gebhart/patrepeval huggingface dataset:
The influence of size and coverage on test suite effectiveness (2009)

We study the relationship between three properties of test suites: size, structural coverage, and fault-finding effectiveness. In particular, we study the question of whether achieving high coverage leads directly to greater effectiveness, or only indirectly through forcing a test suite to be larger. Our experiments indicate that coverage is sometimes correlated with effectiveness when size is controlled for, and that using both size and coverage yields a more accurate prediction of effectiveness than size alone. This in turn suggests that both size and coverage are important to test suite effectiveness. Our experiments also indicate that no linear relationship exists among the three variables of size, coverage and effectiveness, but that a nonlinear relationship does exist.
Anisotropic reverse‐time migration for tilted TI media (2007)

ABSTRACT Seismic anisotropy in dipping shales results in imaging and positioning problems for underlying structures. We develop an anisotropic reverse‐time depth migration approach for P‐wave and SV‐wave seismic data in transversely isotropic (TI) media with a tilted axis of symmetry normal to bedding. Based on an accurate phase velocity formula and dispersion relationships for weak anisotropy, we derive the wave equation for P‐wave and SV‐wave propagation in tilted transversely isotropic (TTI) media. The accuracy of the P‐wave equation and the SV‐wave equation is analyzed and compared with other acoustic wave equations for TTI media. Using this analysis and the pseudo‐spectral method, we apply reverse‐time migration to numerical and physical‐model data. According to the comparison between the isotropic and anisotropic migration results, the anisotropic reverse‐time depth migration offers significant improvements in positioning and reflector continuity over those obtained using isotropic algorithms.
Degree of Vehicle Overloading and its Implication on Road Safety in Developing Countries (2013)

The phenomenon of vehicle overloading is not new and has been discussed in relation to the adverse effects on road pavement damage, road safety and GHG emission. Although much has been said in the context of the more developed countries, there has not been much discussion on vehicle overloading in developing countries. In this study, the extent and degree of vehicle overloading in a developing country is established. Half of the 3-axle trucks were found to be overloaded and the degree of overloading is up to 101% of its legal weight limit! The effect of truck overloading on safety is discussed by establishing the relationship between truck stopping distance and gross vehicle weight for a certain travel speed. Comparison between actual overloading data for 2-axle, 3-axle and 4-axle trucks and the stopping distance illustrates the gravity of the situation which needs a comprehensive and effective strategy from the relevant agencies. Keywords: Road Safety, Vehicle Overloading, Traffic Accidents, Weigh-in-Motion, Stopping Distance
Magnetically complexed collagen nanocomposites (2004)

Rare-earth ions with unfilled 4f shells, Gd3+ (J = ) and Dy3+ (J = ) are bound to glutamic acid residues at the ends of long linear oligopeptides derived from those in naturally occurring collagen proteins. The peptide, which folds into a triple helix about 10 nm long, consists of a sequence 36 amino acids long. The rare-earth–collagen complex self-assembles into layers through a smectic A liquid crystalline phase. The smectic layered structure is retained on drying, and the acidic peptide end blocks localize the rare-earth ions in sheets approximately 1–2 nm thick separated by the collagen-like peptide of the complex. X-ray crystallographic, scanning electron microscopy and optical studies demonstrate the liquid crystallinity of the peptides and the incorporation of the rare-earth ions into sheets between the smectic layers. Magnetic susceptibility (2 K ≤ T ≤ 300 K) and low-temperature isothermal magnetization (0 T ≤ H ≤ 5 T) show the rare-earth–collagen complexes are paramagnetic in the rare-earth concentration range studied (not more than 0.3–0.4 Gd or Dy ion per molecule). This technique of bonding rare-earth ions to oligopeptides, and using the oligopeptide mesophase behaviour to organize attached ions, can be used to tether other rare-earth and/or transition-metal ions, creating layered magnetic structures. The interlayer spacing is dictated solely by the intervening oligopeptide length.
Enhancements to the optimization process in lens design (II) (2001)

The full optimization process includes definition and maintenance of the merit function, selection of optimization strategy, the actual automatic improvement of the system, designer intervention and review of the final results. Well optimized systems are almost always achieved, not by a single run, but by repeated backtracking and re-optimization. A number of improvements to the whole process are presented, both to the damped lest squares algorithm itself and to the 'handling.' The enhancements include extensions to the classical damped least squares. These enhancements have been implemented in the widely used WinLens software package.
Potential hazards of diagnostic radiation. (1977)

