gebhart/patrepeval huggingface dataset:
Postconditioning: A Form of “Modified Reperfusion” Protects the Myocardium by Activating the Phosphatidylinositol 3-Kinase-Akt Pathway (2004)

Brief intermittent episodes of ischemia and reperfusion, at the onset of reperfusion after a prolonged period of ischemia, confer cardioprotection, a phenomenon termed "ischemic postconditioning" (Postcond). We hypothesized that this phenomenon may just represent a modified form of reperfusion that activates the reperfusion injury salvage kinase (RISK) pathway. Isolated perfused rat hearts were subjected to: (a) 35 minutes of ischemia and 120 minutes of reperfusion, and infarct size was determined by tetrazolium staining; or (b) 35 minutes of ischemia and 7 minutes of reperfusion, and the phosphorylation states of Akt, endothelial NO synthase (eNOS), and p70S6K were determined. Postcond reduced infarct size from 51.2+/-3.4% to 31.5+/-4.1% (P<0.01), an effect comparable with ischemic preconditioning (IPC; 27.5+/-2.3%; P<0.01). Of interest, the combined protective effects of IPC and Postcond were not additive (30.1+/-4.8% with IPC+Postcond; P=NS). Inhibiting phosphatidylinositol 3-kinase (PI3K) at reperfusion using LY or Wortmannin (Wort) during the first 15 minutes of reperfusion completely abolished Postcond-induced protection (31.5+/-4.1% with Postcond versus 51.7+/-4.5% with Postcond+LY, P<0.01; 56.2+/-10.1% with Postcond+ Wort; P<0.01), suggesting that Postcond protects the heart by activating PI3K-Akt. Western blot analysis demonstrated that Postcond induced a significant increase in phosphorylation of Akt, eNOS, and p70S6K in an LY- and Wort-sensitive manner. In conclusion, we show for the first time that ischemic Postcond protects the myocardium by activating the prosurvival kinases PI3K-Akt, eNOS, and p70S6K in accordance with the RISK pathway.
Quantification of α-Amylase mRNA in Bacillus subtilis by Nucleic Acid Sandwich Hybridization (1988)

A novel hybridization test for quantification of mRNA from bacterial cells lysed directly in the culture medium was developed and optimized. The method uses two adjacent probes from a DNA fragment of interest in a sandwich hybridization. An unlabeled probe is immobilized on a solid support to capture homologous nucleic acids in the test solution. Hybrid detection is performed with the other, labeled, probe, which can bind to the filter only as a sample-mediated hybrid. We used the Bacillus amyloliquefaciens alpha-amylase gene and its mRNA as models for characterizing gene expression in Bacillus subtilis. To confirm the specificity of mRNA hybridization, nondenatured nucleic acid samples were allowed to react simultaneously with two filters: the mRNA-specific filter containing anti-sense single-stranded DNA and the background filter containing single-stranded DNA of the mRNA sense, respectively. We also developed a rapid enzymatic lysis procedure for B. subtilis, allowing complete degradation of late stationary phase cells grown in rich culture medium, while retaining mRNA molecules of high integrity. The applicability of this rapid lysis procedure and the hybridization method for mRNA analyses in long-term fermentations was demonstrated.
Molecular Genetics of Late‐Onset Alzheimer's Disease (2004)

Late-onset Alzheimer's disease (AD) is a complex and multifactorial disease with the possible involvement of several genes. Apolipoprotein E (APOE), especially the APOE*4 allele, has been established as a strong susceptibility marker that accounts for nearly 30% of the risk in late-onset AD. However, as the APOE*4 allele is neither necessary nor sufficient for the development of AD, it emphasizes the involvement of other genetic and/or environmental factors which, alone or in conjunction with APOE*4, can modify the risk of AD. Recently, genome-wide linkage or linkage disequilibrium studies on late-onset AD have provided informative data for the existence of multiple putative genes for AD on several chromosomes, with the strongest evidence on chromosomes 12, 10, 9 and 6. This paper attempts to review the current progress on the identification of additional genetic loci for late-onset AD.
Computational Analysis of the Evolution of 1‐Deoxy‐D‐xylulose‐5‐phosphate Reductoisomerase, an Important Enzyme in Plant Terpene Biosynthesis (2010)

