gebhart/patrepeval huggingface dataset:
Ultrasonic plaque ablation. A new method for recanalization of partially or totally occluded arteries. (1988)

The potential application of ultrasonic energy for ablation of atherosclerotic plaques was studied in human atherosclerotic arteries with continuous and pulsed delivery of energy. With a prototype ultrasonic wire probe (n = 79 segments), there was gross reduction in vascular lesions as well as microscopic disruption of fibrous and calcified plaques. Normal portions of vessels appeared unaffected by the application of ultrasound. The prototype ultrasonic wire catheter ablated calcific deposits in less than 10 seconds. With this probe, all 26 complete atherosclerotic occlusions 0.5-5 cm in length were recanalized irrespective of the presence of calcium. Twenty-four of the segments were reopened in less than 20 seconds. By light microscopy, the site of plaque ablation was smooth, concave, and conformed to the shape of the probe tip. In 17 samples, there was evidence of thermal injury, and in six of the 79 samples studied with the prototype probe, there was vascular perforation. No vascular perforation occurred without thermal damage, when pulsed (rather than continuous) ultrasonic energy was used (n = 40) or when the duration of application was less than 30 seconds, with power output less than 25 W and with the probe oriented parallel to the wall (n = 26). Thus, by modifying the duration, mode, and magnitude of the ultrasonic power output, thermal injury and vascular perforation may be avoided. In vivo intra-arterial ultrasonic angioplasty of a canine chronic femoral fibrocellular occlusion was also performed. A preliminary in vivo study demonstrated feasibility of the percutaneous application of intra-arterial ultrasonic recanalization. Thus, ultrasonic energy appears to have potential as a method for ablation of occlusive atherosclerotic plaque.
FOXO Proteins Regulate Tumor Necrosis Factor-related Apoptosis Inducing Ligand Expression (2002)

Mutations in PTEN occur in 60-80% of prostate cancers and lead to a constitutive activation of the phosphatidylinositol 3-kinase pathway and a resultant loss of activity of the FOXO family of forkhead transcription factors FKHRL1 and FKHR. To provide insight into the role of PTEN mutations in prostate cancer, we used microarrays to identify genes regulated by FKHRL1 and FKHR in LAPC4 prostate carcinoma cells. These studies revealed that adenoviral overexpression of FKHRL1 and FKHR in the LAPC4 prostate cancer cell line resulted in apoptosis and induced the expression of many genes that affect cellular proliferation or survival. The expression of one of these FOXO-regulated genes, TRAIL, a pro-apoptotic member of the tumor necrosis factor family, was decreased in human metastatic prostate tumors. The altered expression of TRAIL in these tumors correlated directly with decreased PTEN expression and the resultant loss of FKHRL1 and FKHR activity. Analysis of the effects of FOXO proteins on the TRAIL promoter localized the FKHRL1 responsive element of the TRAIL promoter to nucleotides -138 to -121 and demonstrated that TRAIL is a direct target of FKHRL1. These findings suggest that the decreased activity of FKHRL1 and FKHR in prostate cancers resulting from loss of PTEN leads to a decrease in TRAIL expression that may contribute to increased survival of the tumor cells.
Phosphoinositide signalling enzymes in rat liver nuclei: phosphoinositidase C isoform β1 is specifically, but not predominantly, located in the nucleus (1993)

The presence of phosphoinositide-mobilizing enzymes has been investigated in purified rat liver nuclei by radiolabelling and by probing with antibodies. A Ca(2+)-activated phosphoinositidase C (PIC) is present and was shown immunologically to be the beta 1 isoform. No gamma- or delta-PIC was found. However, only 5% of the total beta 1-PIC isoform is nuclear, with the majority being cytosolic. G alpha q and G alpha 11, the suggested physiological activators of beta 1-PIC, were not present. A PtdIns4P 5-kinase is also present, which immunologically is shown to be the C isoform. All of these nuclear inositide enzymes still remained after the removal of the nuclear envelope with Triton X-100, consistent with the concept of an intranuclear inositide cycle [Divecha, Banfic and Irvine (1991) EMBO. J. 10, 3207-3214].
Elevated levels of hyaluronic acid in the sera of women with fibromyalgia. (1997)

HA serum levels in women with FM were significantly elevated compared to healthy controls and patients with RA. This observation suggests that FM is associated with a biochemical abnormality and that serum HA could be a laboratory marker for its diagnosis.
Motor gasolines, summer 1985 (1986)

