gebhart/patrepeval huggingface dataset:
Postconditioning attenuates myocardial ischemia–reperfusion injury by inhibiting events in the early minutes of reperfusion (2004)

(1) Post-con at onset of R reduces myocardial injury; (2) cardioprotection may be mediated, in part, by inhibiting oxidant generation and oxidant mediated injury; (3) the first minute of R in the rat model is critical to cardioprotection by Post-con; and (4) cardioprotection by Post-con may be independent of neutrophil accumulation in AAR. *p<0.05 Post-con vs. Control.
Cholecystokinin Tetrapeptide Induces Panic-like Attacks in Healthy Volunteers (1989)

A total of 31 intravenous injections of the tetrapeptide cholecystokinin (30-33) were carried out in ten healthy subjects. In seven subjects, cholecystokinin-4 provoked a short-lasting (one to four minutes) panic-like attack (an intense unexplainable fear) at doses between 20 and 100 micrograms. In the other three subjects, doses of 80 to 100 micrograms induced severe anxiety, but no panic-like attack. All subjects experienced severe gastrointestinal symptoms. Pretreatment with lorazepam, but not with meprobamate or naloxone, prevented the psychic effects of cholecystokinin-4 in subjects who had experienced a panic-like attack with the same dose of this peptide. Following the peptide injection, levels of plasma free catecholamines, lactate, and glucose were unchanged, whereas levels of plasma cortisol and prolactin were increased. The intravenous injection of the sulfated cholecystokinin octapeptide (26-33) in two subjects (doses of 35 and 40 micrograms, respectively) produced severe gastrointestinal symptoms, but failed to induce any anxiety or panic-like attacks. These preliminary findings suggest that cholecystokinin-4 may have a panic-inducing effect. It remains to be established if this peptide exerts this effect via a direct activation of central cholecystokinin receptors.
Full field automated photoelasticity using two-load-step method (2001)

A new two-load-step approach to the phase-shifting method is presented for the full field determination of both isoclinic and isochro- matic parameters in photoelasticity. The ambiguity that exists in the phase-shifting photoelasticity is overcome by investigating the relation- ships between the phase retardation introduced by two different load steps. The isoclinic angle is automatically determined in the correct range (2p/2, p/2) and the isochromatic parameter is therefore obtained unambiguously. The results obtained from a bending test and an irregu- lar specimen subjected to multiple forces demonstrate the effectiveness of this method. Compared with the load-stepped method (Ekman and Nurse, 1998) or the three-load method (Asundi et al., 2000), this new algorithm is a simpler approach and is easier to execute. © 2001 Society of
TNF-α: A Paradigm of Paradox and Complexity in Multiple Sclerosis and its Animal Models (2010)

TNF-� (tumour necrosis factor-� ) is a pleiotropic cytokine with wide-ranging actions on the immune system and is an important mediator in immune-mediated inflammatory disease states, including multiple sclerosis. TNF-� and its receptors are part of a large and complex superfamily of homologous ligands and receptors, whose many biological func- tions overlap. Investigations have demonstrated the effects of TNF-� at various stages of pathology in multiple sclerosis (MS), including oligodendrocyte death, demyelination, immune cell trafficking, cellular proliferation and major histo- compatibility (MHC) antigen expression. Targeting the TNF-� immunobiological pathway successfully ameliorates dis- ease severity in a number of autoimmune inflammatory conditions except for multiple sclerosis. Anti-TNF-� therapy in experimental autoimmune encephalomyelitis (EAE) showed mixed results, whereas in MS trials it was deleterious. It is clear that TNF-� also has a beneficial role, especially in neuroprotection and regeneration. A clearer understanding of the protective role of TNF-� may be extrapolated from studies in other inflammatory conditions such as stroke and traumatic brain injury.
Amphipathic alpha-helical structure does not predict the ability of receptor-derived synthetic peptides to interact with guanine nucleotide-binding regulatory proteins. (1993)

