gebhart/patrepeval huggingface dataset:
Structure–Activity Studies in a Family of β‐Hairpin Protein Epitope Mimetic Inhibitors of the p53–HDM2 Protein–Protein Interaction (2006)

Inhibitors of the interaction between the p53 tumor-suppressor protein and its natural human inhibitor HDM2 are attractive as potential anticancer agents. In earlier work we explored designing beta-hairpin peptidomimetics of the alpha-helical epitope on p53 that would bind tightly to the p53-binding site on HDM2. The beta-hairpin is used as a scaffold to display energetically hot residues in an optimal array for interaction with HDM2. The initial lead beta-hairpin mimetic, with a weak inhibitory activity (IC(50)=125 microM), was optimized to afford cyclo-(L-Pro-Phe-Glu-6ClTrp-Leu-Asp-Trp-Glu-Phe-D-Pro) (where 6ClTrp=L-6-chlorotryptophan), which has an affinity almost 1,000 times higher (IC(50)=140 nM). In this work, insights into the origins of this affinity maturation based on structure-activity studies and an X-ray crystal structure of the inhibitor/HDM2(residues 17-125) complex at 1.4 A resolution are described. The crystal structure confirms the beta-hairpin conformation of the bound ligand, and also reveals that a significant component of the affinity increase arises through new aromatic/aromatic stacking interactions between side chains around the hairpin and groups on the surface of HDM2.
Machine Learning based Cognitive Communications in White as Well as the Gray Space (2007)

This paper describes new ideas and results on machine learning based cognitive communications in White as well as the Gray space. We combine the concepts of signal processing, communications, pattern classification and machine learning to make a dynamic use of the spectrum such that the emanated signals do not interfere with the existing ones. Unlike other programs such as the neXt Generation (XG) communications program of the Defense Advanced Research Projects Agency (DARPA), where radio scene analysis is carried out to find the spectrum holes also known as the White space, we make use of the White as well as the Gray space for non-interfering signal transmission. Our assumption is that a learning module will facilitate adaptation in the signal classification process, so that the presence of new types of waveforms can be detected, features that best facilitate classification of the previously and newly identified signals can be determined, and waveforms can be generated by using the basis-set orthogonal to the ones present in the environment. Incremental learning and prediction allow knowledge enhancement as more snap-shots of data are processed, resulting in improved decisions. Use of non-competitive policy set results in zero interference with the already existing signals with a modest increase in the White and Gray space utilization. On the other hand competitive policy set utilizes machine learning to predict the future behavior of the signals which results in more than 90% utilization of spectrum at an expense of some interference due to errors in prediction.
Mouse Monoclonal Antibody to Embryonic Antigen: Development, Cross-Reactivity With Rodent and Human Tumors, and Preliminary Polypeptide Characterization<xref ref-type="fn" rid="FN2">2</xref> (1985)

Hybridomas producing IgM and IgG monoclonal antibodies (MoAb) to embryonic or fetal antigens (EA) were obtained in a completely syngeneic system. Lethally irradiated, 13-day-gestation, C57BL/6N mouse fetal cells or KCI extracts of these fetal cells obtained from primaparous donors were used as immunogens in several regimens to induce splenocytes in C57BL/6N mice that were utilized to form the hybridomas following fusion with a mouse myeloma line. Successful growth and cloning of the IgM-producing hybridomas required supplementation with factor(s) produced in the growth medium of the macrophage cell line RAW 264.7. An enzyme-linked immunosorbent assay (ELISA) was employed to screen the primary fusion hybridomas for antibody directed against fetal cell or adult cell determinants with the use of freshly explanted tissues. Glutaraldehyde-fixed fetal cells as well as crude fetal cell membranes were used as EA+ target cells (i.e., cell lines known to activate T-lymphocyte-mediated tumor resistance) in a solid-phase ELISA to perform quantitative ELISA adsorption tests of the MoAb. The anti-EA monoclonal IgM and the IgG detected common, embryo-specific antigen(s) on mouse, hamster, and human fetuses. Term fetal cells and adult normal tissues of the mouse, hamster, and human did not express cross-reactive determinants for the MoAb by absorption analysis and/or by direct binding in ELISA. EA expression as oncofetal antigens could also be detected with the monoclones on several rodent tumor cell lines tested as well as on a variety of human carcinomas but not on a spectrum of normal human tissues with the use of indirect ELISA absorption and affinity gel and sodium dodecyl sulfate-polyacrylamide gel electrophoresis analyses. Fluorescence analysis with the monoclones demonstrated specific reactivity with the surface of EA+ tumor cells in the FACS IV flow cytometer. The responsible antigen was carried on a 44- and a 200-kilodalton polypeptide.
Tagged versus untagged libraries: methods for the generation and screening of combinatorial chemical libraries. (1994)

