gebhart/patrepeval huggingface dataset:
The Cluster Glycoside Effect (2002)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe Cluster Glycoside EffectJoseph J. Lundquist and Eric J. TooneView Author Information Department of Chemistry, Duke University, B120 LSRC, Durham, North Carolina 27708-0317 Cite this: Chem. Rev. 2002, 102, 2, 555–578Publication Date (Web):January 29, 2002Publication History Received18 July 2001Published online29 January 2002Published inissue 1 February 2002https://pubs.acs.org/doi/10.1021/cr000418fhttps://doi.org/10.1021/cr000418fresearch-articleACS PublicationsCopyright © 2002 American Chemical SocietyRequest reuse permissionsArticle Views9600Altmetric-Citations1371LEARN 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:Assays,Carbohydrates,Ligands,Peptides and proteins,Polymers Get e-Alerts
Preparation and Storage of Platelet Concentrates: II. STORAGE VARIABLES INFLUENCING PLATELET VIABILITY AND FUNCTION (1976)

S ummary . Factors affecting the viability and function of stored platelet concentrates have been investigated in a blood component programme. It was found that platelets could be maintained for up to 72 h without bacterial contamination under the following conditions: (1) surgical skin preparation at venipuncture site; (2) blood collection in CPD or ACD anticoagulant in a closed bag system; (3) centrifugation of PRP at 3000 g for 20 min; (4) storage in Fenwal PL‐146, Cutter CL‐2383, or McGaw plastic bags; (5) resuspension of the platelet pellet in 70 ml residual plasma; (6) storage at 22± 2°; and (7) constant gentle mixing throughout storage. Platelet viability as determined by recovery and survival is largely maintained, as is platelet function measured by template bleeding time. Both viability and function of concentrated platelets stored at 4° are severely compromised.
Resonant-microbridge vapor sensor (1986)

A novel integrated vapor sensor is described that incorporates a polycrystalline silicon microbridge coated with a thin polymer film. The microbridge is resonated electrostatically and its vibration is detected capacitively using an integrated NMOS circuit. Vapor uptake by the polymer increases the mass-loading on the microbridge, thereby perturbing the first resonant frequency of the microbridge. In the prototype device, a 150-nm-thick layer of negative photoresist coats a 153-µm-long 1.35-µm-thick polycrystalline silicon microbridge. The phase between the excitation and output voltages at resonance is monitored as the sensor output signal. Exposure to saturated xylene vapor produces a phase shift of -8° with a response time of less than 7 min.
PI3Kδ inhibitor, GS-1101 (CAL-101), attenuates pathway signaling, induces apoptosis, and overcomes signals from the microenvironment in cellular models of Hodgkin lymphoma (2011)

GS-1101 (CAL-101) is an oral PI3Kδ-specific inhibitor that has shown preclinical and clinical activity in non-Hodgkin lymphoma and chronic lymphocytic leukemia. To investigate the potential role of PI3Kδ in Hodgkin lymphoma (HL), we screened 5 HL cell lines and primary samples from patients with HL for PI3Kδ isoform expression and constitutive PI3K pathway activation. Inhibition of PI3Kδ by GS-1101 resulted in the inhibition of Akt phosphorylation. Cocultures with stroma cells induced Akt activation in HL cells, and this effect was blocked by GS-1101. Conversely, production of the stroma-stimulating chemokine, CCL5, by HL cells was reduced by GS-1101. GS-1101 also induced dose-dependent apoptosis of HL cells at 48 hours. Reductions in cell viability and apoptosis were enhanced when combining GS-1101 with the mTOR inhibitor everolimus. Our findings suggest that excessive PI3Kδ activity is characteristic in HL and support clinical evaluation of GS-1101, alone and in combination, as targeted therapy for HL.
Ectodomain Shedding of the Neural Recognition Molecule CHL1 by the Metalloprotease-disintegrin ADAM8 Promotes Neurite Outgrowth and Suppresses Neuronal Cell Death (2004)

