gebhart/patrepeval huggingface dataset:
Immunization with Outer Surface Protein (Osp) A, but Not OspC, Provides Cross-Protection of Mice Challenged with North American Isolates of Borrelia burgdorferi (1997)

The identification of antigens with the capacity to induce a broad spectrum of protective immunity is an important consideration in the design of a Lyme disease vaccine. In this study, the range of protection provided by outer surface protein (Osp) A or OspC vaccination was compared. Mice actively immunized with OspA or OspC were challenged with 3 North American isolates of Borrelia burgdorferi. OspA-immunized mice were fully protected from infection with each of the isolates, whereas mice immunized with OspC were protected from infection with the homologous isolate but not with 2 heterologous isolates. Sequence analysis revealed that the ospA genes from these 3 isolates were >99% homologous, whereas the ospC genes shared only 81%-85% homology. Western blot analysis suggested antigenic heterogeneity associated with OspC but not OspA. These results indicate that genetic and antigenic heterogeneity may limit the usefulness of OspC as a vaccine constituent.
Semaphorin 4D/Plexin-B1 Induces Endothelial Cell Migration through the Activation of PYK2, Src, and the Phosphatidylinositol 3-Kinase–Akt Pathway (2005)

Semaphorins are cell surface and secreted proteins that provide axonal guidance in neuronal tissues and regulate cell motility in many cell types. They act by binding a family of transmembrane receptors known as plexins, which belong to the c-Met family of scatter factor receptors but lack an intrinsic tyrosine kinase domain. Interestingly, we have recently shown that Plexin-B1 is highly expressed in endothelial cells and that its activation by Semaphorin 4D elicits a potent proangiogenic response (J. R. Basile, A. Barac, T. Zhu, K. L. Guan, and J. S. Gutkind, Cancer Res. 64:5212-5224, 2004). In searches for the underlying molecular mechanism, we observed that Semaphorin 4D-stimulated endothelial cell migration requires the activation of the phosphatidylinositol 3-kinase (PI3K)-Akt pathway. Surprisingly, we found that Plexin-B1 stimulates PI3K-Akt through the activation of an intracellular tyrosine kinase cascade that involves the sequential activation of PYK2 and Src. This results in the tyrosine phosphorylation of Plexin-B1, the rapid recruitment of a multimeric signaling complex that includes PYK2, Src, and PI3K to Plexin-B1 and the activation of Akt. These findings suggest that Plexin-B1 may achieve its numerous physiological functions through the direct activation of intracellular tyrosine kinase cascades.
Rearrangements of N-Oxides. A Novel Synthesis of Pyridyl Carbinols and Aldehydes (1954)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTRearrangements of N-Oxides. A Novel Synthesis of Pyridyl Carbinols and AldehydesV. Boekelheide and W. J. LinnCite this: J. Am. Chem. Soc. 1954, 76, 5, 1286–1291Publication Date (Print):March 1, 1954Publication History Published online1 May 2002Published inissue 1 March 1954https://pubs.acs.org/doi/10.1021/ja01634a026https://doi.org/10.1021/ja01634a026research-articleACS PublicationsRequest reuse permissionsArticle Views4680Altmetric-Citations243LEARN 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
Context-Aware Service Selection Using Graph Matching (2009)

Abstract. The current evolution of Ubiquitous Computing and of Service-Oriented Computing is leading to the development of context-aware services. Context-aware services are services whose description is enriched with context information related to the service execution environment, adaptation capabilities, etc. This information is often used for discovery and adaptation purposes. However, context information is naturally dynamic and incomplete, which represents an important issue when comparing service description and user requirements. Actually, uncertainty of context information may lead to inexact matching between provided and required service capabilities, and consequently to the non-selection of services. In order to handle incomplete context information, we propose in this paper a graph-based algorithm for matching contextual service descriptions using similarity measures, allowing inexact matches. Service description and requirements are compared using two kinds of similarity measures: local measures, which compare individually required and provided properties (represented as graph nodes), and global measures, which take into account the context description as a whole, by comparing two graphs corresponding to two context descriptions. 1
Probing Aqueous Surfaces by ToF-SIMS (2011)

We report the first observations of aqueous surfaces by a time-of-flight secondary ion mass spectrometer (ToF-SIMS) via a self-contained microfluidic module compatible in vacuum. The interface uses a microfluidic channel with a 3 {micro}m diameter window into the flowing fluid beneath it. This window supports the liquid against the vacuum by the liquid's surface tension and limits the high-density vapor region traversed by the probe beams to only a few micrometers. We demonstrate detections of aqueous surfaces such as deuterium water and sodium iodide (NaI) solution through the small aperture by ToF-SIMS. Even more, molecular signals (M-H-) of glutamic acid (C5H8NO4-) are observed. ToF-SIMS coupled with the novel interface provides a molecular recognition capability, making it a great choice to detect short-lifetime reaction intermediates in aqueous solutions. This novel microfluidic interface makes multimodal vacuum based analysis of liquid surface possible.
Influence of unsulfonated material and its sulfone content on the physical properties of linear alkylbenzene sulfonates (1988)

