gebhart/patrepeval huggingface dataset:
LIM‐only protein 4 interacts directly with the repulsive guidance molecule A receptor Neogenin (2008)

Repulsive guidance molecule A (RGM A) was recently described as a potent inhibitor of neuroregeneration in a rat spinal cord injury model. The receptor mediating RGM A's repulsive activity was shown to be Neogenin, a member of the Deleted in Colorectal Cancer (DCC) family of netrin receptors. Binding of RGM A to Neogenin induces activation of the small GTPase RhoA and of its effector Rho-kinase by an unknown mechanism. Here we show, that the cytoplasmic tail of Neogenin interacts directly with the transcriptional coactivator LIM domain only 4 (LMO4) in human SH-SY5Y cells, human Ntera neurons, and in embryonic rat cortical neurons. RGM A binding to Neogenin but not binding of Netrin-1, induces release of LMO4 from Neogenin. Down-regulation of LMO4 neutralizes the repulsive activity of RGM A in neuronal cell lines and embryonic rat cortical neurons and prevents RhoA activation. These results show for the first time that an interaction of Neogenin with LMO4 is involved in the RGM A - Neogenin signal transduction pathway for RhoA activation.
Secretory Expression of the Human Serum Albumin Gene in the Yeast, Saccharomyces cerevisiae (1991)

We have fused a cDNA gene encoding mature human serum albumin (HSA) to several secretory leader-encoding sequences. The hybrid genes were cloned into an episomal vector under the control of several yeast promoters and then introduced into yeast cells. The GAL1 promoter in combination with either the native HSA pre-sequence or a modified HSA pre-sequence gave the highest production of immunoreactive HSA, 90 mg/liter being reached in a shake flask culture. The invertase pre-sequence, the mating factor alpha 1 prepro-sequence, and the modified HSA pre-sequence directed accurate processing. In contrast, the chicken lysozyme pre-sequence and the native HSA pre-sequence directed incorrect processing. Episomal vectors were unstable within the host cells under non-selective culture conditions. To improve the plasmid stability, the hybrid genes were incorporated into an integrative vector. Transformants carrying multicopies of the plasmid integrated at the LEU2 locus stably secreted HSA. The highest yield of 65 mg/liter in a shake flask culture was obtained with the combination of the yeast glyceraldehyde-3-phosphate dehydrogenase promoter and the modified HSA pre-sequence. By constructing transformed strains containing multicopies of plasmids integrated at both the chromosome LEU2 and HIS4 loci, we have obtained a stable strain that continuously secretes as much as 85 mg HSA per liter of culture medium.
Introduction to the Theory of Computation (1996)

article Free Access Share on Introduction to the Theory of Computation Author: Michael Sipser PWS Publishing Company PWS Publishing CompanyView Profile Authors Info & Claims ACM SIGACT NewsVolume 27Issue 1March 1996 pp 27–29https://doi.org/10.1145/230514.571645Published:01 March 1996Publication History 174citation6,690DownloadsMetricsTotal Citations174Total Downloads6,690Last 12 Months1,826Last 6 weeks472 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 Alerts New Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
Pulsed laser desorption method for volatilizing thermally labile molecules for supersonic jet spectroscopy (1988)

A technique using pulsed laser desorption is described as a means of volatilizing nonvolatile and thermally labile molecules into the gas phase for entrainment in supersonic jet expansions. By carefully controlling the laser desorption power and by using a glycerol matrix to provide a thin even film of sample, repetitive desorption can be achieved over an extended period for performing jet spectroscopy. Using resonant two-photon ionization spectroscopy while monitoring only the molecular ion in a time-of-flight mass spectrometer, cold sharp spectra are observed for molecules which are difficult to volatilize by conventional heating methods.
Cyclic adenosine monophosphate is a key component of regulatory T cell–mediated suppression (2007)

