gebhart/patrepeval huggingface dataset:
TestSage: Regression Test Selection for Large-Scale Web Service Testing (2019)

Regression testing is an important but expensive activity in software development. Among various types of tests, web service tests are usually one of the most expensive (due to network communications) but widely adopted types of tests in commercial software development. Regression test selection (RTS) aims to reduce the number of tests which need to be retested by only running tests that are affected by code changes. Although a large number of RTS techniques have been proposed in the past few decades, these techniques have not been adopted on large-scale web service testing. This is because most existing RTS techniques either require direct code dependency between tests and code under test or cannot be applied on large scale systems with enough efficiency. In this paper, we present a novel RTS technique, TestSage, that performs RTS for web service tests on large scale commercial software. With a small overhead, TestSage is able to collect fine grained (function level) dependency between test and service under test that do not directly depend on each other. TestSage has also been successfully applied to large complex systems with over a million functions. We conducted experiments of TestSage on a large scale backend service at Google. Experimental results show that TestSage reduces 34% of testing time when running all AEC (Analysis, Execution and Collection) phases, 50% of testing time while running without collection phase. TestSage has been integrated with internal testing framework at Google and runs day-to-day at the company.
Chloroperoxidase (1970)

The spectral changes caused by the addition of hydrogen peroxide and halide salts to chloroperoxidase have been investigated and discussed in relation to the halogenation activity of the enzyme.Chloroperoxidase forms a compound with hydrogen peroxide that is spectrally similar to horseradish peroxidase Compound I.The initial peroxide compound can decompose directly back to the native enzyme in a catalatic reaction or react with ethanol to form acetaldehyde.There is no evidence for the participation of a secondary intermediate in these reactions.The initial peroxide compound also reacts with classical peroxidase donors, such as ascorbate, guaiacol, and pyrogallol.A secondary intermediate is formed in this reaction.Thus, chloroperoxidase exhibits characteristics of both peroxidase and catalase.Chloroperoxidase can catalyze the peroxidative chlorination, bromination, and iodination of appropriate donors.At low pH, the addition of halides causes definite spectral changes in the Soret region of the native enzyme.The spectral changes show the same pH dependence as the halogenation activity.Above the pH optimum of the enzyme, the velocity of the chlorination reaction is approximately proportional to the product of the chloride and hydrogen ion concentrations.A model for the halogenation reactions has been proposed in which halide ions compete with a carboxyl group for a location near the heme group.At low pH, protonation of the car-boxy1 group permits halide ion to supply the negative charge preferred at this location.The close proximity of the halide to the heme enables it to act as a donor for the peroxide compound.The low pH requirement for the binding of halide is responsible for the low pH optimum of the halogenation reactions.
The vitamin D-binding protein gene: quantitation of amplified nucleic acids by ELISA. (1993)

We have utilized enzyme-linked immunosorbent assay (ELISA) to quantitate PCR-amplified DNA. This method was used to measure mRNA for the vitamin D-binding protein (Gc), beta-actin and the transferrin receptor (TR) gene in the Hep3B cell line. Total RNA from Hep3B cells was reverse transcribed to obtain cDNA, which was amplified in the presence of digoxigenin-dUTP by PCR. The PCR products were then hybridized in liquid phase to a biotinylated, nested capture probe for the respective sequences. The hybridized products were bound to a streptavidin-coated ELISA plate and were detected by an alkaline-phosphatase-conjugated antibody to digoxigenin. ELISA standard curves for Gc and control genes, beta-actin and TR, were obtained after PCR amplification of serial dilutions of Hep3B total RNA. As an external standard, an ELISA standard curve for Gc was obtained after PCR amplification of serial dilutions of a full-length Gc cDNA insert obtained from a recombinant plasmid. Thus, we were able to develop a non-isotopic quantitation assay for PCR-amplified DNA that is highly sensitive and has the specificity of hybridization-based methods.
Commereializing medium voltage VFD that utilizes high voltage SiC technology (2017)