The neural cell adhesion molecule "close homologue of L1," termed CHL1, has functional importance in the nervous system. CHL1 is expressed as a transmembrane protein of 185 kDa, and ectodomain shedding releases soluble fragments relevant for its physiological function. Here we describe that ADAM8, a member of the family of metalloprotease disintegrins cleaves a CHL1-Fc fusion protein in vitro at two sites corresponding to release of the extracellular domain of CHL1 in fibronectin (FN) domains II (125 kDa) and V (165 kDa), inhibited by batimastat (BB-94). Cleavage of CHL1-Fc in the 125-kDa fragment was not detectable under non-reducing conditions arguing that cleavage resulting in the 165-kDa fragment is more relevant in releasing soluble CHL1 in vivo. In cells transfected with full-length ADAM8, membrane proximal cleavage of CHL1 was similar and not stimulated by phorbol ester 12-O-tetradecanoylphorbol-13-acetate and pervanadate. No cleavage of CHL1 was observed in cells expressing either inactive ADAM8 with a Glu330 to Gln exchange (EQ-A8), or active ADAM10 and ADAM17. Consequently, processing of CHL1 was hardly detectable in brain extracts of ADAM8-deficient mice but enhanced in a neurodegenerative mouse mutant. CHL1 processed by ADAM8 in supernatants of COS-7 cells and in co-culture with cerebellar granule neurons was very potent in stimulating neurite outgrowth and suppressing neuronal cell death, not observed in cells co-transfected with CHL1/EQ-A8, CHL1/ADAM10, or CHL1/ADAM17. Taken together, we propose that ADAM8 plays an important role in physiological and pathological cell interactions by a specific release of functional CHL1 from the cell surface.
Chirplet representation for audio signals based on model order selection criteria (2009)

In many signal processing applications including Audio and speech processing as well as other research areas of diagnosis of failures in rotating machinery, finding a compact representation of observations signals is often highly desirable. In this respect, chirplets have recently been introduced as an efficient tool for signal representation. However, determining the required number of chirp atoms for the perfect estimation of an observed signal is of great importance. In this research work we study the chirplets signal decomposition to find a compact representation for audio signals of music and speech. The number of chirplets to be used is determined by using the state-of-the-art information criteria. Simulation and experimental results show that by using 4 chirplets are enough for accurate signal representation of music while about 7 to 9 chirplets suffices for speech signal reconstruction. As another application the evaluations are also made on vibration signals. Finally, extracted chirplet atoms are employed to reconstruct the observed signals of music and speech. Subjective tests show acceptable results for signal reconstruction.
Determination of binding constants of diabodies directed against prostate-specific antigen using electrochemiluminescence-based immunoassays (1996)

Two diabody molecules directed against the prostate-specific antigen (PSA) were generated from a combinatorial phage display library. The C-termini of diabodies incorporated the FLAG peptide epitope (P008D diabody) or the myc epitope (P001D). Both diabodies have the same antigen-binding site. Equilibrium-binding constants of these molecules were determined in two immunoassays using the ORIGEN detection system based on electrochemiluminescence. The binding of diabodies to biotinylated PSA was detected with either polyclonal antimouse Fab F(ab')2 or a monoclonal antibody directed against the FLAG epitope. Both detecting antibody preparations were covalently labeled with a ruthenium (II) tris (bipyridyl) moiety, Ru(bpy)3(2+), which allows quantification via an electrochemically triggered light reaction in an ORIGEN analyzer. The binding constants obtained by Scatchard analysis of non-linear curve fitting calculations from electrochemiluminescence immunoassays were compared with data derived from kinetic-binding studies using the BIAcore technology based on surface plasmon resonance. Depending on the detecting antibody, the dissociation constants KD determined at equilibrium with the ORIGEN technology are between 0.1 and 0.4 nM for both diabodies. From the kinetic constants kon and koff measured with the BIAcore instrument KD was calculated to be 0.2 nM for P001D and 0.6 nM for P008D. It is concluded that these two very different methods generate comparable affinity data for the diabodies.
Fas-mediated apoptosis in cultured human eosinophils (1996)

Previous studies have shown that cytokine-dependent eosinophils undergo apoptosis, yet the mechanisms governing this phenomenon remain obscure. Fas antigen is a transmembrane glycoprotein belonging to the tumor necrosis factor receptor family. Cross-linking of Fas antigen in numerous cell types leads to apoptosis. In the present study, we examined the potential role of Fas antigen in the apoptosis of purified blood eosinophils from healthy donors. Cytokine-deprived eosinophils exhibited a time-dependent loss in viability, accompanied by an increase in the number of apoptotic nuclei and in the expression of Fas antigen and its mRNA, as shown by flow cytometry and reverse transcriptase-polymerase chain reaction, respectively. Cross-linking of Fas antigen with an agonistic anti-Fas monoclonal antibody (MoAb) induced a dose- and time-dependent increase in the number of apoptotic nuclei. Furthermore, using an in vitro coculture system, we showed engulfment of anti-Fas MoAb-treated eosinophils by monocyte-derived macrophages. Finally, incubation of eosinophils with the corticosteroid, dexamethasone, induced apoptosis and augmented that triggered by anti-Fas MoAb. Together, these observations suggest that Fas antigen expression and activation is involved in the apoptosis of human eosinophils and may contribute to the resolution of inflammatory allergic reactions in which eosinophil accumulation is a prominent feature.
Structural Insight into the Mode of Action of a Direct Inhibitor of Coregulator Binding to the Thyroid Hormone Receptor (2007)