Over the past two decades the pharmaceutical industry has been driven by the biological sciences. The discovery and description of the biological mechanisms that underlie disease states accompanied by an unraveling of these mechanisms has provided drug, and more recently biotechnological, companies with a barrage of new therapeutic targets. Paradoxically, as a result of such biological and biochemical advances, new sources of drug leads are in short supply. Considerable efforts in trying to create potential drug candidates has led to the parturition of combinatorial chemical libraries. In this review I will examine some of the main technologies for generating and deducing active components from combinatorial libraries that have been segregated into two schools of thought: (i) the creation and decoding of combinatorial libraries by so-called tagged methodologies, and (ii) the production and deconvolution of chemical libraries by untagged protocols.
Asymmetric 1,4-addition of organocuprates to chiral .alpha.,.beta.-unsaturated N-acyl-4-phenyl-2-oxazolidinones: a new approach to the synthesis of chiral .beta.-branched carboxylic acids (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAsymmetric 1,4-addition of organocuprates to chiral .alpha.,.beta.-unsaturated N-acyl-4-phenyl-2-oxazolidinones: a new approach to the synthesis of chiral .beta.-branched carboxylic acidsErnesto Nicolas, K. C. Russell, and Victor J. HrubyCite this: J. Org. Chem. 1993, 58, 3, 766–770Publication Date (Print):January 1, 1993Publication History Published online1 May 2002Published inissue 1 January 1993https://pubs.acs.org/doi/10.1021/jo00055a039https://doi.org/10.1021/jo00055a039research-articleACS PublicationsRequest reuse permissionsArticle Views1556Altmetric-Citations153LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Significance of anti-HBx antibodies in hepatitis B virus infection (1991)

Serological responses to hepatitis B virus-X determinants have been noted in human sera, but conflicting findings concerning the correlation of anti-HBx antibodies with different stages of hepatitis B virus infection or pathological sequelae have been reported. Using an adenovirus-based eukaryotic vector, the 17 kD X protein was efficiently expressed in 293 cells. Cellular extracts containing the eukaryotic X protein have been used to screen for anti-HBx antibodies by immunoblot analysis in a large panel of sera from patients affected by hepatitis B virus chronic hepatitis, hepatocellular carcinoma and acute viral hepatitis. Sera from 32 of 171 (19%) chronic hepatitis B virus patients were positive for anti-HBx antibodies. Only one of thirty-two (3%) HBsAg-negative, anti-HBs/anti-HBc-positive chronic hepatitis serum was anti-HBx positive. Very few sera from primary hepatocellular carcinoma patients showed positivity for anti-HBx (8 of 149 or 5%). Anti-HBx were also detected in 8 of 48 (17%) acute viral hepatitis patients. In the four cases that were followed up weekly, anti-HBx antibodies appeared 3 to 4 wk after the onset of the clinical signs. To compare the X protein expressed in eukaryotic and prokaryotic cells as a substrate for anti-HBx antibody detection, 171 sera were screened with HBx fusion proteins expressed in Escherichia coli. The prokaryotic cell extract test seems to be more sensitive. During the chronic phase of hepatitis B virus infection, the presence of anti-HBx antibodies detected with the eukaryotic cell extract correlates with the presence of well-established markers of ongoing viral replication: serum hepatitis B virus-DNA (p less than 0.001) and intrahepatic HBcAg expression (p less than 0.001).
Hormone and antihormone induce distinct conformational changes which are central to steroid receptor activation. (1992)

