gebhart/patrepeval huggingface dataset:
Production and Characterization of Antibodies Against Synthetic Peptides (2003)

Immunization protocols vary greatly between laboratories. In general, there are no hard and fast rules and most protocols give satisfactory results. The methods described below are designed to give optimal results with minimal injury to the test animal, and we have used them extensively and successfully for several years (1-5). Peptide immunizations differ from those in which the immunogen is a larger macromolecule in that maximal antipeptide titers (which arise rapidly after 2-3 immunizations) do not always coincide with maximal titers against the intact protein (which tend to peak rather later at 4-6 immunizations). Thus, although antipeptide enzyme-linked immunosorbent assays (ELISAs) are useful gages of immune response, there is no substitute for eventual screening on the intact protein (e.g., by immunoprecipitation, Western blotting, and so on). Individual variation in antipeptide response is very marked, so it is advisable to use several animals (three to six) per immunogen. Rabbit responses are generally poorer in specific pathogen-free (SPF) animals, probably reflecting their greater immune naivity. Mouse responses are often best in F(1) crosses (e.g., BALB/c × C57B1/6) rather than pure strains. Alternatively, SJL mice generally respond well.
Retroviral vectors bearing IgG-binding motifs for antibody-mediated targeting of vascular endothelial growth factor receptors (2001)

Targeting retroviral vectors to tumor vasculature is an important goal of cancer gene therapy. In this study, we report a novel targeting approach wherein IgG-binding peptides were inserted into the Moloney murine leukemia virus (MuLV) envelope (env) protein. The modifications on the viral env included replacement of the entire receptor binding region of the viral env with protein A (or ZZ) domains. The truncated env incorporating IgG-binding motifs (known as proteins) provided the targeting function, while the co-expressed wild-type (WT) env protein enabled viral fusion and cell entry. An anti-human VEGF receptor (Flk-1/KDR) antibody served as a molecular bridge, directing the retroviral vector to the endothelial cell. Hence, the IgG-targeted vectors bound to the Flk-1/KDR antibody which in turn bound to VEGF receptors on Kaposi sarcoma, KSY1, endothelial cells. The net effect was increased viral fusion and infectivity of IgG-bound retroviral vectors when compared to non-targeted vectors bearing WT env alone. These data provide the proof of concept that IgG-binding vector/VEGF receptor antibody complexes may be used to enhance retroviral gene delivery to activated endothelial cells.
Structural Elucidation of Scyphostatin, an Inhibitor of Membrane-Bound Neutral Sphingomyelinase (1997)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTStructural Elucidation of Scyphostatin, an Inhibitor of Membrane-Bound Neutral SphingomyelinaseMasahiro Tanaka, Futoshi Nara, Keiko Suzuki-Konagai, Tsuyoshi Hosoya, and Takeshi OgitaView Author Information Biomedical Research Laboratories, Sankyo Co., Ltd. 2-58, Hiromachi 1-chome, Shinagawa-ku Tokyo, 140 Japan Biological Research Laboratories, Sankyo Co., Ltd. 2-58, Hiromachi 1-chome, Shinagawa-ku Tokyo, 140 Japan Tsukuba Research Laboratories, Sankyo Co., Ltd. 33, Miyukigaoka, Tsukuba-shi Ibaraki, 305 Japan Cite this: J. Am. Chem. Soc. 1997, 119, 33, 7871–7872Publication Date (Web):August 20, 1997Publication History Received28 April 1997Revised19 June 1997Published online20 August 1997Published inissue 1 August 1997https://pubs.acs.org/doi/10.1021/ja9713385https://doi.org/10.1021/ja9713385rapid-communicationACS PublicationsCopyright © 1997 American Chemical SocietyRequest reuse permissionsArticle Views480Altmetric-Citations99LEARN 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 SUBJECTS:Alcohols,Chemical structure,Inhibitors,Organic compounds,Peptides and proteins Get e-Alerts
Isolation of an oxygen-sensitive FNR protein of Escherichia coli: interaction at activator and repressor sites of FNR-controlled genes. (1996)

