gebhart/patrepeval huggingface dataset:
The Translocation Inhibitor CAM741 Interferes with Vascular Cell Adhesion Molecule 1 Signal Peptide Insertion at the Translocon (2006)

The cyclopeptolide CAM741 selectively inhibits cotranslational translocation of vascular cell adhesion molecule 1 (VCAM1), a process that is dependent on its signal peptide. In this study we identified the C-terminal (C-) region upstream of the cleavage site of the VCAM1 signal peptide as most critical for inhibition of translocation by CAM741, but full sensitivity to the compound also requires residues of the hydrophobic (h-) region and the first amino acid of the VCAM1 mature domain. The murine VCAM1 signal peptide, which is less susceptible to translocation inhibition by CAM741, can be converted into a fully sensitive signal peptide by two amino acid substitutions identified as critical for compound sensitivity of the human VCAM1 signal peptide. Using cysteine substitutions of non-critical residues in the human VCAM1 signal peptide and chemical cross-linking of targeted short nascent chains we show that, in the presence of CAM741, the N- and C-terminal segments of the VCAM1 signal peptide could be cross-linked to the cytoplasmic tail of Sec61beta, indicating altered positioning of the VCAM1 signal peptide relative to this translocon component. Moreover, translocation of a tag fused N-terminal to the VCAM1 signal peptide is selectively inhibited by CAM741. Our data indicate that the compound inhibits translocation of VCAM1 by interfering with correct insertion of its signal peptide into the translocon.
Cutting Edge: Heat Shock Protein 60 Is a Putative Endogenous Ligand of the Toll-Like Receptor-4 Complex (2000)

Human heat shock protein 60 (hsp60) elicits a potent proinflammatory response in cells of the innate immune system and therefore has been proposed as a danger signal of stressed or damaged cells. We report here that macrophages of C3H/HeJ mice, carrying a mutant Toll-like-receptor (Tlr) 4 are nonresponsive to hsp60. Both the induction of TNF-alpha and NO formation were found dependent on a functional Tlr4 whereas stimulation of macrophages by CpG DNA was Tlr4 independent. We conclude that Tlr4 mediates hsp60 signaling. This is the first report of a putative endogenous ligand of the Tlr4 complex.
득암 최용술에 관한 초고 (2001)

Yong-Sul Chol was born in 1899 in Kwangpyong-ri 150 hwangkan-myon, Youngdong City, Chungbuk Province, Korea. Around 1908 be was separated from bis parents and taken to Japan, where he is believed to have studied Daito Ryu Aiki Jujutsu under Grandmaster Takeda Sokaku for the next 30 years, until Takeda death in 1943. Kintaro Wadanabi was a close friend of Takeda Sokaku and arranged my introduction to him. Takeda Sokaku liked me and feeling great sympathy for my situation, decided to adopt me. Upon my adoption he gave me the Japanese name Yoshida Asao. Yong-Sul Chol was about 11 years old at this time. His home and school were located on Seo Jang Mountain in the area of Akedo. When Yong-Sul Chol was about 28 years old it was arranged by politicians for my teacher and his most outstanding students to travel to Hawaii in order to give an exhibition tour.
Experimental knee pain model in rats and analgesic effect of sodium hyaluronate (SPH). (1988)

Using the model of knee pain reaction induced by intra-articular injection of endogenous pain substances, especially bradykinin (BK) in rats, the mechanism of the analgesic effect of sodium hyaluronate (SPH) was investigated. The simultaneous administration of prostaglandin E2 with BK or hyaluronidase digestion of endogenous hyaluronic acid (HA) in our experiments brought remarkable hyperalgesia on BK-induced knee pain. These results suggest that higher sensitivity to the pain reaction is induced in a diseased joint (higher prostaglandin content, lower concentration and molecular size of HA in synovial fluid) than in a normal one. SPH definitely decreased BK-induced pain, and its analgesic effect was observed for a longer period, depending on its dose in pre-treatment and the degree of its distribution in synovial tissues. As the analgesic effect of SPH was observed in the hyaluronidase-treated joint as well, it is suggested that the increasing viscosity of synovial fluid caused by increasing HA concentration can decrease the pain even without normalizing molecular size of HA in the joint. HA oligomer and other compounds with similar viscosity or with similar polyanionic character as SPH showed no analgesic effect. From these results, it seems that the characteristic steric configurations of higher molecular HA are needed for the manifestation of the analgesic effect. SPH seems to show its analgesic effect by covering pain receptors in synovial tissues and holding endogenous pain substances in its molecule.
Quantitation of Human Immunodeficiency Virus Type 1 in Breast Milk (2003)

