gebhart/patrepeval huggingface dataset:
Autoradiographic distribution of hematoporphyrin derivative in normal and tumor tissue of the mouse. (1981)

The distribution of isotopically labeled hematoporphyrin derivative (HPD) has been studied in mice bearing the spontaneous mammary tumor (fast growing). In stomach, liver, spleen, and pancreas, 3 hr after i.p. injection of [3H]HPD, grains were uniformly distributed over the tissue sections. After 24 hr, the grain density overlying parenchymous areas of these tissues was lower than that over the stromal or reticuloendothelial areas. In the spontaneous mammary tumor (fast growing), higher grain densities were seen over pseudocapsule, stromal septa, and necrotic areas at 3, 6, 12, 24, and 48 hr after injection. At 168 hr postinjection, only isolated stomal cells, presumably macrophages, showed high grain densities. From the temporal changes observed in the distributions of HPD in normal tissues and the relative stability of the distribution seen in the spontaneous mammary tumor (fast growing), we speculate that tissue factors such as vascular permeability, lack of an adequate lymphatic drainage, and nonspecific binding of serum proteins to stromal elements may be responsible for or contribute to the preferential uptake and/or retention of HPD observed in both human and animal tumors.
Leukocyte Extravasation: An Immunoregulatory Role for α- l- Fucosidase? (2008)

Fucosylated oligosaccharides and glycoconjugates have been implicated in several biological events, including the cell-cell adhesion processes that mediate inflammation. Alpha-L-fucosidase (ALF) is an exoglycosidase that is involved in the hydrolytic degradation of alpha-L-fucose from glycoconjugates. In this study, we investigated the potential role of ALF in regulation of leukocyte migration. Measurement of transendothelial migration in response to CCL5 demonstrated that pretreatment of monocytic cells with ALF reduced migration (p = 0.0004) to a greater extent than treatment of the endothelial monolayer (p = 0.0374). Treatment with ALF significantly reduced the adhesion of monocytic cells to immobilized P-selectin.Fc. A murine model of experimental autoimmune uveitis was then used to show that treatment of splenic cells with ALF produced an 8.6-fold decrease in rolling and a 3.2-fold decrease in cell migration across the retinal vasculature. Further in vitro studies demonstrated that treatment of monocytes with the chemokines CCL3 or CCL5 increased the level of mRNA encoding ALF; this was accompanied by the detection of significant increases in both the 51- and 56-kDa components of ALF by Western blotting. Treatment of monocytic cells with ALF for 2 h significantly reduced the cell surface expression of CD31, with a further decrease in expression observed after 5 h (p = 0.002). Thus, CD31 and fucosylated ligands of P-selectin seem to be the candidates through which ALF mediates its effect in vitro. These data identify a previously unrecognized immunoregulatory role for ALF in late stages of inflammation.
Notch signaling controls multiple steps of pancreatic differentiation (2003)

Multiple cell types of the pancreas appear asynchronously during embryogenesis, which requires that pancreatic progenitor cell potential changes over time. Loss-of-function studies have shown that Notch signaling modulates the differentiation of these progenitors, but it remains unclear how and when the Notch pathway acts. We established a modular transgenic system to heritably activate mouse Notch1 in multiple types of progenitors and differentiated cells. We find that misexpression of activated Notch in Pdx1-expressing progenitor cells prevents differentiation of both exocrine and endocrine lineages. Progenitors remain trapped in an undifferentiated state even if Notch activation occurs long after the pancreas has been specified. Furthermore, endocrine differentiation is associated with escape from this activity, because Ngn3-expressing endocrine precursors are susceptible to Notch inhibition, whereas fully differentiated endocrine cells are resistant.
A Rat Monoclonal Antibody That Recognizes Pro- And Active MMP-7 Indicates Polarized Expression In Vivo (2007)