Naturally occurring regulatory T cells (T reg cells) are a thymus-derived subset of T cells, which are crucial for the maintenance of peripheral tolerance by controlling potentially autoreactive T cells. However, the underlying molecular mechanisms of this strictly cell contact-dependent process are still elusive. Here we show that naturally occurring T reg cells harbor high levels of cyclic adenosine monophosphate (cAMP). This second messenger is known to be a potent inhibitor of proliferation and interleukin 2 synthesis in T cells. Upon coactivation with naturally occurring T reg cells the cAMP content of responder T cells is also strongly increased. Furthermore, we demonstrate that naturally occurring T reg cells and conventional T cells communicate via cell contact-dependent gap junction formation. The suppressive activity of naturally occurring T reg cells is abolished by a cAMP antagonist as well as by a gap junction inhibitor, which blocks the cell contact-dependent transfer of cAMP to responder T cells. Accordingly, our results suggest that cAMP is crucial for naturally occurring T reg cell-mediated suppression and traverses membranes via gap junctions. Hence, naturally occurring T reg cells unexpectedly may control the immune regulatory network by a well-known mechanism based on the intercellular transport of cAMP via gap junctions.
LY146032 compared with penicillin G in experimental aortic valve endocarditis caused by group G streptococci (1988)

Rabbits with group G streptococcal aortic endocarditis received no therapy (controls); repeated doses of procaine penicillin G, 300 mg/kg (body weight) per day, administered intramuscularly; or LY146032, a new peptolide antibiotic, 20 mg/kg per day, administered intravenously. Penicillin G and LY146032 reduced mean intravegetation group G streptococcal densities significantly below those observed in controls at both day 3 and day 6 of therapy. Penicillin G effected a more rapid clearance of intravegetation streptococci than LY146032 by day 3, but not by day 6, of therapy.
Alternative Signaling Pathways as Potential Therapeutic Targets for Overcoming EGFR and c-Met Inhibitor Resistance in Non-Small Cell Lung Cancer (2013)

The use of tyrosine kinase inhibitors (TKIs) against EGFR/c-Met in non-small cell lung cancer (NSCLC) has been shown to be effective in increasing patient progression free survival (PFS), but their efficacy is limited due to the development of resistance and tumor recurrence. Therefore, understanding the molecular mechanisms underlying development of drug resistance in NSCLC is necessary for developing novel and effective therapeutic approaches to improve patient outcome. This study aims to understand the mechanism of EGFR/c-Met tyrosine kinase inhibitor (TKI) resistance in NSCLC. H2170 and H358 cell lines were made resistant to SU11274, a c-Met inhibitor, and erlotinib, an EGFR inhibitor, through step-wise increases in TKI exposure. The IC50 concentrations of resistant lines exhibited a 4-5 and 11-22-fold increase for SU11274 and erlotinib, respectively, when compared to parental lines. Furthermore, mTOR and Wnt signaling was studied in both cell lines to determine their roles in mediating TKI resistance. We observed a 2-4-fold upregulation of mTOR signaling proteins and a 2- to 8-fold upregulation of Wnt signaling proteins in H2170 erlotinib and SU11274 resistant cells. H2170 and H358 cells were further treated with the mTOR inhibitor everolimus and the Wnt inhibitor XAV939. H358 resistant cells were inhibited by 95% by a triple combination of everolimus, erlotinib and SU11274 in comparison to 34% by a double combination of these drugs. Parental H2170 cells displayed no sensitivity to XAV939, while resistant cells were significantly inhibited (39%) by XAV939 as a single agent, as well as in combination with SU11274 and erlotinib. Similar results were obtained with H358 resistant cells. This study suggests a novel molecular mechanism of drug resistance in lung cancer.
Soluble forms of the interleukin-6 signal-transducing receptor component gp130 in human serum possessing a potential to inhibit signals through membrane-anchored gp130 (1993)