The distribution and stability of human immunodeficiency virus type 1 (HIV-1) in breast milk (BM) components remain largely unknown. Inhibitory effects, if any, of BM on HIV RNA and DNA PCR amplification are poorly understood. We have addressed these issues by using virus-spiked BM samples from HIV-negative women. BM samples from HIV-negative women were spiked with HIV-1 virions or cells containing a single integrated copy of HIV DNA (8E5/LAV). After incubation under different experimental conditions, viral RNA was detected by the Roche Amplicor UltraSensitive assay in whole-milk, skim milk, and lipid fractions. We found excellent correlation between HIV-1 input copy and recovery in whole milk (r = 0.965, P < 0.0001), skim milk (r = 0.972, P < 0.0001), and the lipid fraction (r = 0.905, P < 0.001). PCR inhibition was observed in less than 10% of the spiked samples. Similar levels of inhibition were noted in BM samples collected from HIV-infected women. HIV proviral DNA was detected in BM samples using real-time PCR (linear correlation between the threshold cycle versus log DNA copy number, >0.982). The effects of incubation duration and temperature and repeated freeze-thaw cycles on HIV RNA recovery were analyzed. HIV RNA levels were remarkably stable in whole milk after three freeze-thaw cycles and for up to 30 h at room temperature. Our findings improve the understanding of the dynamics of HIV detection in BM and the conditions for BM sample collection, storage, and processing.
The Measurement of Matrix and Fracture Properties in Naturally Fractured Cores (1993)

ABSTRACT This paper describes a new laboratory technique to evaluate the properties of a naturally fractured, low permeability core sample. We specifically determine (1) the porosity of the matrix, (2) the permeability of the matrix, (3) the effective width of the fractures, and (4) the permeability of the fractures. New laboratory equipment has been designed and constructed to conduct pressure pulse tests in either a homogeneous or a fractured core sample. Analytical solutions have been developed to model gas flow in a fractured core sample during a pressure pulse test. An automatic history matching program has been developed to analyze the laboratory measured pressure transient data using the analytical solutions. The new technique has been used to measure the matrix and fracture properties in twelve naturally fractured, Devonian Shale cores. The technique we developed in this research is new to the petroleum industry. Our laboratory equipment is unique, and the analytical solutions have not been published in the literature. With this technique, we can measure matrix properties as low as 10−9 md. This is a significant step forward in permeability measurement because the lowest permeability that most existing laboratories can measure is about 10−6 millidarcies.
Formation of Volatile Compounds in Model Experiments with Crude Leek (Allium ampeloprasum Var. Lancelot) Enzyme Extract and Linoleic Acid or Linolenic Acid (2004)

Three continuous assays are described for lipoxygenase (LOX), hydroperoxide lyase (HPL) and alcohol dehydrogenase (ADH) in leek tissue. The catalytic activity of LOX showed significant difference (significance level 5%) between linolenic acid (9.43 x 10(-)(4) katals per kg protein) and linoleic acid (2.53 x 10(-)(4) katals per kg protein), and the pH-optimum of LOX was 4.5-5.5 against linoleic acid. The catalytic activity of HPL was statistically the same for 9-(S)-hydroperoxy-(10E,12Z)-octadecadienoic acid (1.01 x 10(-)(2) katals per kg protein) and 13-(S)-hydroperoxy-(9Z,11E)-octadecadienoic acid (7.69 x 10(-)(3) katals per kg protein). ADH showed a catalytic activity of 5.01 x 10(-)(4) katals/kg of protein toward hexanal. Model experiments with crude enzyme extract from leek mixed with linoleic acid or linolenic acid demonstrated differences in the amount of produced aroma compounds. Linoleic acid resulted in significantly most hexanal, heptanal, (E)-2-heptenal, (E)-2-octenal, (E,E)-2,4-decadienal, pentanol, and hexanol, whereas linolenic acid resulted in significantly most (E)-2-pentenal, (E)-2-hexenal, (E,Z)-2,4-heptadienal, (E,E)-2,4-heptadienal, and butanol. Leek LOX produced only the 13-hydroperoxide of linoleic acid and linolenic acid.
<i>L</i>-Arginine: A Unique Amino Acid for Improving Depressed Wound Immune Function following Hemorrhage (2002)