There are no precise data for determining the extent of somatic damage from small doses of radiation used in diagnostic radiology. Diagnostic radiation given to pregnant women, knowingly or unknowingly, should rarely reach teratogenic levels causing brain and eye abnormalities. Evidence suggests that it does increase the risk of childhood malignancy, especially leukemia. Although rapidly growing tissues seem most susceptible, all radiation probably carries a very small risk of carcinogenesis. Genetic damage is equally difficult to estimate. Diagnostic radiation of females, even in childhood, may be related to an increased incidence of Down's syndrome in older mothers. Radiation also causes point mutations, which may explain the increase of some genetic abnormalities in progeny of older fathers. Whenever an abdominal or pelvic radiograph is ordered before the end of the reproductive period, there must be a potential benefit to balance the small risk involved.
On the Origin of Isoprenoid Biosynthesis (2018)

Isoprenoids and their derivatives represent the largest group of organic compounds in nature and are distributed universally in the three domains of life. Isoprenoids are biosynthesized from isoprenyl diphosphate units, generated by two distinctive biosynthetic pathways: mevalonate pathway and methylerthritol 4-phosphate pathway. Archaea and eukaryotes exclusively have the former pathway, while most bacteria have the latter. Some bacteria, however, are known to possess the mevalonate pathway genes. Understanding the evolutionary history of these two isoprenoid biosynthesis pathways in each domain of life is critical since isoprenoids are so interweaved in the architecture of life that they would have had indispensable roles in the early evolution of life. Our study provides a detailed phylogenetic analysis of enzymes involved in the mevalonate pathway and sheds new light on its evolutionary history. The results suggest that a potential mevalonate pathway is present in the recently discovered superphylum Candidate Phyla Radiation (CPR), and further suggest a strong evolutionary relationship exists between archaea and CPR. Interestingly, CPR harbors the characteristics of both the bacterial-type and archaeal-type mevalonate pathways and may retain signatures regarding the ancestral isoprenoid biosynthesis pathway in the last universal common ancestor. Our study supports the ancient origin of the mevalonate pathway in the three domains of life as previously inferred, but concludes that the evolution of the mevalonate pathway was more complex.
Maurice Cowling, Mill and Liberalism, second edition, Cambridge, Cambridge University Press, 1990, pp. liv + 161. (1991)

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Extensible routers for active networks (2003)

This paper describes our effort to build an extensible router in support of active networks. Our work is driven by two goals: (1) supporting the injection of new functionality into a router, and (2) exploiting commercially available hardware. Our approach is a hierarchical architecture, in which packet flows traverse a range of processing/forwarding paths. This paper both presents the architecture, and describes our experiences implementing the architecture across a combination of general-purpose and network processors.
Eigentransforms for region-based image processing (2005)

Linear transforms such as the DCT are efficient for image compression. While known transforms that approximate the eigentransform are limited to rectangular regions, this paper proposes a model for construction of eigentransforms for arbitrarily-shaped image segments.
Neurochemical, morphological, and neurophysiological abnormalities in retinas of Sandhoff and GM1 gangliosidosis mice (2007)

Retinal abnormalities are well documented in patients with ganglioside storage diseases. The total content and distribution of retinal glycosphingolipids was studied for the first time in control mice and in Sandhoff disease (SD) and GM1 gangliosidosis mice. Light and electron microscopy of the SD and the GM1 retinas revealed storage in ganglion cells. Similar to previous findings in rat retina, GD3 was the major ganglioside in mouse retina, while GM2 and GM1 were minor species. Total ganglioside content was 44% and 40% higher in the SD and the GM1 retinas, respectively, than in the control retinas. Furthermore, GM2 and GM1 content were 11-fold and 51-fold higher in the SD and the GM1 retinas than in the control retinas, respectively. High concentrations of asialo-GM2 and asialo-GM1 were found in the SD and the GM1 retinas, respectively, but were undetectable in the control retinas. The GSL abnormalities in the SD and the GM1 retinas reflect significant reductions in beta-hexosaminidase and beta-galactosidase enzyme activities, respectively. Although electroretinograms appeared normal in the SD and the GM1 mice, visual evoked potentials were subnormal in both mutants, indicating visual impairments. Our findings present a model system for assessing retinal pathobiology and therapies for the gangliosidoses.
Oxygen inhibition of nitrogenase activity in Klebsiella pneumoniae (1993)