Abstract The interleukin-6 (IL-6) signal is transduced through membrane-anchored gp130, which is associated with IL-6 receptor (IL-6R) in the presence of IL-6. Soluble forms of gp130 (sgp130) with molecular weights of 90 and 110 Kd were found in human serum. In the presence of recombinant IL- 6 (rIL-6), serum sgp130 were capable of associating with serum sIL-6R. By the sandwich enzyme-linked immunosorbent assay, healthy human sera was shown to contain 390 +/- 72 ng/mL of sgp130. A mouse pro-B-cell line-derived transfectant, BAF-130, expressing human gp130 was used to examine the function of serum sgp130. When supplemented with rIL-6, human serum induced DNA synthesis in BAF-130 cells, whereas the serum deprived of sIL-6R did not. In contrast, the DNA synthesis induced in BAF-130 cells by rIL-6-supplemented serum was increased when the serum was deprived of sgp130. These results indicated that serum sgp130 could negatively regulate the IL-6 signal. Recently, gp130 has been shown to be involved in the signaling processes of oncostatin M, leukemia inhibitory factor, and ciliary neurotropic factor, in addition to those of IL-6. Recombinant sgp130 showed inhibitory effect on the biologic function of such cytokines. This work implies physiologic roles of naturally produced serum sgp130 in modulating signals through gp130.
Genetic Variability of the Major Histocompatibility Complex Class I Homologue Encoded by Human Cytomegalovirus Leads to Differential Binding to the Inhibitory Receptor ILT2 (2005)

Human cytomegalovirus carries a gene, UL18, that is homologous to cellular major histocompatibility complex (MHC) class I genes. Like MHC class I molecules, the protein product of the UL18 gene associates with beta2-microglobulin, and the stability of this complex depends on peptide loading. UL18 protein binds to ILT2 (CD85j), an inhibitory receptor present on B cells, monocytes, dendritic cells, T cells, and NK cells that also recognizes classical and nonclassical MHC molecules. These observations suggest that UL18 may play a role in viral immune evasion, but its real function is unclear. Since this molecule has similarity with polymorphic MHC proteins, we explored whether the UL18 gene varied between virus isolates. We report here that the UL18 gene varies significantly between virus isolates: amino acid substitutions were found in the predicted alpha1, alpha2, and alpha3 domains of the UL18 protein molecule. We also studied the ability of several variant UL18 proteins to bind to the ILT2 receptor. All of the variants tested bound to ILT2, but there were marked differences in the affinity of binding to this receptor. These differences were reflected in functional assays measuring inhibition of the cytotoxic capacity of NK cells via interaction with ILT2. In addition, the variants did not bind other members of the CD85 family. The implications of these data are discussed.
Identification of an Amino Acid Residue That Lies between the Exofacial Vestibule and Exofacial Substrate-binding Site of the Glut1 Sugar Permeation Pathway (1997)

A valine-to-isoleucine mutation at amino acid residue 197 of Glut2 or the equivalent residue 165 of Glut1 has been shown to impair glucose transport activity. This mutation was originally discovered in the Glut2 gene of a patient with type 2 diabetes. We investigated the mechanism of the effect of this mutation on transport activity via the analysis of Glut1 mutants expressed in Xenopus oocytes combined with cysteine substitution mutagenesis and the use of cysteine-reactive chemical probes. Aliphatic side chain substitutions at position 165 that were bulkier than the native valine residue inhibited glucose transport activity, whereas substitutions of less bulky side chains had little effect on transport, suggesting a role for steric hindrance. A cysteine residue was introduced at position 165 of a functional, cysteine-less Glut1 construct, and this mutant was then tested for inhibition of transport activity by a membrane-impermeant sulfhydryl-specific reagent (p-chloromercuribenzenesulfonate). p-Chloromercuribenzenesulfonate inhibited activity of the Cys165 mutant when it was added to the external buffer but not when it was injected directly into oocytes, indicating that this residue is accessible from the external solvent but not from the cytoplasm. Competition experiments indicated that Cys165 lies near the exofacial substrate-binding site or directly in the sugar permeation pathway. These data provide evidence that the side chain of Val165, which resides in the middle of transmembrane helix 5, juts into the aqueous permeation pathway of Glut1, probably between the exofacial substrate-binding site and the outer vestibule of the pathway.
Inhibition of Human Immunodeficiency Virus Type I Reverse Transcriptase by Suramin-related Compounds (1987)

