasound interventions (2017)

Medical ultrasound imaging robotics systems often comprise of complex control architectures and hardware integration to enable safe human robot interaction. In this paper, we investigate the applicability of a soft robotic end-effector for ultrasound intervention. A novel, parallel design is derived based on the medical requirements, which addresses common shortcomings in both robotic ultrasound systems and soft robotic devices. Individual actuators are developed and characterized and the performance of the overall platform is evaluated in regards to its stiffness and steerability. It is shown that the platform comprises relatively high longitudinal and transversal stiffness, while still being compliant enough to ensure the safety of the patient. The shear stiffness of the platform is 4.2 times greater than the shear stiffness of an individual actuator. The platform is capable of applying loadings of 10N along its longitudinal axis, which makes it suitable for the given application. Furthermore, the workspace of the platform is suitable to robot-guided ultrasound with a maximum platform rotation range of ±14.8°, while only moving ±7mm in space.
Evaluation of methods, instrumentation and materials pertinent to quality assurance filter penetration testing (1984)

Every high efficiency aerosol filter used in the Unites States Department of Energy (DOE) facilities is quality assurance (QA) tested at one of the DOE filter test facilities prior to installation. This testing presently includes measurement of filter penetration at rated airflow using a hot DOP aerosol generator, an Owl aerosol size analyzer, and a scattered-light photometer aerosol concentration monitor. Alternative penetration measurement methods for testing size 5 high efficiency aerosol filters which have rated airflow capacities of 1000 cubic feet/min (cfm, approx. 28 m/sup 3//min) are being studied at Los Alamos National Laboratory. These methods are intended to take advantage of commercially available aerosol instrumentation. A penetration test using a polydisperse aerosol produced with a modified Laskin nozzle aerosol generator was found to have promise as an alternative to the present test method. Such a test eliminates the difficulty in producing a monodisperse challenge aerosol, and takes advantage of state-of-the-art aerosol sizing instruments. Aerosol sizing and concentration measuring capabilities of a laser aerosol spectrometer (LAS) were evaluated with respect to the needs of QA filter penetration testing. An aerosol diluter was selected and evaluated for use with the LAS in making filter penetration measurements. Potential alternative test materials were scrutinized with respect to certain toxicological and physical criteria. Certain of these alternative materials were selected for further evaluation. Results of this evaluation and findings cited in the literature indicate that the selected materials could be easily adapted for use with the modified Laskin aerosol generator.
Predictive and Prognostic Value of Peripheral Blood Cytokeratin-19 mRNA-Positive Cells Detected by Real-Time Polymerase Chain Reaction in Node-Negative Breast Cancer Patients (2006)

Detection of peripheral-blood CK-19 mRNA-positive cells is an independent predictive and prognostic factor for reduced disease-free interval and overall survival, respectively, in node-negative breast cancer patients.
Porous Superabsorbent Hydrogel Composites: Synthesis, Morphology and Swelling Rate (2004)

Abstract Summary: Novel porous hydrogel composites with very high swelling capacity and enhanced rate of water absorption were synthesized in aqueous media at room temperature under normal atmospheric conditions. The porosity was induced through either foaming conducted in the course of polymerization or non‐solvent dewatering of the as‐synthesized gels. Kaolin was incorporated as an inorganic component in the polymerization process. The foaming technique was used to form porosity using three systems of different porogens (porosity generators), i.e. sodium bicarbonate, acetone and their combination. The as‐synthesized gels were dried through oven drying and non‐solvent dewatering. Morphology and swelling rate of the superabsorbent hydrogel composites (SHCs) were studied versus either the porogen system or the drying method. It was found that the simultaneous polymerization‐foaming technique had great influence on the improvement of porosity, morphology of the porous structure and the rate of water absorption. It was also shown that the drying procedure had remarkable influence on preserving the preformed porosity. Methanol as a dewatering solvent produced SHCs with higher porosity and swelling rate in comparison with the porosity of the hydrogels dewatered in acetone. Our invented methodology including simultaneous polymerization and foam formation using dual‐porogen system and the subsequent methanol‐dewatering approach was found to be the most efficient, highly practical, and cost‐effective route for preparing improved superabsorbing hydrogel materials. magnified image
Controllable functionalized carbon fabric for high-performance all-carbon-based supercapacitors (2014)

