gebhart/patrepeval huggingface dataset:
Iron Metabolism and Infection (2007)

The review highlights the intrinsic problems in the acquisition of ferric iron (FeIII) by pathogenic microorganisms, and bacteria in particular, during their infection of animals. Acquisition of iron from host sources, such as ferritin, transferrin, and heme compounds, is discussed. Acquisition can be by direct contact, via a surface receptor protein of the bacterium, with one of the iron-containing compounds, but more frequently iron is acquired by the production of a siderophore. Over 500 different siderophores are now known; they work by having a superior binding power to that of the host iron-containing materials. They literally strip the iron out of these molecules. They are low-molecular-weight (< 1,000 Da) compounds that are produced in response to iron deprivation, which is a primary host defense mechanism against infections. The iron-siderophore complex is small enough to be taken up into the bacterial cells, usually via an active transport process; the iron is removed from the siderophore, normally by a reductive process, and is then incorporated into the various apoproteins of the bacterial cell or is stored within the bacteria in the form of bacterioferritin. To combat the effectiveness of the siderophores, animals may synthesize specific proteins to bind and nullify their action. The role of one such protein, siderocalin (= lipocalin 2), is discussed. However, these countermeasures have, in turn, been thwarted by at least one bacterium, Salmonella, glycosylating its siderophore (enterobactin/enterochelin) so that binding of the modified siderophore (now termed salmochelin) with lipocalin can no longer occur.
A closed-form solution to blind MIMO FIR channel equalization for wireless communication systems based on autocorrelation matching (2004)

The autocorrelation matching method is a second order statistics-based blind MIMO FIR channel equalization technique designed for wireless communication systems using multiple receiving antennas. This paper presents a closed-form solution to the optimal zero-forcing equalizer for the autocorrelation matching method. It can recover a transmitted signal with maximum SNR from an unknown MIMO FIR channel based on the autocorrelation coefficients of the transmitted signal and the autocorrelation matrices of the received signals. Numerical results obtained from intensive computer simulations are also given in this paper, which verify the effectiveness and accuracy of the closed-form solution.
Up-regulation of costimulatory/adhesion molecules by histone deacetylase inhibitors in acute myeloid leukemia cells (2000)

Histone deacetylase inhibitors (HDACIs) have been used to focus on the effects of inducing gene expression through the acetylation of histones which results in chromatin remodeling. The study explored whether HDACIs could induce the expression of costimulatory/adhesion molecules on acute myeloid leukemia (AML) cells, thereby effectively inducing tumor immunity. The expression of CD80, CD86, human leukocyte antigen (HLA)-DR, HLA-ABC, and intracellular adhesion molecule-1 (ICAM-1) was tested in human AML cell lines after the addition of HDACI, sodium butyrate (SB). Generally, increased expression of CD86 was observed by SB treatment in a majority of cell lines, and ICAM-1 was expressed in fewer cell lines. Essentially the same results were obtained using other HDACIs such as FR901228, trichostatin A, and trapoxin A. Quantitation of transcripts of CD86 accompanied with RNA synthesis inhibition assay and nuclear run-on assay revealed that SB up-regulates the CD86 expression transcriptionally. Furthermore, chromatin immunoprecipitation experiments showed that HDACI treatment caused remarkable acetylation on histone H3 and H4 at CD86 promoter chromatin in vivo. In 30 clinical AML samples, CD86 expression was significantly increased (P <.001) by SB treatment, and the expression of HLA-DR and ICAM-1 was moderately increased (P <.05) by SB treatment. Finally, the allogeneic mixed leukocyte reaction (allo-MLR) against HL60 cells pretreated with SB was enhanced 4-fold compared with allo-MLR obtained with non-treated HL60 cells. These results suggest that the immunotherapeutic use of HDACIs may become a novel tool for treatment of AML. (Blood. 2000;96:3847-3856)
Revisión crítica de la patogenia actual de la esclerosis múltiple y futuras direcciones posibles (1999)