Samples for this report were collected from service stations throughout the country and were analyzed in laboratories of various refiners, motor manufacturers, chemical companies, and research institutes. Analytical data for the 1571 motor gasoline and 206 motor gasoline/alcohol blend samples were submitted to the National Institute for Petroleum and Energy Research (NIPER), Bartlesville, Oklahoma, for reporting. This work is jointly funded by the American Petroleum Institute (API) and the United States Department of Energy (DOE), Bartlesville Project Office (DOE cooperative agreement No. FC22-83FE60149). The data are representative of the products of 62 marketers, large and small, which manufacture and supply gasoline. They are tabulated by groups according to brands (unlabeled) and grades for 17 marketing districts into which the country is divided. A map shows the marketing areas, districts, and sampling locations. The report includes trend charts of selected properties of motor fuels over the last twenty-five years. Twelve octane distribution graphs for leaded and unleaded grades of gasoline are presented for areas 1, 2, 3, and 4. The average antiknock (octane) index (R + M)/2 of gasoline sold in the United States during June, July, and August 1985 was 87.4 for unleaded below 90.0, 91.7 for unleaded 90.0 and above, and 88.8 for leaded below 93.0 grades of gasoline. Analyses of motor gasoline containing various alcohols are reported in separate tables beginning with this report. The average antiknock (octane) index (R + M)/2 of gasoline containing alcohols was 88.6 for unleaded below 90.0, 91.4 for unleaded 90.0 and above, and 90.2 for leaded below 93.0 grades of gasoline. 16 figs., 8 tabs.
Noise reduction and speech enhancement via temporal anti-Hebbian learning (2002)

Temporal extensions of both linear and nonlinear anti-Hebbian learning have been shown to be suited to the problem of blind separation of sources from their convolved mixtures. This paper presents a generalized form of anti-Hebbian learning for a partially connected recurrent network based on the maximum likelihood estimation principle. Inspired by features of the binaural unmasking effect the network and associated online adaptation are applied to the enhancement of speech, which is corrupted by interfering noise, competing speech and reverberation. Graded simulations based on speech corrupted with increasingly complex levels of reverberation are reported. It is shown that for high levels of reverberation the proposed method compares favorably with classical adaptive filter approaches to speech enhancement in real acoustic environments.
Metalloproteinase increases in the injured rat spinal cord (2000)

Up-regulation of matrix metalloproteinases MMP-9 and MMP-2 after injury to the spinal cord (SCI) is demonstrated. MMP-9 activity maximized at 12-24 h, and MMP-2 rose at 5 days post-injury. MMP-3 was not detectable by zymographic analysis, so its level of expression was, at most, very low. The level of tissue inhibitor of metalloproteinases in the spinal cord was not altered by injury, perhaps permitting increased MMP-9 and MMP-2 activities in situ. Ablating them with an antibody demonstrated that infiltrating neutrophils were the principal source of MMP-9 activity after spinal cord injury, suggesting that neutrophils utilize that proteinase in responding to spinal cord injury. MMP-9 and MMP-2 probably contribute to breakdown of the extracellular matrix following SCI.
Bombesin, Vasopressin, Lysophosphatidic Acid, and Sphingosylphosphorylcholine Induce Focal Adhesion Kinase Activation in Intact Swiss 3T3 Cells (1998)

Treatment of quiescent Swiss 3T3 cells with bombesin rapidly increased focal adhesion kinase (FAK)-associated tyrosine kinase activity in immune complexes. The effect was rapid (maximum at 2.5 min) and dose dependent (half-maximum response at 0.05 nM). Addition of vasopressin, lysophosphatidic acid, and sphingosylphosphorylcholine also elicited a rapid increase in FAK-associated tyrosine kinase activity. Addition of the selective Src inhibitor pyrazolopyrimidine directly to the in vitro kinase assay potently inhibited Src kinase activity induced by bombesin but did not affect the kinase activity of FAK measured by autophosphorylation or by synthetic substrate phosphorylation in paralell assays. In addition, Src activity was not detected in FAK immunoprecipitates using an optimal Src peptide substrate. Thus, agonist-induced tyrosine kinase activity measured in FAK immunoprecipitates is mediated by FAK activation rather than by co-immunoprecipitating Src. Bombesin-induced FAK activation is not dependent either on protein kinase C or Ca2+ mobilization but was completely blocked by treatment with cytochalasin D or by placing the cells in suspension. These findings indicate that FAK activation requires an intact actin cytoskeleton. Our results demonstrate that agonists that act via 7-transmembrane domain receptors stimulate FAK kinase activation.
Effects of Antithyroid Drugs on Lymphocyte Function in Vitro* (1980)