Research is currently being carried out to develop high-performance solid-state supercapacitors (SCs) with high energy density. One effective method to improve the energy density of the solid-state SC devices is enlarging their operating voltage. Organic electrolytes and asymmetric structure have been employed in supercapacitors to increase their operating voltage. However, they usually suffer from high cost, high toxicity, poor ionic conductivity and complicated manufacturing processes. Herein, a simple oxidation and annealing method is introduced to fabricate functionalized carbon fabric (FCF) electrodes. The as-prepared FCF electrode exhibits a high areal capacitance of 155.8 mF cm−2 and 143.4 mF cm−2 at negative potential and positive potential, respectively. Furthermore, a high-performance and flexible solid-state supercapacitor with high operating voltage (1.6 V) is successfully developed using functionalized carbon fabric as both positive and negative electrode. The FCF-based device has a high capacitance of 134.8 F cm−2 (or 2.41 F cm−3). The maximum volumetric energy density and volumetric power density are 0.83 mW h cm−3 and 1.58 W cm−3, respectively, which are higher than most previously reported CF-based SCs. The proposed FCF electrodes demonstrate exciting possibilities of developing high-performance solid-state supercapacitors with high operating voltage for efficient energy storage.
A theory of typed coercions and its applications (2009)

A number of important program rewriting scenarios can be recast as type-directed coercion insertion. These range from more theoretical applications such as coercive subtyping and supporting overloading in type theories, to more practical applications such as integrating static and dynamically typed code using gradual typing, and inlining code to enforce security policies such as access control and provenance tracking. In this paper we give a general theory of type-directed coercion insertion. We specifically explore the inherent tradeoff between expressiveness and ambiguity--the more powerful the strategy for generating coercions, the greater the possibility of several, semantically distinct rewritings for a given program. We consider increasingly powerful coercion generation strategies, work out example applications supported by the increased power (including those mentioned above), and identify the inherent ambiguity problems of each setting, along with various techniques to tame the ambiguities.
Ballistic transport and velocity overshoot in semiconductors: Part I&#8212;Uniform field effects (1983)

The relationship between ballistic electron transport and velocity overshoot, in semiconductor materials, is clarified. By considering the behavior of electrons in a uniform electric field, we show that while ballistic transport can coexist with velocity overshoot, it is not necessary for overshoot. Furthermore, we show that ballistic transport will not lead to overshoot unless one of the two classic mechanisms for overshoot is also operative.
APPLICATION OF REVERSE OSMOSIS MEMBRANES FOR WATER RECLAMATION WITH VARIOUS PRETREATMENT PROCESSES (2000)

APPLICATION OF REVERSE OSMOSIS MEMBRANES FOR WATER RECLAMATION WITH VARIOUS PRETREATMENT PROCESSESThe City of San Diego is developing new water sources to serve its arid region. In addition, water reclamation is being seriously evaluated by the City to reduce the region's reliance on less dependable imported water. The City adopted the reverse osmosis (RO) process as the foundation of the advanced water treatment of many of their reclamation projects because RO has been shown to accomplish the...Author(s)Paul GagliardoRion P. MerloSamer AdhamR. Shane TrussellRhodes TrussellSourceProceedings of the Water Environment FederationSubjectSession 15 - Natural Systems, Water Reuse and Small Communities: Water Reclamation and Reuse IDocument typeConference PaperPublisherWater Environment FederationPrint publication date Jan, 2000ISSN1938-6478SICI1938-6478(20000101)2000:13L.302;1-DOI10.2175/193864700784607857Volume / Issue2000 / 13Content sourceWEFTECFirst / last page(s)302 - 320Copyright2000Word count303
Effect of Antiepileptic Drugs on Absence‐Like Seizures in the Tremor Rat (1995)

We examined the effects of conventional antiepileptic drugs (AEDs) on absence-like seizures in homozygous tremor rats (tm/tm) to determine if they corresponded pharmacologically to human absence seizures and absence-like seizures in spontaneously epileptic rats (SER: zi/zi, tm/tm) with both tonic convulsive and absence-like seizures. Cortical and hippocampal EEG activity was recorded with chronically implanted electrodes. The effects of AEDS on seizures of the tremor rat showed profiles similar to those observed in human absence seizures and also in absence-like seizures of SER. The absence-like seizures, associated with paroxysmal bursts of 5-7-Hz spike-wave complexes, were inhibited by trimethadione (TMO 200 mg/kg intraperitoneally, i.p.), ethosuximide (ESM 100 and 200 mg/kg, i.p.), valproate (VPA 100 mg/kg, i.p.), and phenobarbital (PB 10 and 20 mg/kg, i.p.). Phenytoin (PHT 20 mg/kg, i.p.) was ineffective. These results are consistent with the conclusion that the tremor rat is a useful model for evaluating new AEDS for human absence seizures.
Approaching MIMO capacity using bitwise Markov Chain Monte Carlo detection (2010)

