gebhart/patrepeval huggingface dataset:
ATOM: a flexible interface for building high performance program analysis tools (1995)

Code instrumentation is a powerful mechanism for understanding program behavior. Unfortunately, code instrumentation is extremely difficult, and therefore has been mostly relegated to building special purpose tools for use on standard industry benchmark suites.

ATOM (Analysis Tools with OM) provides a very flexible and efficient code instrumentation interface that allows powerful, high performance program analysis tools to be built with very little effort. This paper illustrates this flexibility by building five complete tools that span the interests of application programmers, computer architects, and compiler writers.

This flexibility does not come at the expense of performance. Because ATOM uses procedure calls as the interface between the application and the analysis routines, the performance of each tool is similar to or greatly exceeds the best known hand-crafted implementations.
Chondroitinase ABC (Pharmaceutical Grade) for Chemonucleolysis (1996)

In agreement with the current literature, these observations indicate that chondroitinase ABC is safe regarding adverse effects on nerve tissue and blood vessels. The slight reduction in conduction velocity after intrathecal injection of chondroitinase ABC or its vehicle is most likely the result of surgical injury while releasing the nerve roots from the intrathecal fibrous adhesions. Such adhesions may be related to the laminectomy per se, and probably have no pathophysiologic significance.
Fluorescence Quenching of Green Fluorescent Protein during Denaturation by Guanidine (2005)

Fluorescence of green fluorescent protein mutant, 2-5 GFP is observed during denaturation by guanidine. The fluorescence intensity decreases exponentially but the fluorescence lifetime does not change during denaturation. The fluorescence lifetime of the denatured protein is shorter than that of native form. As the protein structure is modified by guanidine, solvent water molecules penetrate into the protein barrel and protonate the chromophore to quench fluorescence. Most fluorescence quenchers do not affect the fluorescence of native form but accelerate the fluorescence intensity decay during denaturation. Based on the observations, a simple model is suggested for the structural change of the protein molecule during denaturation.
Rig animation with a tangible and modular input device (2016)

We propose a novel approach to digital character animation, combining the benefits of tangible input devices and sophisticated rig animation algorithms. A symbiotic software and hardware approach facilitates the animation process for novice and expert users alike. We overcome limitations inherent to all previous tangible devices by allowing users to directly control complex rigs using only a small set (5-10) of physical controls. This avoids oversimplification of the pose space and excessively bulky device configurations. Our algorithm derives a small device configuration from complex character rigs, often containing hundreds of degrees of freedom, and a set of sparse sample poses. Importantly, only the most influential degrees of freedom are controlled directly, yet detailed motion is preserved based on a pose interpolation technique. We designed a modular collection of joints and splitters, which can be assembled to represent a wide variety of skeletons. Each joint piece combines a universal joint and two twisting elements, allowing to accurately sense its configuration. The mechanical design provides a smooth inverse kinematics-like user experience and is not prone to gimbal locking. We integrate our method with the professional 3D software Autodesk Maya ® and discuss a variety of results created with characters available online. Comparative user experiments show significant improvements over the closest state-of-the-art in terms of accuracy and time in a keyframe posing task.
EXPRESSION OF CLASS II MAJOR HISTOCOMPATIBILITY ANTIGENS BY KERATINOCYTES IN CUTANEOUS T CELL LYMPHOMA (1994)

There was no apparent correlation between class II MHC antigen expression and the clinical stage of disease, the type of CTCL skin lesion, or the overall density of the lesional T cell infiltrate. The hierarchy of keratinocyte class II MHC antigen expression observed in this study paralleled that noted in earlier studies of cultured keratinocytes exposed to recombinant interferon-gamma in vitro. This suggests that lesional cytokine levels may be the critical factor governing class II MHC antigen expression by lesional keratinocytes in CTCL.
Mutation in the key enzyme of sialic acid biosynthesis causes severe glomerular proteinuria and is rescued by N-acetylmannosamine (2007)

Mutations in the key enzyme of sialic acid biosynthesis, uridine diphospho-N-acetylglucosamine 2-epimerase/N-acetylmannosamine (ManNAc) kinase (GNE/MNK), result in hereditary inclusion body myopathy (HIBM), an adult-onset, progressive neuromuscular disorder. We created knockin mice harboring the M712T Gne/Mnk mutation. Homozygous mutant (Gne(M712T/M712T)) mice did not survive beyond P3. At P2, significantly decreased Gne-epimerase activity was observed in Gne(M712T/M712T) muscle, but no myopathic features were apparent. Rather, homozygous mutant mice had glomerular hematuria, proteinuria, and podocytopathy. Renal findings included segmental splitting of the glomerular basement membrane, effacement of podocyte foot processes, and reduced sialylation of the major podocyte sialoprotein, podocalyxin. ManNAc administration yielded survival beyond P3 in 43% of the Gne(M712T/M712T) pups. Survivors exhibited improved renal histology, increased sialylation of podocalyxin, and increased Gne/Mnk protein expression and Gne-epimerase activities. These findings establish this Gne(M712T/M712T) knockin mouse as what we believe to be the first genetic model of podocyte injury and segmental glomerular basement membrane splitting due to hyposialylation. The results also support evaluation of ManNAc as a treatment not only for HIBM but also for renal disorders involving proteinuria and hematuria due to podocytopathy and/or segmental splitting of the glomerular basement membrane.
A separability framework for analyzing community structure (2014)