Isoprenoids are a highly diverse and important group of natural compounds. The enzyme 1-deoxy-D-xylulose-5-phosphate reductoisomerase (DXR) catalyzes a key regulatory step in the non-mevalonate isoprenoid biosynthetic pathway in eubacteria and in plant plastids. For example, in Artemisia annua DXR participates in regulation of the biosynthesis of artemisinin, an important antimalarial drug. We performed phylogenetic analysis using DXR protein sequences from a model prokaryote, Escherichia coli, a picoplanktonic alga, Ostreococcus lucimarinus, and higher plants. The functional domain of DXR was conserved, allowing molecular evolutionary comparisons of both prokaryotic and eukaryotic sequences of DXR. Despite this conservation, for some plant species such as Campthoteca acuminata and Arabidopsis thaliana, phylogenetic relationships of their lineages were consistently violated. Our analysis revealed that plant DXR has an N-terminal transit domain that is likely bipartite, consisting of a chloroplast transit peptide (cTP) and a lumen transit peptide (lTP). Several features observed in the lTP suggest that, while DXR is targeted to the chloroplast, it is localized to the thylakoid lumen. These features include a twin arginine motif, a hydrophobic region, and a proline-rich region. The transit peptide also showed putative motifs for a 14-3-3 binding site with a chaperone phosphorylation site at Thr.
Pre-CFU-S quiescence and stem cell exhaustion after cytostatic drug treatment: protective effects of the inhibitory peptide pGlu-Glu-Asp- Cys-Lys (pEEDCK) (1993)

Pre--CFU-S are characterized by their ability to generate spleen colony- forming cells (CFU-S) and by their ability to repopulate the hematopoietic system after damage. We have investigated their response to three consecutive injections of cytosine arabinoside (ara-C), given at t = 0, 12, and 20 hours. Nine hours after treatment, the number of CFU-S and pre--CFU-S was reduced to 10% or 30%, respectively. No pre-- CFU-S were in S-phase at this time, indicating that the pre--CFU-S losses were not caused by direct drug killing. Up to 1 year after treatment, pre--CFU-S were still depleted to 10% of normal, indicating that their proliferative quiescence was permanent. We have previously shown that inhibition of CFU-S recruitment with pGlu-Glu-Asp-Cys-Lys (pEEDCK) makes them ara-C resistant and prevents their decimation. We now found that this also prevented the excessive drainage of the pre-- CFU-S pool, suggesting that pre--CFU-S allocation into active hematopoiesis is triggered by the CFU-S deficit. pEEDCK may thus be applicable as a protector of the hematopoietic repopulation potential against cytostatic drug-induced aplasia. Postchemotherapeutic stimulator treatment with (pEEDCK)2-dimer did not ameliorate pre--CFU-S losses. Long-term culture-initiating cells (LTC-ICs) showed a similar pattern of irreversible reduction after cytostatic drug treatment, which could be prevented by pEEDCK. Our results suggest, that certain subclasses of hematopoietic stem cells (pre--CFU-S) are permanently quiescent and exhaustible and that the capacity for self-renewal is not a necessary property of all stem cell-like cells.
Fibrinogen Cleavage by the Streptococcus pyogenes Extracellular Cysteine Protease and Generation of Antibodies That Inhibit Enzyme Proteolytic Activity (1999)

The extracellular cysteine protease from Streptococcus pyogenes is a virulence factor that plays a significant role in host-pathogen interaction. Streptococcal protease is expressed as an inactive 40-kDa precursor that is autocatalytically converted into a 28-kDa mature (active) enzyme. Replacement of the single cysteine residue involved in formation of the enzyme active site with serine (C192S mutation) abolished detectable proteolytic activity and eliminated autocatalytic processing of zymogen to the mature form. In the present study, we investigated activity of the wild-type (wt) streptococcal protease toward human fibrinogen and bovine casein. The former is involved in blood coagulation, wound healing, and other aspects of hemostasis. Treatment with streptococcal protease resulted in degradation of the COOH-terminal region of fibrinogen alpha chain, indicating that fibrinogen may serve as an important substrate for this enzyme during the course of human infection. Polyclonal antibodies generated against recombinant 40- and 28-kDa (r40- and r28-kDa) forms of the C192S streptococcal protease mutant exhibited high enzyme-linked immunosorbent assay titers but demonstrated different inhibition activities toward proteolytic action of the wt enzyme. Activity of the wt protease was readily inhibited when the reaction was carried out in the presence of antibodies generated against r28-kDa C192S mutant. Antibodies produced against r40-kDa C192S mutant had no significant effect on proteolysis. These data suggest that the presence of the NH(2)-terminal prosegment prevents generation of functionally active antibodies and indicate that inhibition activity of antibodies most likely depends on their ability to bind the active-site region epitope(s) of the protein.
A draft map of the mouse pluripotent stem cell spatial proteome (2016)