This paper discusses system level challenges faced in designing and commercializing a Variable Frequency Drive (VFD) system utilizing high speed, high voltage, and high power density switching devices that incorporate Silicon Carbide (SiC) MOSFET technology.
Substrate Inhibition of <scp>d</scp>-Amino Acid Transaminase and Protection by Salts and by Reduced Nicotinamide Adenine Dinucleotide:  Isolation and Initial Characterization of a Pyridoxo Intermediate Related to Inactivation (1998)

D-Amino acid transaminase, a pyridoxal phosphate (PLP) enzyme, is inactivated by its natural substrate, D-alanine, concomitant with its alpha-decarboxylation [Martinez del Pozo, A., Yoshimura, T., Bhatia, M. B., Futaki, S., Manning, J. M., Ringe, D., and Soda, K. (1992) Biochemistry 31, 6018-6023; Bhatia, M. B., Martinez del Pozo, A., Ringe, D., Yoshimura, T., Soda, K., and Manning, J. M. (1993) J. Biol. Chem. 268, 17687-17694]. beta-Decarboxylation of d-aspartate to d-alanine leads also to this inactivation [Jones, W. M., van Ophem, P. W., Pospischil, M. A., Ringe, D., Petsko, G., Soda, K., and Manning, J. M. (1996) Protein Sci. 5, 2545-2551]. Using a high-performance liquid chromatography-based method for the determination of pyridoxo cofactors, we detected a new intermediate closely related to the inactivation by d-alanine; its formation occurred at the same rate as the inactivation and upon reactivation it reverted to PLP. Conditions were found under which it was characterized by ultraviolet-visible spectral analysis and mass spectroscopy; it is a pyridoxamine phosphate-like compound with a C2 fragment derived from the substrate attached to the C'-4 of the pyridinium ring and it has a molecular mass of 306 consistent with this structure. In the presence of d-serine, slow accumulation of a quinonoid intermediate is also related to inactivation. The inactivation can be prevented by salts, which possibly stabilize the protonated aldimine coenzyme complex. The reduced cofactor, nicotinamide adenine dinucleotide, prevents D-aspartate-induced inactivation. Both of these events also are related to formation of the novel intermediate.
Improving Linewidth Control over Reflective Surfaces Using Heavily Dyed Resists (1986)

Adding high concentrations of soluble dye to photoresists results in greatly improved linewidth control over reflective topography. The linewidth control of 1.25 μm lines (measured as the difference between the widest part of each line and the narrowest) is reduced from 0.24 μm for undyed resist to 0.12 μm for photoresist with a high concentration of dye added. A commercial resist containing a low concentration of Coumarin 6 dye yields an intermediate linewidth control value of 0.20 μm. Wall profiles are unexpectedly straight for heavily dyed resist, exposure latitude is much greater than for undyed resist, and metrology precision is increased sixfold. A commercially available dye is described as a low cost, more soluble alternative to the coumarin dyes now used commercially.
Deformation-free overgrowth of InGaAsP DFB corrugations (1983)

A hybrid LPE/MOCVD growth procedure is described which enables λ = 1.55 μm distributed feedback laser structures to be fabricated without deformation of the corrugated region of the device. Depths of corrugations remaining after overgrowth using this process are typically 1600 Å. Conditions under which deformation does occur are also presented.
Acclimatizing Taxonomic Semantics for Hierarchical Content Classification (2006)

Hierarchical models have been shown to be effective in content classification. However, we observe through empirical study that the performance of a hierarchical model varies with given taxonomies; even a semantically sound taxonomy has potential to change its structure for better classification. By scrutinizing typical cases, we elucidate why a given semantics-based hierarchy does not work well in content classification, and how it could be improved for accurate hierarchical classification. With these understandings, we propose effective localized solutions that modify the given taxonomy for accurate hierarchical classification. We conduct extensive experiments on both toy and real-world data sets, report improved performance and interesting findings, and provide further analysis of algorithmic issues such as time complexity, robustness, and sensitivity to the number of features.
Physical properties of hierarchically ordered self-assembled planar and spherical membranes (2010)