When these three factors are considered, a better explanation is found for the factors which determine the progression of the disability, exhaustion of the inflammatory response, deficient remyelination and the poor correlation between demyelination and the progression of the disease. At the same time, new possibilities for approaches to the treatment and investigation of MS appear.
Particle selection for laser‐accelerated proton therapy feasibility study (2003)

In this paper we present calculations for the design of a particle selection system for laser-accelerated proton therapy. Laser-accelerated protons coming from a thin high-density foil have broad energy and angular spectra leading to dose distributions that cannot be directly used for therapeutic applications. Our solution to this problem is a compact particle selection and collimation device that delivers small pencil beams of protons with desired energy spectra. We propose a spectrometer-like particle selection and beam modulation system in which the magnetic field will be used to spread the protons spatially according to their energies and emitting angles. Subsequently, an aperture will be used to select the protons within a therapeutic window of energy (energy modulation). It will be shown that for the effective proton spatial differentiation, the primary collimation device should be used, which will collimate protons to the desired angular distribution and limit the spatial mixing of different energy protons once they have traveled through the magnetic system. Due to the angular proton distribution, the spatial mixing of protons of different energies will always be present and it will result in a proton energy spread with the width depending on the energy. For 250 MeV protons, the width (from the maximum to the minimum energy) is found to be 50 MeV for the magnetic field configuration used in our calculations. As the proton energy decreases, its energy width decreases as well, and for 80 MeV protons it equals 9 MeV. The presence of the energy width in the proton energy distribution will modify the depth dose curves needed for the energy modulation calculation. The matching magnetic field setup will ensure the refocusing of the selected protons and the final beam will be collimated by the secondary collimator. The calculations presented in this article show that the dose rate that the selection system can yield is on the order of D=260 Gy/min for a field size of 1 x 1 cm2.
Immunohistochemical Detection of Hepatitis C Virus-Infected Hepatocytes in Chronic Liver Disease With Monoclonal Antibodies to Core, Envelope and Ns3 Regions of the Hepatitis C Virus Genome (1992)

The localization of hepatitis C virus-infected hepatocytes in the human liver remains unclear despite the development of a serological assay for the antibody to hepatitis C virus. We studied their localization immunohistochemically with monoclonal antibodies to core, envelope and NS3 antigens of hepatitis C virus. We examined 48 liver biopsy samples from C100–3 antibody-positive patients with chronic liver disease (chronic persistent hepatitis, 5 cases; chronic active hepatitis, 41 cases; cirrhosis, 2 cases) and 12 liver biopsy samples from C100–3 antibody-negative patients with chronic liver disease (type B chronic hepatitis, 8 cases; alcoholic liver disease, 4 cases). In the C100–3 antibody-positive group, positive immunostaining for core antigen, envelope antigen and NS3 antigen was found in 23% (11 of 48), 24% (11 of 45) and 24% (11 of 46), respectively. Negative results were obtained in the C100–3 antibody-negative group. Hepatocytes with positive staining were scattered in the lobules, and they were found in the same regions irrespective of whether the antibody to core antigen, to envelope antigen or to NS3 antigen was used. Each positive cell was strongly stained in the cytoplasm; these decorations disappeared after absorption of the primary antibody with purified antigen. Mean ALT levels in the patients with positive immunostaining for core, envelope or NS3 antigen (174.8 ± 105.7 U/L) tended to be higher than in those with negative immunostaining (142.0 ± 93.8 U/L). On histological evaluation of liver specimens with a scoring system of the histological activity index, intralobular inflammation and fibrosis had higher scores for samples with positive rather than negative immunostaining (p &lt; 0.05). Our findings suggest that inflammation is more severe in liver tissue with hepatitis C virus infection in which more virus is present and that in more advanced chronic liver disease with hepatitis C virus infection, greater amounts of virus are present. (Hepatology 1992;16:306-311.)
Synthesis and adhesive studies of marine polypeptides (1987)