Ninety analogues of suramin have been examined for their ability to inhibit the exogenous reverse transcriptase (RT) of human immunodeficiency virus type I (HIV-I). Of these compounds, 57 inhibited the poly(rC).oligo(dG)-dependent RT activity. Three classes of dose-response curves could be discriminated. Allocation of a compound to one class did not correspond with obvious structural features. Twenty-four substances were superior to suramin in our RT inhibition assay. The RT-inhibitory activity of these compounds did not correlate with their effect against filariae or trypanosomes. Preliminary antiviral evaluation in susceptible human T cells inoculated with HIV-I demonstrated in vitro therapeutic efficacy for some compounds with lower drug-related cellular toxicity than suramin. Certain structural features relevant for the RT-inhibitory effect of these compounds were recognized. Predictions are made for the design of more effective RT inhibitors. Such compounds will help to understand the molecular mechanism of reverse transcription and might be useful in the therapy of retroviral infections.
Ribosome display and related technologies : methods and protocols (2012)

Display technologies have become a very powerful way of generating therapeutic lead molecules and specific reagents for increasing our understanding of biology; however, despite being first described shortly after phage display, the use of ribosome display and related methods have been much less widespread. Since this is in part due to the complexity of the methods, Ribosome Display and Related Technologies: Methods and Protocols seeks to extend their use by collecting expert contributions describing these detailed protocols. The protocols described range from well-established methods that have been used for a decade to generate high affinity antibodies, which are already in the clinic, to methods that are in their early stages of application such as display of peptides incorporating non-canonical amino acids. Written in the highly successful Methods in Molecular Biology™ series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Invaluable and easy to use, Ribosome Display and Related Technologies: Methods and Protocols will be of great benefit to those with general molecular biology or protein engineering experience who wish to select peptides or proteins by display, those with phage display experience who would benefit from the application of ribosome display, as well as those with some ribosome display experience who would like to expand the range of applications to which they are applying the technology
Phosphorylation of 3'-azido-2',3'-dideoxyuridine and preferential inhibition of human and simian immunodeficiency virus reverse transcriptases by its 5'-triphosphate (1989)

3'-Azido-2',3'-dideoxyuridine-5'-triphosphate was found to be a potent and highly selective inhibitor of human immunodeficiency virus type 1 and simian immunodeficiency virus reverse transcriptases. The affinity of 3'-azido-2',3'-dideoxyuridine-5'-triphosphate for the reverse transcriptases was similar to that observed for 3'-azido-3'-deoxythymidine-5'-triphosphate. Both compounds were competitive inhibitors with respect to the normal substrate dTTP and served at least 100 times better as substrates than did dTTP. In contrast, cellular DNA polymerase alpha showed an about 60-times-higher preference for dTTP as substrate than for either inhibitor. The phosphorylation of thymidine in human peripheral blood mononuclear cell extracts was inhibited in a competitive manner by both 3'-azido-2',3'-dideoxyuridine and 3'-azido-3'-deoxythymidine, with apparent inhibition constants of 290 and 3.4 microM, respectively. The Michaelis-Menten constant, Km, for thymidine was 7.0 microM. 3'-Azido-2',3'-dideoxyuridine and 3'-azido-3'-deoxythymidine both served as substrates, with apparent Km values of 67 and 1.4 microM, respectively. The maximal rates of phosphorylation with 3'-azido-2',3'-dideoxyuridine and 3'-azido-3'-deoxythymidine were 40 and 30%, respectively, of the rate with thymidine. The different affinities of 3'-azido-2',3'-dideoxyuridine and 3'-azido-3'-deoxythymidine for the thymidine kinase and the Km values observed with these compounds as substrates may explain the difference in effects on human immunodeficiency virus type 1 replication in infected peripheral blood mononuclear cells observed when equimolar concentrations of the two compounds are compared.
Multiprocessor system for interconnection of Ethernet and FDDI networks using ATM via satellite (1996)

