gebhart/patrepeval huggingface dataset:
Mapping of sites on the Src family protein tyrosine kinases p55blk, p59fyn, and p56lyn which interact with the effector molecules phospholipase C-gamma 2, microtubule-associated protein kinase, GTPase-activating protein, and phosphatidylinositol 3-kinase. (1993)

Engagement of the B-cell antigen receptor complex induces immediate activation of receptor-associated Src family tyrosine kinases including p55blk, p59fyn, p53/56lyn, and perhaps p56lck, and this response is accompanied by tyrosine phosphorylation of distinct cellular substrates. These kinases act directly or indirectly to phosphorylate and/or activate effector proteins including p42 (microtubule-associated protein kinase) (MAPK), phospholipases C-gamma 1 (PLC gamma 1) and C-gamma 2 (PLC gamma 2), phosphatidylinositol 3-kinase (PI 3-K), and p21ras-GTPase-activating protein (GAP). Although coimmunoprecipitation results indicate that the Src family protein tyrosine kinases interact physically with some of these effector molecules, the molecular basis of this interaction has not been established. Here, we show that three distinct sites mediate the interaction of these kinases with effectors. The amino-terminal 27 residues of the unique domain of p56lyn mediate association with PLC gamma 2, MAPK, and GAP. Binding to PI 3-K is mediated through the Src homology 3 (SH3) domains of the Src family kinases. Relatively small proportions of cellular PI 3-K, PLC gamma 2, MAPK, and GAP, presumably those which are tyrosine phosphorylated, bind to the SH2 domains of these kinases. Comparative analysis of binding activities of Blk, Lyn, and Fyn shows that these kinases differ in their abilities to associate with MAPK and PI 3-K, suggesting that they may preferentially bind and subsequently phosphorylate distinct sets of downstream effector molecules in vivo. Fast protein liquid chromatography Mono Q column-fractionated MAPK maintains the ability to bind bacterially expressed Lyn, suggesting that the two kinases may interact directly.
Macrolide biosynthesis. 7. Incorporation of polyketide chain elongation intermediates into methymycin (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMacrolide biosynthesis. 7. Incorporation of polyketide chain elongation intermediates into methymycinDavid E. Cane, Ralph H. Lambalot, P. C. Prabhakaran, and Walter R. OttCite this: J. Am. Chem. Soc. 1993, 115, 2, 522–526Publication Date (Print):January 1, 1993Publication History Published online1 May 2002Published inissue 1 January 1993https://doi.org/10.1021/ja00055a023RIGHTS & PERMISSIONSArticle Views552Altmetric-Citations44LEARN 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 InReddit PDF (707 KB) Get e-Alerts Get e-Alerts
SIMPLIcity: semantics-sensitive integrated matching for picture libraries (2001)

We present here SIMPLIcity (semantics-sensitive integrated matching for picture libraries), an image retrieval system, which uses semantics classification methods, a wavelet-based approach for feature extraction, and integrated region matching based upon image segmentation. An image is represented by a set of regions, roughly corresponding to objects, which are characterized by color, texture, shape, and location. The system classifies images into semantic categories. Potentially, the categorization enhances retrieval by permitting semantically-adaptive searching methods and narrowing down the searching range in a database. A measure for the overall similarity between images is developed using a region-matching scheme that integrates properties of all the regions in the images. The application of SIMPLIcity to several databases has demonstrated that our system performs significantly better and faster than existing ones. The system is fairly robust to image alterations.
Chemoenzymatic synthesis of GM3and GM2gangliosides containing a truncated ceramide functionalized for glycoconjugate synthesis and solid phase applications (2005)