In guanine nucleotide-binding regulatory protein- (G protein) coupled receptors, an amphipathic alpha-helix has been postulated to be the common structural determinant in the NH2- and COOH-terminal portions of the third intracellular loop representing the major interaction site with the G proteins. Here we assessed the ability of six peptides derived from these sites of the human dopamine D1-, D2-, and beta 1-adrenergic receptors to either activate G proteins directly or to uncouple the activity of their respective receptors in a native membrane environment. In addition, the cross-reactivity was analyzed. Nonspecific effects occurring at high concentrations were differentiated from G protein-specific effects. The peptide D2N derived from the NH2-terminal part of the third intracellular loop of the dopamine D2 receptor was the only one capable of specifically reversing the action of its receptor, the dopamine-mediated inhibition of the adenylyl cyclase. Furthermore, only D2N stimulated pertussis toxin-sensitive G proteins. However, D2N as the only peptide exhibiting specific effects did not exhibit the predicted amphipathic alpha-helix observed for mastoparan (Higashijima, T., Burnier, J., and Ross, E. M. (1990) J. Biol. Chem. 265, 14176-14186) as demonstrated by circular dichroism spectroscopy. In contrast, a peptide for which a certain degree of helicality was verified spectroscopically (D1C) was neither active in GTPase and adenylyl cyclase determinations, nor did it block the receptor-mediated cyclase activation. Hence, the amphipathic alpha-helix does not represent the main structural determinant for the receptor-G protein interaction site.
An Application of Convolutional Neural Networks for Automatic Inspection (2006)

Automatic inspection in today's manufacturing is critical to be competitive. In this paper, experimental results from the application of digital filters for defects detection in paper pulp production are shown. These filters have been automatically generated by means of a convolutional neural architecture, that uses a modified back-propagation algorithm. The main subjects discussed are: convolutional top-down spiral architecture, a tool used to automatically generate digital filters, a simple but effective modification to the back-propagation algorithm for this application, and experimental results
Local Fas/APO‐1 (CD95) ligand‐mediated tumor cell killing in vivo (1995)

Fas/APO-1 (CD95) is a cell surface receptor which mediates apoptosis when ligated by specific antibodies or by its recently cloned natural ligand, FasL. We have studied the cytotoxic potential of FasL in vivo using Fas/APO-1-expressing Yac-1 cells as targets. Supernatant harvested from Neuro-2a cells transfected with the murine FasL cDNA contains FasL and transduces a potent apoptotic signal to Yac-1 cells in vitro. Specificity of FasL-mediated cytotoxicity was confirmed by competition assays using soluble Fas or anti-Fas/APO-1 F(ab')2 fragments which specifically interfere with FasL-Fas/APO-1 interactions. Intraperitoneal injection of FasL-containing supernatant efficiently killed Yac-1 target cells which had been implanted in capsules into the peritoneal cavity of mice. Analysis of the target cells revealed DNA fragmentation and nuclear changes typical of apoptosis. As previously shown, intraperitoneal injection of anti-Fas/APO-1 antibodies caused liver failure (Ogasawara, J., Watanabe, F.R., Adachi, M., Matsuzawa, A., Kasugai, T., Kitamura, Y., Itoh, N., Suda, T. and Nagata, S., Nature 1993. 364:806) and was observed at doses which did not reduce Yac-1 cell viability. In contrast, FasL did not induce histopathology in the liver when applied intraperitoneally at doses cytotoxic for Yac-1 cells. However, intravenous administration of FasL induced lethal liver hemorrhages and hepatocyte apoptosis. Thus, locally applied FasL kills tumor cells very efficiently without systemic toxicity and may therefore represent a candidate for local tumor treatment.
Integrating Topics and Syntax (2004)

Statistical approaches to language learning typically focus on either short-range syntactic dependencies or long-range semantic dependencies between words. We present a generative model that uses both kinds of dependencies, and can be used to simultaneously find syntactic classes and semantic topics despite having no representation of syntax or semantics beyond statistical dependency. This model is competitive on tasks like part-of-speech tagging and document classification with models that exclusively use short- and long-range dependencies respectively. 1
Probing Native Protein Structures by Chemical Cross-linking, Mass Spectrometry, and Bioinformatics (2010)

