gebhart/patrepeval huggingface dataset:
Inorganic pyrophosphate-phosphohydrolytic activity associated with rat osseous plate alkaline phosphatase. (1998)

Purified membrane-bound alkaline phosphatase from rat osseous plate hydrolyzed pyrophosphate in the presence of magnesium ions, with a specific activity of 92.7 U/mg. Optimal apparent pH for pyrophosphatase activity was 8.0 and it remained unchanged on increasing the pyrophosphate concentration. In the absence of magnesium ions the enzyme had a Km = 88 microM and V = 36.7 U/mg for pyrophosphate and no inhibition by excess substrate was observed. Pyrophosphatase activity was rapidly destroyed at temperatures above 40 degrees C, but magnesium ions apparently protected the enzyme against denaturation. Sodium metavanadate (Ki = 1.0 mM) was a competitive inhibitor of pyrophosphatase activity, while levamisole (Ki = 8.2 mM) and theophylline (Ki = 7.4 mM) were uncompetitive inhibitors. Magnesium ions (K0.5 = 1.7 microM) stimulated pyrophosphatase activity, while cobalt (Ki = 48.5 microM) and zinc (Ki = 22.0 microM) ions were non-competitive inhibitors. Manganese and calcium ions had no effect on pyrophosphatase activity. The Mw of the pyrophosphatase protein was 130 kDa by gel filtration, but a value of 65 kDa was obtained by dissociative gel electrophoresis, suggesting that it was a dimer of apparently identical subunits. These results suggested that pyrophosphatase activity stems from the membrane-bound osseous plate alkaline phosphatase and not from a different protein.
Kinetic Investigation of Chemokine Truncation by CD26/Dipeptidyl Peptidase IV Reveals a Striking Selectivity within the Chemokine Family (2001)

Chemokines coordinate many aspects of leukocyte migration. As chemoattractants they play an important role in the innate and acquired immune response. There is good experimental evidence that N-terminal truncation by secreted or cell surface proteases is a way of modulating chemokine action. The localization of CD26/dipeptidyl peptidase IV on cell surfaces and in biological fluids, its primary specificity, and the type of naturally occurring truncated chemokines are consistent with such a function. We determined the steady-state catalytic parameters for a relevant selection of chemokines (CCL3b, CCL5, CCL11, CCL22, CXCL9, CXCL10, CXCL11, and CXCL12) previously reported to alter their chemotactic behavior due to CD26/dipeptidyl peptidase IV-catalyzed truncation. The results reveal a striking selectivity for stromal cell-derived factor-1alpha (CXCL12) and macrophage-derived chemokine (CCL22). The kinetic parameters support the hypothesis that CD26/dipeptidyl peptidase IV contributes to the degradation of certain chemokines in vivo. The data not only provide insight into the selectivity of the enzyme for specific chemokines, but they also contribute to the general understanding of CD26/dipeptidyl peptidase IV secondary substrate specificity.
Synthesis of Partially Modified Retro and Retroinverso ψ[NHCH(CF3)]-Peptides (2000)

[reaction: see text] Asymmetric conjugate additions of chiral alpha-amino esters to chiral 4-CF(3) Michael-acceptors were exploited to prepare a small library of enantiomerically pure partially modified retropeptides having a psi[NHCH(CF(3))] unit as a possible mimic of the classical psi(NHCO) retropeptide unit. Yields were nearly quantitative, and the stereoselectivity, which is controlled mainly by the nitrogen nucleophile, was progressively higher with increasing the steric bulk of the alpha-amino ester side-chain R(1).
Death of peripheral CD8+ T cells in the absence of MHC class I is Fas‐dependent and not blocked by Bcl‐xL (2003)