Knowledge of the subcellular distribution of proteins is vital for understanding cellular mechanisms. Capturing the subcellular proteome in a single experiment has proven challenging, with studies focusing on specific compartments or assigning proteins to subcellular niches with low resolution and/or accuracy. Here we introduce hyperLOPIT, a method that couples extensive fractionation, quantitative high-resolution accurate mass spectrometry with multivariate data analysis. We apply hyperLOPIT to a pluripotent stem cell population whose subcellular proteome has not been extensively studied. We provide localization data on over 5,000 proteins with unprecedented spatial resolution to reveal the organization of organelles, sub-organellar compartments, protein complexes, functional networks and steady-state dynamics of proteins and unexpected subcellular locations. The method paves the way for characterizing the impact of post-transcriptional and post-translational modification on protein location and studies involving proteome-level locational changes on cellular perturbation. An interactive open-source resource is presented that enables exploration of these data.
Poly(L‐Lactide) microfilaments enhance peripheral nerve regeneration across extended nerve lesions (2003)

After injury, axonal regeneration occurs across short gaps in the peripheral nervous system, but regeneration across larger gaps remains a challenge. To improve regeneration across extended nerve defects, we have fabricated novel microfilaments with the capability for drug release to support cellular migration and guide axonal growth across a lesion. In this study, we examine the nerve repair parameters of non-loaded filaments. To examine the influence of packing density on nerve repair, wet-spun poly(L-Lactide) (PLLA) microfilaments were bundled at densities of 3.75, 7.5, 15, and 30% to bridge a 1.0-cm gap lesion in the rat sciatic nerve. After 10 weeks, nerve cable formation increased significantly in the filament bundled groups when compared to empty-tube controls. At lower packing densities, the number of myelinated axons was more than twice that of controls or the highest packing density. In a consecutive experiment, PLLA bundles with lower filament-packing density were examined for nerve repair across 1.4- and 1.8-cm gaps. After 10 weeks, the number of successful regenerated nerves receiving filaments was more than twice that of controls. In addition, nerve cable areas for control groups were significantly less than those observed for filament groups. Axonal growth across 1.4- and 1.8-cm gaps was more consistent for the filament groups than for controls. These initial results demonstrate that PLLA microfilaments enhance nerve repair and regeneration across large nerve defects, even in the absence of drug release. Ongoing studies are examining nerve regeneration using microfilaments designed to release neurotrophins or cyclic AMP.
Metabolism of Exogenous Gangliosides GM1 and Chemically Modified GM1 in Mice1 (1988)

Ganglioside GM1(NeuAc), labeled at the C-3 position of sphingosine with tritium, was injected into C3H/He, C57BL/10, B10.AQR mice intraperitoneally. The incorporation and the distribution of the radioactivity in various organs were examined. The injected [3H]GM1(NeuAc) was mainly incorporated in the liver and hydrolyzed sequentially. Sialic acid of ganglioside GM1(NeuAc) and metabolites was converted to N-glycolyl type from N-acetyl type. An appreciable amount of the sphingosine moiety in the administered GM1(NeuAc), moreover, was reutilized, being converted to sphingomyelin, and incorporated into alkyl chain of the ether lipid in phosphatidylethanolamine. The distributions of radioactivity in the metabolites of GM1(NeuAc) administered to the three strains of mice were different from each other. In other organs, GM1(NeuAc) was incorporated and metabolized only slightly. The N-methylamide, at the carboxyl group of the sialic acid, of the labeled ganglioside GM1(GM1(NeuAc)-NMe) was injected into C3H/He mice. Most of the administered [3H]GM1(NeuAc)-NMe was incorporated in the liver, and was metabolized to GM3(NeuAc)-NMe, via GM2(NeuAc)-NMe, within 24 h. GM3(NeuAc)-NMe was the only radioactive compound in the subsequent 10 weeks, but disappeared from the liver gradually. N-Methylamide-modified gangliosides were resistant to hydrolysis by mouse hepatic sialidase, to elongation by glycosyltransferase and to N-glycolylation at N-acetylneuraminic acid by monooxygenase.
Transform coding of arbitrarily-shaped image segments (1993)