Antihormones are potent antagonists of hormone action in vivo, but the mechanism underlying this antagonism is not understood. Several steroid hormones transform (activate) their receptors from a cytosolic, non-DNA binding 8 S sedimentation form to a nuclear, DNA binding 4 S form. Transformation is accompanied by the loss of associated heat shock proteins. We have previously demonstrated that an additional hormone-dependent step, separate from heat shock protein removal, is required for activation of the human progesterone receptor. We have devised an assay in which the human progesterone receptor translated in vitro binds to its specific response element in a hormone-dependent manner. As assessed by limited proteolytic digestion, hormone treatment of the nascent receptor induces a dramatic conformational change within the protein. The conformational change occurs in the absence of DNA and renders the entire ligand binding domain resistant to digestion by proteases. A number of antiprogestins, including RU486, induce an equally dramatic, but distinct, structural alteration of the ligand binding domain. The distinction centers upon the final 30 to 40 amino acids at the carboxyl terminus. The conformational change can be induced by ligand prior to dissociation of the 8 S complex and is not induced by heat shock protein removal in the absence of hormone. Remarkably, virtually identical hormone-induced conformational changes were detected following proteolytic analysis of in vitro translated retinoic acid receptors. Our data indicate that the sole necessary event in the activation of steroid receptors is conformational modification by the ligand. Furthermore, we conclude that transcriptional inactivation of steroid receptors by antihormones involves the induction of an inappropriate structural conformation at the extreme carboxyl terminus of the ligand binding domain.
Soft Core/Shell Packages for Stretchable Electronics (2015)

This paper presents materials and core/shell architectures that provide optimized mechanical properties in packages for stretchable electronic systems. Detailed experimental and theoretical studies quantitatively connect the geometries and elastic properties of the constituent materials to the overall mechanical responses of the integrated systems, with a focus on interfacial stresses, effective modulus, and maximum extent of elongation. Specific results include core/shell designs that lead to peak values of the shear and normal stresses on the skin that remain less than 10 kPa even for applied strains of up to 20%, thereby inducing minimal somatosensory perception of the device on the human skin. Additional, strain‐limiting mesh structures embedded in the shell improve mechanical robustness by protecting the active components from strains that would otherwise exceed the fracture point. Demonstrations in precommercial stretchable electronic systems illustrate the utility of these concepts.
Gadolinium and nephrogenic systemic fibrosis: time to tighten practice (2007)

Nephrogenic systemic fibrosis (NSF) is a relatively new entity, first described in 1997. Few cases have been reported, but the disease has high morbidity and mortality. To date it has been seen exclusively in patients with renal dysfunction. There is an emerging link with intravenous injection of gadolinium contrast agents, which has been suggested as a main triggering factor, with a lag time of days to weeks. Risk factors include the severity of renal impairment, major surgery, vascular events and other proinflammatory conditions. There is no reason to believe that children have an altered risk compared to the adult population. It is important that the paediatric radiologist acknowledges emerging information on NSF but at the same time considers the risk:benefit ratio prior to embarking on alternative investigations, as children with chronic kidney disease require high-quality diagnostic imaging.
IFN-α Enhances Peptide Vaccine-Induced CD8+ T Cell Numbers, Effector Function, and Antitumor Activity (2009)