The interconnection of distributed networks over satellite links employing ATM cell based transmission can be used in the development of emerging high speed networks such as the ITU-T Broadband Integrated Services Digital Network. Issues relating to the segmentation and reassembly mechanisms required to provide the conversion between the formats used within frames on the local area networks and the cells employed over the satellite connection and the management of memory to provide buffer capacity represent challenges with regard to the design of a system providing the bridging services within such an environment. The paper describes the hardware and software architecture of a device constructed to meet these requirements and discusses significant issues addressed during the development.
Enhancing underwater optical imaging by using a low-pass polarization filter (2019)

Object identification in highly turbid optical media depends mainly on the quality of collected images. Underwater images acquired in a turbid environment are generally of very poor quality. Attenuation and backscattering of light by water, by materials dissolved in the water, and by particulate material are the main causes of the degradation of underwater images. It is therefore essential to improve the quality of such images to facilitate object identification. The focus of this paper is to report the principle and validation of a fast and effective method of improving the quality of underwater images. On the one hand, this method uses a polarimetric imaging optical system to reduce the effect of diffusion on the image acquisition. On the other hand, it is based on an optimized version of the dark channel prior (DCP) method that has received a great deal of attention for image dehazing. Results derived from images obtained in a controlled laboratory water tank environment with different turbidity conditions and images from tests using the proposed method at sea demonstrate an ability to significantly improve visibility and reduce runtime by a factor of about 50 for a 4K image when compared to conventional DCP methods.
Production and characterization of bovine interleukin-2. (1984)

A lymphokine analogous to interleukin-2 from other species was generated from bovine suprapharyngeal lymph nodes and characterized biochemically. The isolated material can support the long-term growth of concanavalin A (Con-A) or mixed lymphocyte reaction (MLR)-activated bovine T cells. The material elutes from DEAE-Sephadex at a low salt concentration, approximately 0.075 M, and exhibits molecular weight of approximately 25,000 on Sephadex G-100. When subjected to analysis by sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE), three peaks of activity were observed, corresponding to molecular weights of 14,400, 16,800 and 20,200. Finally, the isolated material exhibited a marked heterogeneity when subjected to chromatofocussing. Three major peaks of activity, with pIs of approximately 5.95, 5.41 and 5.0 are present with peaks of lesser activity at pIs of 5.82, 5.70, 4.73 and 4.20.
Antibodies against specific extracellular epitopes of the glucagon receptor block glucagon binding. (1996)

Polyclonal antibodies were prepared against synthetic peptides corresponding to four different extramembrane segments of the rat glucagon receptor. The antibodies bound specifically to native glucagon receptor as judged by immunofluorescence microscopy of cultured cells expressing a synthetic gene for the receptor. Antibodies to peptides designated PR-15 and DK-12 were directed against amino acid residues 103-117 and 126-137, respectively, of the extracellular N-terminal tail. Antibody to peptide KD-14 was directed against residues 206-219 of the first extracellular loop, and antibody to peptide ST-18, against the intracellular C-terminal tail, residues 468-485. The DK-12 and KD-14 antibodies, but not the PR-15 and ST-18 antibodies, could effectively block binding of 125I-labeled glucagon to its receptor in liver membranes. Incubation of these antibodies with rat liver membranes resulted in both a decrease in the maximal hormonal binding capacity and an apparent decrease in glucagon affinity for its receptor. These effects were abolished in the presence of excess specific peptide antigen. In addition, DK-12 and KD-14 antibodies, but not PR-15 and ST-18 antibodies, interfered with glucagon-induced adenylyl cyclase activation in rat liver membranes and behaved as functional glucagon antagonists. These results demonstrate that DK-12 and KD-14 antibodies are pharmacologically active glucagon antagonists and strongly suggest that residues 126-137 of the N-terminal tail and residues 206-219 of the first extracellular loop contain determinants of ligand binding and may comprise the primary ligand-binding site on the glucagon receptor.