gebhart/patrepeval huggingface dataset:
Human CD38 is associated to distinct molecules which mediate transmembrane signaling in different lineages (1993)

The CD38 antigen displays restricted functional associations with surface molecules involved in immune system and complement. Capping of the CD38 molecule in normal or neoplastic T cells is followed by rapid and specific co-modulation of the CD3-T cell receptor (TcR) complex. In normal and tumor cells of B lineage, CD38 was found to be also associated with surface Ig (sIg) and with the complement receptor 2 (CR2)/CD19 complex. The CD38 molecule expressed by purified natural killer cells displayed an association with the low affinity IgG Fc receptor (Fc gamma RIII) CD16. These observations suggest that specialized areas in the plasma membrane contain co-modulating structures, including different receptors involved in the transduction of extracellular signals. We propose a model whereby TcR, CR2 and CD16 are ligand binding structures in their respective lineages, while CD38 is a molecule involved in the intracellular transduction of the signals.
Arginine methylation of USP9X promotes its interaction with TDRD3 and its anti-apoptotic activities in breast cancer cells (2017)

The Tudor domain-containing proteins are characterized by their specific interactions with methylated protein motifs, including methyl-arginines and methyl-lysines. The Tudor domain-containing protein 3 (TDRD3) is one of the major methyl-arginine effector molecules that recognizes methylated arginine residues on histones and the C-terminal domain of RNA polymerase II, and activates transcription. However, majority of the cellular TDRD3 localizes to the cytoplasm and its functions there are still elusive. Here, we have identified ubiquitin-specific protease 9 X-linked (USP9X) as a TDRD3-interacting protein by GST (glutathione <i>S</i>-transferase) pull-down and co-immunoprecipitation. Detailed characterization suggests that the interaction between TDRD3 and USP9X is mediated through the Tudor domain of TDRD3 and the arginine methylation of USP9X. This interaction plays a critical role in TDRD3 protein stability, as knockdown of USP9X expression leads to increased TDRD3 ubiquitination. We also found that USP9X co-localizes with TDRD3 in cytoplasmic stress granules and this localization is diminished in Tdrd3-null mouse embryonic fibroblast cells, suggesting that TDRD3 is essential for USP9X stress granule localization. Furthermore, we found that one of the USP9X de-ubiquitination targets, myeloid cell leukemia protein 1, is regulated by TDRD3, indicating that TDRD3 potentially regulates USP9X de-ubiquitinase activity. Finally, we show that knockdown of TDRD3 expression sensitizes breast cancer cells to chemotherapeutic drug-induced apoptosis, likely due to its regulation of USP9X. This study provides a novel candidate strategy for targeting apoptosis pathways in cancer therapy.
Cellular Pathways in Response to Ionizing Radiation and Their Targetability for Tumor Radiosensitization (2016)

During the last few decades, improvements in the planning and application of radiotherapy in combination with surgery and chemotherapy resulted in increased survival rates of tumor patients. However, the success of radiotherapy is impaired by two reasons: firstly, the radioresistance of tumor cells and, secondly, the radiation-induced damage of normal tissue cells located in the field of ionizing radiation. These limitations demand the development of drugs for either radiosensitization of tumor cells or radioprotection of normal tissue cells. In order to identify potential targets, a detailed understanding of the cellular pathways involved in radiation response is an absolute requirement. This review describes the most important pathways of radioresponse and several key target proteins for radiosensitization.
Inflammatory Mechanisms in Obesity (2011)

The modern rise in obesity and its strong association with insulin resistance and type 2 diabetes have elicited interest in the underlying mechanisms of these pathologies. The discovery that obesity itself results in an inflammatory state in metabolic tissues ushered in a research field that examines the inflammatory mechanisms in obesity. Here, we summarize the unique features of this metabolic inflammatory state, termed metaflammation and defined as low-grade, chronic inflammation orchestrated by metabolic cells in response to excess nutrients and energy. We explore the effects of such inflammation in metabolic tissues including adipose, liver, muscle, pancreas, and brain and its contribution to insulin resistance and metabolic dysfunction. Another area in which many unknowns still exist is the origin or mechanism of initiation of inflammatory signaling in obesity. We discuss signals or triggers to the inflammatory response, including the possibility of endoplasmic reticulum stress as an important contributor to metaflammation. Finally, we examine anti-inflammatory therapies for their potential in the treatment of obesity-related insulin resistance and glucose intolerance.
Biokinetics of Bone Tracers by Means of Deconvolution Analysis - Comparison of 99mTc MDP, 99mTc DPD and 99mTc EHDP (1982)

