gebhart/patrepeval huggingface dataset:
Practical extraction techniques for Java (2002)

Reducing application size is important for software that is distributed via the internet, in order to keep download times manageable, and in the domain of embedded systems, where applications are often stored in (Read-Only or Flash) memory. This paper explores extraction techniques such as the removal of unreachable methods and redundant fields, inlining of method calls, and transformation of the class hierarchy for reducing application size. We implemented a number of extraction techniques in Jax , an application extractor for Java, and evaluated their effectiveness on a set of large Java applications. We found that, on average, the class file archives for these benchmarks were reduced to 37.5% of their original size. Modeling dynamic language features such as reflection, and extracting software distributions other than complete applications requires additional user input. We present a uniform approach for supplying this input that relies on MEL, a modular specification language. We also discuss a number of issues and challenges associated with the extraction of embedded systems applications.
The <i>Pseudomonas syringae</i> pv. tomato HrpW Protein Has Domains Similar to Harpins and Pectate Lyases and Can Elicit the Plant Hypersensitive Response and Bind to Pectate (1998)

The host-specific plant pathogen Pseudomonas syringae elicits the hypersensitive response (HR) in nonhost plants and secretes the HrpZ harpin in culture via the Hrp (type III) secretion system. Previous genetic evidence suggested the existence of another harpin gene in the P. syringae genome. hrpW was found in a region adjacent to the hrp cluster in P. syringae pv. tomato DC3000. hrpW encodes a 42. 9-kDa protein with domains resembling harpins and pectate lyases (Pels), respectively. HrpW has key properties of harpins. It is heat stable and glycine rich, lacks cysteine, is secreted by the Hrp system, and is able to elicit the HR when infiltrated into tobacco leaf tissue. The harpin domain (amino acids 1 to 186) has six glycine-rich repeats of a repeated sequence found in HrpZ, and a purified HrpW harpin domain fragment possessed HR elicitor activity. In contrast, the HrpW Pel domain (amino acids 187 to 425) is similar to Pels from Nectria haematococca, Erwinia carotovora, Erwinia chrysanthemi, and Bacillus subtilis, and a purified Pel domain fragment did not elicit the HR. Neither this fragment nor the full-length HrpW showed Pel activity in A230 assays under a variety of reaction conditions, but the Pel fragment bound to calcium pectate, a major constituent of the plant cell wall. The DNA sequence of the P. syringae pv. syringae B728a hrpW was also determined. The Pel domains of the two predicted HrpW proteins were 85% identical, whereas the harpin domains were only 53% identical. Sequences hybridizing at high stringency with the P. syringae pv. tomato hrpW were found in other P. syringae pathovars, Pseudomonas viridiflava, Ralstonia (Pseudomonas) solanacearum, and Xanthomonas campestris. DeltahrpZ::nptII or hrpW::OmegaSpr P. syringae pv. tomato mutants were little reduced in HR elicitation activity in tobacco, whereas this activity was significantly reduced in a hrpZ hrpW double mutant. These features of hrpW and its product suggest that P. syringae produces multiple harpins and that the target of these proteins is in the plant cell wall.
Cardiac output and stroke volume estimation using a hybrid of three Windkessel models (2010)

Cardiac output (CO) and stroke volume (SV) are the key hemodynamic parameters to be monitored and assessed in ambulatory and critically ill patients. The purpose of this study was to introduce and validate a new algorithm to continuously estimate, within a proportionality constant, CO and SV by means of mathematical analysis of peripheral arterial blood pressure (ABP) waveforms. The algorithm combines three variants of the Windkessel model. Input parameters to the algorithm are the end-diastolic pressure, mean arterial pressures, inter-beat interval, and the time interval from end-diastolic to peak systolic pressure. The SV estimates from the three variants of the Windkessel model were weighted and integrated to provide beat-to-beat SV estimation. In order to validate the new algorithm, the estimated CO and SV were compared to those obtained through surgically implanted Transonic™ aortic flow probes placed around the aortic roots of six Yorkshire swine. Overall, estimation errors in CO and SV derived from radial ABP were 10.1% and 14.5% respectively, and 12.7% and 16.5% from femoral ABP. The new algorithm demonstrated statistically significant improvement in SV estimation compared with previous methods.
Using Efficient SUPANOVA Kernel for Heart Disease Diagnosis (2006)

