gebhart/patrepeval huggingface dataset:
Molecular cloning of the cDNA which encodes beta-N-acetylhexosaminidase A from Dictyostelium discoideum. Complete amino acid sequence and homology with the human enzyme. (1988)

beta-N-Acetylhexosaminidase A (EC 3.2.1.52), the product of the nag A gene, is a lysosomal enzyme which is developmentally regulated in Dictyostelium discoideum. The enzyme plays a role during the slug stage of development in the maintenance of pseudoplasmodia of normal size. We used a homogeneous preparation of deglycosylated enzyme subunits to generate antibody. The antibody was suitable for screening a lambda gt11 cDNA expression library derived from the mRNA of late log stage axenic cells. We isolated seven positive clones. One of these contains the complete coding sequence of the protein. We also isolated a genomic clone which contains 800 base pairs of 5'-flanking sequence and 728 base pairs of coding sequence. Analysis of the sequences and of primer extension studies indicates an inferred transcript size of 1665 bases which closely matches the 1.8-kilobase mRNA size estimated by Northern blot analysis of poly(A+) mRNA from the organism. The sequence contains an open reading frame which encodes a protein of 59,787 kDa. This equals the apparent molecular weight in sodium dodecyl sulfate-polyacrylamide gels of in vitro translated enzyme. The amino terminus of the purified enzyme appeared to be blocked, but internal peptide sequences were obtained by automated Edman degradation of gel-purified peptides generated by treatment of protein subunits with staphylococcal V-8 protease. These sequences are included in the inferred sequence. In addition to a typical signal sequence, the open reading frame encodes a second candidate transmembrane region, a serine-rich region, and four potential N-glycosylation sites. These are discussed with regard to the localization and processing of the enzyme during its biogenesis. Beginning at amino acid 100 of the Dictyostelium enzyme sequence, 36% of its amino acids are identical to the corresponding sequence of the beta chain, and 33% are identical with those of the alpha chain of human beta-N-acetylhexosaminidase. This is strong evidence that the Dictyostelium enzyme is homologous to the alpha and beta chains of the human enzyme.
Application and Evaluation of Extended Release Technology to Loop Diuretics (2002)

Loop diuretics offer great advantages in treating edematous states associated with congestive heart failure, liver cirrhosis and kidney failure owing to their intense diuretic effect.Evidences suggested the diuretic effect can be exaggerated by careful control of the rate at which loop diuretics are made available to the urinary tubules.If optimally designed, peroral extended release formulation can provide better utilization of the same total dose of loop diuretic, an effect of utmost importance in edematous patients with high resistance to loop diuretics.Bumetanide multiparticulate immediate and extended release formulations were developed and tested in rabbits.A novel multiple response optimization technique based on superimposing contour diagrams was developed and successfully used to optimize bumetanide release.Instability in drug release from multiparticulate formulations after storage warrants in depth investigation of different formulation and processing factors controlling drug release.Curing time, temperature, plasticizer level, coating polymer lipophilicity, and the use of hydrophilic seal coat were explored in this study.The findings proved instability in bumetanide release is attributed to drug migration into the film coat during storage.Careful selection of plasticizer level and curing conditions together with the use of hydrophilic seal coat prevented drug migration and stabilized drug release after storage.When compared to immediate release formulation in rabbits, equivalent amounts of bumetanide were excreted fromboth formulations yet at different rates.The slow delivery of bumetanide from the extended release formulation improved its diuretic and natriuretic efficiencies within the first day after dosing.The activation of compensatory mechanisms is thought to diminish the response to extended release bumetanide formulation within the second day.While providing comparable diuretic and saliuretic effects to that of immediate release formulation, extended release bumetanide formulation can offer the advantage of avoiding the initial, unpleasant and intense diuretic effect experienced with immediate release formulations.5.4.1.3.
Effector protease receptor 1 mediates the mitogenic activity of factor Xa for vascular smooth muscle cells in vitro and in vivo. (1998)