Transfer functions of 99mTc methylene diphosphonate (MDP), 99mTc 2,3-dicarboxypropane-1,1-diphosphonate (DPD) and 99mTc ethane-1-hydroxy-1,1-diphosphonate (EHDP) into bone and extravascular fluid of soft tissues were determined in 5 dogs by deconvolution analysis of the time-course of plasma, soft tissue and bone radioactivity. The transfer rates 5 min after injection--indicating the rapid exchange of the tracer between plasma and the extravascular fluid--decrease in the order MDP greater than EHDP greater than DPD (P less than 0.05). The transfer rates into bone--determined from transfer rates between 30 and 60 min--decreased in a different order, i.e. MDP greater than DPD greater than EHDP (P less than 0.05). The fractional bone uptake of diphosphonates estimated from the ratio of early to late transfer rates was slightly greater for DPD than for MDP and EHDP respectively. The difference between DPD and MDP was not significant (P greater than 0.05). The average bone and soft tissue concentrations of DPD 60 min after injection were greater than that of MDP and EHDP due to different plasma concentrations (DPD greater than EHDP greater than MDP), whereas the bone-to-soft tissue ratios decreased in the sequence MDP greater than DPD greater than EHDP (P less than 0.05).--Our results reveal different biokinetics of MDP, DPD and EHDP explaining variations in osseous and soft tissue uptake suggesting that deconvolution analysis could play an important role in bone scan interpretation.
cAMP-dependent protein kinase defines a family of enzymes (1993)

The structure of the recombinant mouse catalytic subunit of cAMP-dependent protein kinase is reviewed with particular emphasis on the overall features and specific amino acids that are shared by all members of the eukaryotic protein kinase family. The crystal structure of a ternary complex containing both MgATP and a twenty-residue inhibitor peptide defines the precise role of the conserved residues that are clustered at the active site. In addition to catalysing the post-translational modification of other proteins, the catalytic subunit is itself subject to covalent modifications. It is a phosphoprotein and is also myristylated at its amino terminus. The enzyme when crystallized in the presence of detergent shows a detergent molecule bound to an acyl pocket that is presumably occupied by the myristyl moiety in the mammalian enzyme. When expressed in E. coli, the catalytic subunit is autophosphorylated at four sites. Two stable phosphates at Ser338 and Thr197 interact with multiple protein side chains thus explaining why they are inaccessible to phosphatases. Although all substrates and inhibitors of the catalytic subunit share a general minimum consensus sequence, the high affinity binding of protein inhibitors such as the regulatory subunits and the heat stable protein kinase inhibitors require additional determinants that lie beyond the consensus site. These two physiological inhibitors of the catalytic subunit appear to use different sites to achieve high-affinity binding.
Structure of the gene encoding concanavalin A from Canavalia gladiata and its expression in Escherichia coli cells (1990)

We have cloned and sequenced the gene encoding concanavalin A (Con A) from Canavalia gladiata. The sequence covers the whole transcribed region as well as the 5'- and 3'-untranscribed sequences. The coding sequence lacks introns. Con A expressed in Escherichia coli cells was purified by Sephadex G-50 affinity chromatography. The precursor of Con A expressed in E. coli undergoes a peptide cleavage and ligation in the same way as that synthesized during seed maturation.
Expression and localization of GLUT1 and GLUT12 in prostate carcinoma (2003)

GLUT1 and GLUT12 are expressed in human prostate carcinoma cells. One possible rationale for the GLUT1 Golgi association is that it may supply glucose to the Golgi for byproduct incorporation into the prostatic secretory fluid. Further work will investigate the importance of glucose transport and GLUT1 and GLUT12 in prostate carcinoma cell growth.
A constant slew rate Ethernet line driver (2001)

