gebhart/patrepeval huggingface dataset:
CD56 in the Immune System: More Than a Marker for Cytotoxicity? (2017)

Over the past years, the phenotypic and functional boundaries distinguishing the main cell subsets of the immune system have become increasingly blurred. In this respect, CD56 (also known as neural cell adhesion molecule) is a very good example. CD56 is the archetypal phenotypic marker of natural killer cells but can actually be expressed by many more immune cells, including alpha beta T cells, gamma delta T cells, dendritic cells, and monocytes. Common to all these CD56-expressing cell types are strong immunostimulatory effector functions, including T helper 1 cytokine production and an efficient cytotoxic capacity. Interestingly, both numerical and functional deficiencies and phenotypic alterations of the CD56<sup>+</sup> immune cell fraction have been reported in patients with various infectious, autoimmune, or malignant diseases. In this review, we will discuss our current knowledge on the expression and function of CD56 in the hematopoietic system, both in health and disease.
A New Recombinant Single Chain Trispecific Antibody Recruits T Lymphocytes to Kill CEA (Carcinoma Embryonic Antigen) Positive Tumor Cells In Vitro Efficiently (2004)

Anti-tumor associated antigen (TAA).CD3.CD28 trispecific antibody(TsAb) is able to provide two signals for fully and continuously activation of T lymphocytes and recruit them around tumor cells, presenting an attractive concept in tumor immunotherapy. Here, a new single chain trispecific antibody (scTsAb), named CEA-scTsAb, was constructed by fusion of anti-CEA (Carcinoma Embryonic Antigen) single chain antibody (scFv), anti-CD3 scFv and anti-CD28 VH, spaced by polypeptide interlinkers taken from the fragment of constant region (FC) of human IgG and human serum albumin (HSA). It was expressed in Escherichia coli at low temperature (30 degrees C) with up to 50% of the antibody being present in soluble form. After one step of DEAE anion chromatography, the soluble product was sufficiently pure for further in vitro activity assays. First, it was proved that CEA-scTsAb could recognize three antigens (CEA, CD28 and Jurkat cell membrane antigen) specifically and could distinguish antigen positive cells from antigen negative cells in vitro. Then fresh PBMC (peripheral blood mononuclear cells), without being pre-treated by co-stimulatory reagents, such as IL-2 or CD28 mAb, were used as effector cells to test their ability to mediate tumor specific cytolysis of CEA-positive tumor cells, SW1116. It was found by photomicrography that T lymphocytes were attracted to SW1116 cells in the presence of CEA-scTsAb, which resulted in effective cytolysis of tumor cells. As shown by MTT assay, the efficacy of tumor specific cytolysis mediated by CEA-scTsAb related to both the quantity and activation of PBMC. At an effector cells/target cells ratio (E/T) of 5, it was proved by dual-color FACS with propidium iodide (PI) and FITC-annexin V that both necrosis and apoptosis of tumor cells were causes of tumor specific cytolysis. In summary, a new single chain trispecific (CEA x CD3 x CD28) antibody was constructed and characterized carefully in this paper and was found to possess functions: (i) to activate T lymphocytes independently of additional co-stimulatory signal, (ii) to attract activated T lymphocytes around CEA-positive tumor cells, (iii) to attack CEA-positive tumor cells with recruited T lymphocytes. Because it recognizes a widely distributed tumor antigen (CEA), with moderate molecular weight (about 75 kDa) and a simple production procedure, and is able to mediate a high level of tumor specific cytolysis without any additional co-stimulating reagents, CEA-scTsAb is very promising for the task of immunotherapy in future.
Aspirin and salicylate bind to immunoglobulin heavy chain binding protein (BiP) and inhibit its ATPase activity in human fibroblasts (2001)