Productive immune responses require an appropriate environment to support peripheral CD8(+) T cell survival. Although host MHC class I molecules appear to be required for this process, the cellular and molecular requirements have not been comprehensively studied. Using adoptive transfer of 2C/recombinase-activating gene-2 (RAG-2)(-/-) TCR-transgenic T cells, we found that the survival of both naive and effector CD8(+) T cells was dependent upon host expression of the same MHC class I alleles that supported thymic selection. Expression of appropriate MHC class Iby either bone marrow- or non-bone-marrow-derived cells was sufficient, suggesting that professional antigen-presenting cells were not mandatory. In contrast to MHC class I, neither T cell expression of CD28 nor host expression of ICAM-1 was required for peripheral T cell survival. Finally, T cell death in the absence of appropriate host MHC class I was overcome by elimination of Fas signaling but not by overexpression of Bcl-x(L) by CD8(+) T cells. These results suggest that, in the absence of a survival signal provided by engagement of host MHC/self peptide complexes, CD8(+) T cells die via a Fas-dependent, mitochondria-independent pathway.
A fortran language system for mutation‐based software testing (1991)

Abstract Mutation analysis is a powerful technique for testing software systems. The Mothra software testing project uses mutation analysis as the basis for an integrated software testing environment. Mutation analysis requires executing many slightly differing versions of the same program to evaluate the quality of the data used to test the program. The current version of Mothra includes a complete language system that translates a program to be tested into intermediate code so that it and its mutated versions can be executed by an interpreter. In this paper, we discuss some of the unique requirements of a language system used in a mutation‐based testing environment. We then describe how these requirements affected the design and implementation of the Fortran 77 version of the Mothra system. We also describe the intermediate language used by Mothra and the features of the language system that are needed for software testing. The appendices contain a full description of the intermediate language and the mutation operators used by Mothra. The design and implementation techniques that were developed for Mothra are applicable for constructing not just software testing systems, but any type of program analysis system or language system for a special‐purpose application. In particular, we discuss decisions made and techniques developed by the Mothra team that can be useful in such applications as debuggers, program measurement tools, software development environments and other types of program analysis systems.
Interferometric analysis of laser-driven cylindrically focusing shock waves in a thin liquid layer (2016)

Shock waves in condensed matter are of great importance for many areas of science and technology ranging from inertially confined fusion to planetary science and medicine. In laboratory studies of shock waves, there is a need in developing diagnostic techniques capable of measuring parameters of materials under shock with high spatial resolution. Here, time-resolved interferometric imaging is used to study laser-driven focusing shock waves in a thin liquid layer in an all-optical experiment. Shock waves are generated in a 10 µm-thick layer of water by focusing intense picosecond laser pulses into a ring of 95 µm radius. Using a Mach-Zehnder interferometer and time-delayed femtosecond laser pulses, we obtain a series of images tracing the shock wave as it converges at the center of the ring before reemerging as a diverging shock, resulting in the formation of a cavitation bubble. Through quantitative analysis of the interferograms, density profiles of shocked samples are extracted. The experimental geometry used in our study opens prospects for spatially resolved spectroscopic studies of materials under shock compression.
Understanding natural herpes simplex virus immunity to inform next‐generation vaccine design (2016)

Incremental advances in our knowledge of how natural immune control of herpes simplex virus (HSV) develops have yielded insight as to why previous vaccine attempts have only been partially successful, however, our understanding of these pathways, particularly in humans, is still incomplete. Further elucidation of the innate immune events that are responsible for stimulating these effector responses is required to accurately inform vaccine design. An enhanced understanding of the mechanism of action of novel adjuvants will also facilitate the rational choice of adjuvant to optimise such responses. Here we review the reasons for the hitherto partial HSV vaccine success and align these with our current knowledge of how natural HSV immunity develops. In particular, we focus on the innate immune response and the role of dendritic cells in inducing protective T-cell responses and how these pathways might be recapitulated in a vaccine setting.
Phototyping: comprehensive DNA typing for HLA‐A, B, C, DRB1, DRB3, DRB4, DRB5 & DQB1 by PCR with 144 primer mixes utilizing sequence‐specific primers (PCR‐SSP) (1995)