A purpose-built oxystat has been used to study reversible inhibition of nitrogenase by O2 in the facultative anaerobe Klebsiella pneumoniae. C2H2-reducing activity in samples from either an anaerobic glucose-limited or an O2-limited diazotrophic chemostat culture was completely inhibited by exposure to a dissolved O2 concentration (DOC) of 1.5 microM or above. Subsequently, under anaerobic conditions, C2H2-reducing activity returned in the absence of de novo protein synthesis. The amount of activity returning never reached 100% of the initial anaerobic activity before O2 treatment. The degree of reversibility was inversely proportional to the log of DOC during exposure and was decreased by increasing the time of exposure to O2 (about 60% reversibility occurred after a 20 min exposure to 6 microM-O2). The failure to obtain complete recovery of activity was apparently not due to inactivation of the very O2-sensitive pyruvate-flavodoxin oxidoreductase (nifJ product) which provides electrons for nitrogenase activity in vivo. Samples from the O2-limited culture behaved similarly to those limited by glucose. Thus, 'training' of the organism to use O2 during growth does not influence the tolerance of nitrogenase to O2. Since the behaviour towards O2 reported here for K. pneumoniae differs from that known to occur in Azotobacter, the mechanism of protection of nitrogenase from O2 damage may differ in these organisms.
Display of surfaces from volume data (2021)

The application of volume rendering techniques to the display of surfaces from sampled scalar functions of three spatial dimensions is explored. Fitting of geometric primitives to the sampled data is not required. Images are formed by directly shading each sample and projecting it onto the picture plane. Surface shading calculations are performed at every voxel with local gradient vectors serving as surface normals. In a separate step, surface classification operators are applied to obtain a partial opacity for every voxel. Operators that detect isovalue contour surfaces and region boundary surfaces are presented. Independence of shading and classification calculations insures an undistorted visualization of 3-D shape. Non-binary classification operators insure that small or poorly defined features are not lost. The resulting colors and opacities are composited from back to front along viewing rays to form an image. The technique is simple and fast, yet displays surfaces exhibiting smooth silhouettes and few other aliasing artifacts. The use of selective blurring and super-sampling to further improve image quality is also described. Examples from two applications are given: molecular graphics and medical imaging.
Transparent multi-core cryptographic support on Niagara CMT Processors (2009)

How cryptographic functionality has been implemented and made available in application scenarios has evolved over time. Pure software implementations were the obvious first choice, followed by dedicated hardware devices, be it co-processors or hardware accelerators accessible on the main bus. This paper examines aspects of making the next step in this evolution work, namely the use of dedicated cryptographic hardware that's part of multi-core system CPUs. While the inclusion of cryptographic accelerator functionality in the processor chip is not new, this paper investigates the question of how to transparently combine such multi-core cryptographic processor support with higher level software stacks in a commodity operating system that also needs to perform well if such hardware support is not present. We explore this question in the context of the Ultra-SPARC T1 and T2 processor family, chip multi-threaded (CMT) processors that have hardware cryptographic accelerators integrated on-chip with 8-core support for symmetric and asymmetric cryptographic and secure hash operations. The paper presents how a software infrastructure, the Solaris Cryptographic Framework, transparently takes advantage of these chip features and presents a brief comparative study of their performance.
Defining NOTCH3 Target Genes in Ovarian Cancer (2012)

NOTCH3 gene amplification plays an important role in the progression of many ovarian and breast cancers, but the targets of NOTCH3 signaling are unclear. Here, we report the use of an integrated systems biology approach to identify direct target genes for NOTCH3. Transcriptome analysis showed that suppression of NOTCH signaling in ovarian and breast cancer cells led to downregulation of genes in pathways involved in cell-cycle regulation and nucleotide metabolism. Chromatin immunoprecipitation (ChIP)-on-chip analysis defined promoter target sequences, including a new CSL binding motif (N1) in addition to the canonical CSL binding motif, that were occupied by the NOTCH3/CSL transcription complex. Integration of transcriptome and ChIP-on-chip data showed that the ChIP target genes overlapped significantly with the NOTCH-regulated transcriptome in ovarian cancer cells. From the set of genes identified, we showed that the mitotic apparatus organizing protein DLGAP5 (HURP/DLG7) was a critical target. Both the N1 motif and the canonical CSL binding motif were essential to activate DLGAP5 transcription. DLGAP5 silencing in cancer cells suppressed tumorigenicity and inhibited cellular proliferation by arresting the cell cycle at the G(2)-M phase. In contrast, enforced expression of DLGAP5 partially counteracted the growth inhibitory effects of a pharmacologic or RNA interference-mediated NOTCH inhibition in cancer cells. Our findings define direct target genes of NOTCH3 and highlight the role of DLGAP5 in mediating the function of NOTCH3.
B7-H1 Expression Is Associated with Poor Prognosis in Colorectal Carcinoma and Regulates the Proliferation and Invasion of HCT116 Colorectal Cancer Cells (2013)