Many machine learning methods focus on the quality of prediction results as their final purpose. Spline kernel based methods attempt to provide also transparency to the prediction identifying features that are important in the decision process. In this paper, we present a new heuristic for computing efficiently sparse kernel in SUPANOVA. We applied it to a benchmark Boston housing market dataset and to socially important problem of improving the detection of heart diseases in the population using a novel, non-invasive measurement of the heart activities based on magnetic field produced by the human heart. On this data, 83.7% predictions were correct, exceeding the results obtained using the standard Support Vector Machine and equivalent kernels. Equally good results were achieved by the spline kernel on a benchmark Boston housing market dataset.
Morphology Control in Block Copolymer/Polymer Derived Ceramic Precursor Nanocomposites (2008)

Block copolymer−polymer derived ceramic (PDC) precursor nanocomposites were prepared using amorphous poly(isoprene-block-(dimethylamino)ethyl methacrylate) (PI-b-PDMAEMA) and semicrystalline poly(isoprene-block-ethylene oxide) (PI-b-PEO) block copolymers as structure directing agents for poly(ureamethylvinyl)silazane (PUMVS). Studies on hybrid morphologies were performed using small-angle X-ray scattering (SAXS) and transmission electron microscopy (TEM). In the amorphous system, the PUMVS preferentially swells the PDMAEMA, and a systematic increase of the PUMVS to PI-b-PDMAEMA weight ratio resulted in lamellar, hexagonally packed cylindrical and body-centered cubic packed spherical morphologies. Crystallization of PEO in PI-b-PEO/PUMVS hybrids led to crystalline lamellar morphologies over a large range of PUMVS to PI-b-PEO weight ratios. The d-spacing of the PI-b-PEO/PUMVS hybrids increased only slightly upon PUMVS loading, because the strong chain stretching in the PI block is progressively relaxed as the PUMVS swells the PEO. Annealing of the PI-b-PEO/PUMVS system at elevated temperatures led to suppression of the PEO crystallization, resulting in order−order phase transitions.
Drain-Extended FinFET With Embedded SCR (DeFinFET-SCR) for High-Voltage ESD Protection and Self-Protected Designs (2019)

This article presents device design insights and design challenges for drain-extended FinFET devices with embedded silicon-controlled rectifier (SCR) (DeFinFET-SCR), which can be used as an electrostatic discharge (ESD) protection device and a self-protected high-voltage switch/driver for system-on-chip applications. The tradeoff between maximizing ESD robustness without hindering the transistor's operation is discussed in detail. An interplay between parasitic p-n-p turn-on and space charge modulation (SCM) is revealed, which strongly influences the strength of parasitic SCR and its turn-on efficiency during ESD and DC operations. Developed physical insights show that engineering p-n-p turn-on and onset of SCM are the key to maximize ESD robustness without causing early SCR turn-on during transistor operation. Based on new findings and developed physical insights, design guidelines have been derived for ESD robust DeFinFET-SCR.
Exposing server performance to network managers through passive network measurements (2008)

We describe a novel approach to managing the application-level performance of servers within an enterprise network given only passively-collected TCP/IP headers of packets from a link connecting clients to servers. The analysis is driven by constructing, in real-time, a source-level model of the request-response exchanges between each server and all of its clients. By continuously monitoring traffic, we generate a statistical profile of numerous application-layer measures of server performance. Given these measures, and their distributions over time, a network manager can quickly triage server performance problems in generic terms without any knowledge of the servers operation or a priori interaction with the serverpsilas operators. This approach is illustrated by using a continuous, 2-month dataset taken from a border router on the UNC campus to diagnose an actual problem with a UNC web portal.
Multi-Frequency-Spaced Optical Comb Generation by Superposition of Purely Deeply Phase-Modulated Lights (2021)