The development of nuclear hormone receptor antagonists that directly inhibit the association of the receptor with its essential coactivators would allow useful manipulation of nuclear hormone receptor signaling. We previously identified 3-(dibutylamino)-1-(4-hexylphenyl)-propan-1-one (DHPPA), an aromatic beta-amino ketone that inhibits coactivator recruitment to thyroid hormone receptor beta (TRbeta), in a high-throughput screen. Initial evidence suggested that the aromatic beta-enone 1-(4-hexylphenyl)-prop-2-en-1-one (HPPE), which alkylates a specific cysteine residue on the TRbeta surface, is liberated from DHPPA. Nevertheless, aspects of the mechanism and specificity of action of DHPPA remained unclear. Here, we report an x-ray structure of TRbeta with the inhibitor HPPE at 2.3-A resolution. Unreacted HPPE is located at the interface that normally mediates binding between TRbeta and its coactivator. Several lines of evidence, including experiments with TRbeta mutants and mass spectroscopic analysis, showed that HPPE specifically alkylates cysteine residue 298 of TRbeta, which is located near the activation function-2 pocket. We propose that this covalent adduct formation proceeds through a two-step mechanism: 1) beta-elimination to form HPPE; and 2) a covalent bond slowly forms between HPPE and TRbeta. DHPPA represents a novel class of potent TRbeta antagonist, and its crystal structure suggests new ways to design antagonists that target the assembly of nuclear hormone receptor gene-regulatory complexes and block transcription.
Fragmentation of DNA by Nebulization: Figure 1. (2006)

INTRODUCTIONDNA fragmentation is often necessary prior to library construction or subcloning for DNA sequencing. This protocol describes a method for DNA fragmentation by nebulization, in which the fine mist created by forcing a DNA solution through a small hole in the nebulizer unit is collected. The size of the fragments obtained by nebulization is determined chiefly by the speed at which the DNA solution passes through the hole, altering the pressure of the gas blowing through the nebulizer, the viscosity of the solution, and the temperature. Nebulization is easy, quick, and requires only small amounts of DNA (0.5-5 μg). The resulting DNA fragments are distributed over a narrow range of sizes (700-1330 bp). It requires ligation of DNA before nebulization and end-repair afterward.
Multiple actions of β-adrenergic agonists on skeletal muscle and adipose tissue (1989)

Research Article| July 01 1989 Multiple actions of β-adrenergic agonists on skeletal muscle and adipose tissue Y T Yang; Y T Yang *Merck Sharp and Dohme Research Laboratories, Rahway, NJ 07065, U.S.A. Search for other works by this author on: This Site PubMed Google Scholar M A McElligott M A McElligott †Roberts Pharmaceutical Corporation, Meridian Center III, 6 Industrial Way West, Eatontown, NJ 07724, U.S.A. Search for other works by this author on: This Site PubMed Google Scholar Biochem J (1989) 261 (1): 1–10. https://doi.org/10.1042/bj2610001 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Share Icon Share Facebook Twitter LinkedIn Email Cite Icon Cite Get Permissions Citation Y T Yang, M A McElligott; Multiple actions of β-adrenergic agonists on skeletal muscle and adipose tissue. Biochem J 1 July 1989; 261 (1): 1–10. doi: https://doi.org/10.1042/bj2610001 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search nav search search input Search input auto suggest search filter All ContentAll JournalsBiochemical Journal Search Advanced Search This content is only available as a PDF. © 1989 London: The Biochemical Society1989 Article PDF first page preview Close Modal You do not currently have access to this content.
Identification of a new human V lambda gene family--V lambda X. (1994)

Although approximately 40% of Ig light chains in human sera are of the Ig lambda isotype, until recently very little was known about the human Ig lambda gene locus. The genomic structure of the Ig lambda C region has been determined and consists of seven tandemly organized J-C lambda segments. The structure of the region containing the Ig lambda V gene segments is less well defined. Based on amino acid and nucleotide sequence homologies, the V lambda gene segments isolated have been grouped into nine families. Here we report on the isolation of a V lambda gene from the functional rearrangement of a human B lymphoma cell line that has less than 71% nucleotide sequence and 57% deduced amino acid sequence homology to any known V lambda gene. According to the current classification schemes, this gene does not belong to any existing V lambda family. Thus we suggest that this gene belongs to a new V lambda family, V lambda X. The genomic counterpart of the rearranged V lambda gene, and a second member of the family were isolated. The second member is a pseudogene. Southern analysis suggests that the V lambda X family is a small family. The functional V lambda X gene has a consensus heptamer and a nonamer that differs at two sites from the consensus recombination signal sequence. The promoter region contains a consensus TATA box and an octamer that diverge from the consensus sequence by two base pairs.
Survival of coliforms and bacterial pathogens within protozoa during chlorination (1988)

