gebhart/patrepeval huggingface dataset:
Translational regulation of the L11 ribosomal protein operon of Escherichia coli: analysis of the mRNA target site using oligonucleotide-directed mutagenesis. (1984)

The L11 ribosomal protein operon in Escherichia coli consists of the genes for proteins L11 and L1 and is feedback regulated by the translational repressor L1. The mRNA target site for this repression is located close to the translation initiation site of the first L11 cistron. Several mutant plasmid molecules carrying altered nucleotide sequences in the L1 target site were constructed by site-directed in vitro mutagenesis using synthetic oligodeoxyribonucleotides. Specifically, we examined the importance of a presumptive double-stranded stem structure that is common among L1 binding sites on rRNA from a variety of organisms and in L11 mRNA. Mutational alterations that disrupt the stem structure were found to abolish translational regulation as analyzed both in vitro and in vivo. Two of the mutations were combined so that the stem structure was restored but with a different primary nucleotide sequence. This double mutant was shown to restore the original phenotype, the ability to be translationally regulated by L1. These experiments show the importance of the stem structure, but not its primary sequence, for the interaction of L1 with the mRNA and support the concept that mRNA target sites share some structural features with the corresponding ribosomal protein binding sites of rRNA.
Ex vivo expanded peripheral blood progenitor cells provide rapid neutrophil recovery after high-dose chemotherapy in patients with breast cancer (2000)

Ex vivo expanded peripheral blood progenitor cells (PBPCs) have been proposed as a source of hematopoietic support to decrease or eliminate the period of neutropenia after high-dose chemotherapy. CD34 cells were selected from rhG-CSF mobilized PBPCs from patients with breast cancer and were cultured for 10 days in defined media containing 100 ng/mL each of rhSCF, rhG-CSF, and PEG-rhMGDF in 1 L Teflon bags at 20 000 cells/mL. After culture the cells were washed and reinfused on day 0 of transplantation. On day +1, cohort 1 patients (n = 10) also received an unexpanded CD34-selected PBPC product. These patients engrafted neutrophils (absolute neutrophil count, >500/microL) in a median of 6 (range, 5-14) days. Cohort 2 patients (n = 11), who received expanded PBPCs only, engrafted neutrophils in a median of 8 (range, 4-16) days. In comparison, the median time to neutrophil engraftment in a historical control group of patients (n = 100) was 9 days (range, 7-30 days). All surviving patients are now past the 15-month posttransplantation stage with no evidence of late graft failure. The total number of nucleated cells harvested after expansion culture was shown to be the best predictor of time to neutrophil engraftment, with all patients receiving more than 4 x 10(7) cells/kg, engrafting neutrophils by day 8. No significant effect on platelet recovery was observed in any patient. These data demonstrate that PBPCs expanded under the conditions defined can shorten the time to engraftment of neutrophils compared with historical controls and that the rate of engraftment is related to the dose of expanded cells transplanted.
Proteolytic Activity in Anther Extracts of Fertile and Cytoplasmic Male Sterile Petunia (1985)

Proteolytic activity is compared in anther extracts from Petunia parodii fertile and cytoplasmic male sterile lines. It is characterized relative to developmental stage of the anthers, effect of variable incubation times, pH of isolation buffers, and degradation of marker proteins. In fertile anthers, proteolytic activity increases at the end of microsporogenesis and peaks early in microgametogenesis. Degradation is most severe in extracts of fertile anthers and in high molecular weight proteins and reaches its maximum within 20 minutes. Degradation of marker proteins is greatest at pH 5.6 to 8.0 in fertile anther extracts and is eliminated under strong acid conditions (pH 2.8 to 4.0) in both fertile and cytoplasmic male sterile anther extracts. Marker proteins degrade more severely in extracts of fertile anthers; however, the order of substrate sensitivity-myosin > phosphorylase b > bovine serum albumin and ovalbumin > beta-galactosidase-is the same in extracts from fertile and cytoplasmic male sterile anthers.
Pro-autophagic polyphenols reduce the acetylation of cytoplasmic proteins (2012)