We propose multiple-frequency-spaced optical comb generation by superposing deeply phase-modulated lights. A multiple-parallel modulator with pure phase-modulator arms flexibly generates optical combs with any multiplication orders of frequency spacing, powered by interferometric blocking technique.
Rapid Quantification of Trimethylamine (2016)

Sensitive detection of trimethylamine both in aqueous and gaseous phases has been accomplished using an inexpensive colorimetric sensor array. Distinctive color change patterns provide facile discrimination over a wide range of concentrations for trimethylamine with >99% accuracy of classification. Calculated limits of detection are well below the diagnostically significant concentration for trimethylaminuria (fish malodor syndrome). The sensor array shows good reversibility after multiple uses and is able to cleanly discriminate trimethylamine from similar amine odorants. Portable sensing of trimethylamine vapors at ppb concentrations is described using a cell phone camera or a hand-held optoelectronic nose. Application of the sensor array in detecting mouth and skin odor as a potential tool for portable diagnosis of trimethylaminuria is also illustrated.
Visibility Sorting and Compositing for Image-Based Rendering (1997)

We present an efficient algorithm for analyzing synthetic scenes involving a set of moving objects and changing view parameters into a sorted sequence of image layers. The final image is generated by evaluating a 2D image compositing expression on these layers. Unlike previous visibility approaches, we detect and report occlusion cycles rather than splitting to remove them. Such an algorithm has many applications in computer graphics; we demonstrate two: rendering acceleration using image interpolation, and visibility-correct depth of field using image blurring. The algorithm involves an incremental method for identifying mutually occluding sets of objects and computing a visibility sort of these sets. Occlusion queries are accelerated by testing on convex bounding hulls; less conservative tests are also discussed. Kd-trees formed by combinations of directions in object or image space provide an initial cull on potential occluders, and a new incremental algorithm is employed to resolve pairwise occlusions. Mutual occluders are further analyzed to generate an image compositing expression; in the case of nonbinary cycles an expression can always be generated without aggregating the objects into a single layer. Results demonstrate that the algorithm is practical for interactive animation of scenes involving hundreds of objects each comprising hundreds or thousands of polygons.
Subtype Selective Substrates for Histone Deacetylases (2004)

To probe the steric requirements for deacylation, we synthesized lysine-derived small molecule substrates and examined structure-reactivity relationships with various histone deacetylases. Rat liver, human HeLa, and human recombinant class I and II histone deacetylases (HDACs) as well as human recombinant NAD(+)-dependent SIRT1 (class III enzyme) were used in these studies. A benzyloxycarbonyl substituent on the alpha-amino group yielded the highest conversion rates. Replacing the epsilon-acetyl group with larger lipophilic acyl substituents led to a pronounced decrease in conversion by class I and II enzymes; the class III enzyme displayed a greater tolerance. Incubations with recombinant FLAG-tagged human HDACs 1, 3, and 6 showed a distinct subtype selectivity among small molecule substrates. The subtype selectivity of HDAC inhibitors could be predicted with these substrates and an easily obtainable mixture of HDAC subtypes.
Development of Superconducting Fault Current Limiters (2006)

Somewhere in a power utility system, a mishap may cause a short- circuit. The sudden reduction in the power grid's impedance will lead to a surge of current, termed fault current. Sometimes, fault currents can create disasters to power generators, distributors, and consumers. Today, options available for utility companies to handle faults are very limited and compromise the efficiency and increase the cost of the power system. People have been attempting better solutions for fault current control with the application of superconductors. Superconducting fault current limiter (SFCL) is currently the only short-circuit current limiting device capable of associating a low impedance at normal operation to a large impedance at short-circuit conditions, although the SFCL technology still requires further development and techno-economic studies. We started our saturated iron core reactive type SFCL development program in 2002. We fabricated and tested a single phase concept-proof model and a three phase lab testing model in 2004 and 2005 respectively. A 35 kV/100 MVA prototype will be developed in 2006 and will be live -grid tested in 2007. We believe SFCL will address fundamental challenges in power system design. In this paper, we will report the technical data and testing results of the three phase laboratory test model. Some key design parameters of the 35 kV/100 MVA machine will also be presented.
FcRH1: an activation coreceptor on human B cells (2004)

