gebhart/patrepeval huggingface dataset:
A role for CFTR in the elevation of glutathione levels in the lung by oral glutathione administration (2007)

The cystic fibrosis transmembrane conductance regulator (CFTR) protein is the only known apical glutathione (GSH) transporter in the lung. The purpose of these studies was to determine whether oral GSH or glutathione disulfide (GSSG) treatment could increase lung epithelial lining fluid (ELF) GSH levels and whether CFTR plays a role in this process. The pharmacokinetic profile of an oral bolus dose of GSH (300 mg/kg) was determined in mice. Plasma, ELF, bronchoalveolar lavage (BAL) cells, and lung tissue were analyzed for GSH content. There was a rapid elevation in the GSH levels that peaked at 30 min in the plasma and 60 min in the lung, ELF, and BAL cells after oral GSH dosing. Oral GSH treatment produced a selective increase in the reduced and active form of GSH in all lung compartments examined. Oral GSSG treatment (300 mg/kg) resulted in a smaller increase of GSH levels. To evaluate the role of CFTR in this process, Cftr knockout (KO) mice and gut-corrected Cftr KO-transgenic (Tg) mice were given an oral bolus dose of GSH (300 mg/kg) and compared with wild-type mice for changes in GSH levels in plasma, lung, ELF, and BAL cells. There was a twofold increase in plasma, a twofold increase in lung, a fivefold increase in ELF, and a threefold increase in BAL cell GSH levels at 60 min in wild-type mice; however, GSH levels only increased by 40% in the plasma, 60% in the lung, 50% in the ELF, and twofold in the BAL cells within the gut-corrected Cftr KO-Tg mice. No change in GSH levels was observed in the uncorrected Cftr KO mice. These studies suggest that CFTR plays an important role in GSH uptake from the diet and transport processes in the lung.
Advanced Television Systems (1987)

On passe en revue les nouvelles technologies principales appliquees a la television depuis son apparition dans les foyers des Etats-Unis, au debut des annees 60
Translocated EspF protein from enteropathogenic Escherichia coli disrupts host intestinal barrier function (2001)

The mechanisms by which enteropathogenic Escherichia coli (EPEC), an important cause of diarrhea among infants in developing countries, induce symptoms are not defined. EPEC have a type III secretion system required for characteristic attaching and effacing changes that modify the cytoskeleton and apical surface of host cells. Infection of polarized intestinal epithelial cell monolayers by EPEC leads to a loss of transepithelial electrical resistance, which also requires the type III secretion system. We demonstrate here that EspF, a protein that is secreted by EPEC via the type III secretion system, is not required for quantitatively and qualitatively typical attaching and effacing lesion formation in intestinal epithelial cells. However, EspF is required in a dose-dependent fashion for the loss of transepithelial electrical resistance, for increased monolayer permeability, and for redistribution of the tight junction-associated protein occludin. Furthermore, the analysis of EPEC strains expressing EspF-adenylate cyclase fusion proteins indicates that EspF is translocated via the type III secretion system to the cytoplasm of host cells, a result confirmed by immunofluorescence microscopy. These studies suggest a novel role for EspF as an effector protein that disrupts intestinal barrier function without involvement in attaching and effacing lesion formation.
Synthesis of Tamiphosphor (2008)

Tamiphosphor is a neuraminidase inhibitor that is more effective against the H1N1 human influenza virus than tamiflu and equally effective against the recombinant H5N1 (N1BRG14) virus. The synthesis of tamiphosphor depicted uses a Pd-catalyzed phosphonylation of bromo­alkene G to install the phosphonic acid moiety.
Identification of sphingosine kinase 1 (SphK1) as a primary target of icaritin in hepatocellular carcinoma cells (2017)

Hepatocellular carcinoma (HCC) is a highly aggressive neoplasm. We aim to explore the anti-HCC activity by a natural prenylflavonoid icaritin. Icaritin was cytotoxic and pro-apoptotic when added to established (HepG2, KYN-2 and Huh-7 lines) and primary human HCC cells. At the signaling level, icaritin inhibited sphingosine kinase 1 (SphK1) activity in HCC cells, which led to pro-apoptotic ceramide production and JNK1 activation. SphK1 inhibition or silence (by shRNA/microRNA) mimicked icaritin-mediated cytotoxicity, and almost nullified icaritin's activity in HepG2 cells. Reversely, exogenous over-expression of SphK1 sensitized icaritin-induced HepG2 cell apoptosis. In vivo, oral administration of icaritin dramatically inhibited HepG2 xenograft growth in SCID mice. Further, SphK1 activity in icaritin-treated tumors was largely inhibited. In summary, icaritin exerts potent anti-HCC activity in vitro and in vivo. SphK1 inhibition could be the primary mechanism of its actions in HCC cells.
A Functional Polymorphism in the Manganese Superoxide Dismutase Gene and Diabetic Nephropathy (2006)

