gebhart/patrepeval huggingface dataset:
Smart Greybox Fuzzing (2019)

Coverage-based greybox fuzzing (CGF) is one of the most successful approaches for automated vulnerability detection. Given a seed file (as a sequence of bits), a CGF randomly flips, deletes or copies some bits to generate new files. CGF iteratively constructs (and fuzzes) a seed corpus by retaining those generated files which enhance coverage. However, random bitflips are unlikely to produce valid files (or valid chunks in files), for applications processing complex file formats. In this work, we introduce smart greybox fuzzing (SGF) which leverages a high-level structural representation of the seed file to generate new files. We define innovative mutation operators that work on the virtual file structure rather than on the bit level which allows SGF to explore completely new input domains while maintaining file validity. We introduce a novel validity-based power schedule that enables SGF to spend more time generating files that are more likely to pass the parsing stage of the program, which can expose vulnerabilities much deeper in the processing logic. Our evaluation demonstrates the effectiveness of SGF. On several libraries that parse complex chunk-based files, our tool AFLsmart achieves substantially more branch coverage (up to 87 percent improvement) and exposes more vulnerabilities than baseline AFL. Our tool AFLsmart discovered 42 zero-day vulnerabilities in widely-used, well-tested tools and libraries; 22 CVEs were assigned.
Flight Control Systems (2000)

This text consists of two parts - the first providing the fundamentals of flight control system design, the second covering applications of modern control methods. It covers topics such as: industrial consideration for flight control; aircraft modelling; actuation systems; and handling qualities.
Low Temperature Magnetization and Spin Wave Excitations in Amorphous Fe67Co18B₁₄Si₁ (1997)

The temperature dependent saturation magnetization curve of amorphous Fe_(76)Co_(18)B₁₄Si₁ alloy was measured using a SQUID magnetometer and vibrating sample magnetometer from 5 K up to 800 K. Inelastic neutron scattering measurements also have been used to study the long wavelength spin dynamics of this high Tc amorphous ferromagnetic alloy. The magnon dispersion curve exhibit the conventional quadratic relationship E = D (T) q²+△, typical of an isotropic ferromagnet. An estimate of the T = 0 value of spin wave stiffness constant, D (0) ~- 144 meVÅ² value was obtained from a low temperature magnetization curve, which was consistent with the value obtained from the analysis of inelastic neutron scattering data after consideration of its temperature dependence.
Stabilized Gold Nanoparticles by Reduction Using 3,4-Ethylenedioxythiophene-polystyrenesulfonate in Aqueous Solutions:  Nanocomposite Formation, Stability, and Application in Catalysis (2007)

Herein, we report a one-pot synthesis of highly stable Au nanoparticles (AuNPs) using 3,4-ethylenedioxythiophene (EDOT) as a reductant and polystyrene sulfonate (PSS-) as a dopant for PEDOT and particle stabilizer. The synthesis demonstrated in this work entails the reduction of HAuCl4 using EDOT in the presence of PSS-. The formation of AuNPs with concomitant EDOT oxidation is followed by UV-vis spectroscopy at various time intervals. Absorption at 525 nm is due to the surface plasmon band of AuNPs (violet), and broad absorption above 700 nm is due to oxidized PEDOT that was further characterized to be in its highly oxidized (doped) state, using FT-Raman spectroscopy. Transmission electron microscopy shows a polydisperse nature of the particles, and the selected area electron diffraction pattern reveals the polycrystalline nature of AuNPs. With stabilizers such as sodium dodecylsulfate (SDS) (green) and polyvinylpyrrolidone (PVP) (blue), the absorbance around 525 nm was found to be negligibly small, while PSS- showed high absorbance at 525 nm (violet) and above 700 nm (oxidized PEDOT). PSS- also allows complete oxidation of EDOT and serves as an effective dopant for PEDOT. While AuNPs covered by PEDOT alone cannot be dispersed in aqueous solutions, PSS- renders Au-PEDOT water soluble. The hydrodynamic diameter of the nanocomposite estimated from the dynamic light scattering (DLS) measurements increases in the order Na-PSS < SDS < PVP. Interestingly, the color of the Au(nano)-PEDOT/PSS- aqueous dispersion changed reversibly between violet and blue and vice versa on addition of NaOH and HCl, respectively. This reversible color change appears to be a combination effect of acid/base on the properties of PEDOT, in turn changing the environment around the embedded AuNPs. The nanoparticle dispersion also exhibited very high stability in presence of 3.0 M NaCl. Remarkably, the nanocomposite Au(nano)-PEDOT/PSS- was found to function as an effective catalyst to activate the reduction of 4-nitrophenol to 4-aminophenol in the presence of excess NaBH4, and the calculated apparent rate constant value of 4.39 x 10-2 s-1 is found to be higher than those obtained using other nanocomposites with SDS and PVP and comparable to the values reported in the case of other encapsulants.
Characterization of an improved thermal ionization cavity source for mass spectrometry (1999)