Resveratrol is a polyphenol contained in red wine that has been amply investigated for its beneficial effects on organismal metabolism, in particular in the context of the so-called "French paradox," i.e., the relatively low incidence of coronary heart disease exhibited by a population with a high dietary intake of cholesterol and saturated fats. At least part of the beneficial effect of resveratrol on human health stems from its capacity to promote autophagy by activating the NAD-dependent deacetylase sirtuin 1. However, the concentration of resveratrol found in red wine is excessively low to account alone for the French paradox. Here, we investigated the possibility that other mono- and polyphenols contained in red wine might induce autophagy while affecting the acetylation levels of cellular proteins. Phenolic compounds found in red wine, including anthocyanins (oenin), stilbenoids (piceatannol), monophenols (caffeic acid, gallic acid) glucosides (delphinidin, kuronamin, peonidin) and flavonoids (catechin, epicatechin, quercetin, myricetin), were all capable of stimulating autophagy, although with dissimilar potencies. Importantly, a robust negative correlation could be established between autophagy induction and the acetylation levels of cytoplasmic proteins, as determined by a novel immunofluorescence staining protocol that allows for the exclusion of nuclear components from the analysis. Inhibition of sirtuin 1 by both pharmacological and genetic means abolished protein deacetylation and autophagy as stimulated by resveratrol, but not by piceatannol, indicating that these compounds act through distinct molecular pathways. In support of this notion, resveratrol and piceatannol synergized in inducing autophagy as well as in promoting cytoplasmic protein deacetylation. Our results highlight a cause-effect relationship between the deacetylation of cytoplasmic proteins and autophagy induction by red wine components.
Differential inhibition of IL-1 beta activities and receptor binding by monoclonal antibodies mapping within a discrete region of the protein. (1991)

The importance of the region in position 148-192 for the biological activities and receptor-binding capacity of the human IL-1 beta protein has been assessed by the use of mAbs. Four mAbs have been used, which recognize different epitopes within the 148-192 region. None of the mAbs could inhibit binding of IL-1 beta to IL-1RI (expressed on T cells and fibroblasts), suggesting that the 148-192 region does not contain IL-1RI binding sites. Conversely, mAbs Vhp20 (recognizing the fragment 166-169) and BRhD2 (directed to an epitope in the sequence 177-186) recognize sites partially involved in binding to IL-1RII (expressed on B cells, macrophages, and PMN). Only mAbs BRhD2 and FIB 1 (which recognizes an epitope in the sequence 174-186) can inhibit IL-1 beta-induced thymocyte proliferation, whereas all four can inhibit the adjuvant capacity of IL-1 beta in vivo. It is concluded that the region 148-192 encompasses domains important for T cell activation but not for binding to the IL-1RI on T cells, others involved in immunostimulation in vivo, and others important for binding to IL-1RII, although not directly involved in it.
Process intensification: oxidation of benzyl alcohol using a continuous isothermal reactor under microwave irradiation (2005)

In the past two decades, several investigations have been carried out using microwave radiation for performing chemical transformations. These transformations have been largely performed in conventional batch reactors with limited mixing and heat transfer capabilities. The reactions were performed under adiabatic conditions where the enhancements in the reaction rate reported in these publications may be due to the rapid increase in the reaction temperature during the course of the reaction. The concept of process intensification has been used to develop a narrow channel reactor that is capable of carrying out reactions under isothermal conditions while being exposed to microwave irradiation. Oxidation of benzyl alcohol to benzaldehyde has been carried out using the above-mentioned isothermal micro reactor. Results and the findings of this investigation are discussed in this paper.
Viabilities of the Wavelength-Division-Multiplexing Transmission System Over an Optical Fiber Cable (1978)

This paper describes the feasibility and the applicability of the Wavelength-Division-Multiplexing (WDM) system with two types of preliminary WDM transmission experiments. Through this study, it has become clear that WDM technologies play a major role in optical fiber systems and have the possibilities of realizing the various optical fiber transmission systems.
Seven Ways to Preserve the Miracle of Antibiotics (2013)