We have developed a single DNA typing method which uses 144 sequence-specific primer (SSP) reactions to simultaneously detect all known HLA-A, B, C, DRB1, DRB3, DRB4, DRB5 and DQB1 specificities in an allele specific or group specific manner using the same method, reagents, PCR parameters and protocols for all loci. The results from this integrated class I & II method can be visualized on a single photographic or electronic image and hence is described as "Phototyping". Phototyping has an overall resolution greater than or equivalent to good serology and results can be obtained in under 3 hours making the method suitable for genotyping potential cadaver donor peripheral blood without serological backup. This in turn produces the potential for reducing cold ischaemia times in renal transplantation as well as the application of prospective matching to cardiac and liver transplantation. The method has capacity to detect new alleles, for example, novel amplification patterns suggestive of 4 new HLA-B alleles have been detected. The Phototyping set has been used as the sole method of HLA typing for over 1010 individuals. Phototyping is not problem-free; deviations from the standard protocol, poor quality DNA and unsuitable PCR machines can result in individual PCR failures or in incorrect assignment of antigens. Approximately 5% of genotypes were repeated (either partially or fully) because of incomplete or equivocal results.
High-precision liquid chromatography-combustion isotope ratio mass spectrometry (1993)

Online liquid chromatography-combustion high-precision carbon isotope ratio mass spectrometry (LCC-IRMS) is demonstrated for the first time with a direct interface to the liquid source. The interface is based on a continuously coated moving wire which facilitates reproducible solvent removal and analyte combustion, followed by drying of the CO2 and admission to the mass spectrometer. Routine precision and accuracy for compounds analyzed with the interface in the flow injection mode is about delta 13CPDB = 0.5/1000 over the range -28 < delta 13CPDB < 83. Precision in the liquid chromatography mode is routinely approximately 1/1000 and is limited by sample size. This system expands the range of online compound-specific isotope ratio analysis (CSIA) to thermally labile and nonvolatile compounds.
A-coord input (2012)

The human hand can naturally coordinate multiple finger joints, and simultaneously tilt, press and roll a pen to write or draw. For this reason, digital pens are now embedded with auxiliary input sensors to capture these actions. Prior research on auxiliary input channels has mainly investigated them in isolation of one another. In this work, we explore the coordinated use of two auxiliary channels, a class of interaction techniques we refer to as a-coord input. Through two separate experiments, we explore the design space of a-coord input. In the first study we identify if users can successfully coordinate two auxiliary channels. We found a strong degree of coordination between channels. In a second experiment, we evaluate the effectiveness of a-coord input in a task with multiple steps, such as multi-parameter selection and manipulation. We find that a-coord input facilitates coordination even with a complex, aforethought sequential task. Overall our results indicate that users can control at least two auxiliary input channels in conjunction which can facilitate a number of common tasks can on the pen.
Scatter factor stimulates migration of vascular endothelium and capillary-like tube formation (1991)

Scatter factors (SFs) are heat- and trypsin-sensitive cytokines secreted by fibroblastic and vascular smooth muscle cell lines which stimulate motility of normal epithelium, carcinoma cells, and vascular endothelium. Human and mouse SFs have been purified and identified as 90 kD heterodimeric proteins consisting of heavy (58 kD) and light (31 kD) disulfide-bonded subunits. Partial amino acid sequence data from SF-derived tryptic peptides indicate marked sequence homology with hepatocyte growth factors, suggesting a common multigene family. In this chapter we describe the regulation by SF of vascular endothelial cell Chemotaxis and chemokinesis; migration from microcarrier beads to flat surfaces; invasion through porous filters coated with reconstituted basement membrane; secretion of plasminogen activator; and in vitro capillary-like tube formation on a basement membrane surface.
Formation characteristics dictate completion design (1990)

Because horizontal drilling is being applied to more and different types of reservoirs, it is becoming apparent that better completion designs are required to optimize production rates, long-term economics, and ultimate producible reserves. This paper discusses the equipment considerations and the benefits of different completion schemes.
CCR6 Regulation of the Actin Cytoskeleton Orchestrates Human Beta Defensin-2- and CCL20-mediated Restitution of Colonic Epithelial Cells (2009)