Matrix metalloproteinases (MMPs) are a family of enzymes named for their ability to degrade proteins of the extracellular matrix. Here we describe the characterization of a rat monoclonal antibody specifically recognizing one member of this enzyme family, MMP-7. This antibody has been tested for its use in multiple assay types and was shown to be useful for direct enzyme-linked immunosorbent assay (ELISA), Western blotting, immunocytochemistry, and immunohistochemistry of frozen or paraffin-embedded tissues. The antibody has been evaluated for its usefulness with tissues from several different species and, by immunohistochemistry, can detect MMP-7 of human, murine, porcine, and gerbil origin. Immunostaining of MMP-7 in normal tissues or benign tumors of intestinal, breast, and prostatic origin indicates that this protein is normally localized luminally in glandular epithelium. The localization pattern would suggest that in normal or early stage tumors, MMP-7 is most likely not directly involved in extracellular matrix degradation. In contrast, advanced colon tumors show MMP-7 in invading cells at the advancing edge of the tumor.
Stealth Breakpoints (2006)

Microscopic analysis of malicious code (malware) requires the aid of a variety of powerful tools. Chief among them is a debugger that enables runtime binary analysis at an instruction level. One of the important services provided by a debugger is the ability to stop execution of code at an arbitrary point during runtime, using breakpoints. Software breakpoints support an unlimited number of breakpoint locations by changing the code being debugged so that it can be interrupted during runtime. Most, if not all, malware are very sensitive to code modification with self-modifying and/or self-checking (SM-SC) capabilities, rendering the use of software breakpoints limited in their scope. Hardware breakpoints supported by the underlying processor, on the other hand, use a subset of the processor register set and exception mechanisms to provide breakpoints that do not entail code modification. This makes hardware breakpoints the most powerful breakpoint mechanism for malware analysis. However, current processors provide a very limited number of hardware breakpoints (typically 2-4 locations). Thus, a serious restriction is imposed on the debugger to set a desired number of breakpoints without resorting to the limited alternative of software breakpoints. Also, with the ever evolving nature of malware, there are techniques being employed that prevent the use of hardware breakpoints. This calls for a new breakpoint mechanism that retains the features of hardware breakpoints while providing an unlimited number of breakpoints, which cannot be detected or countered. In this paper, we present the concept of stealth breakpoints and discuss the design and implementation of VAMPiRE, a realization of this concept. VAMPiRE cannot be detected or countered and provides unlimited number of breakpoints to be set on code, data, and I/O with the same precision as that of hardware breakpoints. It does so by employing a subtle combination of simple stealth techniques using virtual memory and hardware single-stepping mechanisms that are available on all processors, old and new. This technique makes VAMPiRE portable to any architecture, providing powerful breakpoint ability similar to hardware breakpoints for microscopic malware analysis
hrTis required for cardiovascular development in zebrafish (2002)

The recently identified zebrafish T-box gene hrT is expressed in the developing heart and in the endothelial cells forming the dorsal aorta. Orthologs of hrT are expressed in cardiovascular cells from Drosophila to mouse, suggesting that the function of hrT is evolutionarily conserved. The role of hrT in cardiovascular development, however, has not thus far been determined in any animal model. Using morpholino antisense oligonucleotides, we show that zebrafish embryos lacking hrT function have dysmorphic hearts and an absence of blood circulation. Although the early events in heart formation were normal in hrT morphant embryos, subsequently the hearts failed to undergo looping, and late onset defects in chamber morphology and gene expression were observed. In particular, we found that the loss of hrT function led to a dramatic upregulation of tbx5, a gene required for normal heart morphogenesis. Conversely, we show that overexpression of hrT causes a significant downregulation of tbx5, indicating that one key role of hrT is to regulate the levels of tbx5. Secondly, we found that HrT is required to inhibit the expression of the blood lineage markers gata1 and gata2 in the most posterior lateral plate mesoderm. Finally, we show that HrT is required for vasculogenesis in the trunk, leading to similar vascular defects to those observed in midline mutants such as floating head. hrT expression in the vascular progenitors depends upon midline mesoderm, indicating that this expression is one important component of the response to a midline-derived signal during vascular morphogenesis.
Serum Markers as Tools to Monitor Liver Fibrosis (1998)