Analogues of GM3 and GM2 gangliosides were chemoenzymatically synthesized on a multifunctional ceramide-type tether designed to facilitate diverse strategies for glycoconjugate synthesis. The truncated ceramide aglycon maintains the stereogenic centres of natural ceramide while avoiding extensive hydrophobicity that can hamper synthesis and purification of the glycolipids. Tetanus toxoid and BSA glycoconjugates of these two gangliosides were prepared for immunization of mice, and for solid phase assays to screen for ganglioside-specific antibodies. Inhibition experiments showed that antibodies generated by tetanus toxoid conjugates of GM3 and GM2 exhibited specificity for the carbohydrate epitope and the stereogenic centres of the ceramide.
Expression of Multiple Granzymes by Cytotoxic T Lymphocyte Implies that They Activate Diverse Apoptotic Pathways in Target Cells (2010)

Granzymes play a central role in cytotoxic T lymphocyte and natural killer cell-mediated apoptosis of target cell. Multiple granzymes are found in effector cells, and their mechanisms to lead to apoptosis are different. Effector cells kill target cells via multiple pathways. At least three pathways of apoptosis mediated by granzymes have been found. Moreover, the abnormal activity of granzymes is related to many human diseases, such as autoimmune diseases. Granzymes play an important role in inflammatory response in vivo. The biological features and mechanisms of granzyme A, B, C, K, and M to induce cellular apoptosis are summarized.
In situ synthesis of oligonucleotide microarrays (2004)

This contribution presents a brief overall look of the methods for the preparation of various types of DNA microarrays and a thorough examination of the methods for in situ synthesis of oligonucleotide microarrays.
Environmental Signals Controlling Production of Hemagglutinin/Protease in Vibrio cholerae (2001)

Vibrio cholerae hemagglutinin/protease (Hap) was induced upon nutrient limitation and strongly repressed by glucose. Hap was not produced in a mutant defective in the cyclic AMP (cAMP) receptor protein, suggesting that intracellular cAMP levels mediate Hap expression. No difference was found in Hap production between an rpoS deletion mutant and its isogenic wild-type precursor, indicating that the alternate sigma(s) factor is not essential for Hap expression. Based on these and previous results, we discuss the role of Hap in the pathogenesis of cholera.
Encagement of Gold Nanoclusters in Crosslinked Resorcinarene Shells (2002)

Monolayers of resorcinarene tetraene 1 on gold nano-clusters could be crosslinked by olefin metathesis into a nondesorptive shell. Crosslinking conditions were optimized by monitoring olefin metathesis of 1 by 1H NMR spectroscopy and obtaining empirical rate con-stants. Gel permeation chromatography (GPC) was found to be a useful tool for evaluating the enhanced stability of the encaged nanoparticles; resorcinarene-encapsulated nanoparticles which were not subjected to olefin metathesis did not survive GPC analysis, whereas nanoparticles in crosslinked shells were found to be stable.
Some New Reactions of Methanesulfenyl Chloride1 (1959)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSome New Reactions of Methanesulfenyl Chloride1IRWIN B. DOUGLASSCite this: J. Org. Chem. 1959, 24, 12, 2004–2006Publication Date (Print):December 1, 1959Publication History Published online1 May 2002Published inissue 1 December 1959https://pubs.acs.org/doi/10.1021/jo01094a047https://doi.org/10.1021/jo01094a047research-articleACS PublicationsRequest reuse permissionsArticle Views235Altmetric-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 optionsGet e-Alertsclose Get e-Alerts
Extended CSF cytarabine exposure following intrathecal administration of DTC 101. (1993)

Extended CSF exposure to therapeutic cytarabine concentrations was achieved after a single intraventricular or intralumbar dose of DTC 101, permitting drug administration once every 2 weeks.
Green solvents for sustainable organic synthesis: state of the art (2005)