Salicylic acid (SA), an endogenous signaling molecule of plants, possesses anti-inflammatory and anti-neoplastic actions in human. Its derivative, aspirin, is the most commonly used anti-inflammatory and analgesic drug. Aspirin and sodium salicylate (salicylates) have been reported to have multiple pharmacological actions. However, it is unclear whether they bind to a cellular protein. Here, we report for the first time the purification from human fibroblasts of a approximately 78 kDa salicylate binding protein with sequence identity to immunoglobulin heavy chain binding protein (BiP). The Kd values of SA binding to crude extract and to recombinant BiP were 45.2 and 54.6 microM, respectively. BiP is a chaperone protein containing a polypeptide binding site recognizing specific heptapeptide sequence and an ATP binding site. A heptapeptide with the specific sequence displaced SA binding in a concentration-dependent manner whereas a control heptapeptide did not. Salicylates inhibited ATPase activity stimulated by this specific heptapeptide but did not block ATP binding or induce BiP expression. These results indicate that salicylates bind specifically to the polypeptide binding site of BiP in human cells that may interfere with folding and transport of proteins important in inflammation.
Simple and efficient production of embryonic stem cell-embryo chimeras by coculture. (1993)

A method for the production of embryonic stem (ES) cell-embryo chimeras was developed that involves the simple coculture of eight-cell embryos on a lawn of ES cells. After coculture, the embryos with ES cells attached are transferred to normal embryo culture medium and allowed to develop to the blastocyst stage before reimplantation into foster mothers. Although the ES cells initially attach to the outside of the embryos, they primarily colonize the inner cell mass and its derivatives. This method results in the efficient production of chimeras with high levels of chimerism including the germ line. As embryos are handled en masse and manipulative steps are minimal, this method should greatly reduce the time and effort required to produce chimeric mice.
Kizzle: A Signature Compiler for Exploit Kits (2015)

In recent years, the drive-by malware space has undergone significant consolidation. Today, the most common source of drive-by downloads are the so-called exploit kits. Exploit kits signify a drastic consolidation of the process of malware creation and delivery. This paper presents Kizzle, the first prevention technique specifically designed for finding exploit kits. Our analysis of exploit kits shows that while the actual JavaScript delivered by kits varies greatly, the code observed after it is sufficiently unpacked and deobfuscated varies much less. The approach taken by Kizzle is based in our observation that, while exploit kits change the malware they deliver frequently, kit authors generally \emph{reuse} much of their code from version to version. Ironically, this well-regarded software engineering practice allows us to build a scalable and precise detector that is able to quickly respond to superficial but frequent changes in exploit kits. Kizzle is able to generate anti-virus signatures for detecting exploit kits. These signatures compare favorably to those created by hand by security analysts. Yet Kizzle is highly responsive in that able to automatically generate new {signatures} within hours. %Our approach aims to reduce the imbalance between the attacker who often only needs to make cosmetic changes to their malware to thwart detection, and the defender, whose role requires much manual effort. Our experiments show that Kizzle produces high-accuracy signatures using a scalable cloud-based analysis. When evaluated over a four-week period, false positive rates for Kizzle are under 0.03%, while the false negative rates are under 5%. Both of these numbers compare favorably with the performance of commercial AV engines that use hand-written signatures.
Rapid and delayed effects of epidermal growth factor on gluconeogenesis (1993)