This paper examines near capacity performance of Markov Chain Monte Carlo (MCMC) detectors for multiple-input and multiple-output (MIMO) channels. The proposed MCMC detector (Log-MAP-tb b-MCMC) operates in a strictly bit-wise fashion and adopts Log-MAP algorithm with table look-up. When concatenated with an optimized low-density parity-check (LDPC) code, Log-MAP-tb b-MCMC can operate within 1.2-1.8 dB of the capacity of MIMO systems with 8 transmit/receive antennas at spectral efficiencies up to ¿ = 24 bits/channel use (b/ch). This result improves upon best performance achieved by turbo coded systems using list sphere decoding (LSD) detector by 2.3-3.8 dB, leading to nearly 50% reduction in the capacity gap. Detailed comparisons of the Log-MAP-tb b-MCMC with LSD based detectors demonstrate that MCMC detector is indeed the detector of choice for achieving channel capacity both in terms of performance and complexity.
Investigation of a direct conversion flat panel imager for portal imaging (2001)

Flat-panel based x-ray imaging is an emerging new technology that could be used to significantly improve the quality of on-line portal imagers. There are two types of flat panel imagers: direct and indirect conversion. Previous experimental work on flat panel detectors for portal imaging application used indirect-conversion imagers. In this paper, a direct-conversion amorphous-selenium flat panel imager is investigated for application in portal imaging. The imager has an active imaging area of 14 in. X 17 in., i.e., 3072 X 2560 pixels each with dimensions 139 microm X 139 microm. The spatial frequency dependent detective quantum efficiency of the imager has been measured for a 6 MV beam and found to be amongst the best area detectors investigated for on-line portal imaging. Effects of changing pixel size, as well as possible improvements to both the image quality and convenience of operation are discussed. Comparison with an indirect conversion flat panel imager is also included.
Protection of the ischaemic myocardium by L-propionylcarnitine: effects on the recovery of cardiac output after ischaemia and reperfusion, carnitine transport, and fatty acid oxidation (1986)

The effects of L-propionylcarnitine on the recovery of cardiac contractile performance after global ischaemia and reperfusion were studied in isolated perfused rat hearts. The addition of either 5.5 or 11 mmol X litre-1 L-propionylcarnitine significantly improved the recovery of cardiac output, left ventricular pressure, and dP/dt after 90 min of ischaemia and 15 min of reperfusion. Myocardial adenosine triphosphate and creatine phosphate concentrations were significantly higher in the L-propionylcarnitine treated hearts than in controls, but the concentrations of long chain acyl carnitine and coenzyme A were unaffected. The protecting effects of L-propionylcarnitine were compared with those of L-carnitine and L-acetylcarnitine. A 11 mmol X litre-1 dose of L-propionylcarnitine and L-acetylcarnitine significantly improved the recovery of cardiac output after 90 min of ischaemia and 15 min of reperfusion, but L-carnitine did not. L-Propionylcarnitine was the most protective agent. The effects of these derivatives on L-3H-carnitine transport and 14C-palmitate oxidation were also measured. All of these derivatives competitively inhibited L-3H-carnitine transport in isolated cardiac myocytes, but L-propionylcarnitine was the most potent. Carnitine and L-propionylcarnitine stimulated palmitate oxidation in the homogenate, whereas L-acetylcarnitine inhibited it. In myocytes only L-propionylcarnitine affected palmitate oxidation. These data show that L-propionylcarnitine protects the ischaemic myocardium. Its protection is greater than that for L-carnitine or L-acetylcarnitine, and the difference in effectiveness may relate to the rate of transport into the cells and the effects on fatty acid utilisation.
Thursby: Interstate Cooperation: A Study of the Interstate Compact (1954)

that the development of the jurisdiction of the Consedil d'Etat in France and of similar specialized courts in other European countries is to some extent the result of historical accident rather than of preconceived plans.It would be incorrect, however, to oppose creation of administrative courts on the ground that as a rule they are more subservient to the administration than courts of general jurisdiction.The contrary is often true, at least in Europe.Being more familiar with the administrative machinery and its shortcomings, judges of administrative tribunals are less inclined than other judges to be awed by the prestige of the government.These criticisms of Professor Street's book are matters of opinion, and in any event are minor ones.They cannot detract from the great value of his work.The book deals effectively with some of the more difficult problems of administrative law.It is clear, concise and convincing.It conclusively shows that a careful and intelligent analysis of the provisions of foreign legal systems may be of considerable assistance in improving corresponding provisions of domestic law.This is comparative law at it best.
Effect of nitrogen on the crystal texture and microstructure of sputtered Ni-Fe films (1985)