Four major factors govern the intricacies of community extraction in networks: (1) the literature offers a multitude of disparate community detection algorithms whose output exhibits high structural variability across the collection, (2) communities identified by algorithms may differ structurally from real communities that arise in practice, (3) there is no consensus characterizing how to discriminate communities from noncommunities, and (4) the application domain includes a wide variety of networks of fundamentally different natures. In this article, we present a class separability framework to tackle these challenges through a comprehensive analysis of community properties. Our approach enables the assessment of the structural dissimilarity among the output of multiple community detection algorithms and between the output of algorithms and communities that arise in practice. In addition, our method provides us with a way to organize the vast collection of community detection algorithms by grouping those that behave similarly. Finally, we identify the most discriminative graph-theoretical properties of community signature and the small subset of properties that account for most of the biases of the different community detection algorithms. We illustrate our approach with an experimental analysis, which reveals nuances of the structure of real and extracted communities. In our experiments, we furnish our framework with the output of 10 different community detection procedures, representative of categories of popular algorithms available in the literature, applied to a diverse collection of large-scale real network datasets whose domains span biology, online shopping, and social systems. We also analyze communities identified by annotations that accompany the data, which reflect exemplar communities in various domain. We characterize these communities using a broad spectrum of community properties to produce the different structural classes. As our experiments show that community structure is not a universal concept, our framework enables an informed choice of the most suitable community detection method for identifying communities of a specific type in a given network and allows for a comparison of existing community detection algorithms while guiding the design of new ones.
Mode of action of bradycardic agent, S 16257, on ionic currents of rabbit sinoatrial node cells (1996)

1. The effect of the bradycardic agent S 16257 on the main ionic mechanisms of diastolic depolarization in sinoatrial node cells isolated from rabbit heart, was investigated by the patch-clamp technique in whole-cell and macro-patch recordings. 2. In whole-cell conditions, S 16257 induced a marked exponential use-dependent blockade of the hyperpolarization-activated I(f) current, without shift of the voltage range of its activation curve. The rate of block increased with the drug concentration. The IC50 for the block of I(f) was 2.8 x 10(-6) M. 3. A similar use-dependent decline of I(f) was obtained with 3 microM S 16257, in cell-attached and in inside out macro-patch configurations, suggesting that the bradycardic agent interacts with I(f) channels from the inside of the cell. 4. A high concentration of S 16257 (10 microM) had no detectable effect on T-type calcium current and slightly decreased L-type calcium current (-18.12 +/- 0.66%), without significant use-dependent blockade. 5. S 16257 had no effect on the delayed outward potassium current Ik at 3 microM and slightly decreased it only at high concentrations, -16.3 +/- 1.2% at 10 microM. In contrast, zatebradine, another bradycardic agent, reduced I k by 20.3 +/- 2.5% at 3 microM. 6. In conclusion, S 16257 may lower heart rate without significant negative inotropic action. In comparison with zatebradine, S 16257 had less effect on Ik suggesting less prolongation of repolarization time.
Protective Effect of Different Anti-Rabies Virus VHH Constructs against Rabies Disease in Mice (2014)