The Escherichia coli fnr gene product, FNR, is a DNA binding protein that regulates a large family of genes involved in cellular respiration and carbon metabolism during conditions of anaerobic cell growth. FNR is believed to contain a redox/O2-sensitive element for detecting the anaerobic state. To investigate this process, a fnr mutant that encodes an altered FNR protein with three amino acid substitutions in the N-terminal domain was constructed by site-directed mutagenesis. In vivo, the mutant behaved like a wild-type strain under anaerobic conditions but had a 14-fold elevated level of transcriptional activation of a reporter gene during aerobic cell growth. The altered fur gene was overexpressed in E. coli and the resultant FNR protein was purified to near homogeneity by using anaerobic chromatography procedures. An in vitro Rsa I restriction site protection assay was developed that allowed for the assessment of oxygen-dependent DNA binding of the mutant FNR protein. The FNR protein was purified as a monomer of M(r) 28,000 that contained nonheme iron at 2.05 +/- 0.34 mol of Fe per FNR monomer. In vitro DNase I protection studies were performed to establish the locations of the FNR-binding sites at the narG, narK, dmsA, and hemA promoters that are regulated by either activation or repression of their transcription. The sizes of the DNA footprints are consistent with the binding of two monomers of FNR that protect the symmetrical FNR-recognition sequence TTGAT-nnnnATCAA. Exposure of the FNR protein or protein-DNA complex to air for even short periods of time (approximately 5 min) led to the complete loss of DNA protection at a consensus FNR recognition site. A model whereby the FNR protein exists in the cell as a monomer that assembles on the DNA under anaerobic conditions to form a dimer is discussed.
Role of tumor necrosis factor on toxicity and cytokine production after isolated hepatic perfusion. (2001)

Addition of TNF to melphalan during IHP results in significant differences in post-IHP production of IL-6 and IL-8 with associated changes in mean arterial blood pressure and greater regional toxicity, as reflected in higher levels of serum bilirubin. However, these measurable differences were transient and did not appear to be of major clinical consequence. Prior to its routine use, the benefit of TNF in isolation perfusion should be demonstrated in random assignment trials.
Functions of the TGFβ superfamily in human embryonic stem cells (2005)

The establishment of human embryonic stem (ES) cells has opened possibilities for cell replacement therapy to treat diseases such as diabetes, Parkinson's disease and cardiac myopathies. Self-renewal is one of the essential defining characteristics of stem cells. If stem cells are to have widespread therapeutic applications, it is essential to identify the extrinsic and intrinsic factors maintaining self-renewal, particularly in culture. Insight into the regulation of known self-renewal transcription factors and cross-talk between their upstream signalling pathways is important for a better understanding of how stem cell self-renewal and differentiation are related to downstream target genes. This may lead to the establishment of protocols for obtaining a large supply of ES cells. Here, we review the role that TGFbeta superfamily members are thought to play in self-renewal and differentiation of human and mouse ES cells. We focus on the prototype TGFbeta, TGFbeta1, activin A, nodal and bone morphogenetic proteins and their expression, activity and function in embryonic stem cells.
Palladium(III)-Catalyzed Fluorination of Arylboronic Acid Derivatives (2013)

A practical, palladium-catalyzed synthesis of aryl fluorides from arylboronic acid derivatives is presented. The reaction is operationally simple and amenable to multigram-scale synthesis. Evaluation of the reaction mechanism suggests a single-electron-transfer pathway, involving a Pd(III) intermediate that has been isolated and characterized.
Single-class classification (1975)

Often, when classifying multispectral data, only one class or crop is of interest, such as wheat in the Large Area Crop Inventory Experiment (LACIE). Usual procedures for designing a Bayes classifier require that labeled training samples and therefore ground truth be available for the "class of interest" plus all confusion classes defined by the multispectral data. This paper will consider the problem of designing a two-class Bayes classifier which will classify data into the "class of interest" or the "other" classes but will require only labeled training samples from the "class of interest" to design the classifier. Thus, this classifier minimizes the need for ground truth. For these reasons, the classifier is referred to as a single-class classifier. A procedure for evaluating the overall performance of the single-class classifier in terms of the probability of error will be discussed.
A Ca 2+ -Dependent Transgenic Model of Cardiac Hypertrophy (2001)

