gebhart/patrepeval huggingface dataset:
A locally adaptive region growing algorithm for vascular segmentation (2003)

Abstract To segment vascular structures in 3‐D CTA/MRA images, this article presents a new region growing algorithm based on local cube tracking. In the proposed algorithm, a small local cube is segmented to detect a vessel segment, and the following local cube(s) is determined based on the segmentation result. This procedure is repeated until the segmentation is completed. By confining the segmentation inside each local cube, a robust result can be obtained even in a tubular structure of steadily changing intensity. For segmentation, a locally adaptive and competitive region growing scheme is adopted to obtain well‐defined vessel boundaries. It should be emphasized that the proposed algorithm can detect all branches with practically acceptable computational complexity. In addition, its segmentation result is represented as a tree structure having many branches so that a user may easily correct the result branch‐by‐branch, if necessary. Experimental results from real images prove that the proposed algorithm produces prospective vessel segmentation results for 3‐D CTA/MRA images and segments vessels of various sizes well, including stenoses and aneurysms. © 2003 Wiley Periodicals, Inc. Int J Imaging Syst Technol 13, 208–214, 2003; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/ima.10059
Hepatocyte growth factor–stimulated invasiveness of monocytes (2000)

Hepatocyte growth factor (HGF) is a pluripotent cytokine with mitogenic, motogenic, and morphogenic activity for mainly epithelial and endothelial target cells. We previously demonstrated that the specific HGF receptor, MET, is induced in stimulated peripheral blood monocytes. In this study, we analyzed the functional consequences of MET activation in primary cultures of peripheral blood monocytes from healthy donors. After stimulation of MET-expressing monocytes with recombinant HGF, the gene-expression profile of peripheral blood mononuclear cells and monocytes was significantly modulated, especially with regard to genes involved in cell movement. After stimulation of primary cultured monocytes with HGF, invasion assays showed a significantly increased matrigel invasion rate that was completely abolished by neutralizing antibodies to HGF. The HGF-activated invasiveness and the altered gene-expression profile suggest a proinflammatory role for HGF stimulation of monocytes and support the hypothesis that the HGF/MET signaling system plays an important part in the activation of the nonspecific cellular inflammatory response. (Blood. 2000;95:3964-3969)
The variable genes and gene families of the mouse immunoglobulin κ locus (1999)

In this report 118 mouse Vkappa genes are described which, together with the 22 Vkappa genes reported previously (T. Kirschbaum et al., Eur. J. Immunol. 1998. 28: 1458-1466) amount to 140 genes that had been cloned and sequenced in our laboratory. For 73 of them cDNAs are known, i. e. they have to be considered functional genes, although 10 genes of this group have 1-bp deviations from the canonical promoter, splice site or heptanucleotide recombination signal sequences. Twenty Vkappa genes have been defined as only potentially functional since they do not contain any defect, but no cDNAs have been found (yet) for them. Of the 140 Vkappa genes 47 are pseudogenes. There are indications that two to five Vkappa genes or pseudogenes exist in the kappa locus which we have not yet been able to clone. The 140 Vkappa genes and pseudogenes were assigned to 18 gene families, 4 of them being one-member families. This differs from previous enumerations of the families only by the combination of the Vkappa9 and Vkappa10 families and by the addition of the Vkappa dv gene as a new separate family. Sequence identity usually was 80% or above within the gene families and 55-80% between genes of different families. Many of the mouse Vkappa gene families show significant homologies to the human ones, indicating that in evolution Vkappa gene diversification predated the divergence of the primate and rodent clades.
<title>Wavelets as a tool for the construction of a halftone screen</title> (1995)

Halftoning using a mask presents the advantage of computational simplicity and implementation speed. Blue-noise masks in particular have the additional advantage of producing visually pleasing halftones without periodic artifacts. However, halftones produced with a blue-noise mask are usually grainy and less sharp compared with error diffusion images. In this paper, we present an algorithm for the construction of a 'max-energy' mask that reduces the perceived graininess in the output halftone by controlling the local spectral energy in the dot profiles of the mask, i.e., the binary patterns that results after the mask is thresholded at a constant gray level. Dot profiles of the max-energy mask are shown and an example halftone is compared against a blue-noise mask halftone.
Escherichia coli initiation factor 3 protein binding to 30S ribosomal subunits alters the accessibility of nucleotides within the conserved central region of 16S rRNA (1989)