Rabies virus causes lethal brain infection in about 61000 people per year. Each year, tens of thousands of people receive anti-rabies prophylaxis with plasma-derived immunoglobulins and vaccine soon after exposure. Anti-rabies immunoglobulins are however expensive and have limited availability. VHH are the smallest antigen-binding functional fragments of camelid heavy chain antibodies, also called Nanobodies. The therapeutic potential of anti-rabies VHH was examined in a mouse model using intranasal challenge with a lethal dose of rabies virus. Anti-rabies VHH were administered directly into the brain or systemically, by intraperitoneal injection, 24 hours after virus challenge. Anti-rabies VHH were able to significantly prolong survival or even completely rescue mice from disease. The therapeutic effect depended on the dose, affinity and brain and plasma half-life of the VHH construct. Increasing the affinity by combining two VHH with a glycine-serine linker into bivalent or biparatopic constructs, increased the neutralizing potency to the picomolar range. Upon direct intracerebral administration, a dose as low as 33 µg of the biparatopic Rab-E8/H7 was still able to establish an anti-rabies effect. The effect of systemic treatment was significantly improved by increasing the half-life of Rab-E8/H7 through linkage with a third VHH targeted against albumin. Intraperitoneal treatment with 1.5 mg (2505 IU, 1 ml) of anti-albumin Rab-E8/H7 prolonged the median survival time from 9 to 15 days and completely rescued 43% of mice. For comparison, intraperitoneal treatment with the highest available dose of human anti-rabies immunoglobulins (65 mg, 111 IU, 1 ml) only prolonged survival by 2 days, without rescue. Overall, the therapeutic benefit seemed well correlated with the time of brain exposure and the plasma half-life of the used VHH construct. These results, together with the ease-of-production and superior thermal stability, render anti-rabies VHH into valuable candidates for development of alternative post exposure treatment drugs against rabies.
Classification of multiple cancer types by multicategory support vector machines using gene expression data (2003)

http://www.stat.ohio-state.edu/~yklee/msvm.htm
All-optical Analogue-to-digital Conversion with bitwise signal allocation using a spatial coding method for 3bit grey code (2006)

We propose and demonstrate an all-optical analogue-to-digital conversion with bitwise signal allocation using spatial coding method. It enables to output each bit of a digital signal to a different detector. Preliminary experimental results show that 8-levels analogue signals can be successfully converted into corresponding 3-bit grey codes.
Sulfonamidoglycosylation of glycals. A route to oligosaccharides with 2-aminohexose subunits (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSulfonamidoglycosylation of glycals. A route to oligosaccharides with 2-aminohexose subunitsDavid A. Griffith and Samuel J. DanishefskyCite this: J. Am. Chem. Soc. 1990, 112, 15, 5811–5819Publication Date (Print):July 1, 1990Publication History Published online1 May 2002Published inissue 1 July 1990https://pubs.acs.org/doi/10.1021/ja00171a021https://doi.org/10.1021/ja00171a021research-articleACS PublicationsRequest reuse permissionsArticle Views1293Altmetric-Citations190LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Label-free photoacoustic ophthalmic angiography (2009)

We present label-free functional photoacoustic imaging of the ocular microvasculature in living animals. The anterior segment of an adult mouse was imaged with a laser exposure level well within the American National Standards Institute safety standards. Individual red blood cells traveling along the iris capillaries were clearly resolved, and the hemoglobin oxygen saturation in the iris microvasculature was imaged spectrally. We believe that photoacoustic imaging has the potential to advance the diagnosis and treatment of ocular diseases in humans.
Laboratory services in the context of health care in the 1990's. (1995)

Third in a series of articles on the Clinical Laboratory of the Future, this paper explores the trends affecting the human dimension of laboratory services. The role of the medical laboratory technologist will change along a number of predictable trends over the next five years. Each of these trends is discussed in light of the adjustments to be made over the next five years.
Glycosylation of human IgG antibodies: Relevance to therapeutic applications (2002)

Recent experiences of the bio-pharmaceutical industry illustrate the importance of glycosylation fidelity to the function and pharmokinetics of recombinant glycoproteins. The challenge for in vitro production is considerable since species and tissue specificity is observed for the glycoform(s) of antibody molecules produced in vivo. For recombinant IgG antibody molecules that are intended as therapeutics the challenge is further heightened by the considerable glycoform heterogeneity observed for normal polyclonal IgG and associated variations in biologic function. It is essential, therefore, to demonstrate control over the glycosylation process in the production of recombinant antibodies, produced in vitro (CHO cells etc.) or in vivo (transgenics).
The Insulin-Specific T Cells of Nonobese Diabetic Mice Recognize a Weak MHC-Binding Segment in More Than One Form (2007)

Several naturally occurring anti-insulin CD4 T cells were isolated from islet infiltrates of NOD mice. In accordance with the results of others, these T cells recognized the segment of the beta-chain from residues 9-23. Peptides encompassing the B:(9-23) sequence bound weakly to I-Ag7 in two main contiguous registers in which two residues at the carboxyl end, P20Gly and P21Glu, influenced binding and T cell reactivity. Naturally occurring insulin-reactive T cells exhibited differing reactivities with the carboxyl-terminal amino acids, although various single residue changes in either the flanks or the core segments affected T cell responses. The insulin peptides represent another example of a weak MHC-binding ligand that is highly immunogenic, giving rise to distinct populations of autoimmune T cells.
Sympathetic Innervation of Human Mesenteric Artery and Vein (2008)