The in vitro influence of 6-propylthiouracil (PTU) and methimazole (MMi) on mitogenic activation of human peripheral blood lymphocytes was studied in order to assess whether antithyroid drugs may have an immunomodulatory capacity. Lymphocytes were cultured for 72 h in the presence of phytohaemagglutinin (PHA; 1.25 microgram/ml), concanavalin A (Con A; 5.0 microgram/ml), or pokeweed mitogen (PWM; 2.5 microgram/ml). Antithyroid drugs were added to yield final concentrations of 1-1000 mu mol/liter. High pressure liquid chromatographic analyses verified that the expected drug concentrations in the incubation media were reached and maintained throughout the incubation period. The degree of lymphocyte activation was assessed by measurements of the cellular uptake of [3H]thymidine added after 48 h. PTU (at 1000 mu mol/liter) slightly suppressed PHA- and Con A-induced activation of lymphocytes but enhanced (at 5-500 mu mol/liter) PWM-induced activation. MMI (500-1000 mu mol/liter) enhanced not only PWM-induced activation but (at 1000 mu mol/liter) also enhanced PHA- and Con A-induced activation. Thus, PTU and MMI might interfere with mitogenic activation of lymphocytes. However, the effects were mainly recorded at drug concentrations exceeding those found in blood samples of patients treated with conventional doses.
Bacterial Coinfection in Influenza (2013)

Bacterial coinfection complicated nearly all influenza deaths in the 1918 influenza pandemic and up to 34% of 2009 pandemic influenza A(H1N1) infections managed in intensive care units worldwide. More than 65,000 deaths attributable to influenza and pneumonia occur annually in the United States. Data from 683 critically ill patients with 2009 pandemic influenza A(H1N1) infection admitted to 35 intensive care units in the United States reveal that bacterial coinfection commonly occurs within the first 6 days of influenza infection, presents similarly to influenza infection occurring alone, and is associated with an increased risk of death. Pathogens that colonize the nasopharynx, including Staphylococcus aureus, Streptococcus pneumoniae, and Streptococcus pyogenes, are most commonly isolated. Complex viral, bacterial, and host factors contribute to the pathogenesis of coinfection. Reductions in morbidity and mortality are dependent on prevention with available vaccines as well as early diagnosis and treatment.
Bringing CLARITY to the human brain: visualization of Lewy pathology in three dimensions (2015)

The effective use of CLARITY on large samples of human tissue opens up many potential avenues for detailed pathological and morphological studies.
New enone derivatives of oleanolic acid and ursolic acid as inhibitors of nitric oxide production in mouse macrophages (1997)

New derivatives of 3-oxoolean-1-en-28-oic acid and 3-oxours-1-en-28-oic acid were synthesized. Nine of them showed significant inhibitory activity against interferon-γ-induced nitric oxide production in mouse macrophages when assayed at the 1 μM level. 3,12-Dioxoolean-1,9-dien-28-oic acid (3) had the highest activity (IC50, 0.9 μM).
Fibronectin and proteoglycans as determinants of cell‐substratum adhesion (1979)