Translational initiation factor 3 (IF3) is an RNA helix destabilizing protein which interacts with strongly conserved sequences in 16S rRNA, one at the 3' terminus and one in the central domain. It was therefore of interest to identify particular residues whose exposure changes upon IF3 binding. Chemical and enzymatic probing of central domain nucleotides of 16S rRNA in 30S ribosomal subunits was carried out in the presence and absence of IF3. Bases were probed with dimethyl sulfate (DMS), at A(N-1), C(N-3), and G(N-7), and with N-cyclohexyl-N'-[2-(N-methyl-4-morpholinio)ethyl] carbodiimide p-toluenesulfonate (CMCT), at G(N-1) and U(N-3). RNase T1 and nuclease S1 were used to probe unpaired nucleotides, and RNase V1 was used to monitor base-paired or stacked nucleotides. 30S subunits in physiological buffers were probed in the presence and absence of IF3. The sites of cleavage and modification were detected by primer extension. IF3 binding to 30S subunits was found to reduce the chemical reactivity and enzymatic accessibility of some sites and to enhance attack at other sites in the conserved central domain of 16S rRNA, residues 690-850. IF3 decreased CMCT attack at U701 and U793 and V1 attack at G722, G737, and C764; IF3 enhanced DMS attack at A814 and V1 attack at U697, G833, G847, and G849. Many of these central domain sites are strongly conserved and with the conserved 3'-terminal site define a binding domain for IF3 which correlates with a predicted cleft in two independent models of the 30S ribosomal subunit.
Analysis of Receptor Tyrosine Kinase Internalization Using Flow Cytometry (2008)

The internalization of activated receptor tyrosine kinases (RTKs) by endocytosis and their subsequent down regulation in lysosomes plays a critical role in regulating the duration and intensity of downstream signaling events. Uncoupling of the RTK cMet from ligand-induced degradation was recently shown to correlate with sustained receptor signaling and increased cell tumorigenicity, suggesting that the corruption of these endocytic mechanisms could contribute to increased cMet signaling in metastatic cancers. To understand how cMet signaling for normal cell growth is controlled by endocytosis and how these mechanisms are dysregulated in metastatic cancers, we developed flow cytometry-based assays to examine cMet internalization.
Graft-versus-host-related immunosuppression is induced in mixed chimeras by alloresponses against either host or donor lymphohematopoietic cells. (1988)

Graft-vs.-host (GVH)-related immunosuppression has previously been demonstrated in F1 rodent recipients of parental lymphoid cells, and has been thought to result from an immunologic attack of the donor against the host. Since all cells of such F1 recipients could potentially bear target class I MHC alloantigens, it has not previously been possible to determine precisely the target tissues responsible for development of GVH-related effects. In the present studies we have used mixed allogeneic chimeras as recipients of host or donor-strain lymphocyte inocula, and have made the surprising observation that "GVH-induced" immune unresponsiveness does not require GVH reactivity, per se, but develops in the presence of a one-way alloresponse against lymphohematopoietic cells in either the GVH or the host-versus-graft direction.
Differential effects of SPARC and cationic SPARC peptides on DNA synthesis by endothelial cells and fibroblasts (1993)