B-cell activation and differentiation is regulated through the coordinated function of a dynamic array of cell surface receptors. At different stages in their differentiation, human B cells may express one or more members of a large family of immunoglobulin Fc receptor homologs (FcRH) with regulatory potential. Among these newly identified transmembrane molecules, FcRH1 is unique in having 2 immunoreceptor tyrosine-based activation motif (ITAM)-like motifs in its intracellular domain. Here we used the Fab fragments of new monoclonal anti-FcRH1 antibodies and mRNA analysis to evaluate FcRH1 expression and function during B-cell differentiation. FcRH1 expression begins in pre-B cells, reaches peak levels on naive B cells, and is down-regulated after B cells are activated to begin to form germinal centers. This FcRH1 down-regulation coincides with dramatic enlargement of the pre-germinal center cells, cell cycle entry, and other overt signs of activation that include CD80 and CD86 up-regulation and immunoglobulin D (IgD) down-regulation. In vitro analysis indicates that ligation of FcRH1 leads to its tyrosine phosphorylation and to modest B-cell activation and proliferation. Concomitant FcRH1 ligation enhances B-cell antigen receptor (BCR)-induced Ca(2+) mobilization and proliferation. FcRH1 thus has the potential to serve as an activating coreceptor on B cells.
Dual layer magnetic recording media: a pathway for improving the magnetic and performance characteristics of the storage medium (2005)

In this paper, significant improvements in recording media performance were obtained by utilizing ferromagnetically exchanged coupled bilayers. Two quaternary alloys (CoPtCrTa and CoPtCrB) were employed to achieve high performance recording layer. The net magnetic properties and recording alloy performance were optimized by controlling the thickness ratio.
Selective Detection of Vapor Phase Hydrogen Peroxide with Phthalocyanine Chemiresistors (2008)

The use of hydrogen peroxide as a precursor to improvised explosives has made its detection a topic of critical importance. Chemiresistor arrays comprised of 50 nm thick films of metallophthalocyanines (MPcs) are redox selective vapor sensors of hydrogen peroxide. Hydrogen peroxide is shown to decrease currents in cobalt phthalocyanine sensors while it increases currents in nickel, copper, and metal-free phthalocyanine sensors; oxidation and reduction of hydrogen peroxide via catalysis at the phthalocyanine surface are consistent with the pattern of sensor responses. This represents the first example of MPc vapor sensors being oxidized and reduced by the same analyte by varying the metal center. Consequently, differential analysis by redox contrast with catalytic amplification using a small array of sensors may be used to uniquely identify peroxide vapors. Metallophthalocyanine chemiresistors represent an improvement over existing peroxide vapor detection technologies in durability and selectivity in a greatly decreased package size.
Multi-Fluid Sedimentary Geothermal Energy Systems for Dispatchable Renewable Electricity (2015)

electricity Sedimentary geothermal resources typically have lower temperatures and energy densities than hydrothermal resources, but they often have higher permeability and larger areal extents. Consequently, spacing between injection and production wells is likely to be wider in sedimentary resources, which can result in more fluid pressure loss, increasing the parasitic cost of powering the working fluid recirculation system, compared to hydrothermal systems. For hydrostatic geothermal resources, extracting heat requires that brine be lifted up production wells, such as with submersible pumps, which can consume a large portion of the electricity generated by the power plant. CO2 is being considered as an alternative working fluid (also termed a supplemental fluid) because its advantageous thermophysical properties reduce this parasitic cost, and because of the synergistic benefit of geologic CO2 sequestration (GCS). We expand on this idea by: (1) adding the option for multiple supplemental fluids (N2 as well as CO2) and injecting these fluids to create overpressured reservoir conditions, (2) utilizing up to three working fluids: brine, CO2, and N2 for heat extraction, (3) using a well pattern designed to store supplemental fluid and pressure, and (4) time-shifting the parasitic load associated with fluid recirculation to provide ancillary services (frequency regulation, load following, and spinning reserve) and bulk energy storage (BES).
Effect of the number of cases in image database on the performance of computer-aided diagnosis (CAD) for the detection of pulmonary nodules in chest radiographs (2003)

