gebhart/patrepeval huggingface dataset:
Characterization of a single-chain T-cell receptor expressed in Escherichia coli. (1992)

Despite progress in defining the nature of major histocompatibility complex products that are recognized by the T-cell antigen receptor, the binding properties and structure of the receptor have not been solved. The primary problem has been the difficulty in obtaining sufficient quantities of active receptor. In this report we show that a single-chain T-cell receptor gene can be expressed in Escherichia coli. The protein consists of the variable (V) regions of the alpha and beta chains (V alpha and V beta) encoded by the cytotoxic T-lymphocyte clone 2C (a H-2b anti-H-2d alloreactive cell line) linked by a 25-amino acid flexible peptide. Solubilized extracts that contain the 27-kDa V alpha 3V beta 8 protein are positive in solid-phase immunoassays with the anti-V beta 8 antibody KJ16 and the anti-clonotypic antibody 1B2. Approximately 1% of the protein can be specifically purified on a 1B2-conjugated column. These results indicate that a fraction of the protein is able to fold into a native conformation and that single-chain proteins should be useful not only as immunogens for eliciting anti-T-cell receptor antibodies but in the study of T-cell receptor structure and function.
Fragmentation of clusters sputtered from silver and gold: Molecular dynamics simulations (2005)

Using molecular dynamics simulations and the embedded atom method (EAM) potential we have investigated the sputtered atom clusters produced by 15 keV xenon impacts on silver and 20 keV xenon impacts on gold. Ejected clusters were simulated for long times, up to 0.01--1 \ensuremath{\mu}s, in order to investigate the fragmentation of nascent clusters. The size distributions of nascent and final clusters were calculated and fitted to an inverse power law, resulting in exponents close to 2 and 3, depending on the range of the cluster sizes used. These values are in agreement with other simulations and experiments. The results show that clusters are subject to a dramatic breakup, which makes the size of the largest sputtered cluster go down by a factor of 2--4. Despite this, the exponent in the power law does not change very much from the size distribution of nascent to that of final clusters. Considering the uncertainties, the exponent of the final size distribution is 1.0--1.7 times the exponent of the nascent size distribution.
Probabilistic model for code with decision trees (2016)

In this paper we introduce a new approach for learning precise and general probabilistic models of code based on decision tree learning. Our approach directly benefits an emerging class of statistical programming tools which leverage probabilistic models of code learned over large codebases (e.g., GitHub) to make predictions about new programs (e.g., code completion, repair, etc).
Recipe for e-commerce (1997)

The article focuses on Internet economics and examines some of the more controversial and often misunderstood aspects of shopping on the Web, such as transaction security and the much maligned Magic Cookie. Knowing more about the technologies behind commercial Web transactions can help make the Web a less scary place to type in your credit card number. The Web was never designed to be a transaction oriented environment. The basic transport protocol of the Web-HTTP-is a stateless environment; when combined with TCP/IP's packet switched mechanics, it makes for one heck of a wild ride. Not only can you not connect to and maintain an ongoing session within a Web server, but you can't even maintain a continuous and uninterrupted packet stream with that server. HTTP guarantees that every link you click is a completely new and complete transaction with a beginning and an end, and TCP/IP ensures that every packet composing that brief connection is first accounted for and then immediately forgotten. This environment, while advantageous for some applications, is problematic for conducting online commerce. The difficulty imposed by the Web's stateless environment manifests itself in two primary areas: securing the transaction and payment, and tracking the customer's shopping session. A third but slightly less difficult obstacle is recognizing a customer when they return to a site at another time, which from a marketing perspective is very important. We look at each of these problems and how they are being overcome in today's online commerce environment.
Biological Potential of a Functional Human SNAILRetrogene (2002)

Snail genes encode zinc finger transcription factors required for the development of vertebrate and invertebrate embryos. They trigger epithelial to mesenchymal transitions (EMTs), thereby allowing epithelial cells to emigrate from their place of origin and form tissues such as the mesoderm and the neural crest. Snail genes are also involved in the EMTs responsible for the acquisition of invasiveness during tumor progression. This aspect of their activity is associated with their ability to directly repress E-cadherin transcription. Here we describe the existence of an active human Snail retrogene, inserted within an intron of a novel evolutionarily conserved gene and expressed in different human tissues and cell lines. Functional analyses in cell culture show that this retrogene maintains the potential to induce EMTs, conferring migratory and invasive properties to epithelial cells. In light of this data, we have renamed it SNAIL-like, a new player that must be considered in both physiological and pathological studies of SNAIL function in humans.
Tubulin Post‐Translational Modifications (1997)