A new thermal ionization source for use with a quadrupole mass spectrometer has been designed and characterized. The new source provides significant advantages over the previously reported prototype source and traditional filament-type thermal ionization sources. The operational interface between the source and the quadrupole mass spectrometer has been redesigned. A vacuum interlock, a translational stage, and an adjustable insertion probe are added to improve the source performance. With these modifications, the source is easier to operate while maximizing sample throughput. In this work, the performance of the newly developed source is examined. The ionization efficiencies are measured with a quadrupole mass spectrometer. The efficiency values obtained with this system are comparable to those obtained from a large scale isotope separator. The relationships among the ionization potential, vapor pressure, and measured ionization efficiency results are discussed. The crucible lifetime has been quantitatively estimated by measuring the crucible sputtering rate. Diagnostic studies of the new source show that the crucible position is a crucial parameter for sensitivity and performance. Stability tests demonstrate that the source can be run several weeks at a fixed emission current without significant degradation.
A testbed for experiments with concurrency control primitives in persistent systems (2002)

In current research operating systems, support for objects and the persistence of these objects has been recognised as an important consideration. Research systems provide support for these concepts in the kernel. In these systems a great deal of effort has gone into integrating persistence and object structures with the other low level functions of the operating system. The low level nature of the support ensures that these concepts are in every respect a seamless part of the operating system which interacts sensibly with other components of the system. There has been a tendency in such systems to ignore the issues of concurrency control and resilience, with the attitude that these concepts are well understood by the database community, and as such, can be easily added on top of the system at a later date. A research project is described which aims to investigate the implementation of concurrency control and resilience support at the lowest level of the operating system. Concurrency control and resilience are considered to be sufficiently important and complex issues that they merit support at a low layer of the operating system in the same sense that support for persistence belongs at this level. It is a motivating belief for this project that support for fully fledged concurrency control systems in a truly seamless fashion requires appropriate low level functionality provided by the system. The goal of this project is the identification a set of low level operating system primitives through which a variety of both traditional and more advanced concurrency control methods can be implemented on a persistent store. This goal is being approached through the development of a prototype persistent store which can be used as both an experimental environment and a testbed for the demonstration of the viability of the projects results.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Higher SNR PET image prediction using a deep learning model and MRI image (2019)

PET images often suffer poor signal-to-noise ratio (SNR). Our objective is to improve the SNR of PET images using a deep neural network (DNN) model and MRI images without requiring any higher SNR PET images in training. Our proposed DNN model consists of three modified U-Nets (3U-net). The PET training input data and targets were reconstructed using filtered-backprojection (FBP) and maximum likelihood expectation maximization (MLEM), respectively. FBP reconstruction was used because of its computational efficiency so that the trained network not only removes noise, but also accelerates image reconstruction. Digital brain phantoms downloaded from BrainWeb were used to evaluate the proposed method. Poisson noise was added into sinogram data to simulate a 6 min brain PET scan. Attenuation effect was included and corrected before the image reconstruction. Extra Poisson noise was introduced to the training inputs to improve the network denoising capability. Three independent experiments were conducted to examine the reproducibility. A lesion was inserted into testing data to evaluate the impact of mismatched MRI information using the contrast-to-noise ratio (CNR). The negative impact on noise reduction was also studied when miscoregistration between PET and MRI images occurs. Compared with 1U-net trained with only PET images, training with PET/MRI decreased the mean squared error (MSE) by 31.3% and 34.0% for 1U-net and 3U-net, respectively. The MSE reduction is equivalent to an increase in the count level by 2.5 folds and 2.9 folds for 1U-net and 3U-net, respectively. Compared with the MLEM images, the lesion CNR was improved 2.7 folds and 1.4 folds for 1U-net and 3U-net, respectively. The results show that the proposed method could improve the PET SNR without having higher SNR PET images.
Provably Secure Camouflaging Strategy for IC Protection (2017)