The marine adhesive polydecapeptide (Ala-Lys-Pro-Ser-Tyr-Hyp-Hyp-Thr-Dopa-Lys)n(n ca. 10) has been synthesized by coupling reactions, followed by polycondensation. The O-benzyl, O,O′-dibenzyl, and N-Îµ-2-chlorobenzyloxycarbonyl groups were used to protect the side chains of Ser, Tyr, Hyp, Thr, Dopa, and Lys. The protecting groups were simultaneously cleaved by hydrogen bromide. The bonding strength of the polydecapeptide and other synthetic polypeptides on metals has been measured in water. The bonding strength of the synthesized polydecapeptide exhibited a tensile strength of 28 kg cm–1 on Fe and a compressive shear strength of 3 kg cm–2 on Al2O3, while high molecular weight poly(Lys)·HBr was found to have the highest tensile strength (123 kg cm–2) on Fe, and gelatin the highest compressive shear strength (21 kg cm–2) on Al2O3. The factors important for the effective adhesion on metals are discussed.
Emotional Imagery: Conceptual Structure and Pattern of Somato‐Visceral Response (1980)

ABSTRACT This research examined deductions from a new theory of emotional imagery (Lang, 1979). Two experiments were performed, testing the hypothesis that the conceptual content processed during imagery determines the amplitude and pattern of coincident efferent activity. The image was manipulated by varying the content of the prompting instructions (either stimulus detail or active responding was emphasized in the image script) and by prior imagery training (in which subjects' post‐image verbal reports were shaped to emphasize either stimulus or response material). Three thematic contents were examined: neutral, action, and fear scenes. In Experiment I, a group which received response‐oriented imagery training and response scripts was compared to a stimulus‐oriented group. The results strongly supported the hypothesis: response subjects showed greater physiological activity during imagery, and their efferent pattern generally followed the script content. In Experiment II, one group again received response training and the other, stimulus training. However, half of each group was later tested on response‐structured scripts and the other half on stimulus scripts. Results again supported the hypothesis. As in Experiment I, response‐trained subjects tested on response scripts showed substantial physiological activity. None of the other groups, which received stimulus training and/or stimulus scripts, showed significant physiological responses during imagery. Response‐trained subjects generally rated their imagery as more vivid. Subjects administered response‐oriented scripts reported more emotional arousal than did subjects administered stimulus scripts.
Reaction of tert-butyl hydroperoxide and .alpha.-cumyl hydroperoxide with acetic acid (1974)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTReaction of tert-butyl hydroperoxide and .alpha.-cumyl hydroperoxide with acetic acidW. E. Cass and Arun K. BahlCite this: J. Org. Chem. 1974, 39, 24, 3602–3604Publication Date (Print):November 1, 1974Publication History Published online1 May 2002Published inissue 1 November 1974https://pubs.acs.org/doi/10.1021/jo00938a038https://doi.org/10.1021/jo00938a038research-articleACS PublicationsRequest reuse permissionsArticle Views94Altmetric-Citations2LEARN 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
Growth Recovery on Glucose under Aerobic Conditions of an <i>Escherichia coli</i> Strain Carrying a Phosphoenolpyruvate:Carbohydrate Phosphotransferase System Deletion by Inactivating <i>arcA</i> and Overexpressing the Genes Coding for Glucokinase and Galactose Permease (2007)

In Escherichia coli the phosphotransferase system (PTS) consumes one molecule of phosphoenolpyruvate (PEP) to phosphorylate each molecule of internalized glucose. PEP bioavailability into the aromatic pathway can be increased by inactivating the PTS. However, the lack of the PTS results in decreased glucose transport and growth rates. To overcome such drawbacks in a PTS(-) strain and reconstitute rapid growth on glucose phenotype (Glc(+)), the glk and galP genes were cloned into a plasmid and the arcA gene was inactivated. Simultaneous overexpression of glk and galP increased the growth rate and regenerated a Glc(+) phenotype. However, the highest growth rate was obtained when glk and galP were overexpressed in the arcA(-) background. These results indicated that the arcA mutation enhanced glycolytic and respiratory capacities of the engineered strain.
Identification of cancer-associated gene clusters and genes via clustering penalization (2009)