Type I IFNs, including IFN-alpha, enhance Ag presentation and promote the expansion, survival, and effector function of CD8(+) CTL during viral infection. Because these are ideal characteristics for a vaccine adjuvant, we examined the efficacy and mechanism of exogenous IFN-alpha as an adjuvant for antimelanoma peptide vaccination. We studied the expansion of pmel-1 transgenic CD8(+) T cells specific for the gp100 melanocyte differentiation Ag after vaccination of mice with gp100(25-33) peptide in IFA. IFN-alpha synergized with peptide vaccination in a dose-dependent manner by boosting relative and absolute numbers of gp100-specific T cells that suppressed B16 melanoma growth. IFN-alpha dramatically increased the accumulation of gp100-specific, IFN-gamma-secreting, CD8(+) T cells in the tumor through reduced apoptosis and enhanced proliferation of Ag-specific CD8(+) T cells. IFN-alpha treatment also greatly increased the long-term maintenance of pmel-1 CD8(+) T cells with an effector memory phenotype, a process that required expression of IFN-alpha receptor on the T cells and IL-15 in the host. These results demonstrate the efficacy of IFN-alpha as an adjuvant for peptide vaccination, give insight into its mechanism of action, and provide a rationale for clinical trials in which vaccination is combined with standard-of-care IFN-alpha therapy for melanoma.
Molecular Dynamics: Applications to Proteins (1987)

Molecular dynamics of macromolecules of biological interest began in 1977 with the publication of a paper on the simulation of a small protein, the bovine pancreatic trypsin inhibitor (McCammon et al. 1977). Although the trypsin inhibitor is rather uninteresting from a dynamical viewpoint—its function is to bind to trypsin—experimental and theoretical studies of this model system, the "hydrogen atom" of protein dynamics, served to initiate explorations in this field.
Indirect-drive noncryogenic double-shell ignition targets for the National Ignition Facility: Design and analysis (2002)

Analysis and design of indirect-drive National Ignition Facility double-shell targets with hohlraum temperatures of 200 eV and 250 eV are presented. The analysis of these targets includes the assessment of two-dimensional radiation asymmetry and nonlinear mix. Two-dimensional integrated hohlraum simulations indicate that the x-ray illumination can be adjusted to provide adequate symmetry control in hohlraums specially designed to have high laser-coupling efficiency [Suter et al., Phys. Plasmas 7, 2092 (2000)]. These simulations also reveal the need to diagnose and control localized 10–15 keV x-ray emission from the high-Z hohlraum wall because of strong absorption by the high-Z inner shell. Preliminary estimates of the degree of laser backscatter from an assortment of laser–plasma interactions suggest comparatively benign hohlraum conditions. The application of a variety of nonlinear mix models and phenomenological tools, including buoyancy-drag models, multimode simulations and fall-line optimization, indicates a possibility of achieving ignition, i.e., fusion yields greater than 1 MJ. Planned experiments on the Omega laser will test current understanding of high-energy radiation flux asymmetry and mix-induced yield degradation in double-shell targets.
Isolation and Identification of "Diazepam-Like" Compounds From Bovine Urine (1983)

Attempts to isolate the putative endogenous ligand for the benzodiazepine receptor from bovine urine resulted in the identification of three isoflavans: equol (1), 3',7-dihydroxyisoflavan (2), and 4'-hydroxy-7-methoxyisoflavan (9), as "diazepam-like" compounds. 3-Chloro-9H-carbazole (17) was found to enhance the binding of diazepam in the benzodiazepine receptor binding assay. Pinosylvine monomethyl ether (18), indigo (20), and indirubin (21) were isolated as inactive compounds.
Characterization of a Second Vaccinia Virus mRNA-Decapping Enzyme Conserved in Poxviruses (2007)

Vaccinia virus (VACV) encodes enzymes that cap the 5' end of viral mRNAs, which enhances their stability and translation. Nevertheless, recent studies demonstrated that the VACV D10 protein (VACV-WR_115) decaps mRNA, an enzymatic activity not previously shown to be encoded by a virus. The decapping activity of D10 is dependent on a Nudix hydrolase motif that is also present in the VACV D9 protein (VACV-WR_114), which shares 25% sequence identity with D10. Here, we showed that a purified recombinant VACV D9 fusion protein also decaps mRNA and that this activity was abolished by point mutations in the Nudix hydrolase motif. Decapping was specific for a methylated cap attached to RNA and resulted in the liberation of m7GDP. D9 differed from D10 in requiring a longer capped RNA substrate for optimal activity, having greater sensitivity to inhibition by uncapped RNA, and having lower sensitivity to inhibition by nucleotide cap analogs unattached to RNA. Since D9 is expressed early in infection and D10 late, we suggest that the two proteins enhance mRNA turnover and manipulate gene expression in a complementary and overlapping manner.
Combination treatment with alogliptin and voglibose increases active GLP‐1 circulation, prevents the development of diabetes and preserves pancreatic beta‐cells in prediabetic db/db mice (2009)