The binding of 125I-factor Xa to human aortic smooth muscle cell (SMC) monolayers was studied. At 4 degreesC, 125I-factor Xa bound to a single class of binding sites with a dissociation constant value of 3.6+/-0.7 nM and a binding site density of 11,720+/-1,240 sites/cell (n = 9). 125I-factor Xa binding was not affected by factor X, thrombin, or by DX9065, a direct inhibitor of factor Xa, but was inhibited by factor Xa (IC50 = 5.4+/-0.2 nM; n = 9) and by antibodies specific for the effector cell protease receptor 1 (EPR-1), a well-known receptor of factor Xa on various cell types. A factor X peptide duplicating the inter-EGF sequence Leu83-Leu88-(Gly) blocked the binding of 125I-factor Xa to these cells in a dose-dependent manner (IC50 = 110+/-21 nM). Factor Xa increased phosphoinositide turnover in SMCs and when added to SMCs in culture was a potent mitogen. These effects were inhibited by DX9065 and by antibodies directed against EPR-1 and PDGF. Increased expression of EPR-1 was identified immunohistochemically on SMCs growing in culture and in SMCs from the rabbit carotid artery after vascular injury. When applied locally to air-injured rabbit carotid arteries, antibodies directed against EPR-1 (100 mug/ artery) strongly reduced myointimal proliferation 14 d after vascular injury (65-71% inhibition, P < 0.01). DX9065 (10 mg/kg, subcutaneous) inhibited myointimal proliferation significantly (43% inhibition, P < 0.05). These findings indicate that SMCs express functional high affinity receptors for factor Xa related to EPR-1, which may be of importance in the regulation of homeostasis of the vascular wall and after vascular injury.
Combinatorial chemistry (1995)

G. Lowe, Chem. Soc. Rev., 1995, 24, 309 DOI: 10.1039/CS9952400309
Gene Expression Profiling Of Human Cutaneous Melanoma: Are We There Yet? (2004)

Commentary to: SAGE Identification and Fluorescence Imaging Analysis of Genes and Transcripts in Melanomas and Precursor Lesions Amanda Pfaff Smith, Ashani T. Weeraratna, Justin R. Spears, Paul S. Meltzer and Dorothea Becker and Expression Analysis of Genes identified by Molecular Profiling of VGP Melanomas and MGP Melanoma-Positive Lymph Nodes Shannon L. McDonald, Howard D. Edington, John M. Kirkwood and Dorothea Becker
Arabidopsis cyt1 mutants are deficient in a mannose-1-phosphate guanylyltransferase and point to a requirement of N-linked glycosylation for cellulose biosynthesis (2001)

Arabidopsis cyt1 mutants have a complex phenotype indicative of a severe defect in cell wall biogenesis. Mutant embryos arrest as wide, heart-shaped structures characterized by ectopic accumulation of callose and the occurrence of incomplete cell walls. Texture and thickness of the cell walls are irregular, and unesterified pectins show an abnormally diffuse distribution. To determine the molecular basis of these defects, we have cloned the CYT1 gene by a map-based approach and found that it encodes mannose-1-phosphate guanylyltransferase. A weak mutation in the same gene, called vtc1, has previously been identified on the basis of ozone sensitivity due to reduced levels of ascorbic acid. Mutant cyt1 embryos are deficient in N-glycosylation and have an altered composition of cell wall polysaccharides. Most notably, they show a 5-fold decrease in cellulose content. Characteristic aspects of the cyt1 phenotype, including radial swelling and accumulation of callose, can be mimicked with the inhibitor of N-glycosylation, tunicamycin. Our results suggest that N-glycosylation is required for cellulose biosynthesis and that a deficiency in this process can account for most phenotypic features of cyt1 embryos.
Classification and nomenclature of all human homeobox genes (2007)

We have conducted a comprehensive survey of homeobox genes and pseudogenes in the human genome, described many new loci, and revised the classification and nomenclature of homeobox genes. The classification scheme may be widely applicable to homeobox genes in other animal genomes and will facilitate comparative genomics of this important gene superclass.
Rapid and efficient cloning of Alu-PCR products using uracil DNA glycosylase. (1991)