Abstract Free oil content (unsulfonated matter) in linear alkylbenzene sulfonates has a considerable influence on the physical properties (viscosity and cloud point) of sulfonate slurries. It has been found that a determining factor in this influence is the sulfone content in free oil. This has been observed in several commercial sulfonic acids and confirmed through laboratory sulfonation tests. In order to better understand the effect of the sulfone content, a high performance liquid chromatography method for its determination was developed.
BIOCHEMISTRY OF OXYGEN TOXICITY (1989)

The Hippo pathway was initially discovered in Drosophila melanogaster as a key regulator of tissue growth. It is an evolutionarily conserved signaling cascade regulating numerous biological processes, including cell growth and fate decision, organ size ...Read More
Structure-activity studies of glucagon-like peptide-1. (1994)

A series of analogs of glucagon-like peptide-1 (GLP-1) was made replacing each amino acid with L-alanine to identify side-chain functional groups required for interaction with the GLP-1 receptor. In the case of L-alanine being the parent amino acid, substitution was made with the amino acid found in the corresponding position in glucagon. Binding assays were performed using the cloned rat GLP-1 receptor, and receptor activation was monitored using RIN 2A18 plasma membranes. The analogs that showed the weakest receptor binding were further compared with native GLP-1 by circular dichroism spectroscopy to investigate possible conformational changes. We conclude that the side chains in positions 7, 10, 12, 13, and 15 are directly involved in the receptor interaction while positions 28 and 29 are important for GLP-1 to adapt the conformation recognized by the receptor.
A novel alternate anaplerotic pathway to the glyoxylate cycle in streptomycetes (1997)

ccr encoding crotonyl coenzyme A (CoA) reductase (CCR), which catalyzes the conversion of crotonyl-CoA to butyryl-CoA in the presence of NADPH, was previously cloned from Streptomyces collinus. We now report that a complete open reading frame, designated meaA, is located downstream from ccr. The predicted gene product showed 35% identity with methylmalonyl-CoA mutases from various sources. In addition, the predicted amino acid sequences of S. collinus ccr and meaA exhibit strong similarity to that of adhA (43% identity), a putative alcohol dehydrogenase gene, and meaA (62% identity) of Methylobacterium extorquens, respectively. Both adhA and meaA are involved in the assimilation of C1 and C2 compounds in an unknown pathway in the isocitrate lyase (ICL)-negative Methylobacterium. We have demonstrated that S. collinus can grow with acetate as its sole carbon source even though there is no detectable ICL, suggesting that in this organism ccr and meaA may also be involved in a pathway for the assimilation of C2 compounds. Previous studies with streptomycetes provided a precedent for a pathway that initiates with the condensation of two acetyl-CoA molecules to form butyryl-CoA, which is then transformed to succinyl-CoA with two separate CoB12-mediated rearrangements and a series of oxidations. The biological functions of ccr and meaA in this process were investigated by gene disruption. A ccr-blocked mutant showed no detectable crotonyl-CoA reductase activity and, compared to the wild-type strain, exhibited dramatically reduced growth when acetate was the sole carbon source. An meaA-blocked mutant also exhibited reduced growth on acetate. However, both methylmalonyl-CoA mutase and isobutyryl-CoA mutase, which catalyze the two CoB12-dependent rearrangements in this proposed pathway, were shown to be present in the meaA-blocked mutant. These results suggested that both ccr and meaA are involved in a novel pathway for the growth of S. collinus when acetate is its sole carbon source.
Alternative processing of bovine growth hormone mRNA is influenced by downstream exon sequences. (1989)

In a previous report, we described the presence, in pituitary tissue, of an alternatively processed species of bovine growth hormone mRNA from which the last intron (intron D) has not been removed by splicing (R. K. Hampson and F. M. Rottman, Proc. Natl. Acad. Sci. USA 84:2673-2677, 1987). Using transient expression of the bovine growth hormone gene in Cos I cells, we observed that splicing of intron D was affected by sequences within the downstream exon (exon 5). Deletion of a 115-base-pair FspI-PvuII restriction fragment in exon 5 beginning 73 base pairs downstream of the intron 4-exon 5 junction resulted in cytoplasmic bovine growth hormone mRNA, more than 95% of which retained intron D. This contrasted with less than 5% of the growth hormone mRNA retaining intron D observed with expression of the unaltered gene. Insertion of a 10-base-pair inverted repeat sequence, CTTCCGGAAG, which was located in the middle of this deleted segment, partially reversed this pattern, resulting in cytosolic mRNA from which intron D was predominantly removed. More detailed deletion analysis of this region indicated that multiple sequence elements within the exon 5, in addition to the 10-base-pair inverted repeat sequence, are capable of influencing splicing of intron D. The effect of these exon sequences on splicing of bovine growth hormone precursor mRNA appeared to be specific for the growth hormone intron D. Deletions in exon 5 which resulted in marked alterations in splicing of growth hormone intron D had no effect on splicing when exon 5 of bovine growth hormone was placed downstream of the heterologous bovine prolactin intron D. Deletions in exon 5 which resulted in marked alterations in splicing of growth hormone intron D had no effect on splicing when exon 5 of bovine growth hormone was placed downstream of the heterologous bovine prolactin intron D. The results of this study suggest a unique interaction between sequences located near the center of exon 5 and splicing of the adjacent intron D.
Software refactoring process for adaptive user-interface composition (2010)