Transgenic mice developed hypertrophy and severe cardiomyopathy as a function of age, thus confirming that changes in channel density are sufficient to induce disease. The small, sustained increase in the ingress of Ca(2+) through the calcium channel elevated protein kinase Calpha before the development of hypertrophy, suggesting that protein kinase Calpha plays an important role in triggering hypertrophy.
Yeast 2 µm plasmid copy number is elevated by a mutation in the nuclear gene UBC4 (2001)

The copy number of the Saccharomyces cerevisiae endogenous 2 microm plasmid is under strict control to ensure efficient propagation to the daughter cell without significantly reducing the growth rate of the mother or the daughter cell. A recessive mutation has been identified that resulted in an elevated but stable 2 microm plasmid copy number, which could be complemented by a genomic DNA clone containing the UBC4 gene, encoding an E2 ubiquitin-conjugating enzyme. A ubc4::URA3 deletion resulted in the same elevated 2 microm plasmid copy number. An analysis of the endogenous 2 microm transcripts revealed that the steady-state abundance of REP1, REP2, FLP and RAF were all increased 4-5-fold in the mutant. Analysis of the mutant ubc4 allele identified a single base pair mutation within the UBC4 coding region, which would generate a glutamic acid to lysine amino acid substitution within a region of conserved tertiary structure located within the first alpha-helix of Ubc4p. These investigations represent the first molecular characterization of a mutation within a Saccharomyces cerevisiae nuclear gene shown to affect 2 microm steady-state plasmid copy number and implicate the ubiquitin-dependent proteolytic pathway in host control of 2 microm plasmid copy number.
Low birthweight and adult insulin resistance: the “catch-up growth” hypothesis: Figure 1 (1999)

Epidemiological studies have shown a close correlation between intrauterine growth retardation (IUGR) and the onset of insulin resistance, non-insulin-dependent diabetes mellitus (NIDDM), hypertension, hyperlipidaemia, and cardiovascular diseases in adult life.1-6 To explain this association, the concept of re-programming has been introduced: intrauterine exposure to insufficient nutrient supply during critical periods of fetal life would permanently affect the development and function of the endocrine system, leading to metabolic changes, including reduced insulin sensitivity.5 6 

Although knowledge of the mechanisms involved in the re-programming process might allow new strategies for early prevention of long term metabolic disturbances to be developed, the pathophysiological link between fetal growth impairment and adult diseases is still unclear.

In 1992 Hales and Barker7 proposed the model of the “thrifty phenotype,” suggesting that intrauterine malnutrition would lead to insulin resistance and decreased β cell mass, thus predisposing to NIDDM. According to this hypothesis, the endocrine alterations induced by intrauterine malnutrition are intended to divert the limited nutrient supply to maintain survival and development of vital organs, such as the brain, at the expense of growth.

More recently, the “fetal salvage” hypothesis has been formulated.8 The finding that prepubertal IUGR children show a far greater insulin response than normal birthweight children, challenges the previously proposed β cell hypoplasia. …
New Insights into the Immunopathology of Tuberculosis (1991)

Tuberculosis is characterised by fever, weight loss and necrosis in both lesions and tuberculin skin test sites (Koch phenomenon), although the antigens of Mycobacterium tuberculosis are not directly toxic to the tissues. The tissue damage appears to be due to several interacting factors. First, M. tuberculosis induces an immunoregulatory disorder of which a raised percentage of agalactosyl IgG is a marker. This is seen also in rheumatoid arthritis and Crohn's disease and is associated with tissue-damaging inflammation. Subsequently, several properties of M. tuberculosis exacerbate this disorder by triggering cytokine release, and rendering tissues sensitive to the toxicity of tumor necrosis factor (TNF). Moreover, M. tuberculosis, but not bacillus Calmette-Guérin or several Mycobacterium avium strains, produces a factor which increases the toxicity of TNF for individual cells. Thus, M. tuberculosis may distort the normal protective role of TNF so that this cytokine becomes toxic to the host. The immunoregulatory disorder associated with agalactosyl IgG appears to be susceptible to immunotherapy, so novel types of treatment for the immunopathological component of tuberculosis are being explored.
An Elevation in the Concentration of Free Cytosolic Calcium Is Sufficient to Activate the Oxidative Burst of Granulocytes Primed with Recombinant Human Granulocyte-Macrophage Colony-stimulating Factor (1989)