When normal or SV40-transformed Balb/c 3T3 cells are treated with the Ca++-specific chelator EGTA, they round up and pull away from their footpad adhesion sites to the serum-coated tissue culture substrate, as shown by scanning electron microscope studies. Elastic membranous retraction fibers break upon culture agitation, leaving adhesion sites as substrate-attached material (SAM) (Cells leave "footprints" of substrate adhesion sites during movement by a very similar process.) SAM contains 1-2% of the cell's total protein and phospholipid content and 5-10% of its glucosamine-radiolabeled polysaccharide, most of which is glycosaminoglycan (GAG). By one- and two-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis, there is considerable enrichment in SAM for specific GAGs; for the glycoprotein fibronectin; and for the cytoskeletal proteins actin, myosin, and the subunit protein of the 10 nm-diameter filaments. Fibrillar fibronectin of cellular origin and substratum-bound fibronectin of serum origin (cold-insoluble globulin, CIg) have been visualized by immunofluorescence microscopy. The GAG composition in SAM has been examined under different cellular growth and attachment conditions. Heparan sulfate content correlates with glycopeptide content (derived from glycoprotein). Newly attaching cells deposit SAM with principally heparan sulfate and fibronectin and little of the other GAGs. Hyaluronate and chrondroitin proteoglycans are coordinately deposited in SAM as cells begin spreading and movement over the substrate. Cells attaching to serum-coated or CIg-coated substrates deposited SAM with identical compositions. The proteoglycan nature of the GAGs in SAM has been examined, as well as the ability of proteoglycans to form two classes of reversibly dissociable "supramolecular complexes" - one class with heparan sulfate and glycopeptide-containing material and the second with hyaluronate-chondroitin complexes. Enzymatic digestion of "intact" SAM with trypsin or testicular hyaluronidase indicates that (1) only a small portion of long-term radiolabeled fibronectin and cyto-skeletal protein is bound to the substrate via hyaluronate or chondroitin classes of GAG; (2) most of the fibronectin, cytoskeletal protein and heparan sulfate coordinately resist solubilization; and (3) newly synthesized fibronectin, which is metabolically labile in SAM, is linked to SAM by hyaluronate- and/or chondroitin-dependent binding. All of our studies indicate that heparan sulfate is a direct mediator of adhesion of cells to the substrate, possibly by binding to both cell-surface fibronectin and substrate-bound CIg in the serum coating; hyaluronate-chondroitin complexes in SAM appear to be most important in motility of cells by binding and labilizing fibronectin at the periphery of footpad adhesions, with subsequent cytoskeletal disorganization.
Molecular cloning and functional expression of a novel extracellular lipase from the thermotolerant yeastCandida thermophila (2006)

The thermotolerant yeast Candida thermophila SRY-09 isolated from Thailand produces an extracellular lipase that hydrolyses various triglycerides. To clone the gene encoding the lipase, Saccharomyces cerevisiae was transformed with a C. thermophila genomic library and screened for lipase activity on medium containing olive oil emulsion and rhodamine B. One C. thermophila lipase gene (CtLIP) was found that contained an ORF of 1317 bp encoding a deduced polypeptide of 438 amino acids. Candida thermophila lipase contained a Gly-Asp-Ser-Gln-Gly motif which matched the consensus Gly-X-Ser-X-Gly conserved among lipolytic enzymes. Heterologous expression of the cloned CtLIP under the control of the alcohol oxidase gene (AOX1) promoter in the methylotrophic yeast Pichia pastoris, and enzymatic measurements confirmed the function of the respective protein as a lipase. The recombinant CtLIP could hydrolyse various substrates at high temperature (55 degrees C) with higher efficiency than at 37 or 45 degrees C and preferentially hydrolysed two-positional ester bonds. As with C. thermophila, the heterologously expressed lipase was secreted into the medium by Pichia pastoris.
Evaluation of Methods for the Measurement of Low-Density Lipoprotein Cholesterol (2005)

A high concentration of low-density lipoprotein cholesterol (LDL-C) in plasma is one of the strongest risk factors for atherosclerotic cardiovascular disease and mortality. The most common approach to determining LDL-C in the clinical laboratory is the Friedewald calculation. There is an increased interest to improve the accuracy of LDL-C estimated by this equation. The expert panel convened by National Cholesterol Education Program has recommended the development of accurate direct methods to measure LDL-C. Several homogeneous and fully automated methods have been introduced in recent years that show improved precision and accuracy over earlier methods, especially the Friedewald calculation. Each of the atherogenic particles in plasma--very-low, intermediate-, and low- density lipoprotein--as well as lipoprotein (a), contain one molecule of apolipoprotein B (apoB) and thus, plasma total concentration of apoB reflects the number of atherogenic particles. Several studies suggested that the measurement of apoB could improve the prediction of risk of coronary artery disease. Thus, in addition to the newly developed direct assays, alternative calculation procedures have been proposed that also take into consideration total serum apoB concentration for the estimation of LDL-C and the presence of small, dense LDL particles. The new generation of homogenous methods for the measurement of LDL-C and the use of serum apoB concentration for the estimation of LDL-C can contribute to the accurate LDL-C determination.
Probe Pressure Modulation Algorithm Reduces Extracerebral Contamination in Optical Measurements of Cerebral Blood Flow (2014)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text W. B. Baker, D. R. Busch, A. B. Parthasarathy, R. C. Mesquita, M. Chandra, and A. G. Yodh, "Probe Pressure Modulation Algorithm Reduces Extracerebral Contamination in Optical Measurements of Cerebral Blood Flow," in Biomedical Optics 2014, OSA Technical Digest (online) (Optica Publishing Group, 2014), paper BS3A.52. Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery (2010)