This review describes the enzymes responsible for the post-translational modifications of tubulin, including detyrosination/tyrosination, acetylation/deacetylation, phosphorylation, polyglutamylation, polyglycylation and the generation of non-tyrosinatable alpha-tubulin. Tubulin tyrosine-ligase, which reattaches tyrosine to detyrosinated tubulin, has been extensively characterized and its gene sequenced. Enzymes such as tubulin-specific carboxypeptidase and alpha-tubulin acetyltransferase, required, respectively, for detyrosination and acetylation of tubulin, have yet to be purified to homogeneity and examined in defined systems. This has produced some conflicting results, especially for the carboxypeptidase. The phosphorylation of tubulin by several different types of kinases has been studied in detail but drawing conclusions is difficult because many of these enzymes modify proteins other than their actual substrates, an especially pertinent consideration for in vitro experiments. Tubulin phosphorylation in cultured neuronal cells has proven to be the best model for evaluation of kinase effects on tubulin/microtubule function. There is little information on the enzymes required for polyglutamylation, polyglycylation, and production of non-tyrosinatable tubulin, but the available data permit interesting speculation of a mechanistic nature. Clearly, to achieve a full appreciation of tubulin post-translational changes the responsible enzymes must be characterized. Knowing when the enzymes are active in cells, if soluble or polymerized tubulin is the preferred substrate and the amino acid residues modified by each enzyme are all important. Moreover, acquisition of purified enzymes will lead to cloning and sequencing of their genes. With this information, one can manipulate cell genomes in order to either modify key enzymes or change their relative amounts, and perhaps reveal the physiological significance of tubulin post-translational modifications.
Identification and Expression of Human Cytomegalovirus Transcription Units Coding for Two Distinct Fcγ Receptor Homologs (2002)

Cellular receptors for the Fc domain of immunoglobulin G (IgG) (FcgammaRs) comprise a family of surface receptors on immune cells connecting humoral and cellular immune responses. Several herpesviruses induce FcgammaR activities in infected cells. Here we identify two distinct human cytomegalovirus (HCMV)-encoded vFcgammaR glycoproteins of 34 and 68 kDa. A panel of HCMV strains exhibited a slight molecular microheterogeneity between Fcgamma-binding proteins, suggesting their viral origin. To locate the responsible genes within the HCMV genome, a large set of targeted HCMV deletion mutants was constructed. The mutant analysis allowed the identification of a spliced UL119-UL118 mRNA to encode vFcgammaR gp68 and TRL11/IRL11 to encode vFcgammaR gp34. Both vFcgammaRs are surface resident type I transmembrane glycoproteins. Significant relatedness of sequences in the extracellular chain of gpUL119-118 and gpTRL11 with particular immunoglobulin supergene family domains present in FcgammaR I and FcgammaRs II/III, respectively, indicates a different ancestry and function of gpUL119-118 and gpTRL11. The HCMV-encoded vFcgammaRs highlight an impressive diversification and redundancy of FcgammaR structures.
Automatic segmentation in three-dimensional analysis of fibrovascular pigmentepithelial detachment using high-definition optical coherence tomography (2007)

Automatic segmentation allows for detailed quantitative and topographic analysis of the RPE and the overlying retina. In fPED, the 128 x 512 scanning-pattern shows mild advantages when compared with the 256 x 256 scan. Together with the ability for automatic segmentation, HD-OCT clearly improves the clinical monitoring of chorioretinal disease by adding relevant new parameters. HD-OCT is likely capable of enhancing the understanding of pathophysiology and benefits of treatment for current anti-CNV strategies in future.
Assessment of diagnostic quantitative fluorescent multiplex polymerase chain reaction assays performed on single cells (1998)