Review Articles| August 03 1998 Serum Markers as Tools to Monitor Liver Fibrosis Subject Area: Gastroenterology Akira Hayasaka; Akira Hayasaka First Department of Medicine, Chiba University School of Medicine, Chiba, Japan Search for other works by this author on: This Site PubMed Google Scholar Hiromitsu Saisho Hiromitsu Saisho First Department of Medicine, Chiba University School of Medicine, Chiba, Japan Search for other works by this author on: This Site PubMed Google Scholar Digestion (1998) 59 (4): 381–384. https://doi.org/10.1159/000007493 Article history Published Online: August 03 1998 Content Tools Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn Email Tools Icon Tools Get Permissions Cite Icon Cite Search Site Citation Akira Hayasaka, Hiromitsu Saisho; Serum Markers as Tools to Monitor Liver Fibrosis. Digestion 1 August 1998; 59 (4): 381–384. https://doi.org/10.1159/000007493 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsDigestion Search Advanced Search Keywords: Liver fibrosis, Cirrhosis, Chronic liver disease, Diagnosis, Serum markers, Collagens, Procollagen, Matrix metalloproteinase This content is only available via PDF. 1998Copyright / Drug Dosage / DisclaimerCopyright: All rights reserved. No part of this publication may be translated into other languages, reproduced or utilized in any form or by any means, electronic or mechanical, including photocopying, recording, microcopying, or by any information storage and retrieval system, without permission in writing from the publisher.Drug Dosage: The authors and the publisher have exerted every effort to ensure that drug selection and dosage set forth in this text are in accord with current recommendations and practice at the time of publication. However, in view of ongoing research, changes in government regulations, and the constant flow of information relating to drug therapy and drug reactions, the reader is urged to check the package insert for each drug for any changes in indications and dosage and for added warnings and precautions. This is particularly important when the recommended agent is a new and/or infrequently employed drug.Disclaimer: The statements, opinions and data contained in this publication are solely those of the individual authors and contributors and not of the publishers and the editor(s). The appearance of advertisements or/and product references in the publication is not a warranty, endorsement, or approval of the products or services advertised or of their effectiveness, quality or safety. The publisher and the editor(s) disclaim responsibility for any injury to persons or property resulting from any ideas, methods, instructions or products referred to in the content or advertisements. Article PDF first page preview Close Modal You do not currently have access to this content.
Methylation‐Sensitive Representational Difference Analysis and Its Application to Cancer Research (2003)

Methylation-sensitive representational difference analysis (MS-RDA) was previously established to detect differences in the methylation status of two genomes. This method uses the digestion of genomic DNA with a methylation-sensitive restriction enzyme, HpaII, and PCR to prepare "HpaII-amplicons," followed by RDA. An HpaII-amplicon prepared using betaine and reverse electrophoresis was enriched 3.6-fold (compared with the HpaII-amplicon prepared by the original method) with DNA fragments originating from CpG islands (CGIs). As for the specificity of MS-RDA, it was shown that DNA fragments that are unmethylated in the tester and almost completely methylated in the driver are efficiently isolated. This indicated that genes that are in biallelic methylation or in monoallelic methylation with loss of the other allele are efficiently isolated. Further, by use of two additional methylation-sensitive six-base recognition restriction enzymes, SacII and NarI, more DNA fragments were isolated from CGIs in the 5' regions of genes. After analysis of human lung, gastric, and breast cancers, 12 genes were seen to be silenced and additional genes seen to show decreased expression in association with methylation of genomic regions outside CGIs in the 5' regions of genes. MS-RDA is effective in identifying silenced genes in various cancers.
Mechanisms of Oxidative Damage in Multiple Sclerosis and Neurodegenerative Diseases: Therapeutic Modulation via Fumaric Acid Esters (2012)