In granulocytes harvested from human blood, an elevation of the cytosolic concentration of Ca2+ ions is by itself insufficient to activate the cell's respiratory burst. We report herein that, when granulocytes are "primed" by a 90-min preincubation with the recombinant human hemopoietic growth factor granulocyte-macrophage colony-stimulating factor (GM-CSFrh), elevation of the concentration of cytosolic Ca2+ ions ([Ca2+]i) becomes a more effective transduction signal capable of triggering the generation of substantial quantities of superoxide (O2-) anions by the cell. In these studies, we used four separate and independent maneuvers to induce elevation of [Ca2+]i: 1) depolarization of the cell's electrical potential through obliteration of the transmembrane Na+ and K+ gradients; 2) acidification of the cytoplasm using propionic acid; 3) addition of the calcium ionophore ionomycin; and 4) treatment of the cells with the monoclonal antibody to the C3bi receptor, PMN7C3. In all cases, elevation of [Ca2+]i through these manipulations resulted in the release of substantially greater quantities of O2- by GM-CSFrh-primed granulocytes than by unprimed, control cells. The generation of O2- was in all cases markedly reduced by chelation of either intracellular Ca2+ with 1,2-bis(2-aminophenoxy)ethane-N,N,N',N'-tetraacetic acid or extracellular Ca2+ with [ethylene-bis(oxyethylenenitrilo)]tetraacetic acid. We conclude that during the process of GM-CSFrh priming, the metabolic assembly responsible for O2- anion production in the granulocyte becomes altered in such a way that a subsequent elevation in [Ca2+]i provides a potent signal for its activation.
Study on the Security of Time-Stamping Service Architecture (2009)

NTSC and Uni-trust are constructing the public time-stamping service platform of China. In this paper, we present the architecture of Time-Stamping service and analyze the threats are encountered in each time-stamping system. Then we propose a modified architecture for overcoming these threats. This architecture is relies on a secure time service to obtain a authentic time stamp from the Time Authority, and makes the client obtain a trusted time from the TSA during the time-stamping service. This method improves the security of time service in time-stamping service.
Heparin induces dimerization and confers proliferative activity onto the hepatocyte growth factor antagonists NK1 and NK2. (1996)

Hepatocyte growth factor (HGF) is a potent epithelial mitogen whose actions are mediated through its receptor, the proto-oncogene c-Met. Two truncated variants of HGF known as NK1 and NK2 have been reported to be competitive inhibitors of HGF binding to c-Met, and to function as HGF antagonists (Lokker, N.A., and P.J. Godowski. 1993. J. Biol. Chem. 268: 17145-17150; Chan, A.M., J.S. Rubin, D.P. Bottaro, D.W. Hirschfield, M. Chedid, and S.A. Aaronson. 1991. Science (Wash. DC). 254:1382-1387). We show here, however, that NK1 acts as a partial agonist in mink lung cells. Interestingly, NK1, which is an HGF antagonist in hepatocytes in normal conditions, was converted to a partial agonist by adding heparin to the culture medium. The interaction of NK1 and heparin was further studied in BaF3 cells, which express little or no cell surface heparan sulfate proteoglycans. In BaF3 cells transfected with a plasmid encoding human c-Met, heparin and NK1 synergized to stimulate DNA synthesis and cell proliferation. There was no effect of heparin on the IL-3 sensitivity of BaF3-hMet cells, and no effect of NK1 plus heparin in control BaF3 cells, indicating that the response was specific and mediated through c-Met. The naturally occurring HGF splice variant NK2 also stimulated DNA synthesis in mink lung cells and exerted a heparin-dependent effect on BaF3-hMet cells, but not on BaF3-neo cells. The activating effect of heparin was mimicked by a variety of sulfated glycosaminoglycans. Mechanistic studies revealed that heparin increased the binding of NK1 to BaF3-hMet cells, stabilized NK1, and induced dimerization of NK1. Based on these studies, we propose that the normal agonist activity of NK1 and NK2 in mink lung cells is due to an activating interaction with an endogenous glycosaminoglycan. Consistent with that model, a large portion of the NK1 binding to mink lung cells could be blocked by heparin. Moreover, a preparation of glycosaminoglycans from the surface of mink lung cells induced dimerization of NK1. These data show that the activity of NK1 and NK2 can be modulated by heparin and other related glycosaminoglycans to induce proliferation in cells expressing c-Met.
Applying neural network to robust keyword spotting in speech recognition application (2002)