Thus, L-arginine might improve local wound cell function by decreasing the inflammatory response at the wound site. Since L-arginine protected wound immune cell function this amino acid might represent a novel and useful adjunct to fluid resuscitation for decreasing wound complications following hemorrhage.
Targeting cancer vasculature via endoglin/CD105: a novel antibody-based diagnostic and therapeutic strategy in solid tumours (2009)

Endoglin/CD105 is well acknowledged as being the most reliable marker of proliferation of endothelial cells, and it is overexpressed on tumour neovasculature. Our current knowledge of its structure, physiological role, and tissue distribution suggests that targeting of endoglin/CD105 is a novel and powerful diagnostic and therapeutic strategy in human malignancies, through the imaging of tumour-associated angiogenesis and the inhibition of endothelial cell functions related to tumour angiogenesis. Among biotherapeutic agents, monoclonal antibodies have shown a major impact on the clinical course of human malignancies of different histotypes. Along this line, the potential efficacy of anti-endoglin/CD105 antibodies and their derivatives for clinical purposes in cancer is supported by a large body of available pre-clinical in vitro and in vivo data. In this review, the main findings supporting the translation of antibody-based endoglin/CD105 targeting from pre-clinical studies to clinical applications in human cancer are summarized and discussed.
Tricks with tetramers: how to get the most from multimeric peptide–MHC (2009)

The development of fluorochrome-conjugated peptide-major histocompatibility complex (pMHC) multimers in conjunction with continuing advances in flow cytometry has transformed the study of antigen-specific T cells by enabling their visualization, enumeration, phenotypic characterization and isolation from ex vivo samples. Here, we bring together and discuss some of the 'tricks' that can be used to get the most out of pMHC multimers. These include: (1) simple procedures that can substantially enhance the staining intensity of cognate T cells with pMHC multimers; (2) the use of pMHC multimers to stain T cells with very-low-affinity T-cell receptor (TCR)/pMHC interactions, such as those that typically predominate in tumour-specific responses; and (3) the physical grading and clonotypic dissection of antigen-specific T cells based on the affinity of their cognate TCR using mutant pMHC multimers in conjunction with new approaches to the molecular analysis of TCR gene expression. We also examine how soluble pMHC can be used to examine T-cell activation, manipulate T-cell responses and study allogeneic and superantigen interactions with TCRs. Finally, we discuss the problems that arise with pMHC class II (pMHCII) multimers because of the low affinity of TCR/pMHCII interactions and lack of 'coreceptor help'.
One-Pot Synthesis of Brush-Like Polymers via Integrated Ring-Opening Metathesis Polymerization and Polymerization of Amino Acid N-Carboxyanhydrides (2009)

We report here the integration of ring-opening metathesis polymerization (ROMP) and ring-opening polymerization of the amino acid N-carboxyanhydride (NCA) to allow facile synthesis of brush-like polymers containing polypeptide as the brush side chains. ROMP of N-trimethylsilyl norbornenes rendered the preparation of poly(norbornene)s bearing pendant N-TMS groups. With no need to purify the resulting polymers, such macromolecular initiators could subsequently initiate controlled NCA polymerizations. Brush-like poly(norbornene)s with grafted polypeptides or block copolypeptides were readily obtained with controlled molecular weights and narrow molecular weight distributions. Because numerous ROMP and NCA monomers are widely available, this novel polymerization technique will allow easy access to numerous brush-like hybrid macromolecules with unprecedented properties and broad applications.
Infectious cDNA Clone of the Epidemic West Nile Virus from New York City (2002)