The advancing of reverse engineering techniques has complicated the efforts in intellectual property protection. Proactive methods have been developed recently, among which layout-level integrated circuit camouflaging is the leading example. However, existing camouflaging methods are rarely supported by provably secure criteria, which further leads to an over-estimation of the security level when countering latest de-camouflaging attacks, e.g., the SAT-based attack. In this paper, a quantitative security criterion is proposed for de-camouflaging complexity measurements and formally analyzed through the demonstration of the equivalence between the existing de-camouflaging strategy and the active learning scheme. Supported by the new security criterion, two camouflaging techniques are proposed, including the low-overhead camouflaging cell generation strategy and the AND-tree camouflaging strategy, to help achieve exponentially increasing security levels at the cost of linearly increasing performance overhead on the circuit under protection. A provably secure camouflaging framework is then developed combining these two techniques. The experimental results using the security criterion show that camouflaged circuits with the proposed framework are of high resilience against different attack schemes with only negligible performance overhead.
Electromagnetic contribution to surface enhanced Raman scattering revisited (2003)

Several aspects of the electromagnetic contribution to surface enhanced Raman scattering (SERS) are revisited and analyzed in terms of known concepts and ideas in the field of photonic crystals. A qualitative understanding of some reported SERS phenomena can be achieved by this analysis of the complex energy distribution and spatial localization of surface plasmon resonances in SERS active media. A few of the outstanding issues in the electromagnetic contribution to SERS (like the overwhelming success of nonresonant excitation) can be explained within this framework and, in addition, new physical phenomena utilizing the stimulation or inhibition of the Stokes/anti-Stokes fields are proposed.
Artificial electron acceptors decouple archaeal methane oxidation from sulfate reduction (2016)

The oxidation of methane with sulfate is an important microbial metabolism in the global carbon cycle. In marine methane seeps, this process is mediated by consortia of anaerobic methanotrophic archaea (ANME) that live in syntrophy with sulfate-reducing bacteria (SRB). The underlying interdependencies within this uncultured symbiotic partnership are poorly understood. We used a combination of rate measurements and single-cell stable isotope probing to demonstrate that ANME in deep-sea sediments can be catabolically and anabolically decoupled from their syntrophic SRB partners using soluble artificial oxidants. The ANME still sustain high rates of methane oxidation in the absence of sulfate as the terminal oxidant, lending support to the hypothesis that interspecies extracellular electron transfer is the syntrophic mechanism for the anaerobic oxidation of methane.
Ring-Closing Olefin Metathesis and Radical Cyclization as Competing Pathways (2004)

First and second generation Grubbs' catalyst mediate under otherwise identical conditions two different cyclization modes with high selectivity: a ring-closing metathesis and an atom-transfer radical addition (ATRA) pathway.
Natural Competence and the Evolution of DNA Uptake Specificity (2014)