The growing awareness of the pressing need for greener, more sustainable technologies has focused attention on the use of atom efficient catalytic methodologies for the manufacture of fine chemicals and pharmaceuticals. Another aspect which is receiving increasing attention is the use of alternative reaction media that circumvent the problems associated with many of the traditional volatile organic solvents. The use of nonconventional reaction media also provides opportunities for facilitating the recovery and recycling of the catalyst. The state of the art in the use of alternative reaction media for green, sustainable organic synthesis is reviewed. Liquid–liquid biphasic catalysis provides an industrially attractive method for the recovery and recycling of catalysts as an alternative to the more traditional solid heterogeneous catalysts. Various approaches to liquid–liquid biphasic catalysis—aqueous biphasic, fluorous biphasic, supercritical carbon dioxide, ionic liquids and various combinations thereof—are reviewed and compared. “The best solvent is no solvent” but if a solvent is needed then water has a lot to recommend it and catalysis in aqueous biphasic systems is an industrially attractive methodology which has found broad application. Similarly, supercritical carbon dioxide is an interesting reaction medium in the context of green chemistry and catalysis in various mono- and biphasic systems involving this solvent are reviewed. Fluorous biphasic systems and ionic liquids also have advantages in certain situations and the advantages and limitations of these media are compared. The ultimate in clean catalytic technologies is to telescope multistep syntheses into one-pot in the form of catalytic cascade processes. Examples of such catalytic cascades involving both chemo- and biocatalytic conversions are presented. Biocatalysis has a distinct advantage in this context in that the reactions all take place at or close to ambient temperature and pressure. In emulation of natural processes, where several different enzymes are compartmentalised in the cell, it can be advantageous to immobilise the various catalysts in such a cascade process. In this context, a novel and effective method for the immobilisation of enzymes as cross-linked enzyme aggregates (CLEAs) is discussed and the use of a combi CLEA, containing two enzymes, for the one-pot conversion of benzaldehyde to S-mandelic acid is reported.
Rapid Identification of Dengue Virus Isolates by using Monoclonal Antibodies in an Indirect Immunofluorescence Assay (1983)

Type-specific monoclonal antibodies prepared against the four dengue (DEN) virus serotypes were evaluated for their ability to identify low-passage human and mosquito isolates from Jamaica and West Africa by an indirect immunofluorescence assay. Serotyped human isolates from Jamaican dengue fever patients included 12 DEN-1, two DEN-2, and five DEN-4 viruses. Viruses from West Africa included 84 DEN-2 mosquito strains as well as two DEN-1 and one DEN-2 from humans. Results obtained using the immunofluorescence assay were consistent with virus identifications obtained using the more classical but costly and time-consuming plaque-reduction neutralization test. More viral isolates and higher virus yields were obtained using the C6/36 clone of Aedes albopictus cells rather than LLC-MK2 (monkey kidney) cells. Dengue type-specific monoclonal antibodies detected prototype viral antigens 24-48 hours postinfection in C6/36 cells. This is the first time that monoclonal antibodies have been used to serotype low-passage flavivirus isolates.
Metabolic conversion of CI-1040 turns a cellular MEK-inhibitor into an antibacterial compound (2018)

Abstract Influenza virus (IV) infections cause severe respiratory illnesses that can be complicated by bacterial super-infections. Previously, we identified the cellular Raf-MEK-ERK cascade as a promising antiviral target. Inhibitors of MEK, such as CI-1040, showed potent antiviral activity. However, it remained unclear if this inhibitor and its active form, ATR-002, might sensitize host cells to either IV or secondary bacterial infections. To address these questions, we studied the anti-pathogen activity of ATR-002 in comparison to CI-1040, particularly, its impact on Staphylococcus aureus ( S . aureus ), which is a major cause of IV super-infections. We analysed IV and S . aureus titres in vitro during super-infection in the presence and absence of the drugs and characterized the direct impact of ATR-002 on bacterial growth and phenotypic changes. Importantly, neither CI-1040 nor ATR-002 treatment led to increased bacterial titres during super-infection, indicating that the drug does not sensitize cells for bacterial infection. In contrast, we rather observed reduced bacterial titres in presence of ATR-002. Surprisingly, ATR-002 also led to reduced bacterial growth in suspension cultures, reduced stress- and antibiotic tolerance without resistance induction. Our data identified for the first time that a particular MEK-inhibitor metabolite exhibits direct antibacterial activity, which is likely due to interference with the bacterial PknB kinase/Stp phosphatase signalling system.
Using SV119‐Gold Nanocage Conjugates to Eradicate Cancer Stem Cells Through a Combination of Photothermal and Chemo Therapies (2014)