We report the first full-length infectious clone of the current epidemic, lineage I, strain of West Nile virus (WNV). The full-length cDNA was constructed from reverse transcription-PCR products of viral RNA from an isolate collected during the year 2000 outbreak in New York City. It was cloned into plasmid pBR322 under the control of a T7 promoter and stably amplified in Escherichia coli HB101. RNA transcribed from the full-length cDNA clone was highly infectious upon transfection into BHK-21 cells, resulting in progeny virus with titers of 1 x 10(9) to 5 x 10(9) PFU/ml. The cDNA clone was engineered to contain three silent nucleotide changes to create a StyI site (C to A and A to G at nucleotides [nt] 8859 and 8862, respectively) and to knock out an EcoRI site (A to G at nt 8880). These genetic markers were retained in the recovered progeny virus. Deletion of the 3'-terminal 199 nt of the cDNA transcript abolished the infectivity of the RNA. The plaque morphology, in vitro growth characteristics in mammalian and insect cells, and virulence in adult mice were indistinguishable for the parental and recombinant viruses. The stable infectious cDNA clone of the epidemic lineage I strain will provide a valuable experimental system to study the pathogenesis and replication of WNV.
The Feasibility of Making an Artificial Vagina at the Time of Anterior Exenteration (1973)

At the time of an anterior exenteration a space was successfully maintained in the pelvis for a vagina using a balsa wood splint covered with an amniotic membrane. Re-epithelialization occurred under the membrane by squamous cells from the vulva making it unnecessary to make an artificial vagina with asplit thickness graft.
Production of mouse lymphotoxin by phytohemagglutinin-stimulated spleen cells requires two cell fractions (1982)

The appearance of lymphotoxin in the culture fluid of phytohemagglutinin (PHA)-stimulated mouse spleen cells required two cell fractions that were separated by adherence to plastic. Upon stimulation with PHA, neither cell fraction alone produced significant amounts of lymphotoxin; however, when the cell fractions were combined and then stimulated with PHA, full activity was produced. Cytotoxic activity was not fully restored by combining PHA-stimulated cultured fluids from adherent and nonadherent cell fractions. This indicated that the cytotoxic activity was not the result of two factors, one produced by each cell fraction, that acted on the target cells, but rather, two cells interacted to produce lymphotoxin. Treatment of the unfractionated spleen cells with monoclonal anti-Thy1.2 and complement before PHA stimulation greatly reduced the production of lymphotoxin and indicated that at least one of the cells was a T cell. Lymphotoxin production was partially restored by the addition of nonadherent cells to the anti-Thy1.2-treated cells, suggesting that the T cell was nonadherent. Treatment of unfractionated cells with either silica or carrageenan had no effect on the subsequent production of lymphotoxin by PHA, suggesting that the adherent cell was not actively phagocytic.
Simian virus 40 tandem repeated sequences as an element of the early promoter. (1981)

On the late side of the simian virus 40 (SV40) DNA replication origin are several sets of tandem repeated sequences, the largest of which is 72 base pairs long. The role of these sequences was examined through construction of deletion mutants of SV40. A mutant from which one of the 72-base-pair repeated units was removed is viable upon transfection of monkey kidney cells with viral DNA. Extension of this deletion into the second repeated unit, however, leads to nonviability, as recognized by the absence of early transcription and of tumor antigen production. These observations indicate that the 72-base-pair repeated sequences form an essential element in the early viral transcriptional promoter and explain the inability of such a deleted genome to complement an early temperature-sensitive mutant of SV40, tsA, as well as the failure to replicate its DNA. In a parallel experiment it was found that the extended deletion mutant was also unable to complement a late temperature-sensitive mutant of SV40, tsB. This suggests that the extended mutant is also defective in DNA replication or late transcription (or both).
Two Binding Orientations for Peptides to the Src SH3 Domain: Development of a General Model for SH3-Ligand Interactions (1994)

Solution structures of two Src homology 3 (SH3) domain-ligand complexes have been determined by nuclear magnetic resonance. Each complex consists of the SH3 domain and a nine-residue proline-rich peptide selected from a large library of ligands prepared by combinatorial synthesis. The bound ligands adopt a left-handed polyproline type II (PPII) helix, although the amino to carboxyl directionalities of their helices are opposite. The peptide orientation is determined by a salt bridge formed by the terminal arginine residues of the ligands and the conserved aspartate-99 of the SH3 domain. Residues at positions 3, 4, 6, and 7 of both peptides also intercalate into the ligand-binding site; however, the respective proline and nonproline residues show exchanged binding positions in the two complexes. These structural results led to a model for the interactions of SH3 domains with proline-rich peptides that can be used to predict critical residues in complexes of unknown structure. The model was used to identify correctly both the binding orientation and the contact and noncontact residues of a peptide derived from the nucleotide exchange factor Sos in association with the amino-terminal SH3 domain of the adaptor protein Grb2.
Sphingosine Mediates the Immediate Negative Inotropic Effects of Tumor Necrosis Factor-α in the Adult Mammalian Cardiac Myocyte (1997)