Positive B7-H1 expression is an independent predictor for colorectal carcinoma prognosis. Moreover, knockdown of B7-H1 can inhibit cell proliferation, migration and invasion.
A Novel Concept of Dye Application for Dyeing and Printing (1965)

A new method of dyeing and printing textiles is described in which the dye is bound to the fibre by means of a compound of high molecular weight. The advantages and disadvantages of existing methods of dyeing and printing textiles are surveyed and possible methods of combining dyes chemically with binders are discussed, with particular reference to the preparation of film–forming copolymers containing interpolymerised dye. Dyes containing acrylic groups have been found to be the most suitable. The application of such copolymers to textiles is considered; the colorations obtained have higher fastness to rubbing and to solvents than pigment dyeings and prints, but the light fastness is generally somewhat lower.
Modification mechanism of cerium on the Al-18Si alloy (2006)

在不同扔的状态下面的高级低共熔体的 Al-Si 合金上的稀土元素铈(Ce ) 的效果被光显微镜和量的图象分析学习了。尺寸和在铸造物的主要的硅的数量随 melt 的增加的 Ce 的增加减少，这被发现。好 facetted 形状的从分叉的形状的同时主要的硅变化。尽管在铸造物的最容易溶解的硅上的修正也随 melt 的增加的 Ce 的增加改善，离开主要的硅的最容易溶解的硅上的修正的效果在到主要的硅的最容易溶解的硅结束上是比那更明显的。修正机制借助于扫描详细被分析电子显微镜与精力装备了 X 光检查和热力学分析的散分析，它在反应和反应平衡的标准吉布斯精力在变化上包括了分析。
Rat Brain Protein Kinase C: Purification, Antibody Production, and Quantification in Discrete Regions of Hippocampus (1989)

Protein kinase C (PKC), a calcium- and phospholipid-dependent kinase, is highly enriched in rat brain, where it may function in signal transduction processes. We purified rat brain PKC to homogeneity by a three-column procedure of diethylaminoethyl-cellulose, phenyl-Sepharose, and protamine-agarose with a yield of 16% and a final specific activity of 9,600 pmol of [3H]phorbol-12,13-dibutyrate bound/mg of protein. The pure protein consisted of a doublet of 80 and 78 kilodaltons. Rabbit antibodies prepared against a beta-type PKC synthetic peptide sequence (RAKIGQGTKAPEEKTANTISK) showed high specificity and sensitivity for PKC and recognized only the 78-kilodalton form of PKC. Micropunches (300 microns in diameter) of rat hippocampal subregions were solubilized in sodium dodecyl sulfate (SDS) sample buffer, electrophoresed on SDS-10% polyacrylamide gels, and transferred to nitrocellulose. PKC was visualized by 125I-protein A autoradiography and quantified by densitometry. The highest concentrations of PKC were found in the CA1 pyramidal cell layer (0.43 +/- 0.04 OD), with the lowest amounts in the CA3 and CA4 pyramidal cell layers (0.11 +/- 0.02 and 0.085 +/- 0.006 OD, respectively). These results demonstrate a simple way of preparing antibodies against domains of PKC. We also describe a procedure for quantifying the relative amounts of PKC in discrete brain regions.
Hamiltonian Simulation by Uniform Spectral Amplification (2017)