This work reports the effect of nitrogen in the sputtering gas on the crystal texture and microstructure of 1 μ thick 81/19 Ni–Fe films sputter deposited on silica glass and silicon. X-ray diffraction, transmission electron microscopy, and scanning auger microprobe analysis have been used to characterize films’ properties. The films show (111) and (002) crystals orientations. Upon increasing the nitrogen content of the sputtering gas, the amount of (111) crystal texture decreases; whereas the amount of (002) crystal texture shows a maxima at about 0.1% nitrogen. The microstructural analysis of films shows that the presence of nitrogen in the sputtering gas promotes fine grain size. The mechanism of crystal texture development with an increase in the amount of nitrogen in the sputtering gas is discussed.
Compressible, Turbulent Flow with Boundary-Layer Heat Addition (2005)

One proposed method of achieving a reduction in viscous drag or skin friction in scramjet combustors is through hydrogen combustion in the boundary layer. Previous experimental work performed at the University of Queensland indicated that drag reductions of 80% were possible. This paper studies the effects of heat release on supersonic boundary layers at conditions typically found within the combustor duct of a scramjet using a three-dimensional turbulent compressible flow solver with a finite volume formulation for the solution of the compressible Navier-Stokes equations. Large-Eddy Simulation (LES) using the approximate deconvolution model includes the effects of turbulence. Three conditions of a supersonic, perfect gas, flat-plate boundary layers are studied. The first condition is a validation case at Mach 2.88 with a Reynolds number of 2 × 10 (based on incoming boundary layer thickness, Re). The next two cases are Mach 4.42 and 4.21 flows with Reynolds number (Re) of 8.4 × 10 and 6.3 × 10 respectively. The results obtained for all three cases compare very well with experimental and theoretical data and give insight into the changes in turbulent kinetic energy and stress profiles that occur in the processes of drag reduction via heat addition.
Repeatability and Reproducibility in Proteomic Identifications by Liquid Chromatography−Tandem Mass Spectrometry (2009)

The complexity of proteomic instrumentation for LC-MS/MS introduces many possible sources of variability. Data-dependent sampling of peptides constitutes a stochastic element at the heart of discovery proteomics. Although this variation impacts the identification of peptides, proteomic identifications are far from completely random. In this study, we analyzed interlaboratory data sets from the NCI Clinical Proteomic Technology Assessment for Cancer to examine repeatability and reproducibility in peptide and protein identifications. Included data spanned 144 LC-MS/MS experiments on four Thermo LTQ and four Orbitrap instruments. Samples included yeast lysate, the NCI-20 defined dynamic range protein mix, and the Sigma UPS 1 defined equimolar protein mix. Some of our findings reinforced conventional wisdom, such as repeatability and reproducibility being higher for proteins than for peptides. Most lessons from the data, however, were more subtle. Orbitraps proved capable of higher repeatability and reproducibility, but aberrant performance occasionally erased these gains. Even the simplest protein digestions yielded more peptide ions than LC-MS/MS could identify during a single experiment. We observed that peptide lists from pairs of technical replicates overlapped by 35-60%, giving a range for peptide-level repeatability in these experiments. Sample complexity did not appear to affect peptide identification repeatability, even as numbers of identified spectra changed by an order of magnitude. Statistical analysis of protein spectral counts revealed greater stability across technical replicates for Orbitraps, making them superior to LTQ instruments for biomarker candidate discovery. The most repeatable peptides were those corresponding to conventional tryptic cleavage sites, those that produced intense MS signals, and those that resulted from proteins generating many distinct peptides. Reproducibility among different instruments of the same type lagged behind repeatability of technical replicates on a single instrument by several percent. These findings reinforce the importance of evaluating repeatability as a fundamental characteristic of analytical technologies.
Comparative Measurements on Loudspeaker Distortion: Current vs. Voltage Control (2017)

Abstract Modulation and harmonic distortion produced by ordinary moving-coil direct-radiator drive units are measured under current control and voltage control. A realistic two-tone test signal is used to investigate the detrimental effect of the voice coil electromotive forces on the voltage-to-current conversion that is critical with voltage control. Dramatic improvements in distortion performance are obtained with current control. Current nonlinearities in voltage-controlled speakers are shown to be the dominant source of modulation and odd harmonic distortions at signal frequencies above the fundamental resonance region. Currents in conductive voice coil formers also seem to be significant sources of distortion; with current control and non-conductive formers, odd harmonics and related modulation products virtually vanished in the upper midrange.