An analog bias circuit consisting of two transistors, three current sources, and one resistor facilitates the design of an Ethernet line driver. The rise time is insensitive to process variations and temperature variations, Rise-time accuracy is 223 ppm//spl deg/C over a temperature range of 140/spl deg/C. This line driver has been fabricated in 0.35-/spl mu/m CMOS.
A macroscopic view of the melt-blowing process for producing microfibers (1988)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA macroscopic view of the melt-blowing process for producing microfibersRobert L. ShambaughCite this: Ind. Eng. Chem. Res. 1988, 27, 12, 2363–2372Publication Date (Print):December 1, 1988Publication History Published online1 May 2002Published inissue 1 December 1988https://pubs.acs.org/doi/10.1021/ie00084a021https://doi.org/10.1021/ie00084a021research-articleACS PublicationsRequest reuse permissionsArticle Views889Altmetric-Citations123LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Herpes Simplex Virus 2 UL45 Is a Type II Membrane Protein (1998)

In addition to eleven glycoproteins, the herpes simplex virus type 2 (HSV-2) genome encodes several proteins with potential membrane-spanning segments but no asparagine-linked carbohydrates. One of these is UL45. Fractionation of infected cells showed that HSV-2 UL45 is an integral membrane protein, and analysis of UL45 mutants with potential glycosylation sites showed that it has a type II membrane orientation, the first HSV protein known to have this orientation. Furthermore, it is detectable in infected cells at a time similar to that when glycoproteins gB and gD are detected, consistent with a role in cell-cell fusion, which has previously been found for HSV-1 UL45.
Role of Thiols in Radioprotection: Radiation Chemical Aspects (1989)

Using the technique of pulse radiolysis, it has been demonstrated that thiyl radicals (RS.) derived from glutathione (GSH), cysteine (CYSH), penicillamine (PnSH) and 2-mercaptoethanol (ME) interact with oxygen at a high rate. The resulting transient absorption, with a maximum around 540-560 nm, is characteristic of the sulphur peroxyl radical (RSOO.). The yield and the kinetic of formation of RSOO. further support our previous suggestion that thiyl/O2 reaction is an equilibrium. The redox properties of RSOO. are discussed on the basis of the interaction with reductants. Studies on the radio-induced enzyme inactivation in the presence of thiols seem to suggest a damaging role for RSOO. radicals.
Photonic band gap materials: a semiconductor for light (2003)

Summary form only given. I review and discuss the role of three-dimensional light localization in the development of integrated optics on a photonic crystal micro-chip. The control and selective inhibition of spontaneous emission in a three dimensional photonic band gap material offers the possibility of developing novel active devices on such a chip.
Microspectrometer with slab-waveguide transmission gratings (1996)

An integrated transmission diffraction grating in a planar optical waveguide is presented for broadband spectroscopic analysis of liquids and gases. Silicon oxynitride slab waveguides on silicon substrates with low optical loss in the visible range are combined with a phase transmission grating exhibiting a blaze effect at 500 nm to achieve high-efficiency diffraction and high spectral dispersion. Collimated white light propagates through the waveguide and couples into air at a stepped formed planar grating. The beams of each adjacent step interfere constructively at the focal line of a cylindrical lens, its focal line positioned perpendicular to the waveguide plane. We used a common silicon photodiode array to detect the spectral data. Our approach is to develop a compact and economic spectrometer without moving parts that can be applied for UV-visible analysis and near-infrared industrial process control as well.
Glycopeptide profiling of human urinary erythropoietin by matrix-assisted laser desorption/ionization mass spectrometry (1997)