The mechanical properties and water permeability of hierarchical self-assembling membranes and sacs formed from oppositely charged high molecular weight hyaluronic acid (HA) and small molecule peptide amphiphiles (PAs) were studied. Techniques to make reproducible 2D planar membranes and 3D spherical sacs from these materials were developed while membrane inflation and osmotic swelling were used to quantify the mechanical properties and water permeability of these structures. It was found that incubation time and concentration of HA used had an effect on the area modulus and water permeability of the membranes. These factors also affected the kinetics of membrane growth as evidenced in SEM micrographs, which showed differences in the structure. Area modulus of membranes changed from about 6 N m−1 for the lower weight percent HA system at the shortest incubation time of 3 minutes, up to 12 N m−1 for the higher weight percent HA system at the longest incubation time of 60 minutes. Water permeability decreased with incubation time, but the lower weight percent HA system showed a lower water permeability when compared to the higher weight percent HA system at the same incubation time. This type of characterization and understanding of the structure–property relationships in self-assembling systems are necessary steps in both using these structures for specific applications and applying this knowledge to design new and better materials in the future.
An introduction to electrical resistivity in geophysics (2001)

Physicists are finding that the skills they have learned in their training may be applied to areas beyond traditional physics topics. One such field is that of geophysics. This paper presents the electrical resistivity component of an undergraduate geophysics course at Radford University. It is taught from a physics perspective, yet the application of the theory to the real world is the overriding goal. The concepts involved in electrical resistivity studies are first discussed in a general sense, and then they are studied through the application of the relevant electromagnetic theory. Since geology majors comprise the bulk of the students in this class, the math used is only that which is typically required of geology majors. The final results are given in a form that practicing geophysicists may use in the field. A method is presented for constructing an inexpensive apparatus for measuring electrical resistivity in both a tabletop laboratory setting and in the field. This apparatus is truly “plug and play” since its assembly and use requires only the most basic knowledge of electronics. This apparatus is tested in a tabletop laboratory setting as well as in two field surveys.
P4-MACsec: Dynamic Topology Monitoring and Data Layer Protection with MACsec in P4-SDN (2019)

We propose P4-MACsec to protect network links between P4 switches through automated deployment of MACsec, a widespread IEEE standard for securing Layer 2 infrastructures. It is supported by switches and routers from major manufacturers and has only little performance limitations compared to VPN technologies such as IPsec. P4-MACsec introduces a data plane implementation of MACsec including AES-GCM encryption and decryption directly on P4 switches. P4-MACsec features a two-tier control plane structure where local controllers running on the P4 switches interact with a central controller. We propose a novel secure link discovery mechanism that leverages protected LLDP frames and the two-tier control plane structure for secure and efficient management of a global link map. Automated deployment of MACsec creates secure channel, generates keying material, and configures the P4 switches for each detected link between two P4 switches. It detects link changes and performs rekeying to provide a secure, configuration-free operation of MACsec. In this paper, we review the technological background of P4-MACsec and explain its architecture. To demonstrate the feasibility of P4-MACsec, we implement it on the BMv2 P4 software switch and validate the prototype through experiments. We evaluate its performance through experiments that focus on TCP throughput and round-trip time. We publish the prototype and experiment setups on Github.
Comprehensive DNA methylation analysis of human peripheral blood leukocytes and lymphoblastoid cell lines (2011)

DNA methylation is involved in development and in human diseases. Genomic DNA derived from lymphoblastoid cell lines (LCLs) is commonly used to study DNA methylation. There are potential confounding factors regarding the use of LCL-derived DNA, however, such as Epstein-Barr (EB) viral infection and artifacts induced during cell culture. Recently, several groups compared the DNA methylation status of peripheral blood leukocytes (PBLs) and LCLs and concluded that the DNA methylation profiles between them might be consistent. To confirm and extend theses results, we performed a comprehensive DNA methylation analysis using both PBLs and LCLs derived from the same individuals. Using the luminometric methylation assay, we revealed that the global DNA methylation level was different between PBLs and LCLs. Furthermore, the direction of change was not consistent. Comparisons of genome-wide DNA methylation patterns of promoter regions revealed that methylation profiles were largely conserved between PBLs and LCLs. A preliminary analysis in a small number of samples suggested that the methylation status of an LCL may be better correlated with PBLs from the same individual than with LCLs from other individuals. Expectedly, DNA methylation in promoter regions overlapping with CpG islands was associated with gene silencing in both PBLs and LCLs. With regard to methylation differences, we found that hypermethylation was more predominant than hypomethylation in LCLs compared with PBLs. These findings suggest that LCLs should be used for DNA methylation studies with caution as the methylation patterns of promoter regions in LCLs are not always the same as those in PBLs.
Applications of iodonium salts and iodonium ylides as precursors for nucleophilic fluorination in Positron Emission Tomography (2013)