Identification of genes associated with cancer development and progression using microarray data is challenging because of the high dimensionality and cluster structure of gene expressions. Here the clusters are composed of multiple genes with coordinated biological functions and/or correlated expressions. In this article, we first propose a hybrid approach for clustering gene expressions. The hybrid approach uses both pathological pathway information and correlations of gene expressions. We propose using the group bridge, a novel clustering penalization approach, for analysis of cancer microarray data. The group bridge approach explicitly accounts for the cluster structure of gene expressions, and is capable of selecting gene clusters and genes within those selected clusters that are associated with cancer. We also develop an iterative algorithm for computing the group bridge estimator. Analysis of three cancer microarray datasets shows that the proposed approach can identify biologically meaningful gene clusters and genes within those identified clusters.
Highly Efficient Drug Delivery with Gold Nanoparticle Vectors for in Vivo Photodynamic Therapy of Cancer (2008)

A highly efficient drug vector for photodynamic therapy (PDT) drug delivery was developed by synthesizing PEGylated gold nanoparticle conjugates, which act as a water-soluble and biocompatible "cage" that allows delivery of a hydrophobic drug to its site of PDT action. The dynamics of drug release in vitro in a two-phase solution system and in vivo in cancer-bearing mice indicates that the process of drug delivery is highly efficient, and passive targeting prefers the tumor site. With the Au NP-Pc 4 conjugates, the drug delivery time required for PDT has been greatly reduced to less than 2 h, compared to 2 days for the free drug.
Indirect-drive radiation uniformity in tetrahedral hohlraums (1996)

Tetrahedral hohlraums, by which are understood spherical hohlraums with four laser entrance holes (LEH’s) placed at or near the vertices of a tetrahedron, are proposed for the National Ignition Facility (NIF) [J. Lindl, Phys. Plasmas 2, 3933 (1995)] and the upgraded OMEGA laser [T. R. Boehly et al., Rev. Sci. Instrum. 66, 508 (1995)]. All but four of the 48 NIF beams can irradiate a tetrahedral hohlraum, assuming that 72 beam ports are provided to accommodate direct drive. On OMEGA, the target chamber provides an exact tetrahedral symmetry, permitting the irradiation of tetrahedral hohlraums with all 60 beams. Hohlraum designs are optimized using a new three-dimensional view-factor program called Buttercup, which traces all beam paths through the hohlraum and calculates the radiation flux on the capsule for different values of the albedo. Good irradiation uniformity (∼2% rms) can be obtained on the capsule at all times during the implosion, even with identical beam temporal histories, in contrast to the case of cylindrical hohlraums where ‘‘beam phasing’’ is needed.
Bevacizumab in the Treatment of Breast Cancer: Rationale and Current Data (2004)