Adaptive user-interface composition is the ability of a software system to: (a) compose its user-interface at runtime according to a given deployment profile; and (b) to possibly drop running components and activate better alternatives in their place in response to deployment profile modifications. While adaptive behavior has gained interest for a wide range of software products and services, its support is very demanding requiring adoption of user-interface architectural patterns from the early software design stages. While previous research addressed the issue of engineering adaptive systems from scratch, there is an important methodological gap since we lack processes to reform existing non-adaptive systems towards adaptive behavior. We present a stepwise transformation process of user-interface software by incrementally upgrading relevant class structures towards adaptive composition by treating adaptive behavior as a cross-cutting concern. All our refactoring examples have emerged from real practice.
Effect of "Ground Truth" on Image Binarization (2012)

Image binarization has a large effect on the rest of the document image analysis processes in character recognition. Algorithm development is still a major focus of research. Evaluation of image binarization has been done by comparison of the result of OCR systems on images binarized by different methods. That has been criticized in that the binarization alone is not evaluated, but rather how it interacts with the downstream processes. Recently pixel accurate "ground truth" images have been introduced for use in binarization algorithm evaluation. This has been shown to be open to interpretation. The choice of binarization ground truth affects the binarization algorithm design, either directly if design is by automated algorithm trying to match the provided ground truth, or indirectly if human designers adjust their designs to perform better on the provided data. Three variations in pixel accurate ground truth were used to train a binarization classifier. The performance can vary significantly depending on choice of ground truth, which can influence binarization design choices.
ORGANIC COATINGS: SCIENCE AND TECHNOLOGY VOLUME 1: FILM FORMATION, COMPONENTS AND APPEARANCE (1993)

"ORGANIC COATINGS: SCIENCE AND TECHNOLOGY VOLUME 1: FILM FORMATION, COMPONENTS AND APPEARANCE." Drying Technology, 11(6), p. 1477
Stationary objects in multiple object tracking (2007)

This paper presents an approach to detect stationary foreground objects in naturally busy surveillance video scenes with several moving objects. Our approach is inspired by human's visual cognition processes and builds upon a multi-tier video tracking paradigm with main layers being the spatially based "peripheral tracking" loosely corresponding to the peripheral vision and the object based "vision tunnels " for focused attention and analysis of tracked objects. Humans allocate their attention to different aspects of objects and scenes based on a defined task. In our model, a specific processing layer corresponding to allocation of attention is used for detection of objects that become stationary. The static object layer, a natural extension of this framework, detects and maintains the stationary foreground objects by using the moving object and scene information from Peripheral Tracker and the Scene Description layers. Simple event detection modules then use the enduring stationary objects to determine events such as Parked Vehicles or Abandoned Bags.
Low Density Lipoprotein Receptor-related Protein and Factor IXa Share Structural Requirements for Binding to the A3 Domain of Coagulation Factor VIII (2003)

Low-density lipoprotein receptor-related protein (LRP) is an endocytic receptor that binds multiple distinct ligands, including blood coagulation factor VIII (FVIII). FVIII is a heterodimeric multidomain protein that consists of a heavy chain (domains A1, a1, A2, a2, and B) and a light chain (domains a3, A3, C1, and C2). Both chains contribute to high-affinity interaction with LRP. One LRP-interactive region has previously been located in the C2 domain, but its affinity is low in comparison with that of the entire FVIII light chain. We now have compared a variety of FVIII light chain derivatives with the light chain of its homolog FVa for LRP binding. In surface plasmon resonance studies employing LRP cluster II, the FVa and FVIII light chains proved different in that only FVIII displayed high-affinity binding. Because the FVIII a3-A3-C1 fragment was effective in associating with LRP, this region was explored for structural elements that are exposed but not conserved in FV. Competition studies using synthetic peptides suggested that LRP binding involves the FVIII-specific region Lys(1804)-Ala(1834) in the A3 domain. In line with this observation, LRP binding was inhibited by a recombinant antibody fragment that specifically binds to the FVIII sequence Glu(1811)-Lys(1818). The role of this sequence in LRP binding was further tested using a FVIII/FV chimera in which sequence Glu(1811)-Lys(1818) was replaced with the corresponding sequence of FV. Although this chimera still displayed residual binding to LRP cluster II, its affinity was reduced. This suggests that multiple sites in FVIII contribute to high-affinity LRP binding, one of which is the FVIII A3 domain region Glu(1811)-Lys(1818). This suggests that LRP binding to the FVIII A3 domain involves the same structural elements that also contribute to the assembly of FVIII with FIXa.
Borehole flexural modes in anisotropic formations (1994)