Chemical cross-linking of reactive groups in native proteins and protein complexes in combination with the identification of cross-linked sites by mass spectrometry has been in use for more than a decade. Recent advances in instrumentation, cross-linking protocols, and analysis software have led to a renewed interest in this technique, which promises to provide important information about native protein structure and the topology of protein complexes. In this article, we discuss the critical steps of chemical cross-linking and its implications for (structural) biology: reagent design and cross-linking protocols, separation and mass spectrometric analysis of cross-linked samples, dedicated software for data analysis, and the use of cross-linking data for computational modeling. Finally, the impact of protein cross-linking on various biological disciplines is highlighted.
Localization and characterization of the gene encoding release factor RF3 in Escherichia coli. (1994)

Two protein release factors (RFs) showing codon specificity, RF1 and RF2, are known to be required for polypeptide chain termination in Escherichia coli. A third protein component has also been described that stimulates termination in vitro, but it has remained uncertain whether this protein, RF3, participates in termination in vivo or is essential to cell growth. We report (i) the purification and N-terminal sequencing of RF3; (ii) the isolation of transposon insertion mutants similar to miaD, a suppressor of a leaky UAA mutation affecting the gene miaA, leading to enhanced nonsense suppression; (iii) the localization of the affected gene on the physical map of the chromosome; and (iv) the cloning and sequencing of the wild-type gene, providing proof that it encodes the factor RF3. We designate the gene prfC. Two transposon insertions were shown to interrupt the coding sequence of prfC, at codons 287 and 426. The enhanced nonsense suppression in the insertion mutants shows that the product participates in termination in vivo. The isolation of such mutants strongly suggests that the gene product is not essential to cell viability, though cell growth is affected. RF3 is a protein with a molecular weight of 59,460 containing 528 amino acids and displays much similarity to elongation factor EF-G, a GTP binding protein necessary for ribosomal translocation, and other GTP binding proteins known or thought to interact with the ribosome.
Scanning magnetoresistance microscopy (1996)

We have developed a new scanning magnetic microscopy which uses commercial magnetoresistive (MR) record/playback heads as sense probes. Two-dimensional magnetic images are constructed by bringing the MR head into physical contact with the sample, and then acquiring MR voltage while the head is raster scanned using a high resolution (∼1 nm), linearized positioning stage. With currently available MR heads, an upper bound on the spatial resolution is 0.1×2.0 μm. This technique has broad applications beyond the magnetic storage media for which these heads were designed. In addition to magnetic imaging, this instrument can also be used to evaluate contact record and playback processes.
6-DoF Haptic Rendering Using Continuous Collision Detection between Points and Signed Distance Fields (2016)

We present an algorithm for fast continuous collision detection between points and signed distance fields, and demonstrate how to robustly use it for 6-DoF haptic rendering of contact between objects with complex geometry. Continuous collision detection is often needed in computer animation, haptics, and virtual reality applications, but has so far only been investigated for polygon (triangular) geometry representations. We demonstrate how to robustly and continuously detect intersections between points and level sets of the signed distance field. We suggest using an octree subdivision of the distance field for fast traversal of distance field cells. We also give a method to resolve continuous collisions between point clouds organized into a tree hierarchy and a signed distance field, enabling rendering of contact between rigid objects with complex geometry. We investigate and compare two 6-DoF haptic rendering methods now applicable to point-versus-distance field contact for the first time: continuous integration of penalty forces, and a constraint-based method. An experimental comparison to discrete collision detection demonstrates that the continuous method is more robust and can correctly resolve collisions even under high velocities and during complex contact.
An Empirical Evaluation of Some Articulatory and Cognitive Aspects of Marking Menus (1993)