Vascular endothelial growth factor (VEGF) has emerged as a key target for the treatment of cancer. As the ligand to the VEGF receptor, it plays a central role in promoting tumor angiogenesis. Overexpression of VEGF leads to poor outcomes in patients with breast cancer and other tumors. Preclinical studies have shown that the humanized monoclonal antibody to VEGF, bevacizumab (Avastin; Genentech, Inc., South San Francisco, CA), can reduce tumor angiogenesis and inhibit the growth of solid tumors, either alone or in combination with chemotherapy. As a single agent or added to vinorelbine, bevacizumab has produced encouraging results in phase II clinical trials in patients with refractory metastatic breast cancer. When added to capecitabine chemotherapy in a phase III trial, bevacizumab produced a greater response rate, but did not prolong progression-free survival. This may reflect the late disease stage and poor prognostic factors in the patient population. A large, ongoing, phase III, cooperative group trial is evaluating the effect of bevacizumab in combination with paclitaxel as first-line therapy for metastatic disease. The adverse effect profile of bevacizumab differs from that of cytotoxic chemotherapy and includes hypertension, proteinuria, thrombosis, and epistaxis.
Direct Stereo- and Enantiocontrolled Synthesis of Vicinal Stereogenic Quaternary Carbon Centers. Total Syntheses of meso- and (−)-Chimonanthine and (+)-Calycanthine (1999)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTDirect Stereo- and Enantiocontrolled Synthesis of Vicinal Stereogenic Quaternary Carbon Centers. Total Syntheses of meso- and (−)-Chimonanthine and (+)-CalycanthineLarry E. Overman, Daniel V. Paone, and Brian A. StearnsView Author Information Department of Chemistry, 516 Rowland Hall University of California Irvine, California 92697-2025 Cite this: J. Am. Chem. Soc. 1999, 121, 33, 7702–7703Publication Date (Web):August 6, 1999Publication History Received24 May 1999Published online6 August 1999Published inissue 1 August 1999https://pubs.acs.org/doi/10.1021/ja991714ghttps://doi.org/10.1021/ja991714grapid-communicationACS PublicationsCopyright © 1999 American Chemical SocietyRequest reuse permissionsArticle Views3685Altmetric-Citations200LEARN 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 SUBJECTS:Cyclization,Diols,Heck reaction,Molecular structure,Redox reactions Get e-Alerts
Control of developmental transcription factor sigma F by sporulation regulatory proteins SpoIIAA and SpoIIAB in Bacillus subtilis. (1990)

The sporulation operon spoIIA of Bacillus subtilis consists of three cistrons called spoIIAA, spoIIAB, and spoIIAC. Little is known about the function of spoIIAA and spoIIAB, but spoIIAC encodes a sigma factor called sigma F, which is capable of directing the transcription in vitro of genes that are expressed in the forespore chamber of the developing sporangium. We now report that the products of the spoIIA operon constitute a regulatory system in which SpoIIAA is an antagonist of SpoIIAB (or otherwise counteracts the effect of SpoIIAB) and SpoIIAB is, in turn, an antagonist of SpoIIAC (sigma F). This conclusion is based on the observations that (i) overexpression of spoIIAB inhibits sigma F-directed gene expression, (ii) a mutation in spoIIAB stimulates sigma F-directed gene expression, (iii) a mutation in spoIIAA blocks sigma F-directed gene expression, and (iv) a mutation in spoIIAB relieves the block in sigma F-directed gene expression caused by a mutation in spoIIAA. The SpoIIAA/SpoIIAB/SpoIIAC regulatory system could play a role in controlling the timing of sigma F-directed gene expression and/or could be responsible for restricting sigma F-directed gene expression to the forespore chamber of the sporangium.
Delivering quantum dots to cells: bioconjugated quantum dots for targeted and nonspecific extracellular and intracellular imaging (2010)

Bioconjugated nanomaterials offer endless opportunities to advance both nanobiotechnology and biomedical technology. In this regard, semiconductor nanoparticles, also called quantum dots, are of particular interest for multimodal, multifunctional and multiplexed imaging of biomolecules, cells, tissues and animals. The unique optical properties, such as size-dependent tunable absorption and emission in the visible and NIR regions, narrow emission and broad absorption bands, high photoluminescence quantum yields, large one- and multi-photon absorption cross-sections, and exceptional photostability are the advantages of quantum dots. Multimodal imaging probes are developed by interfacing the unique optical properties of quantum dots with magnetic or radioactive materials. Besides, crystalline structure of quantum dots adds scope for high-contrast X-ray and TEM imaging. Yet another unique feature of a quantum dot is its spacious and flexible surface which is promising to integrate multiple ligands and antibodies and construct multi-functional probes for bioimaging. In this critical review, we will summarize recent advancements in the preparation of biocompatible quantum dots, bioconjugation of quantum dots, and applications of quantum dots and their bioconjugates for targeted and nonspecific imaging of extracellular and intracellular proteins, organelles and functions (181 references).