Antibiotic resistance is a well-acknowledged crisis with no clearly defined comprehensive, national corrective plan. We propose a number of interventions that, collectively, could make a large difference. These include collection of data to inform decisions, efforts to reduce antibiotic abuse in people and animals, great emphasis on antibiotic stewardship, performance incentives, optimal use of newer diagnostics, better support for clinical and basic resistance-related research, and novel methods to foster new antibiotic development.
Hetero-arylboroxines: the first rational synthesis, X-ray crystallographic and computational analysis (2008)

A novel series of hetero-arylboroxines were synthesized and structurally characterized by X-ray diffraction, NMR and computational analysis. The solid-state structures of the hetero-arylboroxines represent the first report of AB(2)-type hetero-arylboroxines.
Interference phenomenon determines the color in an organic light emitting diode (1997)

We report on electroluminescence from two-layer organic diodes made of poly(3-methyl-4-octylthiophene) and 2-(4-biphenylyl)-5-(4-tert-butylphenyl)-1,2,4-oxadiazole films between electrodes of indium tin oxide and Ca/Al. The diodes emitted light in the green-blue range; the electroluminescence spectra varied between diodes with different thicknesses of the polymer and molecular layers. The optical phenomena were simulated with a model accounting for interference effects; simulated results showed that the electroluminescence from the organic diode can be due neither to luminescence of the polymer nor of the molecular layer. These model simulations, together with electrochemical measurements, can be interpreted as evidence for an indirect optical transition at the polymer/molecule interface that only occurs in a strong electric field. We label this transition an electroplex.
Identification ofLactobacillus plantarumGenes That Are Induced in the Gastrointestinal Tract of Mice (2004)

Lactobacillus plantarum is a flexible and versatile microorganism that inhabits a variety of environmental niches, including the human gastrointestinal (GI) tract. Moreover, this lactic acid bacterium can survive passage through the human or mouse stomach in an active form. To investigate the genetic background of this persistence, resolvase-based in vivo expression technology (R-IVET) was performed in L. plantarum WCFS1 by using the mouse GI tract as a model system. This approach identified 72 L. plantarum genes whose expression was induced during passage through the GI tract as compared to laboratory media. Nine of these genes encode sugar-related functions, including ribose, cellobiose, sucrose, and sorbitol transporter genes. Another nine genes encode functions involved in acquisition and synthesis of amino acids, nucleotides, cofactors, and vitamins, indicating their limited availability in the GI tract. Four genes involved in stress-related functions were identified, reflecting the harsh conditions that L. plantarum encounters in the GI tract. The four extracellular protein encoding genes identified could potentially be involved in interaction with host specific factors. The rest of the genes are part of several functionally unrelated pathways or encode (conserved) hypothetical proteins. Remarkably, a large number of the functions or pathways identified here have previously been identified in pathogens as being important in vivo during infection, strongly suggesting that survival rather than virulence is the explanation for the importance of these genes during host residence.
A 1.8-V 10-Gb/s fully integrated CMOS optical receiver analog front-end (2005)

A fully integrated 10-Gb/s optical receiver analog front-end (AFE) design that includes a transimpedance amplifier (TIA) and a limiting amplifier (LA) is demonstrated to require less chip area and is suitable for both low-cost and low-voltage applications. The AFE is fabricated using a 0.18-/spl mu/m CMOS technology. The tiny photo current received by the receiver AFE is amplified to a differential voltage swing of 400 mV/sub (pp)/. In order to avoid off-chip noise interference, the TIA and LA are dc-coupled on the chip instead of ac-coupled though a large external capacitor. The receiver front-end provides a conversion gain of up to 87 dB/spl Omega/ and -3dB bandwidth of 7.6 GHz. The measured sensitivity of the optical receiver is -12dBm at a bit-error rate of 10/sup -12/ with a 2/sup 31/-1 pseudorandom test pattern. Three-dimensional symmetric transformers are utilized in the AFE design for bandwidth enhancement. Operating under a 1.8-V supply, the power dissipation is 210 mW, and the chip size is 1028 /spl mu/m/spl times/1796 /spl mu/m.
Maturation-Dependent Expression and Function of the CD49d Integrin on Monocyte-Derived Human Dendritic Cells (2000)