Oxidative stress plays a crucial role in many neurodegenerative conditions such as Alzheimer's disease, amyotrophic lateral sclerosis and Parkinson's as well as Huntington's disease. Inflammation and oxidative stress are also thought to promote tissue damage in multiple sclerosis (MS). Recent data point at an important role of anti-oxidative pathways for tissue protection in chronic-progressive MS, particularly involving the transcription factor nuclear factor (erythroid-derived 2)-related factor 2 (Nrf2). Thus, novel therapeutics enhancing cellular resistance to free radicals could prove useful for MS treatment. Here, fumaric acid esters (FAE) are a new, orally available treatment option which had already been tested in phase II/III MS trials demonstrating beneficial effects on relapse rates and magnetic resonance imaging markers. In vitro, application of dimethylfumarate (DMF) leads to stabilization of Nrf2, activation of Nrf2-dependent transcriptional activity and abundant synthesis of detoxifying proteins. Furthermore, application of FAE involves direct modification of the inhibitor of Nrf2, Kelch-like ECH-associated protein 1. On cellular levels, the application of FAE enhances neuronal survival and protects astrocytes against oxidative stress. Increased levels of Nrf2 are detected in the central nervous system of DMF treated mice suffering from experimental autoimmune encephalomyelitis (EAE), an animal model of MS. In EAE, DMF ameliorates the disease course and improves preservation of myelin, axons and neurons. Finally, Nrf2 is also up-regulated in the spinal cord of autopsy specimens from untreated patients with MS, probably as part of a naturally occurring anti-oxidative response. In summary, oxidative stress and anti-oxidative pathways are important players in MS pathophysiology and constitute a promising target for future MS therapies like FAE.
Cascade-type flow of lignocellulosic components through the phase-separation system. (2001)

For the successive total utilization of lignocellulosics, the phase-separation system has been developed. A key of this system is the phase-separation treatment with phenol compounds and concentrated acid. Without heating and pressing, the cell wall with IPN structures is separated into the lignin-based polymers (lignophenols) and carbohydrates within 1 hour. The functionality of materials can be controlled by the properties of phenol and acid in the phase-separation system. The lignophenols had unique properties that conventional lignins did not have. Furthermore, the functionality of lignophenols was controllable using the intramolecular switching function (cleavages of C2-aryl ether linkages by nucleophilic attack of C1-phenolic nuclei to C2). The carbohydrates can be converted to functional oligo-saccharides, simple sugars, alcohols etc. The phase-separation system would form the basis of an advanced molecular-level refining and recycling system for forestry products.
The structure of insulin receptor and its subunits. Evidence for multiple nonreduced forms and a 210,000 possible proreceptor. (1982)

We have identified the subunits of the insulin receptor using immunoprecipitation by antibodies to the insulin receptor after either biosynthetic or surface labeling of cultured human lymphocytes (IM-9). With this approach, we have found there are two major, Mr = 135,000 (alpha), Mr = 95,000 (beta) and one minor, Mr = 210,000 (gamma) subunit. Peptide mapping clearly demonstrates that the major peptides of the alpha and beta subunits are different, whereas similarities exist in the peptide fragments of the gamma subunit and the alpha and beta subunits after limited proteolysis. The gamma subunit, however, is not simply a disulfide heterodimer of alpha and beta subunits, since this subunit was not reduced by 100 mM dithiothreitol plus 5% 2-mercaptoethanol, or even under more potent denaturing conditions, such as 8 M guanidine-HCL and mercaptoethanol at pH 10.5. In nonreduced gels, free insulin receptor subunits are observed, as well as two higher molecular weight bands of Mr = 520,000 and 350,000. On reduction, the 520,000 band was composed primarily of Mr = 210,000 and 95,000 subunits, whereas the 350,000 band was composed primarily of Mr = 135,000 and 95,000 subunits. These data suggest that the two major subunits of the insulin receptor (alpha and beta) are distinct. In addition, there is a third component of the receptor identifiable of 210,000 which may be a proreceptor or some closely associated effector protein. Furthermore, it appears that in the native state several kinds of disulfide oligomers of these subunits exist. These findings suggest a complex model for insulin receptor synthesis and insertion into the membrane.
Size Fractionation of Metal Nanoparticles by Membrane Filtration (2005)

A novel thin film composite nanofiltration (NF) membrane is fabricated by coating a conventional ultrafiltration membrane with a self-assembling amphiphilic graft copolymer. The NF membranes are used in the fractionation of gold nanoparticles to achieve a well-defined particle cutoff diameter and reduced size dispersity (see Figure).
Cytotoxic activity of an interleukin 6-Pseudomonas exotoxin fusion protein on human myeloma cells. (1988)