By incorporating dUMP residues into the 5' end of PCR primers, one can generate products which, after treatment with uracil DNA glycosylase (UDG), contain 3' overhangs. These overhangs can be annealed to vector molecules with complementary overhangs generated in a similar fashion and transformed directly into Escherichia coli without the need for ligase. We have tested this method of ligation-independent cloning by using UDG to create complementary single-stranded sticky ends between vector and Alu-PCR products generated from cosmid clones containing DNA from human chromosome 21. Using a single primer, Alu-PCR amplifies the sequence between appropriately oriented, repetitive (Alu) sequences in human DNA that are no more than 2 to 3 kb apart. Nineteen Alu-PCR products were observed in four human chromosome 21 cosmids. Thirteen of these products were detected among 48 subclones picked at random after cloning of the Alu-PCR products using UDG. The size or abundance of an Alu-PCR product did not appear to affect significantly the efficiency of cloning. Eight of the subclones were tested and all hybridized to human chromosome 21 DNA. UDG cloning should prove to be a general PCR cloning method that allows one to rapidly subclone small fragments from human genomic DNA.
81: Enhancing the in vivo expansion of adoptively transferred EBV-CTL with lymphodepleting CD45 monoclonal antibodies in NPC patients (2007)

Background: Treatment of Epstein Barr virus (EBV)-positive nasopharyngeal carcinoma (NPC) with polyclonal EBV-specific cytotoxic T cells (EBV-CTL) has been promising, producing disease stabilization and complete remissions in patients with low disease burden. However, infused EBV-CTL did not expand significantly in vivo, limiting their antitumor activity. One strategy to enhance the in vivo expansion of adoptively transferred CTL is to reduce the lymphocyte pool prior to T cell infusion. This should result in homeostatic proliferation of the infused T cells restoring the lymphoid compartment. A pair of monoclonal antibodies, targeted to the CD45 antigen (CD45 MAbs), were used to selectively lymphodeplete patients prior to stem cell transplantation. These produced marked reduction in circulating lymphoid and myeloid cells while largely sparing marrow progenitors. We therefore hypothesized that administration of CD45 MAbs will lymphodeplete NPC patients and allow for in vivo expansion of adoptively transferred EBV-CTL. Study design: The primary objective of this Phase I clinical trial is to determine the safety of escalating doses of EBV-CTL after CD45 MAbs infusion in EBV-positive NPC patients. The secondary objective is to determine the expansion, persistence and antitumor effects of infused EBV-CTL. Results: Eight patients with advanced stage, refractory/relapsed NPC have been treated with autologous EBV-CTL (2×107-1×108 cells/m2per infusion). Patients received between 1 - 5 CTL infusions, which were well tolerated, although one developed transient swelling at a pre-existing metastatic disease site. Infusion of CD45 MAbs resulted in a transient period of neutropenia (ANC <0.5×109/L), which resolved within 48 hours. The absolute lymphocyte count decreased 4-fold and approached baseline within 14 days post infusion. In 6 of 8 patients, we detected increased IL-15 serum levels, a cytokine important for lymphocyte proliferation. In 3 out of 8 patients EBV-CTL expanded 2.5 to 21-fold within 8 weeks post infusion as determined by IFN-γ Elispot assays. Clinically, 1 patient had a complete response (>9 months), 3 had stable disease for 2 - 16 months, and 4 had progressive disease. Conclusion: Treatment of EBV-positive NPC with EBV-CTL appears to be safe and can be associated with significant anti-tumor activity. Administration of CD45 MAbs prior to EBV-CTL infusion resulted in transient lymphodepletion and can aid in the expansion of adoptively transferred CTL.
The novel fragment of tyrosyl tRNA synthetase, mini‐ TyrRS, is secreted to induce an angiogenic response in endothelial cells (2007)

Aminoacyl tRNA synthetases--enzymes that catalyze the first step of protein synthesis--in mammalian cells are now known to have expanded functions, including activities in signal transduction pathways, such as those for angiogenesis and inflammation. The native synthetases themselves are procytokines, having no signal transduction activities. After alternative splicing or natural proteolysis, specific fragments that are potent cytokines and that interact with specific receptors on cell surfaces are released. In this manner, a natural fragment of human tyrosyl tRNA synthetase (TyrRS), mini-TyrRS, has been shown to act as a proangiogenic cytokine. The mechanistic basis for the action of mini-TyrRS in angiogenesis has yet to be established. Here, we show that mini-TyrRS is exported from endothelial cells when they are treated with tumor necrosis factor-alpha. Mini-TyrRS binds to vascular endothelial cells and activates an array of angiogenic signal transduction pathways. Mini-TyrRS-induced angiogenesis requires the activation of vascular endothelial growth factor receptor-2 (VEGFR2/Flk-1/KDR). Mini-TyrRS stimulates VEGFR2 phosphorylation in a VEGF-independent manner, suggesting VEGFR2 transactivation. Transactivation of VEGFR2 and downstream angiogenesis require an intact Glu-Leu-Arg (ELR) motif in mini-TyrRS, which is important for its cytokine activity. These studies therefore suggest a mechanism by which mini-TyrRS induces angiogenesis in endothelial cells and provide further insight into the role of mini-TyrRS as a link between translation and angiogenesis.
Dental follicle stem cells and tissue engineering (2010)