To determine whether activation of the neutral sphingomyelinase pathway was responsible for the immediate (<30 min) negative inotropic effects of tumor necrosis factor-alpha (TNF-alpha), we examined sphingosine levels in diluent and TNF-alpha-stimulated cardiac myocytes. TNF-alpha stimulation of adult feline cardiac myocytes provoked a rapid (<15 min) increase in the hydrolysis of [14C]sphingomyelin in cell-free extracts, as well as an increase in ceramide mass, consistent with cytokine-induced activation of the neutral sphingomyelinase pathway. High performance liquid chromatographic analysis of lipid extracts from TNF-alpha-stimulated cardiac myocytes showed that TNF-alpha stimulation produced a rapid (<30 min) increase in free sphingosine levels. Moreover, exogenous D-sphingosine mimicked the effects of TNF-alpha on intracellular calcium homeostasis, as well as the negative inotropic effects of TNF-alpha in isolated contracting myocytes; time course studies showed that exogenous D-sphingosine produced abnormalities in cell shortening that were maximal at 5 min. Finally, blocking sphingosine production using an inhibitor of ceramidase, n-oleoylethanolamine, completely abrogated the negative inotropic effects of TNF-alpha in isolated contracting cardiac myocytes. Additional studies employing biologically active ceramide analogs and sphingosine 1-phosphate suggested that neither the immediate precursor of sphingosine nor the immediate metabolite of sphingosine, respectively, were likely to be responsible for the immediate negative inotropic effects of TNF-alpha. Thus, these studies suggest that sphingosine mediates the immediate negative inotropic effects of TNF-alpha in isolated cardiac myocytes.
Cerebrospinal fluid is drained primarily via the spinal canal and olfactory route in young and aged spontaneously hypertensive rats (2014)

We have demonstrated a contrast-enhanced CT technique for measuring and visualising CSF dynamics in vivo. These results indicate substantial drainage of CSF via spinal and olfactory routes, but there was little evidence of drainage via sagittal sinus arachnoid granulations in either young or aged animals. The data suggests that spinal and olfactory routes are the primary routes of CSF drainage and that sagittal sinus arachnoid granulations play a minor role, even in aged rats with higher ICP.
Change in ascorbate radical production in an irradiated experimental tumor with increased tumor size. (1996)

We have reported that ascorbate radical (Asc.-) could serve as an indicator of the amount of hydroxyl radical and superoxide produced by irradiation in vivo. Using this method, we investigated the relationship between tumor size and Asc.- production after irradiation (10 Gy) and between tumor size and the radical-scavenging ability of WR-2721 (300 mg/kg). Asc.- was measured in normal muscle and SCC-VII tumors transplanted into mice (n = 6). In tumors, the increase in Asc.- significantly decreased with increasing tumor size (r = -0.483; P < 0.05). The increase in Asc.- production after irradiation was more inhibited by WR-2721 in normal muscle tissue than in tumor tissue at various sizes. In tumors, the increase in Asc.- was less inhibited by WR-2721 with increasing tumor size. These results demonstrate that the increase in radical production after irradiation and drug distribution decreased with increasing tumor size and that WR-2721 has excellent differential protection. This method is expected to measure changes in the amounts of local hydroxyl radical and superoxide modified by a change of tumor environment or drug administration.
<title>Using fractal compression scheme to embed a digital signature into an image</title> (1997)

With the increase in the number of digital networks and recording devices, digital images appear to be a material, especially still images, whose ownership is widely threatened due to the availability of simple, rapid and perfect duplication and distribution means. It is in this context that several European projects are devoted to finding a technical solution which, as it applies to still images, introduces a code or watermark into the image data itself. This watermark should not only allow one to determine the owner of the image, but also respect its quality and be difficult to revoke. An additional requirement is that the code should be retrievable by the only mean of the protected information. In this paper, we propose a new scheme based on fractal coding and decoding. In general terms, a fractal coder exploits the spatial redundancy within the image by establishing a relationship between its different parts. We describe a way to use this relationship as a means of embedding a watermark. Tests have been performed in order to measure the robustness of the technique against JPEG conversion and low pass filtering. In both cases, very promising results have been obtained.