Abstract A perturbation method of solution is an efficient way of analyzing elastic wave propagation along a borehole in anisotropic formations. The perturbation model allows us to calculate changes in the modal dispersion curves caused by the differences in elastic constants between the anisotropic formation of interest and a reference, or unperturbed, isotropic formation. The equivalent isotropic constants in the reference formation are obtained from the appropriate compressional-and shear-wave velocities for the selected propagation and polarization directions of the flexural mode. This choice of the unperturbed solution means that the required perturbation is minimal, resulting in enhanced accuracy of the perturbed solution. Computational results are presented for the dispersion curves of borehole flexural waves in a transversely isotropic (TI) formation as a function of borehole deviation from the TI symmetry axis. In addition, radial distributions of displacement and stress fields associated with the flexural wave are obtained as a function of frequency. These provide qualitative information on the radial depth of investigation with flexural wave logging. The flexural wave excitation function is a measure of the energy that a source converts to flexural motion. We deduce an expression for the flexural wave excitation and show that its bandlimited characteristic is influenced by both the borehole diameter and formation parameters. From the dispersion curves and excitation functions, we can compute the flexural waveforms caused by a dipole source with arbitrary orientation in the borehole. In the numerical computations, we have used the unperturbed mode shapes for an equivalent isotropic medium together with the perturbed dispersion relations caused by the formation anisotropy.
Heterosubtypic Neutralizing Monoclonal Antibodies Cross-Protective against H5N1 and H1N1 Recovered from Human IgM+ Memory B Cells (2008)

The human monoclonal CR6261 described in this study could be developed for use as a broad spectrum agent for prophylaxis or treatment of human or avian influenza infections without prior strain characterization. Moreover, the CR6261 epitope could be applied in targeted vaccine strategies or in the design of novel antivirals. Finally our approach of screening the IgM(+) memory repertoire could be applied to identify conserved and functionally relevant targets on other rapidly evolving pathogens.
A secure payment system for electronic commerce (1999)

Security is an important factor for the wide acceptance of electronic commerce services. Special security mechanisms are needed for the implementation of secure electronic payment systems that permit the integration of electronic transactions. In the framework of the information brokerage system that has been developed by the GAIA project of the European union a number of such mechanisms have been proposed and implemented. As a result, an integrated secure electronic payment system is provided that covers a number of different payment methods preserving maximum security of electronic transactions.
MET Exon 14 Alterations in Lung Cancer: Exon Skipping Extends Half-Life (2016)

MET exon 14 alterations are a diverse group of mutations, many of which disrupt splice acceptor or donor sites leading to exon 14 skipping, impaired receptor degradation, and oncogenic transformation. These alterations are clinically targetable with MET-directed therapy. Clin Cancer Res; 22(12); 2832-4. ©2016 AACRSee related article by Tong et al., p. 3048.
Soluble adhesion molecule P-selectin and endothelial dysfunction in essential hypertension (1995)

This study suggests that hypertensives have high plasma fibrinogen levels, platelet dysfunction (which could contribute to atherogenesis, as indicated by raised soluble P-selectin levels) and endothelial dysfunction (as indicated by high von Willebrand factor levels), which are related to diastolic blood pressure. These factors may act synergistically to increase atherogenesis and may explain the high risk of atherosclerotic vascular disease in hypertensives.
Reduction of the false‐positive rate in newborn screening by implementation of MS/MS‐based second‐tier tests: The Mayo Clinic experience (2004–2007) (2007)

The continued expansion of newborn screening programmes to include additional conditions increases the responsibility of newborn screening laboratories to provide testing with the highest sensitivity and specificity to allow for identification of affected patients while minimizing the false-positive rate. Some assays and analytes are particularly problematic. Over recent years, our laboratory tried to improve this situation by developing second-tier tests to reduce false-positive results in the screening for congenital adrenal hyperplasia (CAH), tyrosinaemia type I, methylmalonic acidaemias, homocystinuria, and maple syrup urine disease (MSUD). Beginning in 2004, this approach was applied to Mayo's newborn screening programme and resulted in a false-positive rate of 0.09%, a positive predictive value of 41%, and a positive detection rate of 1 affected case in 1672 babies screened.