Oxidative stress has been suggested to contribute to the development of diabetic nephropathy. Manganese superoxide dismutase (MnSOD) protects the cells from oxidative damage by scavenging free radicals. The demand for antioxidants is increased by smoking, which could disturb the balance between antioxidants and radicals. The present study aimed to determine whether a valine/alanine polymorphism in MnSOD (V16A, rs4880), alone or in combination with smoking, can contribute to development of diabetic nephropathy in 1,510 Finnish and Swedish patients with type 1 diabetes. Overt diabetic nephropathy (n = 619) was defined as having an albumin excretion rate (AER) >200 microg/min or renal replacement therapy; incipient diabetic nephropathy was defined as having an AER of 20-200 microg/min (n = 336). The control subjects had diabetes duration of >or=20 years, without albuminuria (AER <20 microg/min) and without antihypertensive treatment (n = 555). In addition to male sex and elevated A1C, smoking was significantly associated with diabetic nephropathy (overt plus incipient), odds ratio (OR) 2.00 (95% CI 1.60-2.50). When controlling for age at onset, diabetes duration, A1C, smoking, and sex, the Val/Val genotype was associated with an increase in risk of diabetic nephropathy (1.32 [1.00-1.74], P = 0.049). When evaluating the combined effect of genotype and smoking, we used logistic regression with stratification according to smoking status and genotype. The high-risk group (ever smoking plus Val/Val genotype) had 2.52 times increased risk of diabetic nephropathy (95% CI 1.73-3.69) compared with the low-risk group, but no departure from additivity was found. Our results indicate that smoking and homozygosity for the MnSOD Val allele is associated with an increased risk of diabetic nephropathy, which supports the hypothesis that oxidative stress contributes to the development of diabetic nephropathy.
<title>Can invisible watermarks resolve rightful ownerships?</title> (1997)

Digital watermarks have been proposed in recent literature as the means for copyright protection of multimedia data. In this paper we address the capability of invisible watermarking schemes to resolve copyright ownerships. We will show that rightful ownerships cannot be resolved by current watermarking schemes alone. In addition, in the absence of standardization of watermarking procedures, anyone can claim ownership of any watermarked image. Specifically, we provide counterfeit watermarking schemes that can be performed on a watermarked image to allow multiple claims of rightful ownerships. We also proposed non-invertible watermarking schemes in this paper and discuss in general the usefulness of digital watermarks in identifying the rightful copyright owners. The results, coupled with the recent attacks on some image watermarks, further imply that we have to carefully re-think our approaches to invisible watermarking of images, and re- evaluate the promises, applications and limitations of such digital means of copyright protection.
Human anti-V2 monoclonal antibody that neutralizes primary but not laboratory isolates of human immunodeficiency virus type 1 (1994)

A human immunoglobulin G1 lambda monoclonal antibody (MAb), 697-D, was developed that recognizes the V2 region of human immunodeficiency virus type 1 (HIV-1) gp120. Substitutions at amino acid positions 176/177, 179/180, 183/184, and 192 to 194 in the V2 loop of gp120 each completely abolished the binding capacity of 697-D in an enzyme-linked immunosorbent assay format. Competition analysis with three different neutralizing murine anti-V2 MAbs confirmed the specificity of 697-D. The 697-D epitope is primarily conformation dependent, although there was weak reactivity of the MAb with a V2 peptide spanning residues 161 to 180. Treatment of recombinant gp120 HIVIIIB with sodium metaperiodate, which oxidizes carbohydrates, abolished the binding of the MAb, showing the dependence of the epitope on intact carbohydrates. The broad reactivity of 697-D was displayed by its binding to the gp120 molecules from four of four laboratory isolates and five of five primary isolates. The MAb 697-D neutralized three out of four primary isolates but failed to neutralize any of four laboratory strains of HIV-1. 697-D and a human anti-V3 MAb, 447-52-D, displayed similar potency in neutralizing primary isolates, indicating that the V2 region of gp120, like the V3 region and the CD4-binding domain, can induce potent neutralizing antibodies against HIV-1 in humans.
Yield Evaluation of 10-kA/cm$^{2}$ Nb Multi-Layer Fabrication Process Using Conventional Superconducting RAMs (2007)