Adult stem cells are multipotent and can be induced experimentally to differentiate into various cell lineages. Such cells are therefore a key part of achieving the promise of tissue regeneration. The most studied stem cells are those of the hematopoietic and mesenchymal lineages. Recently, mesenchymal stem cells were demonstrated in dental tissues, including dental pulp, periodontal ligament, and dental follicle. The dental follicle is a loose connective tissue that surrounds the developing tooth. Dental follicle stem cells could therefore be a cell source for mesenchymal stem cells. Indeed, dental follicle is present in impacted teeth, which are commonly extracted and disposed of as medical waste in dental practice. Dental follicle stem cells can be isolated and grown under defined tissue culture conditions, and recent characterization of these stem cells has increased their potential for use in tissue engineering applications, including periodontal and bone regeneration. This review describes current knowledge and recent developments in dental follicle stem cells and their application.
From tubes to drops: droplet-based microfluidics for ultrahigh-throughput biology (2013)

Droplet-based microfluidics holds enormous potential for transforming the way that many biological screens are performed by affording unprecedented increases in screening throughput and reductions in reagent usage. In this paper, we describe this maturing field and the pioneering work that has laid the foundation for its application to ultrahigh-throughput biological analysis. We begin by introducing the basic elements of the approach and describe the numerous microfluidic components that have been developed for droplet manipulation, with special emphasis on the ones most useful for ultrahigh-throughput analysis. We conclude with a discussion of the first demonstrations of this approach to perform novel, ultrahigh-throughput biological screens.
The Fluid Mosaic Model of the Structure of Cell Membranes (1972)

A fluid mosaic model is presented for the gross organization and structure of the proteins and lipids of biological membranes. The model is consistent with the restrictions imposed by thermodynamics. In this model, the proteins that are integral to the membrane are a heterogeneous set of globular molecules, each arranged in an amphipathic structure, that is, with the ionic and highly polar groups protruding from the membrane into the aqueous phase, and the nonpolar groups largely buried in the hydrophobic interior of the membrane. These globular molecules are partially embedded in a matrix of phospholipid. The bulk of the phospholipid is organized as a discontinuous, fluid bilayer, although a small fraction of the lipid may interact specifically with the membrane proteins. The fluid mosaic structure is therefore formally analogous to a two-dimensional oriented solution of integral proteins (or lipoproteins) in the viscous phospholipid bilayer solvent. Recent experiments with a wide variety of techniqes and several different membrane systems are described, all of which abet consistent with, and add much detail to, the fluid mosaic model. It therefore seems appropriate to suggest possible mechanisms for various membrane functions and membrane-mediated phenomena in the light of the model. As examples, experimentally testable mechanisms are suggested for cell surface changes in malignant transformation, and for cooperative effects exhibited in the interactions of membranes with some specific ligands. Note added in proof: Since this article was written, we have obtained electron microscopic evidence (69) that the concanavalin A binding sites on the membranes of SV40 virus-transformed mouse fibroblasts (3T3 cells) are more clustered than the sites on the membranes of normal cells, as predicted by the hypothesis represented in Fig. 7B. T-here has also appeared a study by Taylor et al. (70) showing the remarkable effects produced on lymphocytes by the addition of antibodies directed to their surface immunoglobulin molecules. The antibodies induce a redistribution and pinocytosis of these surface immunoglobulins, so that within about 30 minutes at 37 degrees C the surface immunoglobulins are completely swept out of the membrane. These effects do not occur, however, if the bivalent antibodies are replaced by their univalent Fab fragments or if the antibody experiments are carried out at 0 degrees C instead of 37 degrees C. These and related results strongly indicate that the bivalent antibodies produce an aggregation of the surface immunoglobulin molecules in the plane of the membrane, which can occur only if the immunoglobulin molecules are free to diffuse in the membrane. This aggregation then appears to trigger off the pinocytosis of the membrane components by some unknown mechanism. Such membrane transformations may be of crucial importance in the induction of an antibody response to an antigen, as well as iv other processes of cell differentiation.
Characterization of rat LECAM‐1 (L‐selectin) by the use of monoclonal antibodies and evidence for the presence of soluble LECAM‐1 in rat sera (1993)