Article Transform coding of arbitrarily-shaped image segments Share on Authors: Shih Fu Chang View Profile , David G. Messerschmitt View Profile Authors Info & Claims MULTIMEDIA '93: Proceedings of the first ACM international conference on MultimediaSeptember 1993 Pages 83–90https://doi.org/10.1145/166266.166275Published:01 September 1993 23citation664DownloadsMetricsTotal Citations23Total Downloads664Last 12 Months2Last 6 weeks1 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
Tight Junction Proteins Form Large Complexes and Associate with the Cytoskeleton in an ATP Depletion Model for Reversible Junction Assembly (1997)

A key feature of the ischemic epithelial cell phenotype is the disruption of tight junctions (TJ). In a Manin-Darby canine kidney cell model for ischemia-reperfusion/hypoxia-reoxygenation injury which employs inhibitors of glycolysis (2-deoxy-D-glucose) and oxidative phosphorylation (antimycin A), transepithelial electrical resistance, a measure of TJ integrity, dropped rapidly, correlating well with declining ATP levels. Although immunocytochemical studies revealed only subtle changes in the distribution of the TJ proteins, zonula occludens (ZO)-1, ZO-2, and cingulin, examination of the Triton X-100 solubilities of these proteins, an indicator of cytoskeletal association, revealed a striking shift of all three TJ proteins into the insoluble pool, consistent with increased cytoskeletal interaction during ATP depletion. In addition, rate-zonal centrifugation analysis of a detergent-soluble fraction showed an increase in the amount of ZO-1 and ZO-2 in high density fractions following ATP depletion, providing further evidence for association of TJ proteins into a large complex possibly involving the cytoskeleton. Analysis of immunoprecipitation data from [35S]methionine-labeled cells revealed that ATP depletion led to the association of a 240-kDa protein with the ZO-1-containing complex. Western blots of this protein immunoprecipitated with anti-ZO-1 antibodies confirmed its identity as fodrin, a protein believed to link membrane and other proteins to the actin-based cytoskeleton. Together, our data suggest that in the absence of major immunocytochemical changes, ATP depletion leads TJ proteins to form large insoluble complexes and associate with the cytoskeleton. We propose a model in which a key, potentially regulated, step in the generation of the ischemic epithelial cell phenotype is the interaction between TJ proteins and fodrin and/or other cytoskeletal proteins.
Confinement and Sleep Deprivation Effects on Propensity to Take Risks (2009)

During the night of sleep deprivation, risk-taking propensity decreases and remains stable the following day in the confinement condition while it increases after the baseline period. In a confined environment under a normal sleep-wake schedule, impulsiveness increases in men and women.
Movement of air in the electric wind of the corona discharge (1961)

The mechanism of gas movement in the electric wind is considered herein, and an approximate theory presented which relates relevant electrical and aerodynamic quantities. Among others, these relationships are shown to hold for an electrostatic blower, operating on the electric-wind principle: Gas velocity is a linear function of voltage and is proportional to the square root of current; if the density of the gas is not too low, the efficiency of electrokinetic conversion near sparkover is proportional to the square root of the density, and the velocity at constant current is independent of the density; near sparkover efficiency is independent of voltage; velocity increases slowly as additional blowers are stacked in series; the ozone concentration of blower air resulting from the corona discharge is an increasing function of electric-wind velocity. The forms of the equations relating these variables are found to hold in a variety of cases, even though assumed boundary conditions are not observed experimentally. The practical utility of an electrostatic blower is limited by an efficiency of operation in the neighborhood of 1%.
Cyclometalated Iridium(III) Aquo Complexes:  Efficient and Tunable Catalysts for the Homogeneous Oxidation of Water (2007)