The susceptibility of coliform bacteria and bacterial pathogens to free chlorine residuals was determined before and after incubation with amoebae and ciliate protozoa. Viability of bacteria was quantified to determine their resistance to free chlorine residuals when ingested by laboratory strains of Acanthamoeba castellanii and Tetrahymena pyriformis. Cocultures of bacteria and protozoa were incubated to facilitate ingestion of the bacteria and then were chlorinated, neutralized, and sonicated to release intracellular bacteria. Qualitative susceptibility of protozoan strains to free chlorine was also assessed. Protozoa were shown to survive and grow after exposure to levels of free chlorine residuals that killed free-living bacteria. Ingested coliforms Escherichia coli, Citrobacter freundii, Enterobacter agglomerans, Enterobacter cloacae, Klebsiella pneumoniae, and Klebsiella oxytoca and bacterial pathogens Salmonella typhimurium, Yersinia enterocolitica, Shigella sonnei, Legionella gormanii, and Campylobacter jejuni had increased resistance to free chlorine residuals. Bacteria could be cultured from within treated protozoans well after the time required for 99% inactivation of free-living cells. All bacterial pathogens were greater than 50-fold more resistant to free chlorine when ingested by T. pyriformis. Escherichia coli ingested by a Cyclidium sp., a ciliate isolated from a drinking water reservoir, were also shown to be more resistant to free chlorine. The mechanism that increased resistance appeared to be survival within protozoan cells. This study indicates that bacteria can survive ingestion by protozoa. This bacterium-protozoan association provides bacteria with increased resistance to free chlorine residuals which can lead to persistence of bacteria in chlorine-treated water. We propose that resistance to digestion by predatory protozoa was an evolutionary precursor of pathogenicity in bacteria and that today it is a mechanism for survival of fastidious bacteria in dilute and inhospitable aquatic environments.
A method of comparing the areas under receiver operating characteristic curves derived from the same cases. (1983)

Receiver operating characteristic (ROC) curves are used to describe and compare the performance of diagnostic technology and diagnostic algorithms. This paper refines the statistical comparison of the areas under two ROC curves derived from the same set of patients by taking into account the correlation between the areas that is induced by the paired nature of the data. The correspondence between the area under an ROC curve and the Wilcoxon statistic is used and underlying Gaussian distributions (binormal) are assumed to provide a table that converts the observed correlations in paired ratings of images into a correlation between the two ROC areas. This between-area correlation can be used to reduce the standard error (uncertainty) about the observed difference in areas. This correction for pairing, analogous to that used in the paired t-test, can produce a considerable increase in the statistical sensitivity (power) of the comparison. For studies involving multiple readers, this method provides a measure of a component of the sampling variation that is otherwise difficult to obtain.
Efficient Amortised Bayesian Inference for Hierarchical and Nonlinear Dynamical Systems (2019)

We introduce a flexible, scalable Bayesian inference framework for nonlinear dynamical systems characterised by distinct and hierarchical variability at the individual, group, and population levels. Our model class is a generalisation of nonlinear mixed-effects (NLME) dynamical systems, the statistical workhorse for many experimental sciences. We cast parameter inference as stochastic optimisation of an end-to-end differentiable, block-conditional variational autoencoder. We specify the dynamics of the data-generating process as an ordinary differential equation (ODE) such that both the ODE and its solver are fully differentiable. This model class is highly flexible: the ODE right-hand sides can be a mixture of user-prescribed or "white-box" sub-components and neural network or "black-box" sub-components. Using stochastic optimisation, our amortised inference algorithm could seamlessly scale up to massive data collection pipelines (common in labs with robotic automation). Finally, our framework supports interpretability with respect to the underlying dynamics, as well as predictive generalization to unseen combinations of group components (also called "zero-shot" learning). We empirically validate our method by predicting the dynamic behaviour of bacteria that were genetically engineered to function as biosensors. Our implementation of the framework, the dataset, and all code to reproduce the experimental results is available at https://www.github.com/Microsoft/vi-hds .
RFX: new tools for real-time MHD control (2004)

RFX has been recently modified to improve its capability of controlling different MHD phenomena by means of fast, feedback controlled amplifiers and distributed radial field inductors. The paper, after summarizing the principal results obtained in the past by means of active control of magnetic fields in RFX, describes the recent modifications to the machine and the improvements to the power supplies and to the magnetic diagnostics. The old thick shell has been replaced by a much thinner shell, whose electromagnetic time constants are much shorter than pulse duration, and a system of 192 radial field coils has been added, covering the whole torus surface. Then the paper describes the models used to design the new real-time control system of RFX and gives some preliminary results obtained, with the same techniques, on the EXTRAP-T2R device. The basic choices about the technologies adopted for the new RFX control system are discussed with reference to the general problem of real-time control of MHD instabilities in magnetic fusion devices. Finally, the paper defines the main objectives of the RFX scientific programme aimed at exploiting these new tools.