Many bacteria are naturally competent, able to actively transport environmental DNA fragments across their cell envelope and into their cytoplasm. Because incoming DNA fragments can recombine with and replace homologous segments of the chromosome, competence provides cells with a potent mechanism of horizontal gene transfer as well as access to the nutrients in extracellular DNA. This review starts with an introductory overview of competence and continues with a detailed consideration of the DNA uptake specificity of competent proteobacteria in the Pasteurellaceae and Neisseriaceae. Species in these distantly related families exhibit strong preferences for genomic DNA from close relatives, a self-specificity arising from the combined effects of biases in the uptake machinery and genomic overrepresentation of the sequences this machinery prefers. Other competent species tested lack obvious uptake bias or uptake sequences, suggesting that strong convergent evolutionary forces have acted on these two families. Recent results show that uptake sequences have multiple "dialects," with clades within each family preferring distinct sequence variants and having corresponding variants enriched in their genomes. Although the genomic consensus uptake sequences are 12 and 29 to 34 bp, uptake assays have found that only central cores of 3 to 4 bp, conserved across dialects, are crucial for uptake. The other bases, which differ between dialects, make weaker individual contributions but have important cooperative interactions. Together, these results make predictions about the mechanism of DNA uptake across the outer membrane, supporting a model for the evolutionary accumulation and stability of uptake sequences and suggesting that uptake biases may be more widespread than currently thought.
Field Observations of Tree Injection (1988)

This paper examines tree injection from the view point of the contracting arborist. Contract arborists are responsible for applying the art and science of tree injection, as developed by the utility foresters, city arborists and chemical manufacturers to its commercial phase. In making a commercial application of plant growth regulators to trees, specifically those trimmed around electrical wires, the contract arborist has encountered a multitude of unexpected situations. These operational problems continually hinder the practice, development and refinement of this new science or management tool. Problems of tree physiology and program implementation were not solved until the desired material could be placed in the tree accurately and consistently. Today many equipment variations exist, each filling a perceived need in the search for reliable trunk injection equipment.
Microelectrode study of gallium deposition from Chlorogallate melts (1990)

Abstract Microelectrodes are used to extract thermodynamic, transport, and kinetic data for the gallium trichloride/1‐methyl‐3‐ethylimidazolium chloride room‐temperature molten salt that has been used by the authors to form GaAs thin films. The gallium electrodeposition process, which must be understood for the analysis of the GaAs deposition process, is simulated numerically. A plausible gallium deposition mechanism is identified. Microcylinder electrodes are shown to be advantageous for the acquisition of physicochemical constants. Microdisk electrodes are employed to investigate current oscillation phenomena that appear to be related to metal crystallization processes.
<i>Staphylococcus aureus</i>clumping factor B (ClfB) promotes adherence to human type I cytokeratin 10: implications for nasal colonization (2002)

Staphylococcus aureus is an important cause of sepsis in both community and hospital settings, a major risk factor for which is nasal carriage of the bacterium. Eradication of carriage by topical antibiotics reduces sepsis rates in high-risk individuals, an important strategy for the reduction of nosocomial infection in targeted patient populations. Understanding the mechanisms by which S. aureus adheres to nasal epithelial cells in vivo may lead to alternative methods of decolonization that do not rely on sustained antimicrobial susceptibility. Here, we demonstrate for the first time that the S. aureus surface-expressed protein, clumping factor B (ClfB), promotes adherence to immobilized epidermal cytokeratins in vitro. By expressing a range of S. aureus adhesins on the surface of the heterologous host Lactococcus lactis, we demonstrated that adherence to epidermal cytokeratins was conferred by ClfB. Adherence of wild-type S. aureus was inhibited by recombinant ClfB protein or anti-ClfB antibodies, and S. aureus mutants defective in ClfB adhered poorly to epidermal cytokeratins. Expression of ClfB promoted adherence of L. lactis to human desquamated nasal epithelial cells, and a mutant of S. aureus defective in ClfB had reduced adherence compared with wild type. ClfB also promoted adherence of L. lactis cells to a human keratinocyte cell line. Cytokeratin 10 molecules were shown by flow cytometry to be exposed on the surface of both desquamated nasal epithelial cells and keratinocytes. Cytokeratin 10 was also detected on the surface of desquamated human nasal cells using immunofluorescence, and recombinant ClfB protein was shown to bind to cytokeratin K10 extracted from these cells. We also showed that ClfB is transcribed by S. aureus in the human nares. We propose that ClfB is a major determinant in S. aureus nasal colonization.
Molecular Studies of Voltage-gated Potassium Channels (1990)