Intestinal inflammation is exacerbated by defects in the epithelial barrier and subsequent infiltration of microbes and toxins into the underlying mucosa. Production of chemokines and antimicrobial peptides by an intact epithelium provide the first line of defense against invading organisms. In addition to its antimicrobial actions, human beta defensin-2 (HBD2) may also stimulate the migration of dendritic cells through binding the chemokine receptor CCR6. As human colonic epithelium expresses CCR6, we investigated the potential of HBD2 to stimulate intestinal epithelial migration. Using polarized human intestinal Caco2 and T84 cells and non-transformed IEC6 cells, HBD2 was equipotent to CCL20 in stimulating migration. Neutralizing antibodies confirmed HBD2 and CCL20 engagement to CCR6 were sufficient to induce epithelial cell migration. Consistent with restitution, motogenic concentrations of HBD2 and CCL20 did not induce proliferation. Stimulation with those CCR6 ligands leads to calcium mobilization and elevated active RhoA, phosphorylated myosin light chain, and F-actin accumulation. HBD2 and CCL20 were unable to stimulate migration in the presence of either Rho-kinase or phosphoinositide 3-kinase inhibitors or an intracellular calcium chelator. Together, these data indicate that the canonical wound healing regulatory pathway, along with calcium mobilization, regulates CCR6-directed epithelial cell migration. These findings expand the mechanistic role for chemokines and HBD2 in mucosal inflammation to include immunocyte trafficking and killing of microbes with the concomitant activation of restitutive migration and barrier repair.
A computer model of cellular interactions in the immune system (1992)

The power of modern computers allows the modeling and simulation of complex biological systems. The last decade has seen the emergence of a growing number of simulations of the immune system. In this article, Franco Celada and Philip Seiden present a model that, they suggest, is rich enough to allow computer experiments to be used as practical adjuncts to the usual biological experiments, at a saving of cost and time.
Metabolism and chemotherapeutic activity of 9-beta-D-arabinofuranosyl-2-fluoroadenine against murine leukemia L1210 and evidence for its phosphorylation by deoxycytidine kinase. (1980)

The 2-fluoro derivative of 9-beta-D-arabinofuranosyladenine (2-F-ara-A) and its soluble 5'-formate and 5'-phosphate derivatives were therapeutically effective against the parent leukemia L1210 (L1210/0). 2-F-ara-A and 9-beta-D-arabinofuranosyladenine 5'-formate were inactive aginst a 1-beta-D-arabinofuranosylcytosine-resistant subline (L1210/ara-C) that was deficient in deoxycytidine kinase. Deoxycytidine prevented 2-F-ara-A-induced inhibition of proliferation of L1210/0 cells in culture and alleviated 2-F-ara-a inhibition of DNA synthesis. After treatment of mice with 9-beta-D-arabinofuranosyladenine 5'-formate, intracellular levels of the 5'-triphosphate of 9-beta-D-arabinofuranosylfluoroadenine in leukemia cells were more than 10 times higher in L1210/0 cells than in L1210/ara-C cells. Similar results were obtained in this line of leukemia cells from mice treated with the 5'-monophosphate of 9-beta-D-arabinofuranosyl-2-fluoroadenine. Thus, L1210/ara-C cells deficient in deoxycytidine kinase activity were also deficient in capacity to phosphorylate 2-F-ara-A. Kinase activity from L1210/0 cells for deoxycytidine and for 2-F-ara-A coeluted from calcium phosphate cellulose and from diethylaminoethyl cellulose columns and had similar mobility on gel electrophoresis. Deoxyadenosine kinase was clearly separated from deoxycytidine kinase. Deoxycytidine competed with 2-F-ara-A for phosphorylation by the partially purified enzyme from L1210 cells. These results indicate that 2-F-ara-A is phosphorylated to the 5'-monophosphate by deoxycytidine kinase of leukemia L1210 cells.
Superoxide dismutase activities of an iron porphyrin and other iron complexes (1979)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSuperoxide dismutase activities of an iron porphyrin and other iron complexesRobert F. Pasternack and Barry HalliwellCite this: J. Am. Chem. Soc. 1979, 101, 4, 1026–1031Publication Date (Print):February 1, 1979Publication History Published online1 May 2002Published inissue 1 February 1979https://doi.org/10.1021/ja00498a038RIGHTS & PERMISSIONSArticle Views464Altmetric-Citations146LEARN 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 InReddit PDF (729 KB) Get e-Alertsclose Get e-Alerts
The Percentage of n‐3 Highly Unsaturated Fatty Acids in Total HUFA as a Biomarker for Omega‐3 Fatty Acid Status in Tissues (2007)