This review summarizes the applications of iodonium compounds in the rapidly developing field of Positron Emission Tomography (PET). Reactions of diaryliodonium salts with fluoride anion have found wide practical application in PET as a fast and convenient method for the introduction of the radioactive [ 18 F]-fluoride into radiotracer molecules. The best synthetic methods for the preparation of iodonium precursors for PET are described, the mechanistic aspects of nucleophilic fluorination reaction are discussed, and specific examples of the preparation of PET radioligands are provided.
SNARE Protein-Dependent Glutamate Release from Astrocytes (2000)

We investigated the cellular mechanisms underlying the Ca(2+)-dependent release of glutamate from cultured astrocytes isolated from rat hippocampus. Using Ca(2+) imaging and electrophysiological techniques, we analyzed the effects of disrupting astrocytic vesicle proteins on the ability of astrocytes to release glutamate and to cause neuronal electrophysiological responses, i.e., a slow inward current (SIC) and/or an increase in the frequency of miniature synaptic currents. We found that the Ca(2+)-dependent glutamate release from astrocytes is not caused by the reverse operation of glutamate transporters, because the astrocyte-induced glutamate-mediated responses in neurons were affected neither by inhibitors of glutamate transporters (beta-threo-hydroxyaspartate, dihydrokainate, and L-trans-pyrrolidine-2,4-dicarboxylate) nor by replacement of extracellular sodium with lithium. We show that Ca(2+)-dependent glutamate release from astrocytes requires an electrochemical gradient necessary for glutamate uptake in vesicles, because bafilomycin A(1), a vacuolar-type H(+)-ATPase inhibitor, reduced glutamate release from astrocytes. Injection of astrocytes with the light chain of the neurotoxin Botulinum B that selectively cleaves the vesicle-associated SNARE protein synaptobrevin inhibited the astrocyte-induced glutamate response in neurons. Therefore, the Ca(2+)-dependent glutamate release from astrocytes is a SNARE protein-dependent process that requires the presence of functional vesicle-associated proteins, suggesting that astrocytes store glutamate in vesicles and that it is released through an exocytotic pathway.
A bovine ephemeral fever vaccine incorporating adjuvant Quil A: a comparative study using adjuvants Quil A, aluminium hydroxide gel and dextran sulphate (1985)

Various vaccines containing the 919 strain of ephemeral fever virus were evaluated in experimental calves and in commercial cattle. The vaccine virus was mixed with one of the adjuvants, Quil A (a saponin derivative), aluminium hydroxide gel, dextran sulphate or combinations of these. The response of experimental calves was evaluated by measuring the production of neutralising antibodies and by resistance to challenge with virulent virus; the response of commercial cattle was judged only by the production of neutralising antibody. Twelve calves given two doses of vaccine containing Quil A produced neutralising antibodies to bovine ephemeral fever virus and all were resistant to challenge with virulent virus given 28 to 76 days after the second vaccination. The vaccine given in three of these calves also contained aluminium hydroxide gel. Six of eight unvaccinated control calves succumbed to experimental challenge. In commercial cattle (17 to 26 animals per group) the serological response after two doses of vaccine containing Quil A or Quil A and dextran sulphate was significantly better than that after vaccines containing only dextran sulphate or after vaccines containing combinations of aluminium hydroxide gel and Quil A. The adjuvant Quil A alone was tested in cattle and shown to produce a transient soft swelling at the injection site as well as a rise in rectal temperature of greater than 1 degree C one day after inoculation. At least 99.99 per cent of viral infectivity was destroyed when the vaccine was mixed with Quil A, suggesting that live virus may not be essential in the immunogenicity of the vaccine. This vaccine overcame two of the problems associated with previous attenuated vaccines tested in Australia; the necessity for adjuvant and virus to be mixed immediately before use and the large volume of the vaccine.
Angiotensin converting enzyme is the main contributor to angiotensin I–II conversion in the interstitium of the isolated perfused rat heart (2001)