A word spotting recognition system is developed using an artificial neural network based on the Quickprop algorithm to recognize the keyword "collect" corrupted by white Gaussian noise in continuous speech. The neural network is constructed with 420 input nodes, 70 hidden neurons and 1 output neuron. A sigmoid function is used for activation function. Two phrases, one with the keyword and the other without are used for training. Ten phrases are used for testing on the trained network in which five versions are associated with each phrase. Misclassification happens to the original version of one phrase containing the keyword and false alarms happen to two phrases without the keyword.
Studies on antidiabetic agents. II. Synthesis of 5-(4-(1-methylcyclohexylmethoxy)-benzyl)thiazolidine-2,4-dione (ADD-3878) and its derivatives. (1982)

More than 100 5-substituted thiazolidine-2, 4-diones were prepared and their hypoglycemic and hypolipidemic activities were evaluated with genetically obese and diabetic mice, yellow KK. The structure-activity relationship study showed that the 5-(4-oxybenzyl) moiety is essential for substantial activity. Among these compounds, 5-(4-cyclohexylmethoxy) benzylthiazolidine-2, 4-dione (47), 5-[4-(1-methylcyclohexylmethoxy) benzyl]-thiazolidine-2, 4-dione (49, ADD-3878) and 5-{4-[2-(3-pyridyl) ethoxy] benzyl} thiazolidine-2, 4-dione (59) exhibited the most favorable properties in terms of activity and toxicity.
Detection of cholera enterotoxin activity in suckling hamsters (1978)

For detection of cholera enterotoxin activity, suckling hamster, mouse, and rat models were compared. It was found that not only suckling mice but also suckling rats and hamsters were sensitive to cholera enterotoxin. Among these models, suckling hamsters were the most sensitive and gave positive results with about 1/100 the cholera toxin seen in suckling mice and rats.
Global ocean carbon uptake: magnitude, variability and trends (2013)

Abstract. The globally integrated sea–air anthropogenic carbon dioxide (CO2) flux from 1990 to 2009 is determined from models and data-based approaches as part of the Regional Carbon Cycle Assessment and Processes (RECCAP) project. Numerical methods include ocean inverse models, atmospheric inverse models, and ocean general circulation models with parameterized biogeochemistry (OBGCMs). The median value of different approaches shows good agreement in average uptake. The best estimate of anthropogenic CO2 uptake for the time period based on a compilation of approaches is −2.0 Pg C yr−1. The interannual variability in the sea–air flux is largely driven by large-scale climate re-organizations and is estimated at 0.2 Pg C yr−1 for the two decades with some systematic differences between approaches. The largest differences between approaches are seen in the decadal trends. The trends range from −0.13 (Pg C yr−1) decade−1 to −0.50 (Pg C yr−1) decade−1 for the two decades under investigation. The OBGCMs and the data-based sea–air CO2 flux estimates show appreciably smaller decadal trends than estimates based on changes in carbon inventory suggesting that methods capable of resolving shorter timescales are showing a slowing of the rate of ocean CO2 uptake. RECCAP model outputs for five decades show similar differences in trends between approaches.
Syndecan 3 Intramembrane Proteolysis Is Presenilin/γ-Secretase-dependent and Modulates Cytosolic Signaling (2003)

The syndecans play critical roles in several signal transduction pathways. The core proteins of these heparan sulfate proteoglycans are characterized by highly conserved transmembrane and intracellular domains which are required for signaling across the membrane and for interaction with cytosolic proteins. However, regulatory mechanisms controlling these functions remain largely unknown. Here we show that, upon ligand-induced primary proteolytic cleavage within the ectodomain, the intracellular domain of syndecan 3 is released by regulated intramembrane proteolysis. The cleavage is mediated by presenilin/gamma-secretase complex and negatively regulates the plasma membrane targeting of the transcriptional cofactor CASK.