We have refined polymerase chain reaction (PCR) assays for the detection of sickle cell anaemia, the delta F 508 deletion causing cystic fibrosis, and the IVS1-110 mutation leading to beta thalassaemia, allowing them to be successfully performed upon single cells using fluorescent primers. We have also assessed the possibility of detecting aneuploidies of chromosomes 13, 18 and 21 using a quantitative fluorescent polymerase chain reaction (QF-PCR) with primers flanking polymorphic short tandem repeat (STR) markers. Trisomies were readily diagnosed by the detection of tri-allelic patterns. However some heterozygote normal and trisomic diallelic patterns did not produce the expected ratios of amplified PCR products due to preferential DNA sequence amplification. Total allelic drop out (ADO) did not occur with any of the cells tested. Multiplex QF-PCR assays can be performed on a single cell in under 6 h and simultaneously provide diagnosis of single gene defects, sex determination and an indication of selected chromosome aneuploidy.
Dynamic smoothing in cross‐well tomography (1993)

PreviousNext No AccessSEG Technical Program Expanded Abstracts 1993Dynamic smoothing in cross‐well tomographyAuthors: Tamas NemethFuhao QinEgon NormarkTamas NemethUniversity of Utah, Fuhao QinUniversity of Utah, and Egon NormarkUniversity of Aarhus, Denmarkhttps://doi.org/10.1190/1.1822331 SectionsAboutPDF/ePub ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinked InRedditEmail Permalink: https://doi.org/10.1190/1.1822331FiguresReferencesRelatedDetailsCited ByFirst-break vertical seismic profiling tomography for Vinton Salt DomeHua-wei Zhou26 May 2006 | GEOPHYSICS, Vol. 71, No. 3 SEG Technical Program Expanded Abstracts 1993ISSN (print):1052-3812 ISSN (online):1949-4645Copyright: 1993 Pages: 1396 publication data© 1993 Copyright © 1993 Society of Exploration GeophysicistsPublisher:Society of Exploration Geophysicists HistoryPublished: 10 Feb 2005 CITATION INFORMATION Tamas Nemeth, Fuhao Qin, and Egon Normark, (1993), "Dynamic smoothing in cross‐well tomography," SEG Technical Program Expanded Abstracts : 118-121. https://doi.org/10.1190/1.1822331 Plain-Language Summary PDF DownloadLoading ...
Specific Hippocampal Volume Reductions in Individuals at Risk for Alzheimer’s Disease (1997)

Our goal was to ascertain the involvement of the temporal lobe in the preclinical (not yet diagnosable) stages of dementia of the Alzheimer's type (DAT) by using MRI-derived volumes. We assessed anatomical subdivisions of the temporal lobe on three groups of carefully screened age- and education-matched elderly individuals: 27 normal elderly (NL), 22 individuals with minimal cognitive impairment (MCI), who did not fulfill DAT criteria but were regarded at high risk for future DAT, and 27 DAT individuals. We found hippocampal volume reductions of 14% for the MCI and 22% for the DAT group compared to the NL group. Utilizing regression analyses and after accounting for gender head size-age, generalized atrophy (CSF), and other temporal lobe subvolumes, the hippocampal volume separated NL from MCI individuals, correctly classifying 74%. For NL and MCI groups combined the hippocampal volume was the only temporal lobe subvolume related to delayed recall memory performance. When contrasting MCI and DAT individuals, the fusiform gyrus volume uniquely improved the ability of the hippocampal volume to separate MCI from DAT individuals from 74 to 80%. Our cross-sectional data suggest that, within the temporal lobe, specific hippocampal volume reductions separated the group at risk for DAT from the normal group. By the time impairments are sufficient to allow a diagnosis of DAT to be made, in addition to the medial temporal lobe volume reductions, the lateral temporal lobe is also showing volume reductions, most saliently involving the fusiform gyrus.
Acute Intraoperative Arterial Elongation: Histologic, Morphologic, and Vascular Reactivity Studies (1994)