The site-specific glycan heterogeneity of human urinary erythropoietin was investigated by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). Owing to the small amount of protein available, a strategy combining optimal sensitivity and specificity was used. Erythropoietin was reduced, S-alkylated and digested with endoproteinase Lys C. The peptides were separated by reversed-phase high-performance liquid chromatography and the molecular masses of the peptides determined by MALDI-MS. The peptides were identified by comparing the experimental masses with the masses predicted from the cDNA derived amino acid sequence. Glycopeptides were identified from the mass spectra based on the peak pattern caused by the glycan heterogeneity. They were further characterized after treatment with neuraminidase and endoproteases. All N-glycosylation sites exhibited fucose-containing complex-type glycans. The N-glycosylation sites at Asn38 and Asn83 are mainly occupied by tetraantennary glycans, whereas Asn24 is occupied by a mixture of bi-, tri- and tetraantennary glycans. A molecular mass glycoprofile for each glycosylation site was established based on the relative peak intensities observed in the MALDI mass spectra of the desialylated glycopeptides.
Nickel-catalysed electrochemical reductive deprotection of allyl ethers (1995)

The selective deprotection of a series of functionalized alkyl and aryl allyl ethers to the parent alcohols or phenols, under non-hydrolytic conditions, is effected by the combination of electrochemistry and catalysis by NiII–bipyridine complexes.
The Centromere: Hub of Chromosomal Activities (1995)

Centromeres are the structures that direct eukaryotic chromosome segregation in mitosis and meiosis. There are two major classes of centromeres. Point centromeres, found in the budding yeasts, are compact loci whose constituent proteins are now beginning to yield to biochemical analysis. Regional centromeres, best described in the fission yeast Schizosaccharomyces pombe, encompass many kilobases of DNA and are packaged into heterochromatin. Their associated proteins are as yet poorly understood. In addition to providing the site for microtubule attachment, centromeres also have an important role in checkpoint regulation during mitosis.
A simple and novel method for RNA‐seq library preparation of single cell cDNA analysis by hyperactive Tn5 transposase (2012)

Here, we tested the applicability of hyperactive Tn5-mediated library preparation to deep sequencing of single cell cDNA, optimized the protocol, and compared it with the conventional method based on sonication. This new technique does not require any expensive or special equipment, which secures wider availability. A library was constructed from only 100 ng of cDNA, which enables the saving of precious specimens. Only a few steps of robust enzymatic reaction resulted in saved time, enabling more specimens to be prepared at once, and with a more reproducible size distribution among the different specimens. The obtained RNA-seq results were comparable to the conventional method. Thus, this Tn5-mediated preparation is applicable for anyone who aims to carry out deep sequencing for single cell cDNAs.
Classification and phylogeny of hydrogenases (2001)

Hydrogenases (H2ases) catalyze the reversible oxidation of molecular hydrogen and play a central role in microbial energy metabolism. Most of these enzymes are found in Archaea and Bacteria, but a few are present in Eucarya as well. They can be distributed into three classes: the [Fe]-H2ases, the [NiFe]-H2ases, and the metal-free H2ases. The vast majority of known H2ases belong to the first two classes, and over 100 of these enzymes have been characterized genetically and/or biochemically. Compelling evidence from sequences and structures indicates that the [NiFe]- and [Fe]-H2ases are phylogenetically distinct classes of proteins. The catalytic core of the [NiFe]-H2ases is a heterodimeric protein, although additional subunits are present in many of these enzymes. Functional classes of [NiFe]-H2ases have been defined, and they are consistent with categories defined by sequence similarity of the catalytic subunits. The catalytic core of the [Fe]-H2ases is a ca. 350-residue domain that accommodates the active site (H-cluster). A few monomeric [Fe]-H2ases are barely larger than the H-cluster domain. Many others are monomeric as well, but possess additional domains that contain redox centers, mostly iron-sulfur. Some [Fe]-H2ases are oligomeric. The modular structure of H2ases is strikingly illustrated in recently unveiled sequences and structures. It is also remarkable that most of the accessory domains and subunits of H2ases have counterparts in other redox complexes, in particular NADH-ubiquinone oxidoreductase (Complex I) of respiratory chains. Microbial genome sequences are bringing forth a significant body of additional H2ase sequence data and contribute to the understanding of H2ase distribution and evolution. Altogether, the available data suggest that [Fe]-H2ases are restricted to Bacteria and Eucarya, while [NiFe]-H2ases, with one possible exception, seem to be present only in Archaea and Bacteria. H2ase processing and maturation involve the products of several genes which have been identified and are currently being characterized in the case of the [NiFe]-H2ases. In contrast, near to nothing is known regarding the maturation of the [Fe]-H2ases. Inspection of the currently available genome sequences suggests that the [NiFe]-H2ase maturation proteins have no similar counterparts in the genomes of organisms possessing [Fe]-H2ases only. This observation, if confirmed, would be consistent with the phylogenetic distinctiveness of the two classes of H2ases. Sequence alignments of catalytic subunits of H2ases have been implemented to construct phylogenetic trees that were found to be consistent, in the main, with trees derived from other data. On the basis of the comparisons performed and discussed here, proposals are made to simplify and rationalize the nomenclature of H2ase-encoding genes.
Multi-Material Freeform Fabrication of Active Systems (2008)