To achieve larger scale and higher speed single flux quantum (SFQ) circuits, we have been developing a 10-kA/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> Nb multi-layer fabrication process composed of more than six pla- narized Nb layers, an Nb/AlO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</sub> /Nb junction layer, a Mo resistor layer, and SiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> insulator layers. To evaluate reliability of the fabrication process, we have designed superconducting random access memories (RAMs) with four different memory capacities: 256, IK, 4 K, and 16 K bits. Although the circuit configuration of these RAMs is almost the same as that of previously developed ones that have conventional latching devices, we modified the circuit parameters and layout design based on specifications of the new fabrication process. We have obtained operations for the 256-bit RAM with a bit yield of 100%, the lK-bit RAM with a bit yield of 99.8%, and the 4K-bit RAM with a bit yield of 96.7%. The number of defects in the 4K-bit RAM was estimated to be approximately 10. We confirmed that evaluations using the RAMs were effective at detecting defects due to the fabrication process.
[Measurement of neonatal ventricular size]. (1993)

Ultrasound imaging of the brain was carried out in 59 normal full-term infants in the nursery on the 3rd-7th postpartum days. The mean width of the lateral ventricles, third ventricles, brain hemispheres, and the mean distance from the most lateral extent of the lateral ventricle to the falx were 0.24 +/- 0.08cm, 0.26 +/- 0.07cm, 4.20 +/- 0.17cm, and 1.08 +/- 0.25cm, respectively. The mean area of the lateral ventricular body was 0.11 +/- 0.08cm2. There was no significant difference of ventricular size between vaginal delivery and cesarean section infants. The relation of ventricular size to occipitofrontal circumference was significant (r = 0.44, P < 0.01).
FTIR microscopy of biological cells and tissue: data analysis using resonant Mie scattering (RMieS) EMSC algorithm (2012)

Transmission and transflection infrared microscopy of biological cells and tissue suffer from significant baseline distortions due to scattering effects, predominantly resonant Mie scattering (RMieS). This scattering can also distort peak shapes and apparent peak positions making interpretation difficult and often unreliable. A correction algorithm, the resonant Mie scattering extended multiplicative signal correction (RMieS-EMSC), has been developed that can be used to remove these distortions. The correction algorithm has two key user defined parameters that influence the accuracy of the correction. The first is the number of iterations used to obtain the best outcome. The second is the choice of the initial reference spectrum required for the fitting procedure. The choice of these parameters influences computational time. This is not a major concern when correcting individual spectra or small data sets of a few hundred spectra but becomes much more significant when correcting spectra from infrared images obtained using large focal plane array detectors which may contain tens of thousands of spectra. In this paper we show that, classification of images from tissue can be achieved easily with a few (<10) iterations but a reliable interpretation of the biochemical differences between classes could require more iterations. Regarding the choice of reference spectrum, it is apparent that the more similar it is to the pure absorption spectrum of the sample, the fewer iterations required to obtain an accurate corrected spectrum. Importantly however, we show that using three different non-ideal reference spectra, the same unique correction solution can be obtained.
Post-translational Fate of a Mucin-like Leukocyte Sialoglycoprotein (CD43) Aberrantly Expressed in a Colon Carcinoma Cell Line (1997)