Most reports on the effects of epidermal growth factor (EGF) on gluconeogenesis have indicated that such effects depend on the substrate used and are only observable after a lag time of 30-40 min. Recently, an immediate and transient effect of EGF on glucose synthesis was described in a perfused liver system. Here we extend the study of the effect of EGF on gluconeogenesis to isolated hepatocytes from fasted rats. The delayed effect of EGF on gluconeogenesis was studied by adding the substrate 40 min after the peptide. Under these conditions EGF increased glucose synthesis from pyruvate, decreased it when the substrate was lactate or glycerol and did not modify gluconeogensis from fructose or dihydroxyacetone. EGF did not affect the metabolic flux through glycolysis, determined as the production of lactate+pyruvate from 30 mM glucose. Furthermore, EGF did not modify the metabolic flux through pyruvate kinase, determined as the production of lactate+pyruvate from 1 mM dihydroxyacetone. The differing effects of EGF on gluconeogenesis depending on the substrate used can be explained by the effects of EGF on the cytosolic redox state (measured as the lactate/pyruvate ratio). About 20 min after the addition of EGF, the mitochondrial redox state (measured as the 3-hydroxybutyrate/acetoacetate ratio) decreased. This effect of EGF was blocked by ammonium, which also abolished the effect of the peptide on gluconeogenesis. Thus the effect of EGF at the mitochondrial level appears to be necessary for its effects on gluconeogenesis. Taken together, our results indicate that the delayed effects of EGF on gluconeogenesis are secondary to the effects of the peptide at both the mitochondrial and cytosolic levels. In addition to these delayed effects, we observed that EGF rapidly and transiently stimulated glucose synthesis from lactate, decreased the cytosolic redox state and increased oxygen consumption. All of these rapid effects required the presence of extracellular calcium and disappeared in the presence of rotenone, suggesting that this rapid effect of EGF on gluconeogenesis is secondary to the stimulation of mitochondrial respiration.
A fully synthetic human Fab antibody library based on fixed VH/VL framework pairings with favorable biophysical properties (2013)

This report describes the design, generation and testing of Ylanthia, a fully synthetic human Fab antibody library with 1.3E+11 clones. Ylanthia comprises 36 fixed immunoglobulin (Ig) variable heavy (VH)/variable light (VL) chain pairs, which cover a broad range of canonical complementarity-determining region (CDR) structures. The variable Ig heavy and Ig light (VH/VL) chain pairs were selected for biophysical characteristics favorable to manufacturing and development. The selection process included multiple parameters, e.g., assessment of protein expression yield, thermal stability and aggregation propensity in fragment antigen binding (Fab) and IgG1 formats, and relative Fab display rate on phage. The framework regions are fixed and the diversified CDRs were designed based on a systematic analysis of a large set of rearranged human antibody sequences. Care was taken to minimize the occurrence of potential posttranslational modification sites within the CDRs. Phage selection was performed against various antigens and unique antibodies with excellent biophysical properties were isolated. Our results confirm that quality can be built into an antibody library by prudent selection of unmodified, fully human VH/VL pairs as scaffolds.
Quantitative Analysis of Human Red Blood Cell Proteome (2017)

Red blood cells (RBCs) are the most abundant cell type in the human body. RBCs and, in particular, their plasma membrane composition have been extensively studied for many years. During the past decade proteomics studies have extended our knowledge on RBC composition; however, these studies did not provide quantitative insights. Here we report a large-scale proteomics investigation of RBCs and their "white ghost" membrane fraction. Samples were processed using the multienzyme digestion filter-aided sample preparation (MED-FASP) and analyzed using Q-Exactive mass spectrometer. Protein abundances were computed using the total protein approach (TPA). The validation of the data with stable isotope-labeled peptide-based protein quantification followed. Our in-depth analysis resulted in the identification of 2650 proteins, of which 1890 occurred at more than 100 copies per cell. We quantified 41 membrane transporter proteins spanning an abundance range of five orders of magnitude. Some of these, including the drug transporter ABCA7 and choline transporters SLC44A1 and SLC44A2, have not previously been identified in RBC membranes. Comparison of protein copy numbers assessed by proteomics showed a good correlation with literature data; however, abundances of several proteins were not consistent with the classical references. Because we validated our findings by a targeted analysis using labeled standards, our data suggest that some older reference data from a variety of biochemical approaches are inaccurate. Our study provides the first "in-depth" quantitative analysis of the RBC proteome and will promote future studies of erythrocyte structure, functions, and disease.
Sequence-based in silico analysis of well studied Hepatitis C Virus epitopes and their variants in other genotypes (particularly genotype 5a) against South African human leukocyte antigen backgrounds (2012)