The accurate mapping of reads that span splice junctions is a critical component of all analytic techniques that work with RNA-seq data. We introduce a second generation splice detection algorithm, MapSplice, whose focus is high sensitivity and specificity in the detection of splices as well as CPU and memory efficiency. MapSplice can be applied to both short (<75 bp) and long reads (≥ 75 bp). MapSplice is not dependent on splice site features or intron length, consequently it can detect novel canonical as well as non-canonical splices. MapSplice leverages the quality and diversity of read alignments of a given splice to increase accuracy. We demonstrate that MapSplice achieves higher sensitivity and specificity than TopHat and SpliceMap on a set of simulated RNA-seq data. Experimental studies also support the accuracy of the algorithm. Splice junctions derived from eight breast cancer RNA-seq datasets recapitulated the extensiveness of alternative splicing on a global level as well as the differences between molecular subtypes of breast cancer. These combined results indicate that MapSplice is a highly accurate algorithm for the alignment of RNA-seq reads to splice junctions. Software download URL: http://www.netlab.uky.edu/p/bioinfo/MapSplice.
Effect of antifungal agents on lipid biosynthesis and membrane integrity in Candida albicans (1987)

Eight antifungal agents were examined for effects on lipid biosynthesis and membrane integrity in Candida albicans. Lipids were labeled in vivo or in vitro with [14C]acetate and analyzed by thin-layer and gas chromatography. Membrane integrity was measured by a recently developed [14C]aminoisobutyric acid radiolabel release assay. The imidazole antifungal agents miconazole, econazole, clotrimazole, and ketoconazole, at concentrations inhibiting ergosterol biosynthesis (0.1 microM), decreased the ratio of unsaturated to saturated fatty acids in vivo but not in vitro. Similarly, naftifine, tolnaftate, and the azasterol A25822B, at concentrations inhibiting ergosterol biosynthesis (10, 100, and 1 microM, respectively), decreased the ratio of unsaturated to saturated fatty acids in vivo only. This suggests that the effect on fatty acids observed with ergosterol biosynthesis inhibitors may be secondary to the effect on ergosterol. With imidazoles, oleic acid antagonized inhibition of cell growth but not inhibition of ergosterol. This suggests that, with the C-14 demethylase inhibitors, decreased unsaturated fatty acids, rather than decreased ergosterol, are responsible for growth inhibition. Cerulenin, previously reported to be a potent inhibitor of both fatty acid and ergosterol biosynthesis, was found in the present study to inhibit the former (at 5 microM) but not the latter (up to 100 microM). Of the antifungal agents tested, econazole and miconazole (at 100 microM) produced complete release of [14C]aminoisobutyric acid, which is consistent with membrane damage.
Breathomics—exhaled volatile organic compound analysis to detect hepatic encephalopathy: a pilot study (2016)

The current diagnostic challenge with diagnosing hepatic encephalopathy (HE) is identifying those with minimal HE as opposed to the more clinically apparent covert/overt HE. Rifaximin, is an effective therapy but earlier identification and treatment of HE could prevent liver disease progression and hospitalization. Our pilot study aimed to analyse breath samples of patients with different HE grades, and controls, using a portable electronic (e) nose. 42 patients were enrolled; 22 with HE and 20 controls. Bedside breath samples were captured and analysed using an uvFAIMS machine (portable e-nose). West Haven criteria applied and MELD scores calculated. We classify HE patients from controls with a sensitivity and specificity of 0.88 (0.73-0.95) and 0.68 (0.51-0.81) respectively, AUROC 0.84 (0.75-0.93). Minimal HE was distinguishable from covert/overt HE with sensitivity of 0.79 and specificity of 0.5, AUROC 0.71 (0.57-0.84). This pilot study has highlighted the potential of breathomics to identify VOCs signatures in HE patients for diagnostic purposes. Importantly this was performed utilizing a non-invasive, portable bedside device and holds potential for future early HE diagnosis.
Structure of Malhamensilipin A, an Inhibitor of Protein Tyrosine Kinase, from the Cultured Chrysophyte Poterioochromonas malhamensis (1994)

A new chlorosulfolipid, malhamensilpin A [1] was isolated from the cultured chrysophyte Poterioochromonas malhamensis. Malhamensilipin A was demonstrated to be a modest inhibitor of pp60v-src protein tyrosine kinase. The structure was determined by detailed spectral analysis to be a novel C24 hexachloro lipid containing a vinyl sulfate ester (2,11,12,13,15,16-hexachloro-14-hydroxy-n-tetracos-1E-enol-1-sulfa te).