Dendritic cells (DC) are highly specialized APC that are critical for the initiation of T cell-dependent immune responses. DC exert a sentinel function while immature and, after activation by inflammatory stimuli or infectious agents, mature and migrate into lymphoid organs to prime T cells. We have analyzed integrin expression on monocyte-derived DC (MDDC) and found that expression of CD49d integrins (CD49d/CD29 and CD49d/beta7) was induced/up-regulated during TNF-alpha- or LPS-initiated MDDC maturation, reflecting the induction/up-regulation of CD49d and beta7 mRNA. CD49d mRNA steady-state level increased more than 10 times during maturation, with the highest levels observed 24 h after TNF-alpha treatment. CD49d integrin expression conferred mature MDDC with an elevated capacity to adhere to the CS-1 fragment of fibronectin, and also mediated transendothelial migration of mature MDDC. Up-regulation of CD49d integrin expression closely paralleled that of the mature DC marker CD83. CD49d integrin expression was dependent on cell maturation, as its induction was abrogated by N:-acetylcysteine, which inhibits NF-kappaB activation and the functional and phenotypic maturation of MDDC. Moreover, CD49d integrin up-regulation and MDDC maturation were prevented by SB203580, a specific inhibitor of p38 mitogen-activated protein kinase, but were almost unaffected by the mitogen-activated protein/extracellular signal-related kinase kinase 1/2 inhibitor PD98059. Our results support the existence of a link between functional and phenotypic maturation of MDDC and CD49d integrin expression, thus establishing CD49d as a maturation marker for MDDC. The differential expression of CD49d on immature and mature MDDC might contribute to their distinct motility capabilities and mediate mature DC migration into lymphoid organs.
Improved definition image expansion (1992)

A method for nonlinear image expansion is introduced. The method preserves the discontinuities of the original image, therefore producing an expanded image with improved definition. The maximum a posteriori (MAP) estimation technique that is proposed results in the constrained optimization of a convex functional. The expanded image produced from this method will be shown to be aesthetically and quantitatively superior to images expanded by the standard methods of replication, linear interpolation, and cubic B-spline expansion.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Diagnosing attention-deficit/hyperactivity disorder in children. (1998)

Attention-deficit/hyperactivity disorder (ADHD) is a heterogeneous behavioral disorder of uncertain etiology that is always evident first in childhood. The correct diagnosis of the ADHD patient thus requires familiarity with how the diagnosis should be established across the life span. This article provides a description of the DSM-IV syndrome of ADHD, information on prevalence, and an overview of standard methods used in office practice to diagnose ADHD in children. These practice parameters will be examined in the light of the practitioner's current concerns about the validity of the diagnosis.
Development and characterization of a monoclonal antibody specific for human basophils and the identification of a unique secretory product of basophil activation. (1999)

Despite increasing evidence that basophils can infiltrate into inflamed tissues during allergic reactions, determination of the extent of infiltration and elucidation of their role in allergic disease has been frustrated by the lack of reliable means for detecting this cell type in tissues. In the present study, we report on a new monoclonal antibody specific for basophils and on the initial characterization of the antigen it recognizes. Basophils were isolated from peripheral blood by Percoll density gradient centrifugation and a positive-selection immunomagnetic procedure and injected into mice to produce monoclonal antibodies. A hybridoma clone, designated BB1, secreted antibody of the IgG2a isotype; this antibody bound selectively to basophils on immunocytochemistry but did not react with any other cell type or tissue structure, although it did stain a proportion of cells from the basophilic cell line KU812F. In sections of mixed populations of peripheral blood cells, similar numbers of cells stained with Alcian blue dye and BB1 over a wide range of basophil purity. BB1 antibody was effective in identifying basophils in sections of mixed cells or in tissues after fixation with ethanol, Carnoy's solution, or formalin. Staining of basophils with BB1 gave a granular appearance, although flow cytometry indicated that some antigen was also present on the surface of the cell. Activation of these cells with anti-IgE antibody or with the calcium ionophore A23187 provoked release of the antigen in parallel with that of histamine. BB1 antibody did not, by itself, stimulate histamine release. The molecular mass of the antigen was determined on Hedrick-Smith gels to be 124+/-11 kd. This new monoclonal antibody will be a valuable experimental tool in future studies, allowing the reliable detection of basophils in tissues of patients with allergic and chronic inflammatory disease; in addition, the antigen it identifies has potential as a unique marker of basophil activation.
Middle East Respiratory Syndrome Coronavirus in Bats, Saudi Arabia (2013)