A blood biomarker of omega-3 fatty acid intake and tissue status could serve as a modifiable risk factor for cardiovascular disease. The percentage of omega-3 highly unsaturated fatty acid (HUFA > or = 20 carbons and > or =3 double bonds) in the total HUFA pool (the n-3 HUFA score) was examined as a potential blood biomarker of omega-3 fatty acids in tissues. The fatty acid composition of total lipid extracts (TLE) and phospholipid (PL) fractions were determined for plasma and erythrocytes samples of human subjects (n = 20) and the n-3 HUFA score and the sum of eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) were compared. Omega-3 fatty acids in blood and tissues of rats (n = 31) and pigs (n = 48) were also determined and the associations were compared. The n-3 HUFA score is more consistent across plasma and erythrocytes, with strong correlations between TLE and PL in plasma (r = 0.93) and erythrocytes (r = 0.94). The n-3 HUFA score was less variable and blood levels correlated strongly with various animal tissues. The n-3 HUFA score is a useful blood biomarker that does not require the isolation of the PL class thereby supporting high throughput analyses. The strength of association between the n-3 HUFA score and disease risk needs to be examined.
Machine Learning for Secure Device Personalization Using Blockchain (2018)

Recently, there is a growing trend towards machine learning models that run on client devices such as smartphones, with constraints such as model size and time. Often, the user data on client devices is considered private and so cannot be uploaded to an external server for processing and running the model. Blockchain provides a new way of sharing data that is secure and decentralized. In this paper, we provide a way to use blockchain to run a machine learning model in a decentralized way using various nodes to compute part of the learning task. We apply our system in a smart home IoT setting to generate user customizations based on user activity prediction for IoT devices. We use distributed association rule mining to generate the rules of user activity from the device logs. We describe the system architecture and simulate the system using Ethereum based tools.
An AR System with Intuitive User Interface for Manipulation and Visualization of 3D Medical Data (2004)

We report on a stereoscopic video-see-through augmented reality system which we developed for medical applications. Our system allows interactive in-situ visualization of 3D medical imaging data. For high-quality rendering of the augmented scene we utilize the capabilities of the latest graphics card generations. Fast high-precision MPR generation ("multiplanar reconstruction") and volume rendering is realized with OpenGL 3D textures. We provide a tracked hand-held tool to interact with the medical imaging data in its actual location. This tool is represented as a virtual tool in the space of the medical data. The user can assign different functionality to it: select arbitrary MPR cross-sections, guide a local volume rendered cube through the medical data, change the transfer function, etc. Tracking works in conjunction with retroreflective markers, which frame the workspace for head tracking respectively are attached to instruments for tool tracking. We use a single head-mounted tracking camera, which is rigidly fixed to the stereo pair of cameras that provide the live video view of the real scene. The user's spatial perception is based on stereo depth cues as well as on the kinetic depth cues that he receives with the viewpoint variations and the interactive data visualization. The AR system has a compelling real-time performance with 30 stereo-frames/second and exhibits no time lag between the video images and the augmenting graphics. Thus, the physician can interactively explore the medical imaging information in-situ.
Amelioration of Experimental Lipid Keratopathy by Photochemically Induced Thrombosis of Feeder Vessels (1987)

The photochemical interaction between intravenously injected rose bengal dye and 514.5-nm argon laser irradiation was employed to initiate permanent thrombotic occlusions in the corneal neovasculature of rabbit eyes with experimentally induced lipid keratopathy. This photothrombotic procedure did not produce corneal edema or polymorphonuclear leukocyte infiltration, as was found in previous studies employing laser-induced photocoagulation. Thus, by means of the new technique, we avoided the formation of additional neovascularization and lipid deposition. Vascular occlusion by photothrombosis, effected with 8.5 times less incident intensity and 27.5 times less total light exposure than with photocoagulation, yielded an average reduction of corneal cholesterol content of 36% as opposed to an increase of 24% found with previous argon laser photocoagulation.