We investigated the effect of the number of cases included in an image database on development of a computer-aided diagnosis (CAD) scheme for the detection of lung nodules, in terms of the performance of the CAD scheme. A total number of 1000 chest radiographs with nodules was used in this study. All images were divided randomly into subsets consisting of the same number of cases from different sources. The subsets we used in this study were 10 sets of 100 cases, 5 sets of 200 cases, and 2 sets of 500 cases. The entire database and all of the subsets were tested by use of the same CAD scheme, but with different parameter settings for consistency tests. When the sensitivities of the CAD scheme for each subset were kept at a level of 70.0 %, the numbers of false positives per image were 0.1 for 100 cases, 0.6 for 200 cases, 2.9 for 500 cases, and 6.2 for 1000 cases. Therefore, the performance of the CAD scheme in detecting lung nodules was strongly affected by the number of cases used. We conclude that a large-scale image database is needed for reliable evaluation of the performance of CAD.
Replication and inclusion body characteristics of two Lymantria dispar nuclear polyhedrosis virus plaque variants (1991)

Propagation of Autographa californica nuclear polyhedrosis virus in cell culture results in the generation of a mutant virus, termed few polyhedra. This plaque variant is characterized by a high budded virus titer, the formation of few polyhedral inclusion bodies (PIBs), and the production of PIBs exhibiting a low potency against its natural host. The isolation and study of a few polyhedra variant of Lymantria dispar nuclear polyhedrosis virus (LdNPV) could lead to a means of enhancing viral potency against the gypsy moth.
Application of thermosensitive polymers as a new embolic material for intravascular neurosurgery (1996)

Application of thermosensitive polymers as an embolic material for intravascular neurosurgery was investigated. We intended to use thermosensitive polymers to occlude vessels by precipitation in response to body temperature. Copolymers of N-isopropylacrylamide (NIPAM) and N-n-propylacrylamide (NPAM) were selected as thermosensitive polymers. To determine the optimal lower critical soluble temperature (LCST) for the embolic material, we developed an in vitro flow model. In this study the copolymers with an LCST of 24-26 degrees C showed appropriate precipitation. To prove the occlusion of vessels in vivo, we injected the copolymers into a rabbit kidney through a microcatheter. The extent of embolization was judged by angiography and histological examination. An acute toxicity test of the copolymer of NIPAM and NPAM was performed in comparison with that of the NIPAM monomer. The copolymer used in this paper showed no acute toxicity in mice. Water solubility, non-adhesiveness, and non-toxicity are the advantages of the use of thermosensitive polymers as an embolic material. By changing the LCST, various embolic materials can be designed. Based on our results, we believe that the application of thermosensitive polymers as a new embolic material is very promising.
Cloning and DNA sequence analysis of<i>bmpC</i>, a gene encoding a potential membrane lipoprotein of<i>Borrelia burgdorferi</i> (1994)

Immunoscreening of a lambda gt11 genomic library of Borrelia burgdorferi expressed in Escherichia coli permitted detection of a clone containing a partial sequence of a B. burgdorferi gene encoding a protein with significant homology to TmpC of Treponema pallidum. Subsequent cloning and DNA sequence analysis revealed an open reading frame encoding a protein with 353 amino acid residues. The open reading frame is preceded by putative promoter sequences and a ribosome binding site, and is initiated with a TTG. The putative protein shares 26% identity with TmpC, contains a signal peptidase II sequence, and is also homologous to the gene products of the recently described bmpA and bmpB of B. burgdorferi. This gene has been designated bmpC. Additional sequencing and restriction analysis indicate that it is located at approximately 400 kbp on the chromosomal map of B. burgdorferi, immediately upstream of bmpA and bmpB.
Quasi-single-mode homogeneous 31-core fibre (2015)

A homogeneous 31-core fibre with a cladding diameter of 230 μm for quasi-single-mode transmission is designed and fabricated. LP <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">01</sub> -crosstalk of -38.4 dB/11 km at 1550 nm is achieved by using few-mode trench-assisted cores.