The cloning and characterization of the voltage-activated Shaker potassium channel gene in Drosophila have led to the identification of structural elements involved in potassium channel gating. As found for the voltage-activated sodium channel, the S4 segment, located in the conserved core of the protein, plays a central role in voltage-dependent activation. Potassium channels appear to be formed by the assembly of several polypeptides into multisubunit channels. This is directly analogous to the proposed folding of the four internally homologous pseudosubunits of sodium and calcium channels. The amino- and carboxy-terminal regions of Shaker channels are specialized for, and appear to interact in, inactivation gating. This interaction probably includes interaction between subunits, as may be said for the role in inactivation gating of the junction between the carboxyl terminus of the third domain and amino terminus of the fourth domain of sodium channel (Vassilev et al. 1988). The capacity for coassembly in potassium channels extends not only to the alternatively spliced products of the same gene, but also to the products of different genes. Heteromultimeric channels that are formed in this way have kinetic and pharmacological properties that differ from homomultimers of their constituents and, as such, broaden the functional diversity of channels that can be produced by any given number of compatible potassium channel genes.
A Study on the Value-turn of Independent Bookstores - Based on the 2010s (2020)

본 연구는 국내 독립서점의 수치적 증가를 독립서점의 가치적 전환이라는 관점에서 논증하기 위해 빅데이터 분석을 통하여 시기별 독립서점의 의미 변화를 살펴보았다. 연구결과, 독립서점의 의미는 2010년대 초반 기술발전으로 인한 시장 영역의 할인 경쟁의 심화로 오프라인 서점이 위기를 맞이하면서 정책의 영역으로 편입되기 시작하였으며, 2010년대 중반에는 정책적 영역(G)과 문화적 영역이 결합된 형태로 가격 중심에서 콘텐츠 중심의 소비로 변화하고 있는 것으로 나타났다. 마지막으로 2010년대 후반에는 문화적 영역과 사회적 영역이 결합된 형태로, 지역과의 연계가 강화되고 있음을 확인할 수 있었다. 이러한 독립서점과 지역의 연계는 지역커뮤니티에 영향을 주고 도서관 등 책을 매개로 다양한 협력을 가능케하여 지역의 네트워크 허브로서 기능할 수 있을 뿐 아니라 지역 랜드마크로 부상할 수 있음을 확인하였다.This study demonstrates the numerical increase in independent bookstores in Korea in view of the value-turn of independent bookstores. For this purpose, we examined the changes in the value and meaning of independent bookstores in Korea analyzed media articles through big data analysis. As a result of the study, the change in the meaning of independent bookstores faced a crisis in the early- 2010s due to the intensification of discount competition in the Market field due to technological development. Also the meaning of independent bookstores began to be combined in the Government field. Secondly, in the mid-2010s, it was found that the policy of the Government (G) and the Cultural field were combined to change the content-oriented consumption from the price center. Finally, in the late 2010s, a combination of Cultural and Social fields confirmed the strengthening of regional connections. This connection between independent bookstores and regions has been confirmed to affect region communities, enable various cooperation through books such as libraries, and function as a network hub in the region, as well as to emerge as a region landmark.
The antibacterial effects of terpene alcohols on and their mode of action (2004)

The study was made of the antibacterial effects of three terpene alcohols on Staphylococcus aureus, focusing on the leakage of K+ ions and toxicity over time. The leakage of K+ ions was monitored continuously with a K+-electrode. Our results suggested that the terpene alcohols, namely, farnesol, nerolidol and plaunotol might act on cell membranes. The rank order of effectiveness, farnesol>nerolidol>plaunotol, was the same in the toxicity assay and in the examination of the leakage of K+ ions, when we considered the initial rate and the amount of leaked K+ ions. The rank order agreed with the results of a growth-inhibition assay reported previously. The antibacterial activity reflected the initial rate of leakage of K+ ions, suggesting that damage to cell membranes might be one of the major modes of action of these terpene alcohols. The results also demonstrated that the initial rate of leakage and the amount of leaked K+ ions are useful as indices of the antibacterial activities of hydrophobic compounds.