While in vivo and in vitro studies are needed to confirm immunogenic epitopes, in silico HCV epitope vaccine design which takes into account HCV variation and host allele frequency will maximize population coverage in different ethnic groups.
Absorption of Intact Oligosaccharide in Health and Disease (1974)

Conference Article| October 01 1974 Absorption of Intact Oligosaccharide in Health and Disease IAN S. MENZIES IAN S. MENZIES 1Department of Chemical Pathology, St Thomas's Hospital, London SE1 7EH, U.K. Search for other works by this author on: This Site PubMed Google Scholar Biochem Soc Trans (1974) 2 (5): 1042–1047. https://doi.org/10.1042/bst0021042 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn MailTo Cite Icon Cite Get Permissions Citation IAN S. MENZIES; Absorption of Intact Oligosaccharide in Health and Disease. Biochem Soc Trans 1 October 1974; 2 (5): 1042–1047. doi: https://doi.org/10.1042/bst0021042 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 JournalsBiochemical Society Transactions Search Advanced Search This content is only available as a PDF. © 1974 Biochemical Society1974 Article PDF first page preview Close Modal You do not currently have access to this content.
Graphite/Liquid Mixed Matrices for Laser Desorption/Ionization Mass Spectrometry (1996)

A combination of liquid matrix and graphite particulates (2 μm) has been proposed as a method suitable for the laser desorption/ionization mass spectrometry of peptides and proteins (Sunner, J.; et al. Anal. Chem. 1995, 67, 4335). Here we demonstrate the potential of this approach as a straightforward, and very general, method of achieving the ultraviolet laser desorption/ionization of a broad range of intermediate weight analytes. The desorption/ionization mechanism, the influence of preparative procedures, and the breadth of application of this methodology have been investigated. A simple and robust preparative procedure is presented for the analysis of proteins, oligosaccharides, and synthetic polymers. Detection sensitivities are in the femtomole region for lower molecular weight peptides and oligosaccharides. The graphite acts as an energy transfer medium by absorbing the UV radiation, leading to thermal desorption of the liquid matrix and analyte. The liquid matrix was observed to fulfill several important roles. In the case of peptides and proteins, which preferentially form protonated molecular ions, it acts as a protonating agent. It also enhances the signal intensities of cationized species (e.g., polysaccharides and polar polymers) by assisting their desorption. An excess of liquid matrix serves to cool the analyte during the desorption step and minimize decomposition. The presence of liquid matrices increases the sample lifetime at a particular desorption spot, minimizing the time-consuming search for "hot spots". The addition of cationizing salts has been shown to improve the quality of mass spectra obtained for polar polymers and extend the range of materials that can be investigated to include apolar synthetic polymers.
Incidence of c-Ki-ras activation in N-methyl-N-nitrosourea-induced mammary carcinomas in pituitary-isografted mice. (1992)

We found previously that mouse mammary epithelial cells cultured in the presence of the mammogenic hormones progesterone and prolactin and treated with the carcinogen N-methyl-N-nitrosourea produced a high frequency of hyperplastic alveolar nodules and carcinomas with squamous metaplasia upon transplantation to syngeneic mice. The majority of these mammary transformants had an activated c-Ki-ras proto-oncogene with a specific point mutation in codon 12 (G35 to A35). To determine whether these in vitro findings parallel mammary carcinogenesis in vivo, virgin female mice were pituitary isografted to increase their circulating levels of progesterone and prolactin. The pituitary isograft results in an increase in proliferation, leading to lobulo-alveolar development and differentiation of the mammary epithelial cells. Five weeks after pituitary isografting, the mice were treated with a single injection of N-methyl-N-nitrosourea (50 micrograms/g body weight). Greater than 90% of the N-methyl-N-nitrosourea-treated mice developed mammary carcinomas between 3 and 7 months after treatment. The majority (75%) of the carcinomas had histopathology identical to that of tumors induced in vitro in the presence of progesterone and prolactin. A number of the mammary cancers (17%) induced in pituitary-isografted mice also had the identical point mutation in the c-Ki-ras proto-oncogene found in the in vitro studies. These results suggest that the hormonal milieu around the time of carcinogen exposure affects not only the incidence and phenotype of the mammary transformants but also the molecular events associated with mammary carcinogenesis.
Targeting of the Bmi-1 Oncogene/Stem Cell Renewal Factor by MicroRNA-128 Inhibits Glioma Proliferation and Self-Renewal (2008)