We have characterized the rat LECAM-1 (L-selectin) by the use of newly generated hamster anti-rat LECAM-1 monoclonal antibodies (mAb) (HRL1, HRL2, HRL3, HRL4), with respect to the biochemistry, cellular distribution and function, and developed an ELISA system to detect the soluble form of rat LECAM-1. In the rat, lymphocyte and neutrophil LECAM-1 have apparent molecular masses of 65 and 62 kDa, respectively, and differential glycosylation may account for the molecular heterogeneity. Readily detectable levels of LECAM-1 are expressed on peripheral blood lymphocytes and neutrophils, but not on thymocytes. Lymphocyte LECAM-1 is rapidly shed from the cell surface upon cell activation with PMA, but not with interleukin (IL)-8. In contrast, neutrophil LECAM-1 showed rapid shedding upon stimulation with phorbol 12-myristate 13-acetate (PMA) or IL-8. Concomitantly there is up-regulated expression of Mac-1 in PMA- and IL-8-stimulated neutrophils. Neutrophil rolling in mesenteric venules was significantly inhibited by administration of function-blocking anti-rat LECAM-1 mAb HRL3, but not by non-blocking HRL4, indicating that LECAM-1 plays a significant role in leukocyte rolling. Given that LECAM-1 is rapidly shed from the cell surface, we attempted to develop an ELISA system for detecting LECAM-1 is soluble form, and measured the levels in experimental autoimmune uveitis. The circulating levels of LECAM-1 increased from day 4, which preceded the appearance of clinical signs of uveitis and remained high until uveitis subsided, suggesting that soluble LECAM-1 is potentially a useful parameter to monitor certain types of inflammatory or immune disorders.
Determining computable scenes in films and their structures using audio-visual memory models (2000)

In this paper we present novel algorithms for computing scenes and within-scene structures in films. We begin by mapping insights from film-making rules and experimental results from the psychology of audition into a computational scene model. We define a computable scene to be a chunk of audio-visual data that exhibits long-term consistency with regard to three properties: (a) chromaticity (b) lighting (c) ambient sound. Central to the computational model is the notion of a causal, finite-memory viewer model. We segment the audio and video data separately. In each case we determine the degree of correlation of the most recent data in the memory with the past. The respective scene boundaries are determined using local minima and aligned using a nearest neighbor algorithm. We introduce a periodic analysis transform to automatically determine the structure within a scene. We then use statistical tests on the transform to determine the presence of a dialogue. The algorithms were tested on a difficult data set: five commercial films. We take the first hour of data from each of the five films. The best results: scene detection: 88% recall and 72% precision, dialogue detection: 91% recall and 100% precision.
Hepatitis B Virus Core Particles as Epitope Carriers (1995)

HBV core (HBc) particle is one of the most intensively studied particulate carriers for the insertion of foreign peptide sequences. Recombinant HBc protein expressed from the cloned gene undergoes the correct folding in a large variety of bacterial, yeast, insect and mammalian cells. Unique assembly properties and shape of 30/34-nm HBc particles allow substantial insertions into their primary structure without loss of their capsid-forming ability. N- and C-terminal regions, as well as the immunodominant loop in the middle of the molecule are widely accepted as targets for the introduction of foreign epitopes, ensuring retention and even enhancement of the original immunological activity of inserted sequences. Special sets of display vectors have been constructed on the basis of the cloned HBc gene. Epitope sequences of viral (BLV, FeLV, FMDV, HBV, HCV, HIV-1, HRV2, MCMV, PV-1, SIV) and nonviral (human chorionic gonadotropin) origin have been studied as model display moieties.