It is suggested that in humans with an upright stance, the mesenteric venous system plays a particularly important role in controlling mesenteric capacitance, which is reflected by their dense innervation. It is speculated that transmitters released from perivascular nerves supplying the human mesenteric arteries may play a long-term (trophic) role in addition to short-term signalling roles.
Supramolecular Origins of Product Selectivity for Methanol-to-Olefin Catalysis on HSAPO-34 (2001)

Ethylene selectivity in methanol-to-olefin (MTO) catalysis is related to the number of methyl groups on benzene rings trapped in the nanocages of the preferred catalyst HSAPO-34. By correlating the time evolutions of the catalysts' 13C NMR spectra and the volatile product distribution following abrupt cessation of methanol flow, we discovered that (in the absence of other adsorbates) propene is favored by methylbenzenes with four to six methyl groups but ethylene is predominant from those with two or three methyl groups. We substantially increased ethylene selectivity by operating at lower methanol partial pressures or higher temperatures, either of which reduces the steady-state average methyl substitution. As a step toward a kinetic analysis of the MTO reaction on HSAPO-34, we treated each nanocage with a methylbenzene molecule as a supramolecule capable of unimolecular dissociation into ethylene or propene and a less highly substituted methylbenzene. Addition of a water molecule to a nanocage containing a methylbenzene produces a distinct supramolecule with unique properties. Indeed, co-feeding water with methanol significantly increased the average number of methyl groups per ring at steady state relative to identical conditions without additional water, and also increased ethylene selectivity, apparently through transition state shape selectivity.
Ketomethylene pseudopeptide analogs of substance P: synthesis and biological activity (1986)

Two pseudopeptide analogues [Bz-(RS)Phe8 psi (COCH2)Gly9]SP8-11 (I) and [pGlu6,(RS)Phe8 psi (COCH2)Gly9]SP6-11 (II) of the substance P related C-terminal hexapeptide [pGlu6]SP6-11 were prepared as follows. The pseudodipeptidic unit H(RS)Phe psi (COCH2)GlyOH was synthesized by using a modified Dakin-West reaction between Bz-Phe-OH and monomethyl succinoyl chloride. The N alpha-protected pseudopeptidic unit was then incorporated into the appropriate peptide by using various coupling methods. The two pseudopeptide analogues were purified, characterized, and tested for their biological activity and inhibitory effect on SP degrading enzymes. Analogue II was a full agonist contracting the isolated guinea pig ileum with a potency of 70% compared to the parent hexapeptide [pGlu6]SP6-11. It was also a potent inhibitor of SP degrading activity in rat diencephalon membranes with a Ki of 20 microM whereas analogue I was a weak inhibitor.
Three-dimensional localization precision of the double-helix point spread function versus astigmatism and biplane (2010)

Wide-field microscopy with a double-helix point spread function (DH-PSF) provides three-dimensional (3D) position information beyond the optical diffraction limit. We compare the theoretical localization precision for an unbiased estimator of the DH-PSF to that for 3D localization by astigmatic and biplane imaging using Fisher information analysis including pixelation and varying levels of background. The DH-PSF results in almost constant localization precision in all three dimensions for a 2 μm thick depth of field while astigmatism and biplane improve the axial localization precision over smaller axial ranges. For high signal-to-background ratio, the DH-PSF on average achieves better localization precision.
Gas Purification and Measurement at the PPT Level (1991)

Impurity levels in the low parts‐per‐trillion (ppt) are possible to measure by atmospheric pressure ionization mass spectrometry. These impurity levels are achieved by the use of getter‐based point‐of‐use purifiers for argon and nitrogen over a wide range of operating conditions, including room temperature operation. At these low impurity levels, the necessity for using ultraclean technology principles, such as all‐metal construction, the elimination of dead zones, and the reduction of outgassing by the use of techniques such as oxygen passivation, is clearly demonstrated, especially to achieve moisture levels near the 100 ppt range.
Artificial Enzymes (1996)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTArtificial EnzymesYukito Murakami, Jun-ichi Kikuchi, Yoshio Hisaeda, and Osamu HayashidaView Author Information Department of Chemical Science and Technology, Faculty of Engineering, Kyushu University and Institute for Fundamental Research in Organic Chemistry, Kyushu University, Fukuoka 812-81, Japan Cite this: Chem. Rev. 1996, 96, 2, 721–758Publication Date (Web):March 28, 1996Publication History Received20 July 1995Revised20 November 1995Published online28 March 1996Published inissue 1 January 1996https://pubs.acs.org/doi/10.1021/cr9403704https://doi.org/10.1021/cr9403704research-articleACS PublicationsRequest reuse permissionsArticle Views7724Altmetric-Citations638LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Hydrophobicity,Ions,Organic compounds,Peptides and proteins,Vesicles Get e-Alerts