MicroRNAs (miR) show characteristic expression signatures in various cancers and can profoundly affect cancer cell behavior. We carried out miR expression profiling of human glioblastoma specimens versus adjacent brain devoid of tumor. This revealed several significant alterations, including a pronounced reduction of miR-128 in tumor samples. miR-128 expression significantly reduced glioma cell proliferation in vitro and glioma xenograft growth in vivo. miR-128 caused a striking decrease in expression of the Bmi-1 oncogene, by direct regulation of the Bmi-1 mRNA 3'-untranslated region, through a single miR-128 binding site. In a panel of patient glioblastoma specimens, Bmi-1 expression was significantly up-regulated and miR-128 was down-regulated compared with normal brain. Bmi-1 functions in epigenetic silencing of certain genes through epigenetic chromatin modification. We found that miR-128 expression caused a decrease in histone methylation (H3K27me(3)) and Akt phosphorylation, and up-regulation of p21(CIP1) levels, consistent with Bmi-1 down-regulation. Bmi-1 has also been shown to promote stem cell self-renewal; therefore, we investigated the effects of miR-128 overexpression in human glioma neurosphere cultures, possessing features of glioma "stem-like" cells. This showed that miR-128 specifically blocked glioma self-renewal consistent with Bmi-1 down-regulation. This is the first example of specific regulation by a miR of a neural stem cell self-renewal factor, implicating miRs that may normally regulate brain development as important biological and therapeutic targets against the "stem cell-like" characteristics of glioma.
Realistic modeling for facial animation (1995)

Article Realistic modeling for facial animation Share on Authors: Yuencheng Lee University of Toronto, Department of Computer Science, 10 King's College Road, Toronto, ON, Canada University of Toronto, Department of Computer Science, 10 King's College Road, Toronto, ON, CanadaView Profile , Demetri Terzopoulos University of Toronto, Department of Computer Science, 10 King's College Road, Toronto, ON, Canada University of Toronto, Department of Computer Science, 10 King's College Road, Toronto, ON, CanadaView Profile , Keith Waters Digital Equipment Corporation, Cambridge Research Lab., One Kendall Square, Cambridge, MA Digital Equipment Corporation, Cambridge Research Lab., One Kendall Square, Cambridge, MAView Profile Authors Info & Claims SIGGRAPH '95: Proceedings of the 22nd annual conference on Computer graphics and interactive techniquesSeptember 1995 Pages 55–62https://doi.org/10.1145/218380.218407Online:15 September 1995Publication History 499citation4,950DownloadsMetricsTotal Citations499Total Downloads4,950Last 12 Months84Last 6 weeks9 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
Modulation of Hepatitis C Virus Genome Replication by Glycosphingolipids and Four-Phosphate Adaptor Protein 2 (2014)

Like most viruses with a positive-sense RNA genome, HCV replicates its RNA on remodeled host membranes composed of lipids hijacked from various internal membrane compartments. During infection, HCV induces massive production and retargeting of the PI4P lipid to its replication complex. However, the role of PI4P in HCV replication is not well understood. In this study, we have shown that FAPP2, a PI4P effector and glycosphingolipid-binding protein, is recruited to the HCV replication complex and is required for HCV genome replication and replication complex formation. More importantly, this study demonstrates, for the first time, the crucial role of glycosphingolipids in the HCV life cycle and suggests a link between PI4P and glycosphingolipids in HCV genome replication.