The source of human infection with Middle East respiratory syndrome coronavirus remains unknown. Molecular investigation indicated that bats in Saudi Arabia are infected with several alphacoronaviruses and betacoronaviruses. Virus from 1 bat showed 100% nucleotide identity to virus from the human index case-patient. Bats might play a role in human infection.
Agonist-Receptor-Arrestin, an Alternative Ternary Complex with High Agonist Affinity (1997)

The rapid decrease of a response to a persistent stimulus, often termed desensitization, is a widespread biological phenomenon. Signal transduction by numerous G protein-coupled receptors appears to be terminated by a strikingly uniform two-step mechanism, most extensively characterized for the beta2-adrenergic receptor (beta2AR), m2 muscarinic cholinergic receptor (m2 mAChR), and rhodopsin. The model predicts that activated receptor is initially phosphorylated and then tightly binds an arrestin protein that effectively blocks further G protein interaction. Here we report that complexes of beta2AR-arrestin and m2 mAChR-arrestin have a higher affinity for agonists (but not antagonists) than do receptors not complexed with arrestin. The percentage of phosphorylated beta2AR in this high affinity state in the presence of full agonists varied with different arrestins and was enhanced by selective mutations in arrestins. The percentage of high affinity sites also was proportional to the intrinsic activity of an agonist, and the coefficient of proportionality varies for different arrestin proteins. Certain mutant arrestins can form these high affinity complexes with unphosphorylated receptors. Mutations that enhance formation of the agonist-receptor-arrestin complexes should provide useful tools for manipulating both the efficiency of signaling and rate and specificity of receptor internalization.
Large-Scale Investigation of Base Excision Repair Genetic Polymorphisms and Lung Cancer Risk in a Multicenter Study (2005)

Our results do not support a major independent role of BER gene polymorphisms in lung cancer risk. However, we cannot exclude the possibility that the OGG1 Ser326Cys and XRCC1 Arg194Trp polymorphisms play minor roles in lung carcinogenesis.
Structural and therapeutic insights from the species specificity and in vivo antithrombotic activity of a novel αIIb-specific αIIbβ3 antagonist (2009)

We previously reported on a novel compound (Compound 1; RUC-1) identified by high-throughput screening that inhibits human alphaIIbbeta3. RUC-1 did not inhibit alphaVbeta3, suggesting that it interacts with alphaIIb, and flexible ligand/rigid protein molecular docking studies supported this speculation. We have now studied RUC-1's effects on murine and rat platelets, which are less sensitive than human to inhibition by Arg-Gly-Asp (RGD) peptides due to differences in the alphaIIb sequences contributing to the binding pocket. We found that RUC-1 was much less potent in inhibiting aggregation of murine and rat platelets. Moreover, RUC-1 potently inhibited fibrinogen binding to murine platelets expressing a hybrid alphaIIbbeta3 receptor composed of human alphaIIb and murine beta3, but not a hybrid receptor composed of murine alphaIIb and human beta3. Molecular docking studies of RUC-1 were consistent with the functional data. In vivo studies of RUC-1 administered intraperitoneally at a dose of 26.5 mg/kg demonstrated antithrombotic effects in both ferric chloride carotid artery and laser-induced microvascular injury models in mice with hybrid halphaIIb/mbeta3 receptors. Collectively, these data support RUC-1's specificity for alphaIIb, provide new insights into the alphaIIb binding pocket, and establish RUC-1's antithrombotic effects in vivo.