Cancer stem cells (CSCs) are believed to be responsible for the long-term growth of a tumor, as well as its metastasis and recurrence after conventional therapies. Here, it is demonstrated that the sigma-2 receptor is overexpressed on the surface of breast CSCs, and thus could serve as a biomarker for the purpose of targeting. Breast CSCs are targeted with Au nanocages (AuNCs) by functionalizing their surfaces with SV119, a synthetic small molecule capable of binding to the sigma-2 receptor with high specificity. The interiors of the AuNCs could also be loaded with an anticancer drug to be selectively delivered to breast CSCs and released in a controllable fashion. The results demonstrate that the SV119-AuNC conjugate can serve as a new platform to carry out photothermal and chemo therapies simultaneously, eradicating breast CSCs more effectively through a synergetic effect.
Actinium-225 for Targeted α Therapy: Coordination Chemistry and Current Chelation Approaches (2018)

The α-emitting radionuclide actinium-225 possesses nuclear properties that are highly promising for use in targeted α therapy (TAT), a therapeutic strategy that employs α particle emissions to destroy tumors. A key factor, however, that may hinder the clinical use of actinium-225 is the poor understanding of its coordination chemistry, which creates challenges for the development of suitable chelation strategies for this ion. In this article, we provide an overview of the known chemistry of actinium and a summary of the chelating agents that have been explored for use in actinium-225-based TAT. This overview provides a starting point for researchers in the field of TAT to gain an understanding of this valuable therapeutic radionuclide.
17O Quantitative Nuclear Magnetic Resonance Spectroscopy of Gasoline and Oxygenated Additives (2003)

17O Nuclear magnetic resonance (NMR) spectroscopy allows exclusive detection and direct quantification of oxygenates in gasoline unaffected by its hydrocarbon content, using the internal standard quantitative NMR (QNMR) method. Chemical shifts of 24 oxygen-containing compounds as potential additives and contaminants have been measured in gasoline and corrected values of δO 18.1 and 3.9 determined for neat methyl tert-butyl ether (MTBE) and neat di-n-butyl ether, respectively. Quantification of ethanol in gasoline can be readily achieved by 17O QNMR with dimethyl sulfone as an internal standard reference material, at the levels currently used in retail gasolines (1−20%). In addition, the simultaneous detection and quantification of the oxygenates methanol, ethanol, 2-propanol, tert-butyl alcohol, and MTBE in gasoline has been established to further demonstrate the specificity of the method. 17O NMR has distinct advantages over 1H and 13C QNMR methods, and although it cannot reliably differentiate 1-propanol, 1-butanol, 1-pentanol, and isopentyl alcohol, 17O NMR does allow the rapid and unambiguous identification of unexpected oxygenates such as acetates and ketones found as contaminants in some retail gasoline.
Restraining Infarct Expansion Preserves Left Ventricular Geometry and Function After Acute Anteroapical Infarction (1999)