SPARC (secreted protein, acidic and rich in cysteine), also known as osteonectin, is an extracellular Ca+2-binding glycoprotein that inhibits the incorporation of [3H]-thymidine and delays the onset of S-phase in synchronized cultures of bovine aortic endothelial (BAE) cells. This effect appears not to be dependent on the functional properties of SPARC associated with changes in cell shape or inhibition of cell spreading. In this study we investigate the conditions under which cell cycle modulation occurs in different types of cells. Human umbilical vein endothelial cells, a transformed fetal BAE cell line, and bovine capillary endothelial cells exhibited a sensitivity to SPARC and a cationic peptide from a non-Ca+2-binding region of SPARC (peptide 2.1, 0.2-0.8 mM) similar to that observed in BAE cells. In contrast, human foreskin fibroblasts and fetal bovine ligament fibroblasts exhibited an increase in the incorporation of [3H]-thymidine in the presence of 25 microM-0.2 mM peptide 2.1; inhibition was observed at concentrations in excess of 0.4 mM. This biphasic modulation could be further localized to a sequence of 10 amino acids comprising the N-terminal half of peptide 2.1. A synthetic peptide from another cationic region of SPARC (peptide 2.3) increased [3H]-thymidine incorporation by BAE cells and fibroblasts in a dose-dependent manner. In endothelial cells, a stimulation of 50% was observed at a concentration of 0.01 mM; fibroblasts required approximately 100-fold more peptide 2.3 for levels of stimulation comparable to those obtained in endothelial cells. The observation that SPARC and unique SPARC peptides can differentially influence the growth of fibroblasts and endothelial cells in a concentration-dependent manner suggests that SPARC might regulate proliferation of specific cells during wound repair and remodeling.
Cell adhesion peptides alter smooth muscle cell adhesion, proliferation, migration, and matrix protein synthesis on modified surfaces and in polymer scaffolds (2002)

The effects of cell adhesion peptides (RGDS, KQAGDV, VAPG) on vascular smooth muscle cells grown on modified surfaces and in tissue-engineering scaffolds were examined. Cells were more strongly adhered to surfaces modified with adhesive ligands than to control surfaces (no ligand or a nonadhesive ligand). Cell migration was higher on surfaces with 0.2 nmol/cm(2) of adhesive ligand than on control surfaces, but it was lower on surfaces with 2.0 nmol/cm(2) of adhesive ligand than it was on control surfaces. Further, cell proliferation was lower on adhesive surfaces than it was on control surfaces, and it decreased as the ligand density increased. Similarly, in the peptide-grafted hydrogel scaffolds, cell proliferation was lower in scaffolds containing the adhesive peptides than it was in control scaffolds. After 7 days of culture, more collagen per cell was produced in control scaffolds than in scaffolds containing adhesive peptides. In addition, collagen production decreased in the scaffolds as the ligand concentration increased. While modification of a surface or scaffold material with adhesive ligands initially increases cell attachment, it may be necessary to optimize cell adhesion simultaneously with proliferation, migration, and matrix production.
Behavior of Slender Steel-Concrete Composite Columns Wrapped with FRP Jackets (2011)

This paper studies the influence of slenderness on the behavior of steel-concrete composite columns encased in fiber-reinforced polymer (FRP) jackets. The composite columns are composed of steel I-sections that are partially encased by concrete and fully wrapped with epoxy-saturated glass and carbon FRP sheets. A total of nine specimens were tested with different slenderness parameters and heights ranging between 500 and 3,000 mm. The confining pressure provided by the FRP jacket and the composite action between the constituent materials resulted in an enhanced compressive behavior of the composite columns. The compressive strength, elastic axial stiffness, and energy dissipation capacity of the composite columns increased by a ratio of up to 5.2, 2.5, and 14.0, respectively, compared with that of the bare steel columns counterparts. A capacity curve, which shows the compressive strength of the composite columns for various slenderness parameters, was developed based on the experimental results.
ChemInform Abstract: Fluorinated Organic Peroxides ‐ Their Decomposition Behavior and Applications (1994)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Localization of pregnancy-associated plasma protein-A and colocalization of pregnancy-associated plasma protein-A messenger ribonucleic acid and eosinophil granule major basic protein messenger ribonucleic acid in placenta. (1994)

The presence of PAPP-A mRNA and PAPP-A subunit protein in placental X cells and syncytiotrophoblasts indicates that both X cells and syncytiotrophoblasts synthesize the PAPP-A subunit, whereas only X cells synthesize proMBP.
Establishment of B cell hybridomas with B cell surface antigens. (1982)