This study focuses on the histomorphologic damage produced by an acute elongation process, as well as on quantifying the alterations in arterial contractility following the application of this technique. Light microscopy and scanning electron microscopy studies were prepared from expanded and non-expanded pig superficial femoral arteries (SFA) harvested immediately following expansion, and again at 24- and 72-hr intervals. Histologically, the expanded vessels showed minor, patchy, endothelial slough, but not fragmentation of the internal or external elastic lamina. At 24 hr, the endothelium showed reactive changes, but no evidence of smooth-muscle necrosis of the tunica media was observed. At 72 hr, healing of the endothelium was evident by SEM. Similar specimens, also from the SFA, were harvested and placed in organ chambers immediately following expansion and 24 hr later, to measure contractility when exposed to alpha-adrenergic agonists. The vessels were exposed to the contractile agonists, phenylephrine and 5-hydroxytryptamine, which evoked similar concentration-dependent increases in tension in both the expanded group and the controls. From these observations, the authors conclude that acute intraoperative elongation of arteries results in only minor endothelial damage, without affecting the inherent contractility of the vessel wall.
Oxidative Metabolism in Pediococcus pentosaceus III. Glucose Dehydrogenase System (1965)

Lee, Chin K. (North Carolina State of the University of North Carolina, Raleigh), and Walter J. Dobrogosz. Oxidative metabolism in Pediococcus pentosaceus. III. Glucose dehydrogenase system. J. Bacteriol. 90:653-660. 1965.-A method was developed for the purification of glucose dehydrogenase from Pediococcus pentosaceus Az-25-5. The procedures included treatments with protamine sulfate, ammonium sulfate, and heat in addition to acid precipitation, calcium phosphate adsorption and elution, and diethylaminoethyl-Sephadex column chromatography. The final preparation thus obtained was purified 255-fold and exhibited both similarities and dissimilarities to the same enzyme isolated from other sources. The enzyme is absolutely specific for nicotinamide adenine dinucleotide phosphate (NADP) as a cofactor, and oxidizes only glucose or its analogue 2-deoxyglucose via the following reversible reaction: beta-d-glucose + NADP right harpoon over left harpoon d-glucono-delta-lactone + NADPH(2) + H(+). K(m) values were 2.3 x 10(-2) for glucose and 2 x 10(-4) for NADP. Monovalent cations were required for stability of the enzyme and stimulated activity. The pH optimum was 7.0, and the equilibrium constant was determined to be 13.4 x 10(-7) at pH 6.4. Among the Lactobacillaceae, glucose dehydrogenase activity was found to be essentially limited to members of the genus Pediococcus. Studies on the enzymatic composition of P. pentosaceus viewed in conjunction with other available data led to the conclusion that this enzyme is not involved to any significant extent in the energy metabolism of this organism.
Regulatory control of the terminal complement proteins at the surface of human endothelial cells: neutralization of a C5b-9 inhibitor by antibody to CD59 (1990)

Functionally inhibitory antibody to the plasma membrane complement inhibitor CD59 has been used to investigate control of the terminal complement proteins at the endothelial cell surface. Antibodies against purified human erythrocyte CD59 (polyclonal anti-CD59 and monoclonal antibodies [MoAbs] 1F1 and 1F5) were found to bind specifically to monolayers of cultured human umbilical vein endothelial cells, and by Western blotting to recognize an 18- to 21-Kd endothelial protein. When bound to the endothelial monolayer, anti-CD59 (immunoglobulin G or Fab fragment) potentiated membrane pore formation induced upon C9 binding to C5b-8, and augmented the C5b-9-induced cellular responses, including stimulated secretion of von Willebrand factor and expression of catalytic surface for the prothrombinase enzyme complex. Although potentiating endothelial responses to the terminal complement proteins, anti-CD59 had no effect on the response of these cells to stimulation by histamine. Taken together, these data suggest that human endothelial cells express the CD59 cell surface inhibitor of the terminal complement proteins, which serves to protect these cells from pore-forming and cell-stimulatory effects of the C5b-9 complex. These data also suggest that the inactivation or deletion of this cell surface regulatory molecule would increase the likelihood for procoagulant changes in endothelium exposed to complement activation in plasma.
Quantitative Determination of Δ9-THC, CBG, CBD, Their Acid Precursors and Five Other Neutral Cannabinoids by UHPLC-UV-MS (2017)