Background —Expansion of an acute myocardial infarction predicts progressive left ventricular (LV) dilatation, functional deterioration, and early death. This study tests the hypothesis that restraining expansion of an acute infarction preserves LV geometry and resting function. Methods and Results —In 23 sheep, snares were placed around the distal left anterior descending and second diagonal coronary arteries. In 12 sheep, infarct deformation was prevented by Marlex mesh placed over the anticipated myocardial infarct. Snared arteries were occluded 10 to 14 days later. Serial hemodynamic measurements and transdiaphragmatic quantitative echocardiograms were obtained up to 8 weeks after anteroapical infarction of 0.23 of LV mass. In sheep with mesh, circulatory hemodynamics, stroke work, and end-systolic elastance return to preinfarction values 1 week after infarction and do not change subsequently. Ventricular volumes and ejection fraction do not change after the first week postinfarction. Control animals develop large anteroapical ventricular aneurysms, increasing LV dilatation, and progressive deterioration in circulatory hemodynamics and ventricular function. At week 8, differences in LV end-diastolic pressure, cardiac output, end-diastolic and end-systolic volumes, ejection fraction, stroke work, and end-systolic elastance are significant ( P &lt;0.01) between groups. Conclusions —Preventing expansion of acute myocardial infarctions preserves LV geometry and function.
Dielectric Constant and Loss Data (1972)

This report includes data on high temperature organic crystals, ceramics, and glasses. Additional sections include plastic materials with less heat resistance. (P.S.-PL)
Leptin Transport Across the Blood-Brain Barrier: Implications for the Cause and Treatment of Obesity (2001)

Leptin has emerged as a major regulator of adiposity. Leptin is released into the blood from fat cells and circulates to the brain where it crosses the blood-brain barrier (BBB) to act at receptors within the central nervous system to affect appetite, thermogenesis, and a number of other actions. In humans and in many rodent models, resistance to leptin appears to be a chief cause of obesity. Determining the cause of leptin resistance is fundamental to developing strategies for the use of leptin in obesity. The literature characterizing the transport of leptin across the BBB is reviewed. This literature strongly suggests that the cause of leptin resistance is due a decreased transport of leptin across the BBB in obese humans and rodents. The main cause of this resistance appears to be an impairment in the activity of the transporter rather than just simply saturation at higher doses. Strategies to overcome impaired BBB transport are reviewed, including the use of allosteric regulators and the delivery of material by the intrathecal route.
The Adaptable Major Histocompatibility Complex (MHC) Fold: Structure and Function of Nonclassical and MHC Class I–Like Molecules (2013)

The MHC fold is found in proteins that have a range of functions in the maintenance of an organism's health, from immune regulation to fat metabolism. Well adapted for antigen presentation, as seen for peptides in the classical MHC molecules and for lipids in CD1 molecules, the MHC fold has also been modified to perform Fc-receptor activity (e.g., FcRn) and for roles in host homeostasis (e.g., with HFE and ZAG). The more divergent MHC-like molecules, such as some of those that interact with the NKG2D receptor, represent the minimal MHC fold, doing away with the α3 domain and β2m while maintaining the α1/α2 platform domain for receptor engagement. Viruses have also co-opted the MHC fold for immune-evasive functions. The variations on the theme of a β-sheet topped by two semiparallel α-helices are discussed in this review, highlighting the fantastic adaptability of this fold for good and for bad.
A Bayesian Model for Biclustering with Applications (2010)

Summary The paper proposes a Bayesian method for biclustering with applications to gene microarray studies, where we want to cluster genes and experimental conditions simultaneously. We begin by embedding bicluster analysis into the framework of a plaid model with random effects. The corresponding likelihood is then regularized by the hierarchical priors in each layer. The resulting posterior, which is asymptotically equivalent to a penalized likelihood, can attenuate the effect of high dimensionality on cluster predictions. We provide an empirical Bayes algorithm for sampling posteriors, in which we estimate the cluster memberships of all genes and samples by maximizing an explicit marginal posterior of these memberships. The new algorithm makes the estimation of the Bayesian plaid model computationally feasible and efficient. The performance of our procedure is evaluated on both simulated and real microarray gene expression data sets. The numerical results show that our proposal substantially outperforms the original plaid model in terms of misclassification rates across a range of scenarios. Applying our method to two yeast gene expression data sets, we identify several new biclusters which show the enrichment of known annotations of yeast genes.