This paper describes the biosynthesis of L-CanAg, a mucin-like glycoprotein which carries the carcinoma-associated carbohydrate epitope sialyl-Lewis a and is secreted by the colon adenocarcinoma cell line COLO 205. Recently, it has been shown that L-CanAg is a novel glycoform of CD43, a surface sialoglycoprotein normally found only on hematopoietic cells. Immunoprecipitation with alpha-GPEP18, a novel antiserum against the cytoplasmic domain of CD43, detected a transmembrane form of L-CanAg carrying sialyl-Lewis a. Cell surface biotinylation experiments demonstrated the presence of transmembrane L-CanAg at the plasma membrane and that COLO 205, unlike the leukocyte cell line HL-60, contained significant amounts of glycosylated intracellular CD43. Immunoprecipitation of phosphate-labeled COLO 205 cells revealed that membrane-bound L-CanAg, like leukocyte CD43, is a phosphoprotein. Interestingly, both surface- and phosphate-labeled L-CanAg were eluted earlier from a gel filtration column than their unlabeled counterparts, indicating that this method could separate membrane-bound L-CanAg from its soluble form. Immunoprecipitations of pulse-chase-labeled COLO 205 lysates fractionated by gel filtration showed that decrease in membrane-bound L-CanAg was concomitant with an increase in the intracellular soluble form. Together, these data indicate that transmembrane L-CanAg is fully glycosylated and phosphorylated before the extracellular domain is cleaved off and stored inside the cell before exocytosis.
A novel role for thyroid hormone, glucocorticoids and retinoic acid in timing oligodendrocyte development (1994)

The timing of oligodendrocyte differentiation is thought to depend on an intrinsic clock in oligodendrocyte precursor cells that counts time or cell divisions and limits precursor cell proliferation. We show here that this clock mechanism can be separated into a counting component and an effector component that stops cell proliferation: whereas the counting mechanism is driven by mitogens that activate cell-surface receptors, the effector mechanism depends on hydrophobic signals that activate intracellular receptors, such as thyroid hormones, glucocorticoids and retinoic acid. When purified oligodendrocyte precursor cells are cultured at clonal density in serum-free medium in the presence of mitogens but in the absence of these hydrophobic signals, the cells divide indefinitely and do not differentiate into postmitotic oligodendrocytes. In the absence of mitogens, the precursor cells stop dividing and differentiate prematurely into oligodendrocytes even in the absence of these hydrophobic signals, indicating that these signals are not required for differentiation. The levels of these signals in vivo may normally regulate the timing of oligodendrocyte differentiation, as the maximum number of precursor cell divisions in culture depends on the concentration of such signals and injections of thyroid hormone into newborn rats accelerates oligodendrocyte development. As thyroid hormone, glucocorticoids and retinoic acid have been shown to promote the differentiation of many types of vertebrate cells, it is possible that they help coordinate the timing of differentiation by signalling clocks in precursor cells throughout a developing animal.
On-Line, Real-Time Measurements of Cellular Biomass using Dielectric Spectroscopy (2000)

Introduction All else being equal, the productivity of a biological process is determined by the quantity of biomass present. There is therefore a major requirement for the accurate measurement and control of the biomass within fermentors, at both laboratory and industrial scales. Presently the range of sensors available that can be used in situ and reliably for the monitoring and regulation of biotechnological processes in general is rather limited. These sensors normally rely upon physical (e.g. optical, mechanical and electrical) or chemical variables (e.g. pH and concentration) rather than biological ones per se (Sarra et al., 1996; Pons, 1991). However only physical methods allow the on-line, real-time estimation of biomass (Harris and Kell, 1985). As well as physical methods, any easily determinable chemical that is produced or consumed by cells at an essentially constant rate during cell growth may also be used to assess biomass, e.g. carbon dioxide evolution and oxygen consumption. In these indirect methods biomass is then calculated based upon mass balances, stoichiometric relationships or empirical constants. However, this type of approach has the great disadvantage that it does not generally discriminate between biomass and necromass (Kell et al., 1990). Even if biomass was easily measurable there is still the question of what is biologically relevant information for fermentation control and how can one define and quantify it (e.g. metabolism, viability, vitality, morphology) (Kell et al., 1987; Kell, 1987a;
Apolipoprotein A-I, Phospholipid Vesicles, and Cyclodextrins as Potential Anti-Atherosclerotic Drugs: Delivery, Pharmacokinetics, and Efficacy (2000)