We describe marking menus, an extension of pie menus, which are well suited for stylus-based interfaces. Pie menus are circular menus subdivided into sectors, each of which might correspond to a different command. One moves the cursor from the center of the pie into the desired sector. Marking menus are invisible pie menus in which the movement of the cursor during a selection leaves an "ink trail" similar to a pen stroke on paper. The combination of a pie menu and a marking menu supports an efficient transition from novice to expert performance. Novices can "pop-up" a pie menu and make a selection, whereas experts can simply make the corresponding mark without waiting for the menu to appear. This article describes an experiment in which we explored both articulatory and cognitive aspects of marking menus for different numbers of items per menu and using different input devices (mouse, trackball, and stylus). The articulatory aspects are how well subjects could execute the physical actions necessary to select from pie marking menus. Articulatory aspects were investigated by presenting one group of subjects with the task of selecting from fully visible menus. Because one feature of marking menus is that users should be able to select from them without seeing the menus (by making a mark), we also ran two groups of subjects with invisible pie menus: one group with an ink trail and one without. These subjects were therefore faced with the task of either mentally representing the menu or associating marks with the commands they invoked through practice. These then are the cognitive aspects to which we refer. Our results indicate that subjects' performance degraded as the number of items increased. When menus were hidden, however, subjects performance did not degrade as rapidly when menus contained even numbers of items. We also found subjects performed better with the mouse and stylus than with the trackball.
Effect of Anular Repair on the Healing Strength of the Intervertebral Disc (2000)

Direct repair of anular incisions in the lumbar spine does not significantly alter the healing strength of the intervertebral disc after lumbar discectomy.
Logistic Regression Models (2009)

Logistic Regression Models presents an overview of the full range of logistic models, including binary, proportional, ordered, partially ordered, and unordered categorical response regression procedures. Other topics discussed include panel, survey, skewed, penalized, and exact logistic models. The text illustrates how to apply the various models t
Entangling flux qubits with a bipolar dynamic inductance (2004)

We propose a scheme to implement controllable coupling between two flux qubits using the screening current response of a dc superconducting quantum interference device (SQUID). The coupling strength is adjusted by the current bias applied to the SQUID and can be varied continuously from positive to negative values, allowing cancellation of the direct mutual inductance between the qubits. We show that this variable coupling scheme permits efficient realization of universal quantum logic. The same SQUID can be used to determine the flux states of the qubits.
Protein folding in the bacterial periplasm (1997)

Free access1 April 1997 Share on Protein folding in the bacterial periplasmAuthors: D Missiakas, S RainaAuthors Info & AffiliationsDOI: https://doi.org/10.1128/jb.179.8.2465-2471.1997 PDF/EPUB
Aminocyclopropenium Ions: Synthesis, Properties, and Applications (2013)

This review covers the preparation, physical properties, and applications of cyclopropenium ions bearing one, two, or three amino substituents. It provides a description of the most reliable methods to access these unique structures as well as a discussion of the reactivity profiles of the common subtypes. 1 Introduction 2 Preparation 3 Properties 3.1 Stability 3.2 Redox Behavior 3.3 Ion Pair Strain 4 Reactions 5 Applications 5.1 Ionic Liquids 5.2 Metal Complexes 5.2.1 TDAC π-Complexes 5.2.2 BDAC σ-Complexes 5.2.3 Cyclopropenimine Ligands 5.2.4 BDAC–Phosphorus Ligands 5.3 Brønsted Bases 6 Conclusion
A Comparison of the Performance and Application Differences Between Manual and Automated Patch-Clamp Techniques (2012)

The patch clamp technique is commonly used in electrophysiological experiments and offers direct insight into ion channel properties through the characterization of ion channel activity. This technique can be used to elucidate the interaction between a drug and a specific ion channel at different conformational states to understand the ion channel modulators' mechanisms. The patch clamp technique is regarded as a gold standard for ion channel research; however, it suffers from low throughput and high personnel costs. In the last decade, the development of several automated electrophysiology platforms has greatly increased the screen throughput of whole cell electrophysiological recordings. New advancements in the automated patch clamp systems have aimed to provide high data quality, high content, and high throughput. However, due to the limitations noted above, automated patch clamp systems are not capable of replacing manual patch clamp systems in ion channel research. While automated patch clamp systems are useful for screening large amounts of compounds in cell lines that stably express high levels of ion channels, the manual patch clamp technique is still necessary for studying ion channel properties in some research areas and for specific cell types, including primary cells that have mixed cell types and differentiated cells that derive from induced pluripotent stem cells (iPSCs) or embryonic stem cells (ESCs). Therefore, further improvements in flexibility with regard to cell types and data quality will broaden the applications of the automated patch clamp systems in both academia and industry.
Z39Ig is expressed on macrophages and may mediate inflammatory reactions in arthritis and atherosclerosis (2006)