The exponential speedups promised by Hamiltonian simulation on a quantum computer depends crucially on structure in both the Hamiltonian $\hat{H}$, and the quantum circuit $\hat{U}$ that encodes its description. In the quest to better approximate time-evolution $e^{-i\hat{H}t}$ with error $ε$, we motivate a systematic approach to understanding and exploiting structure, in a setting where Hamiltonians are encoded as measurement operators of unitary circuits $\hat{U}$ for generalized measurement. This allows us to define a \emph{uniform spectral amplification} problem on this framework for expanding the spectrum of encoded Hamiltonian with exponentially small distortion. We present general solutions to uniform spectral amplification in a hierarchy where factoring $\hat{U}$ into $n=1,2,3$ unitary oracles represents increasing structural knowledge of the encoding. Combined with structural knowledge of the Hamiltonian, specializing these results allow us simulate time-evolution by $d$-sparse Hamiltonians using $\mathcal{O}\left(t(d \|\hat H\|_{\text{max}}\|\hat H\|_{1})^{1/2}\log{(t\|\hat{H}\|/ε)}\right)$ queries, where $\|\hat H\|\le \|\hat H\|_1\le d\|\hat H\|_{\text{max}}$. Up to logarithmic factors, this is a polynomial improvement upon prior art using $\mathcal{O}\left(td\|\hat H\|_{\text{max}}+\frac{\log{(1/ε)}}{\log\log{(1/ε)}}\right)$ or $\mathcal{O}(t^{3/2}(d \|\hat H\|_{\text{max}}\|\hat H\|_{1}\|\hat H\|/ε)^{1/2})$ queries. In the process, we also prove a matching lower bound of $Ω(t(d\|\hat H\|_{\text{max}}\|\hat H\|_{1})^{1/2})$ queries, present a distortion-free generalization of spectral gap amplification, and an amplitude amplification algorithm that performs multiplication on unknown state amplitudes.
Design and performance of a piezoelectric actuated precise rotary positioner (2006)

Industries including semiconductor, biotechnology, and nanotechnology are seeking compact and reliable nanometer resolution positioning techniques. To address this demand, this article presents a friction-drive rotary stage driven by a piezoelectric transducer (PZT) actuator. This stage includes a multilayer PZT actuator, the Scott-Russell mechanism, an actuation stage, a preload spring, and an output shaft. Its rotary positioning is accomplished by the stick-slip effect between the wire electrodischarge-machining rotary stage and the output shaft. Finite element analysis and Taguchi optimization method were extensively conducted to analyze the displacement, stress, and vibration behavior for optimum design. As shown by the experimental results, the stage achieved a resolution of 0.13μrad and a speed of 0.15°∕h by tuning of the preload spring.
Use of a Green Fluorescent Protein as a Marker for Human Immunodeficiency Virus Type 1 Infection (1997)

We constructed a recombinant human immunodeficiency virus type 1 (HIV-1) provirus called R7-GFP that expresses a modified form of a green fluorescent protein (GFP) from the jellyfish Aequorea victoria by substituting GFP-coding sequences for Nef-coding sequences. Alanine was substituted for serine at amino acid position 65 in the modified GFP, resulting in markedly increased fluorescence at an excitation wavelength of 488 nm as compared to wild-type GFP. The replication kinetics of R7-GFP were identical to that measured with an isogenic, nef-negative strain lacking GFP. Expression of GFP by replication-competent HIV-1 allowed simultaneous quantitation of viral infection and cell surface CD4 levels, revealing rapid and nearly complete CD4 downregulation on R7-GFP-infected PBMCs.
Using Augmented Virtuality for Remote Collaboration (2004)

This paper describes the concept, prototypical implementation, and usability evaluation of the Augmented Virtuality (AV)-based videoconferencing (VC) system cAR/PE!. We present a solution that allows three participants at different locations to communicate over a network in an environment simulating a traditional face-to-face meeting. Integrated into the AV environment are live video streams of the participants spatially arranged around a virtual table, a large virtual presentation screen for 2D display and application sharing, and 3D geometry (models) within the room and on top of the table. We describe the general concept and application scenario as well as the actual hardware setup, the implementation, and the use of the system in its current state. Results of two usability studies with 87 subjects are presented that show the general usability of our approach as well as good overall satisfaction. Parts of the work described here were presented as a poster at the second International Symposium on Mixed and Augmented Reality (Regenbrecht, Ott, Wagner, Lum, Kohler, et al., 2003. An Augmented Virtuality Approach to 3D Videoconferencing. Poster at 2nd Int. Symp. on Mixed and Aug. Reality, Tokyo.).