A chimeric toxin composed of human interleukin 6 (IL-6) attached to a portion of Pseudomonas exotoxin (PE) devoid of its own cell recognition domain has been produced in Escherichia coli. The fusion protein (IL-6-PE40) is cytotoxic to a human myeloma cell line expressing IL-6 receptors but has no effect on IL-6 receptor-negative cells. The specificity of IL-6-PE40 cytotoxicity was demonstrated through competition with excess IL-6 and neutralization with an antibody to IL-6. IL-6-PE40 may be useful in the selective elimination of myeloma cells and other cells with high numbers of IL-6 receptors.
Distinctive Glycerophospholipid Profiles of Human Seminoma and Adjacent Normal Tissues by Desorption Electrospray Ionization Imaging Mass Spectrometry (2011)

Desorption electrospray ionization mass spectrometry (DESI-MS) has been successfully used to discriminate between normal and cancerous human tissue from different anatomical sites. On the basis of this, DESI-MS imaging was used to characterize human seminoma and adjacent normal tissue. Seminoma and adjacent normal paired human tissue sections (40 tissues) from 15 patients undergoing radical orchiectomy were flash frozen in liquid nitrogen and sectioned to 15 μm thickness and thaw mounted to glass slides. The entire sample was two-dimensionally analyzed by the charged solvent spray to form a molecular image of the biological tissue. DESI-MS images were compared with formalin-fixed, hematoxylin and eosin (H&E) stained slides of the same material. Increased signal intensity was detected for two seminolipids [seminolipid (16:0/16:0) and seminolipid (30:0)] in the normal tubule testis tissue; these compounds were undetectable in seminoma tissue, as well as from the surrounding fat, muscle, and blood vessels. A glycerophosphoinositol [PI(18:0/20:4)] was also found at increased intensity in the normal testes tubule tissue when compared with seminoma tissue. Ascorbic acid (i.e., vitamin C) was found at increased amounts in seminoma tissue when compared with normal tissue. DESI-MS analysis was successfully used to visualize the location of several types of molecules across human seminoma and normal tissues. Discrimination between seminoma and adjacent normal testes tubules was achieved on the basis of the spatial distributions and varying intensities of particular lipid species as well as ascorbic acid. The increased presence of ascorbic acid within seminoma compared with normal seminiferous tubules was previously unknown.
Optical Fish Tracking In Fishways Using Neural Networks (2010)

One of the main issues in Computer Vision is to extract the movement of one or several points or objects of interest in an image or video sequence to conduct any kind of study or control process. Different techniques to solve this problem have been applied in numerous areas such as surveillance systems, analysis of traffic, motion capture, image compression, navigation systems and others, where the specific characteristics of each scenario determine the approximation to the problem. This paper puts forward a Computer Vision based algorithm to analyze fish trajectories in high turbulence conditions in artificial structures called vertical slot fishways, designed to allow the upstream migration of fish through obstructions in rivers. The suggested algorithm calculates the position of the fish at every instant starting from images recorded with a camera and using neural networks to execute fish detection on images. Different laboratory tests have been carried out in a full scale fishway model and with living fishes, allowing the reconstruction of the fish trajectory and the measurement of velocities and accelerations of the fish. These data can provide useful information to design more effective vertical slot fishways.
Mass Spectrometry of Intracellular and Membrane Proteins Using Cleavable Detergents (2003)

Detergents have been used to enhance the solubility of hydrophobic biomolecules for decades. Despite the widespread use of detergents in biochemistry, the presence of these molecules often complicates further analysis by mass spectrometry. This study presents a solution to this problem by outlining a method utilizing a novel cleavable detergent, 3-[3-(1,1-bisalkyloxyethyl)pyridin-1-yl]propane-1-sulfonate (PPS). This detergent can be used to extract protein contained within the interior of the cell by disrupting cell membranes. Once the proteins are free from the cell, PPS also assists in protein solubilization by shielding the hydrophobic regions of the newly extracted protein from unfavorable interactions with water. The added advantage of PPS over conventional detergents such as sodium dodecyl sulfate or n-octylglucoside is that the detergent properties that interfere with MALDI mass spectrometry can be eliminated prior to analysis. PPS was found to improve sensitivity in MALDI analyses of both soluble proteins and membrane proteins without degrading spectral quality. The virtues of this strategy were applied to whole cell extracts. Analysis of these extracts resulted in an overall increase in both the number of peaks observed and overall signal intensity.