Z39Ig is a transmembrane protein containing two Ig homology domains with unknown functions. Immunohistochemical analyses of human carotid atherosclerotic plaques detected Z39Ig staining in areas rich in foamy macrophages. Z39Ig staining was also observed in macrophages in the lining layers and sublining areas of rheumatoid arthritis synovium. Z39Ig staining in the osteoarthritis synovium was restricted to macrophages in the lining layers. To identify the role(s) of Z39Ig in the function of macrophages, we used human monocytic cell lines TF-1A (Z39Ig-negative) and THP-1 (Z39Ig-positive). The expression of Z39Ig was induced in TF-1A cells ,when they were differentiated into macrophages by treatment with PMA. The stimulation of PMA-treated TF-1A or THP-1 cells with immobilized anti-Z39Ig mAb induced the secretion of IL-8 and matrix metalloproteinase (MMP)-9, which was dependent on NF-kappaB activation. These data indicate that the macrophage Z39Ig is involved in the pathogenesis of inflammatory diseases through chemokine induction, which will promote the migration of inflammatory cells into the lesion area, and MMP-9 induction, which will contribute to cartilage destruction or extracellular matrix degradation.
Design and Synthesis of Novel Magnetic Core−Shell Polymeric Particles (2008)

A novel synthetic strategy was developed for the preparation of magnetic core-shell (MCS) particles consisting of hydrophobic poly(methyl methacrylate) cores with hydrophilic chitosan shells and gamma-Fe2O3 nanoparticles inside the cores via copolymerization of methyl methacrylate from chitosan in the presence of vinyl-coated gamma-Fe2O3 nanoparticles. The magnetic core-shell particles were characterized with transmission electron microscopy, field-emission scanning electron microscopy, particle size and zeta-potential measurements, vibrating sample magnetometry, and atomic force microscopy, respectively. The MCS particles were less than 200 nm in diameter with a narrow size distribution (polydispersity = 1.09) and had a good colloidal stability (critical coagulation concentration = 1.2 M NaCl at pH 6.0). Magnetization study of the particles indicated that they exhibited superparamagnetism at room temperature and had a saturation magnetization of 2.7 A m2/kg. The MCS particles were able to form a continuous film on a glass substrate, where magnetic nanoparticles could evenly disperse throughout the film. Thus, these new materials should be extremely useful in various applications.
Some Critics and the Vulgar Error (1965)

Everyone who has ever been enchanted by the writ ten wordâand this surely includes everyone who has ever attempted to teach itâhas given at least a passing thought to the question: Wherein lies the difference be tween the language of poetry and the language of prose?
Formation of adamantan-1-ols by the reactions of adamantanes with 2,3-dichloro-5,6-dicyano-p-benzoquinone (DDQ) in trifluoromethanesulfonic acid (2001)

Adamantanes were treated with DDQ in trifluoromethanesulfonic acid followed by hydrolysis to give adamantan-1-ols in good yields.
Applying 3D seismic in a complex mountainous area of Tarim Basin (2002)

Complex surface and subsurface conditions in China's northern Tarim Basin make it impossible to record good 3D seismic data with conventional acquisition geometry. In addition, the thickness of the low-velocity layer varies from 3 to 150 m, making 3D static corrections a challenge.
Intravascular metabolism of normal and mutant mouse immunoglobulin molecules (1990)

The metabolism of IgG immunoglobulins in the body is tightly regulated in order to maintain their intravascular concentration. Different subclasses may have different intravascular half-lives, and in the mouse, passively administered IgG2b disappears from the circulation more rapidly than IgG2a. We have attempted to localize the sequences in the constant region which are responsible for this difference by examining the intravascular metabolism of mutant immunoglobulins that were generated in tissue culture and have undergone deletions of individual constant region domains or contain different combinations of gamma 2b and gamma 2a CH2 and CH3 domains. Our results suggest that the regulation of intravascular metabolism is complex but indicate that sequences in the CH3 domain are important in determining the different intravascular half-lives of IgG2b and IgG2a antibodies in the mouse.