In the intact rat heart, ACE is the main contributor to angiotensin I to angiotensin II conversion, both in the coronary vascular bed and the interstitium. Cardiac ACE is not limited to the coronary vascular endothelium.
Thermal Decomposition Behavior of Hydrated Magnesium Dodecahydrododecaborates (2009)

MgB12H12 is an intermediate in the hydrogen desorption and sorption processes of magnesium borohydride, which is an important candidate material for hydrogen storage. It is thus highly desirable to synthesize anhydrous MgB12H12 in order to study its properties and its role in the hydrogenation and dehydrogenation of magnesium borohydride. Contrary to the literature claim, we find that anhydrous MgB12H12 cannot be obtained from simple thermal decomposition of Mg(H2O)6B12H12·6H2O (1) which has different thermal decomposition behavior from that of most hydrated alkali and alkaline earth salts of dodecahydrododecaborates. Thermal decomposition of 1 involves both dehydration and dehydrogenation processes in three steps, resulting in the formation of complexes Mg(H2O)6B12H12 (2), Mg(H2O)3B12H12 (3), and Mg(μ-OH)xB12H12−x (4) that were characterized by XRD, IR, and 11B NMR. Dehydrogenation was also confirmed by both the generation of hydrogen observed in TPD-MS spectra and the formation of polyhydroxylated complexes.
Design and application of a class of sensors to monitor Ca <sup>2+</sup> dynamics in high Ca <sup>2+</sup> concentration cellular compartments (2011)

Quantitative analysis of Ca(2+) fluctuations in the endoplasmic/sarcoplasmic reticulum (ER/SR) is essential to defining the mechanisms of Ca(2+)-dependent signaling under physiological and pathological conditions. Here, we developed a unique class of genetically encoded indicators by designing a Ca(2+) binding site in the EGFP. One of them, calcium sensor for detecting high concentration in the ER, exhibits unprecedented Ca(2+) release kinetics with an off-rate estimated at around 700 s(-1) and appropriate Ca(2+) binding affinity, likely attributable to local Ca(2+)-induced conformational changes around the designed Ca(2+) binding site and reduced chemical exchange between two chromophore states. Calcium sensor for detecting high concentration in the ER reported considerable differences in ER Ca(2+) dynamics and concentration among human epithelial carcinoma cells (HeLa), human embryonic kidney 293 cells (HEK-293), and mouse myoblast cells (C2C12), enabling us to monitor SR luminal Ca(2+) in flexor digitorum brevis muscle fibers to determine the mechanism of diminished SR Ca(2+) release in aging mice. This sensor will be invaluable in examining pathogenesis characterized by alterations in Ca(2+) homeostasis.
Elemental‐Sulfur‐Mediated Facile Synthesis of a Covalent Triazine Framework for High‐Performance Lithium–Sulfur Batteries (2016)

A covalent triazine framework (CTF) with embedded polymeric sulfur and a high sulfur content of 62 wt % was synthesized under catalyst- and solvent-free reaction conditions from 1,4-dicyanobenzene and elemental sulfur. Our synthetic approach introduces a new way of preparing CTFs under environmentally benign conditions by the direct utilization of elemental sulfur. The homogeneous sulfur distribution is due to the in situ formation of the framework structure, and chemical sulfur impregnation within the micropores of CTF effectively suppresses the dissolution of polysulfides into the electrolyte. Furthermore, the triazine framework facilitates electron and ion transport, which leads to a high-performance lithium-sulfur battery.
Solving small and large scale constraint satisfaction problems using a heuristic-based microgenetic algorithm (2002)

Microgenetic algorithms (MGAs) are genetic algorithms that use a very small population size (population size < 10). Recently, interest in MGAs has grown because, for some problems, they are able to find solutions with fewer evaluations than genetic algorithms with larger population sizes. This paper introduces two heuristic-based MGAs which quickly find solutions to constraint satisfaction problems. Both of these algorithms outperform a well-known algorithm, the iterative descent method, on most instances of the N-queens problem. We compare these three algorithm on the basis of the mean number of evaluations needed to find solutions to several instances of the N-queens problem.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>