M12.4, one of several B lymphomas derived from BALB/c mice, was mutagenized with ethyl methanesulfonate in vitro. M12.4.1, a subline of the mutant cells, was sensitive to hypoxanthine-aminopterin-thymidine selective medium and was fused with normal splenic B lymphocytes of C57BL/6ByJ mice. The hybridomas obtained from this fusion were shown to express mu heavy chain, H-2KbDb, Iad, and Iab on the cell surface by analyses of flow microfluorometry and a cytotoxicity assay, although parental M12.4.1 lacked mu heavy chain on the cell membrane. These results demonstrate that the B cell hybridomas with B cell surface antigens have been established in vitro. IgM molecules on the cell surface of the hybridomas were shown to originate from normal B cells of C57BL/6ByJ mice by flow microfluorometry analyses after staining with fluorescein-labeled Bet 1, a monoclonal rat antibody that recognizes Igh-6.5, a mouse IgM allotypic determinant. These hybridomas could generate IgM-secreting cells at the high frequency (more than 10% of the cultured cells) when stimulated with bacterial lipopolysaccharide. On the other hand, parental M12.4.1 did not develop any IgM-secreting cells under the same conditions. These findings suggest that these B cell hybridomas with B cell surface antigens may be a good model for the study of B cell differentiation.
Precursor role of arachidonic acid in release of slow reacting substance from rat basophilic leukemia cells. (1977)

The release of slow reacting substance (SRS) from rat basophilic leukemia cells (RBL-1) by the ionophore A23187 (5-10 mug/ml) was stimulated 5-fold by arachidonate and inhibited 78% by 5,8,11,14-eicosatetraynoate (an inhibitor of both fatty acid cyclooxygenase and lipoxygenase). Linoleic acid and linolenic acid both inhibited SRS formation, whereas indomethacin (a cyclooxygenase inhibitor) had no effect. Radiolabel from [14C]- or [3H]arachidonate was incorporated into SRS as indicated by comigration of radioactivity and bioreactivity in several chromatographic systems after purification to apparent radiochemical homogeneity. The radiolabeled SRS was clearly separated chromatographically from other known arachidonate metabolites. Thus, SRS appears to be a previously undescribed product of arachidonic acid metabolism, probably formed through the lipoxygenase pathway. The ability to prepare purified, biosynthetically labeled, SRS should be of considerable help in further studies of its structure, biologic function, and catabolism.
Complete Protection Against Interleukin-1β–Induced Functional Suppression and Cytokine-Mediated Cytotoxicity in Rat Pancreatic Islets In Vitro Using an Interleukin-1 Cytokine Trap (2006)

Cytokines, particularly interleukin (IL)-1beta, have been postulated to cause beta-cell destruction in type 1 diabetes. We tested the efficacy of an IL-1 cytokine trap in counteraction of suppressive and toxic effects after exposure of rat pancreatic islets in vitro to IL-1beta. The IL-1 cytokine trap used herein comprised extracellular domains of the IL-1 receptor accessory protein and the human IL-1 receptor 1 arranged inline and fused to the Fc portion of human IgG1. Groups of isolated rat pancreatic islets were maintained in medium culture with or without IL-1beta (150 pmol/l) for 48 hours in the absence or presence of the IL-1 trap at 1-, 10-, or 100-fold excess the molar concentration of the cytokine. IL-1beta alone induced a strong inhibition of insulin secretion and glucose oxidation rate and a marked increase in medium nitrite accumulation as an indicator of nitric oxide generation. When the IL-1 trap was used at a ratio 10:1 or 100:1, a complete protection against these effects were observed. Moreover, the IL-1 trap (100:1) blocked the increased islet cell death seen in islets treated with a combination of IL-1beta + tumor necrosis factor-alpha + interferon-gamma as well as functional suppression induced by the cytokine combination. In conclusion, we show that addition of an IL-1 trap can protect rat pancreatic islets in vitro against noxious effects induced by IL-1beta. Exploring the IL-1 trap in relevant animal models of type 1 diabetes represents an interesting future intervention strategy.
Structure and Mechanism of Helicases and Nucleic Acid Translocases (2007)