High-density lipoprotein (HDL) is a reliable predictor for susceptibility to cardiovascular disease. Since apolipoprotein A-I (apoA-I) is the major protein of HDL, it is worthwhile to evaluate the potential of this protein to reduce the lipid burden of lesions observed in the clinic. While a large body of data emanates from in vitro and cell culture studies with apoA-I, few animal and lesser clinical trials examining the potential of this apolipoprotein to induce cholesterol (and other lipid) efflux exist. Lessons may be learned from studies with other lipid acceptors such as phospholipid vesicles (PLVs, liposomes) and cyclodextrins (CDs). Additionally, the combination of apoA-I with other effluxing agents, alteration of the composition of the lipoprotein, or a remodeling of the protein structure of the apolipoprotein to be administered in vivo may result in increased efficacy. The usage of this apolipoprotein in a therapeutic context has to follow the conventional sequence of events: an evaluation of the biodistribution, safety, and dose-response of the protein in animal trials before clinical trials. The review also considers the potential of cyclodextrins and PLVs to induce reverse cholesterol transport in vivo and discusses the potential of CDs as delivery agents for genetic constructs, such as plasmids and oligonucleotides.
GPU-assisted high-resolution, real-time 3-D shape measurement (2006)

This paper describes a Graphics Processing Unit (GPU)-assisted real-time three-dimensional shape measurement system. Our experiments demonstrated that the absolute coordinates calculation and rendering speed of a GPU is more than four times faster than that of a dual CPU workstation with the same graphics card. By implementing the GPU into our system, we realized simultaneous absolute coordinate acquisition, reconstruction and display at 30 frames per second with a resolution of approximately 266K points per frame. Moreover, a 2+1 phase-shifting algorithm was employed to alleviate the measurement error caused by motion. Applications of the system include medical imaging, manufacturing, entertainment, and security.
The glycine receptor deficiency of the mutant mouse spastic: evidence for normal glycine receptor structure and localization (1986)

Homozygotes of the mutant mouse spastic exhibit reduced binding of 3H-strychnine to homogenates from various regions of the CNS compared with unaffected littermates (White and Heller, 1982). Here we report evidence that the spastic mutation coincides with a reduced concentration and an unaltered structure of the glycine receptor in spinal cord. Scatchard analysis of 3H-strychnine binding revealed a single binding site with a Bmax of 267 +/- 62 fmol/mg protein for spastic and of 864 +/- 220 fmol/mg protein for control mice; no difference was found for the corresponding KD values. Also Ki values of glycine for 3H-strychnine binding and displacement of 3H-strychnine by beta-alanine and taurine were indistinguishable for both preparations. Photoaffinity labeling of synaptic membranes with 3H-strychnine identified an Mr = 48,000 polypeptide in both control and spastic mouse membranes. Tryptic digestion of these membranes produced radiolabeled peptide fragments of identical molecular weights, suggesting that the proteolytic cleavage sites around the antagonist binding site are conserved in the mutant glycine receptor protein. Glycine receptors from both control and mutant mice were purified by affinity chromatography on aminostrychnine agarose. SDS/PAGE revealed three polypeptides of Mr = 48,000, 58,000, and 93,000 in both receptor preparations. Monoclonal antibodies directed against different subunits of the glycine receptor were applied to an enzyme-linked immunosorbent assay. The same pattern of immunoreactivity was obtained for glycine receptor from spinal cord of spastic homozygotes, control mice, and rats, suggesting conservation of the antigenic epitopes in the mutant receptor.(ABSTRACT TRUNCATED AT 250 WORDS)
A Gibbs Sampling Method to Detect Overrepresented Motifs in the Upstream Regions of Coexpressed Genes (2002)

Microarray experiments can reveal important information about transcriptional regulation. In our case, we look for potential promoter regulatory elements in the upstream region of coexpressed genes. Here we present two modifications of the original Gibbs sampling algorithm for motif finding (Lawrence et al., 1993). First, we introduce the use of a probability distribution to estimate the number of copies of the motif in a sequence. Second, we describe the technical aspects of the incorporation of a higher-order background model whose application we discussed in Thijs et al. (2001). Our implementation is referred to as the Motif Sampler. We successfully validate our algorithm on several data sets. First, we show results for three sets of upstream sequences containing known motifs: 1) the G-box light-response element in plants, 2) elements involved in methionine response in Saccharomyces cerevisiae, and 3) the FNR O(2)-responsive element in bacteria. We use these data sets to explain the influence of the parameters on the performance of our algorithm. Second, we show results for upstream sequences from four clusters of coexpressed genes identified in a microarray experiment on wounding in Arabidopsis thaliana. Several motifs could be matched to regulatory elements from plant defence pathways in our database of plant cis-acting regulatory elements (PlantCARE). Some other strong motifs do not have corresponding motifs in PlantCARE but are promising candidates for further analysis.