Cannabinoids are a group of terpenophenolic compounds in the medicinal plant <i>Cannabis sativa</i> (Cannabaceae family). Cannabigerolic acid, Δ<sup>9</sup>-tetrahydrocannabinolic acid A, cannabidiolic acid, Δ<sup>9</sup>-tetrahydrocannabinol, cannabigerol, cannabidiol, cannabichromene, and tetrahydrocannabivarin are major metabolites in the classification of different strains of <i>C. sativa</i>. Degradation or artifact cannabinoids cannabinol, cannabicyclol, and Δ<sup>8</sup>-tetrahydrocannabinol are formed under the influence of heat and light during processing and storage of the plant sample. An ultrahigh-performance liquid chromatographic method coupled with photodiode array and single quadruple mass spectrometry detectors was developed and validated for quantitative determination of 11 cannabinoids in different <i>C. sativa</i> samples. Compounds 1: - 11: were baseline separated with an acetonitrile (with 0.05% formic acid) and water (with 0.05% formic acid) gradient at a flow rate of 0.25 mL/min on a Waters Cortec UPLC C18 column (100 mm × 2.1 mm I. D., 1.6 µm). The limits of detection and limits of quantitation of the 11 cannabinoids were below 0.2 and 0.5 µg/mL, respectively. The relative standard deviation for the precision test was below 2.4%. A mixture of acetonitrile and methanol (80 : 20, <i>v</i>/<i>v</i>) was proven to be the best solvent system for the sample preparation. The recovery of all analytes was in the range of 97 - 105%. A total of 32 <i>Cannabis</i> samples including hashish, leaves, and flower buds were analyzed.
Refractory T-Cell Anergy and Rapidly Fatal Progressive Multifocal Leukoencephalopathy After Prolonged CTLA4 Therapy (2017)

Progressive multifocal leukoencephalopathy (PML) is a deadly demyelinating disease due to central nervous system replication of the human polyomavirus JC virus (JCV) in immunosuppressed patients. The only effective therapeutic approach is to restore anti-JCV T-cell responses. In this study, we describe a case of rapidly fatal PML with JCV T-cell anergy in a renal transplant patient treated with CTLA4-Ig (belatacept, a CD28-B7 costimulation blocker and T-cell anergy inducer). T-cell anergy could not be reversed despite several therapeutic approaches. Progressive multifocal leukoencephalopathy secondary to biotherapy-induced T-cell anergy may thus represent a subset of PML with major resistance to anti-JCV immune recovery.
Degradation of poly(ethylene oxide) (1960)

Abstract The degradation of high polymers of ethylene oxide in aqueous and organic solutions is accelerated by strong acids, certain oxidizing agents, ultraviolet light, and certain heavy metal ions. The effectiveness of the latter two components is related to the solution stability of various polymer samples upon long‐term, natural aging. These facts are interpreted by assuming that poly(ethylene oxide) degrades primarily by autoxidation, giving hydroperoxides which decompose by polymer chain cleavage. Certain oxidizable materials and compounds which form stable free radicals are effective in retarding the solution viscosity decrease. Aqueous polymer solutions containing alcohols, such as isopropyl alcohol, are very stable to all of the normally detrimental aging conditions. The effectiveness of the alcohol is related to the theoretical ease with which the α‐hydrogen atom is extracted, and, consequently, these effects are interpreted in view of the selective autoxidation of the alcohol present. Other types of stabilizers were investigated.
Serologic changes following B lymphocyte depletion therapy for rheumatoid arthritis (2003)

Following B lymphocyte depletion in patients with RA, a positive clinical response occurred in correlation with a significant drop in the levels of CRP and autoantibodies. Antibacterial antibody levels were relatively well maintained. B lymphocyte return preceded relapse in all patients. There was also a temporal relationship between clinical relapse and rises in autoantibody levels. Although these observations are consistent with a role for B lymphocytes in the pathogenesis of RA, the precise mechanisms involved remain unclear.
Computer translation of IUPAC systematic organic chemical nomenclature. 3. Syntax analysis and semantic processing (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTComputer translation of IUPAC systematic organic chemical nomenclature. 3. Syntax analysis and semantic processingD. I. Cooke-Fox, G. H. Kirby, and J. D. RaynerCite this: J. Chem. Inf. Comput. Sci. 1989, 29, 2, 112–118Publication Date (Print):May 1, 1989Publication History Published online1 May 2002Published inissue 1 May 1989https://pubs.acs.org/doi/10.1021/ci00062a011https://doi.org/10.1021/ci00062a011research-articleACS PublicationsRequest reuse permissionsArticle Views94Altmetric-Citations20LEARN 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 options Get e-Alerts