Helicases and translocases are a ubiquitous, highly diverse group of proteins that perform an extraordinary variety of functions in cells. Consequently, this review sets out to define a nomenclature for these enzymes based on current knowledge of sequence, structure, and mechanism. Using previous definitions of helicase families as a basis, we delineate six superfamilies of enzymes, with examples of crystal structures where available, and discuss these structures in the context of biochemical data to outline our present understanding of helicase and translocase activity. As a result, each superfamily is subdivided, where appropriate, on the basis of mechanistic understanding, which we hope will provide a framework for classification of new superfamily members as they are discovered and characterized.
Stability of protein production from recombinant mammalian cells (2003)

One of the most important criteria for successful generation of a therapeutic protein from a recombinant cell is to obtain a cell line that maintains stability of production. If this is not achieved it can generate problems for process yields, effective use of time and money, and for regulatory approval of products. However, selection of a cell line that sustains stability of production over the required time period may be difficult to achieve during development of a therapeutic protein. There are several studies in the literature that have reported on the instability of protein production from recombinant cell lines. The causes of instability of production are varied and, in many cases, the exact molecular mechanisms are unknown. The production of proteins by cells is modulated by molecular events at levels ranging from transcription, posttranscriptional processing, translation, posttranslational processing, to secretion. There is potential for regulation of stability of protein production at many or all of these stages. In this study we review published information on stability of protein production for three industrially important cell lines: hybridoma, Chinese hamster ovary (CHO), and nonsecreting (NS0) myeloma cell lines. We highlight the most likely molecular loci at which instability may be engendered and indicate other areas of protein production that may affect stability from mammalian cells. We also outline approaches that could help to overcome the problems associated with unpredictable expression levels and maximized production, and indicate the consequences these might have for stability of production.
Patch32: a system for automated client OS updates (1998)

The adage chain is only as strong as its weakest is true for network security, the link being the host on the network. To secure a network, hosts must be thoughtfully installed and kept updated with the appropriate patches. For hosts running Microsoft Windows 95® or Microsoft Windows NT Workstation® keeping patches current is problematic.

Unlike most Unix variants, neither Windows 95 nor NT Workstation ship with a network extensible update mechanism. Though third party solutions are available, they can be costly to implement for large networks. This paper presents a free update mechanism for hosts running Windows 9x or NT Workstation served by Samba (see Appendix A).

Developed to patch Microsoft's 32 bit operating systems, the name Patch32 was adopted. Patch32 was developed for an existing network dominated by Sun Microsystems' SPARC servers running Solaris®, however, Patch32 can be used in any environment that provides SMB file services.
Extension of a Diffusion Model for Holographic Photopolymers (1995)

(1995). Extension of a Diffusion Model for Holographic Photopolymers. Journal of Modern Optics: Vol. 42, No. 12, pp. 2571-2573.
NR2B Selective NMDA Antagonists: The Evolution of the Ifenprodil-Type Pharmacophore (2006)

The quest for NR2B subtype selective NMDA antagonists started almost twenty years ago. The structure of ifenprodil, the prototype of this group of compounds, inspired many medicinal chemists in several research units. Different approaches led to the identification of the pharmacophore and several distinct classes of compounds containing this pharmacophore. From these studies a few drug candidates emerged and clinical trials proved the viability of the concept. This article attempted to follow the evolution from ifenprodil, a multiple ligand, to selective NR2B antagonists.
<title>High-speed template matching algorithm using contour information</title> (1992)

We propose a new high speed template matching algorithm named edge point template matching (EPTM), which can match one gray image to another closely similar image and detect small differences between them. This method uses location, strength, and direction of contours in the template image. They are stored in a one-dimensional array. This reduced template makes the computational cost lower than previous methods which have a two- dimensional template. Generally, this kind of template reduction causes a mismatch when the image is disturbed. Contour dilation of the target image improves this situation. By applying the coarse-fine algorithm and the sequential similarity detection algorithm, our method is approximately 300 times faster than the well known cross-correlation technique. A simple hardware architecture is enough to implement the algorithm, and it is possible to execute matching a 400 X 400 template on a 512 X 512 target image within 200 msec.