Current Solid Freeform Fabrication (SFF) technologies can manufacture, directly from digital data, end-use mechanical parts in an increasingly wide variety of engineering materials. However, commercial SFF systems remain costly, complex, proprietary, and are limited to working with one or two proprietary materials during the course of building a part, hindering their broader application and the impact of the technology. The work we present here demonstrates (1) that SFF systems can employ many materials and multiple processes during the course of building a single object, (2) that such systems can produce complete, active, electromechanical devices, rather than only mechanical parts, and (3) that such multi-material SFF systems can be made accessible to, and are of interest to the general public. We have developed a research-oriented, multi-material SFF system and employed it to produce not only mechanical parts, but complete and functional Zn-air batteries, electrical wiring, flexible circuit boards, strain-gages, electromagnets, electroactive polymer actuators, organic-polymer transistors, and electromechanical relays. We have also developed and published the Fab@Home Model 1 open-source, multi-material, freeform fabrication system design. The Fab@Home project has received broad public and media attention, and more than 100 Model 1 machines have been built by individuals around the world.
Glycosidase-catalysed synthesis of oligosaccharides: a two-step synthesis of the core trisaccharide of N-linked glycoproteins using the β-N-acetylhexosaminidase and the β-mannosidase from Aspergillus oryzae (1996)

Using a partially purified β-mannosidase from Aspergillus oryzae, a β-mannosyl unit is trasferred from p-nitrophenyl β-D-mannopyranoside 5 to di-N-acetylchitobiose 4 to give the core trisaccharide β-D-Manp-(1→4)-β-D-GlcpNAc-(1→4)-D-GlcpNAc 6 of the N-linked glycoproteins.
N-Glycans on the Nipah Virus Attachment Glycoprotein Modulate Fusion and Viral Entry as They Protect against Antibody Neutralization (2012)

Nipah virus (NiV) is the deadliest known paramyxovirus. Membrane fusion is essential for NiV entry into host cells and for the virus' pathological induction of cell-cell fusion (syncytia). The mechanism by which the attachment glycoprotein (G), upon binding to the cell receptors ephrinB2 or ephrinB3, triggers the fusion glycoprotein (F) to execute membrane fusion is largely unknown. N-glycans on paramyxovirus glycoproteins are generally required for proper protein conformational integrity, transport, and sometimes biological functions. We made conservative mutations (Asn to Gln) at the seven potential N-glycosylation sites in the NiV G ectodomain (G1 to G7) individually or in combination. Six of the seven N-glycosylation sites were found to be glycosylated. Moreover, pseudotyped virions carrying these N-glycan mutants had increased antibody neutralization sensitivities. Interestingly, our results revealed hyperfusogenic and hypofusogenic phenotypes for mutants that bound ephrinB2 at wild-type levels, and the mutant's cell-cell fusion phenotypes generally correlated to viral entry levels. In addition, when removing multiple N-glycans simultaneously, we observed synergistic or dominant-negative membrane fusion phenotypes. Interestingly, our data indicated that 4- to 6-fold increases in fusogenicity resulted from multiple mechanisms, including but not restricted to the increase of F triggering. Altogether, our results suggest that NiV-G N-glycans play a role in shielding virions against antibody neutralization, while modulating cell-cell fusion and viral entry via multiple mechanisms.