A series of bis-phenylpyridine, bis-aquo iridium(III) complexes is herein shown to robustly and efficiently catalyze the oxidation of water to dioxygen in the presence of a sacrificial oxidant. Through substitution on the cyclometalating ligands of these complexes, it is shown that a broad range of oxidation potentials can be achieved within this class of catalyst. Parallel, dynamic monitoring of oxygen evolution, made possible by equipping reaction vessels with pressure-voltage transducers, facilitates correlation of these complexes' ionization potentials with their respective activity toward water oxidation. The importance of these catalysts lies in (A) their ability to oxidize water in a purely aqueous medium, (B) their simplicity of design, (C) their durability, and (D) the ease with which they can be tuned to accommodate the electrochemical needs of photosensitizers in hypothetical photochemical water oxidation and full artificial photosynthetic schemes.
Stretchable Piezoelectric Nanoribbons for Biocompatible Energy Harvesting (2012)

The development of a method for integrating highly efficient energy conversion materials onto flexible, stretchable, and biocompatible substrates could yield breakthroughs in implantable or wearable energy harvesting systems. Being electromechanically coupled, piezoelectric crystals represent a particularly interesting subset of smart materials which can function as sensors, actuators, bioMEMS devices, and energy converters. Yet, the most efficient piezoelectrics are rigid and brittle in nature, while the crystallization of these materials generally requires high temperatures for maximal performance. These inherent material properties render corresponding devices incompatible with temperature-sensitive soft materials such as plastic, rubber, and tissue. Nanotechnology provides a route for overcoming these dichotomies, by altering the mechanics of materials while simultaneously improving their performance. Here, we present a scalable and parallel route for interfacing crystalline piezoelectric nanoribbons of lead zirconate titanate (PZT) with stretchable rubbers over macroscopic areas. The nanoribbons are fabricated via the recently developed PENCiL approach, which allows for controllable, location-determinant PZT nanoribbon arrays hierarchically patterned over wafer scales. Fundamental characterization of the ribbons by piezoresponse force microscopy indicates that their electromechanical energy conversion metrics are among the highest reported on a flexible medium and enhanced by the nanoscale mechanics of the hybrid system. Finally, integration into energy harvesting devices reveals the ability to generate power from bodily motion such as finger tapping. The excellent performance of the piezo-ribbon assemblies coupled with stretchable, biocompatible rubber may enable exciting avenues in fundamental research and novel applications.
Tissue vaccines for cancer (2007)

Most tumors, including prostate carcinoma, are heterogeneous mixtures of neoplastic cells and supporting stromal matrix. Attempts to vaccinate as a means to treat or prevent cancer have typically relied on use of a single antigen or cell type. In the case of whole-cell vaccines, clonal populations of cancer cells are grown in culture and harvested for vaccine material. However, it is clear from microarray data that neoplastic cells grown in culture are greatly different from those found in vivo. Tissue vaccines are harvested directly from tumors and are used to immunize the animal or the patient. They are antigenically rich, in that they are comprised of not only neoplastic cells but also supporting stromal matrix; furthermore, they include antigens that may be expressed only in vivo and which may be critical to a successful immune response to the cancer. For these reasons, the idea that tissue vaccines for cancer have potentially great utility has merit and should be explored further.
Bioactivity of flavonoids. (1997)

Flavonoids are benzo-gamma-pyrone derivatives of plant origin. They possess wide spectrum of biological activity. From the therapeutical point of view the most important are their antioxidant properties. These are the result of high propensity to electron transfer, ferrous ions chelating activity and direct scavenging of reactive oxygen species. Flavonoids inhibit enormous number of enzymes. From the pharmacological point of view inhibition of cyclooxygenase and lipoxygenases as well as scavenging of superoxide anions seem to be essential. Flavonoids are antiinflammatory agents as the result of diminished formation of proinflammatory mediators (prostaglandins, leukotrienes, reactive oxygen species, nitric oxide). They are also antithrombotic owing to their ability to scavenge superoxide anions. These anions are strong inhibitors of prostacyclin production. Removal of superoxide anions by flavonoids facilitates antiaggregatory PGI2 formation. Superoxide anions generate proagregatory isoprostanes. The antiaggregatory effect of flavonoids may be due to the limitation of formation of isoprostanes. Empirical use of flavonoids as drugs acquired recently scientific confirmation.
Art and Photography (1984)

Watson outlines some of the debates regarding the relationship of photography and art. Includes statements by and biographical notes on ten artists.