Chronic treatment with alogliptin in combination with voglibose concurrently increased active GLP-1 circulation, increased insulin secretion, decreased glucagon secretion, prevented the onset of the disease, and preserved pancreatic beta-cells and islet structure in prediabetic db/db mice.
Noise in MEMS (2009)

This review provides a comprehensive recap of noise research in MEMS. Some background on noise and on MEMS is provided. We review noise production mechanisms, and highlight work on the theory and modeling of noise in MEMS. Then noise measurements in the specific types of MEMS are reviewed. Inertial MEMS (accelerometers and angular rate sensors), pressure and acoustic sensors, optical MEMS, RF MEMS, surface acoustic wave devices, flow sensors, and chemical and biological MEMS, as well as data storage devices and magnetic MEMS, are reviewed. We indicate opportunities for additional experimental and computational research on noise in MEMS.
Gold nanotags for combined multi-colored Raman spectroscopy and x-ray computed tomography (2009)

Multi-color gold-nanoparticle-based tags (nanotags) are synthesized for combined surface-enhanced Raman spectroscopy (SERS) and x-ray computed tomography (CT). The nanotags are synthesized with quasi-spherical gold nanoparticles encoded with a reporter dye (color), each with a unique Raman spectrum. A library of nanotags with six different colors were synthesized for a range of gold nanoparticle sizes and an optimum size has been established to yield the largest SERS intensity and x-ray attenuation that is higher than the iodinated CT contrast agents used in clinics. Proof-of-principle in vivo imaging results with nanotags are presented that, for the first time, demonstrates the combined in vivo dual modality imaging capability of SERS and CT with a single nanoparticle probe.
Prophylactic and Therapeutic Efficacy of Human Monoclonal Antibodies against H5N1 Influenza (2007)

These studies provide proof of concept that fully human mAbs with neutralizing activity can be rapidly generated from the peripheral blood of convalescent patients and that these mAbs are effective for the prevention and treatment of H5N1 infection in a mouse model. A panel of neutralizing, cross-reactive mAbs might be useful for prophylaxis or adjunctive treatment of human cases of H5N1 influenza.
Use of an indwelling catheter for examining cardiovascular responses to pericardial administration of bradykinin in rat (1995)

These results demonstrate that pericardial administration of BK produces a tachycardia and pressor effect in awake and alpha-chloralose-anesthetized rats and a tachycardia and depressor effect in pentobarbital-anesthetized rats. These responses appear to be mediated through activation of BK (presumably B2) receptors on cardiac vagal and sympathetic afferents, and may include a direct action of BK on the heart. This model of pericardial administration of pharmacologic agonists may be useful in studies of cardiac pain and reflex responses.
Analysis of the targeting of the hypermutational machinery and the impact of subsequent selection on the distribution of nucleotide changes in human V rearrangements (1998)

B cells are unique in that they generate and tolerate a high rate of mutations in their antigen receptor genes and employ these mutations as a basis of avidity maturation. The precise role of the mutational machinery versus subsequent selection in determining the frequency and distribution of mutations has not been fully analyzed. To address these issues, the influence of the intrinsic mutational machinery and subsequent selection on the frequency and distribution of mutations in the expressed human immunoglobulin repertoire was analyzed. Analysis of non-productively rearranged VH genes from individual human B cells provided an opportunity to examine the immediate impact of somatic hypermutation without superimposed selective influences. Comparison with the frequency and distribution of mutations in the productively rearranged human VH genes permitted an estimate of the influences of subsequent selection.