gebhart/patrepeval huggingface dataset:
Five polymorphic microsatellite VNTRs on the human X chromosome. (1990)

The human genome contains approximately 50,000 copies of an interspersed repeat with the sequence (dT.dG/dA.dC)n, where n = approximately 10-60. We and others have found that several of these repeats have variable lengths in different individuals, with allelic fragments varying in size by multiples of 2 bp. These "microsatellite" variable number of tandem repeats (VNTRs) may be scored by PCR, using unique flanking primers to amplify the repeat-containing regions and resolving the products on DNA sequencing gels. Since few VNTRs have been found on the X chromosome, we screened a flow-sorted X chromosome-specific genomic library for microsatellites. Approximately 25% of the phage clones hybridized to a poly (dT-dG).poly(dA-dC) probe. Of seven X-linked microsatellites present in positive phages, five are polymorphic and three have both eight or more alleles and heterozygosities exceeding 75%. Using PCR to amplify genomic DNAs from hybrid cell panels, we confirmed the X localization of these VNTRs and regionally mapped four of them. The fifth VNTR was regionally mapped by virtue of its tight linkage to DXS87 in Centre du Polymorphisme Humain families. We conclude that whatever factors limit the occurrence of "classical" VNTRs and RFLPs on the X chromosome do not appear to operate in the case of microsatellite VNTRs.
Antipeptide antisera define neutralizing epitopes on the adenovirus hexon (1992)

The adenovirus (Ad) hexon contains both group-and type-specific antigenic determinants. To identify the latter, peptides were synthesized corresponding to residues 281 to 292 from loop 1 and 441 to 455 from loop 2 of the Ad2 hexon. These sequences display type-specific variation and have been shown by X-ray crystallography to be present on the surface of the virion. Antisera raised against the peptides bound both peptide and the native hexon in ELISA, and blocked virus infectivity, as determined by immunofluorescence or neutralization assays. The loop 1 peptide was shown to inhibit binding of the corresponding antiserum to the native hexon in ELISA and to abolish its neutralizing activity. Neither the loop 1- nor loop 2-specific antiserum neutralized the infectivity of Ad4 or Ad40. Neutralization did not appear to result from aggregation of virus particles and thus their inability to attach to the cell, because virions treated with immune serum were internalized to the same extent as those treated with preimmune serum. Examination of the immune response elicited by Ad2 infection revealed that antibodies directed against the L1 and L2 epitopes were also present in human serum. Thus, the variable regions exposed on the surface of the Ad2 hexon represent type-specific neutralizing antigenic determinants.
Postendocytic trafficking of epidermal growth factor-receptor complexes is mediated through saturable and specific endosomal interactions. (1994)

Intracellular trafficking of the epidermal growth factor receptor (EGF-R) is regulated by receptor occupancy. To investigate this, we developed an assay to study endosomal sorting under steady-state conditions. Using a cell line transfected with EGF-R variants, we found that the fraction of internalized EGF.EGF-R complexes sorted to lysosomes was a function of the number of intracellular complexes and required sequences in the cytoplasmic domain of the receptor. As the number of intracellular occupied wild-type receptors increased from 3 x 10(2) to 2 x 10(5)/cell, the fraction of internalized EGF that was degraded dropped from 70 to 20%. Transforming growth factor-alpha, which dissociates from the EGF-R at endosomal pH, was degraded to a uniform extent of approximately 50% at all intracellular ligand concentrations. EGF internalized by receptors lacking a cytoplasmic domain (c'647) was degraded to an extent of only 5-10% independent of the number of intracellular complexes. Mutant receptors truncated either at residues 1022 or 973 displayed sorting patterns intermediate between wild-type and c'647 receptors. Despite large differences in their internalization rates, the fractional sorting patterns of c'1022 and c'973 receptors were indistinguishable. Receptor tyrosine kinase activity appeared to have a small effect on sorting pattern, but only in the context of full-length receptors. Our results indicate that the default pathway of internalized receptors is rapidly recycling and that lysosomal targeting of occupied EGF-R is due to endosomal retention that is both specific and saturable. In addition, internalization and endosomal retention of EGF-R appear to be mediated by distinct structural elements.
Comparison of the suppressive effects of interleukin-10 and interleukin-4 on synovial fluid macrophages and blood monocytes from patients with inflammatory arthritis. (1995)

This study determined the potential capacity of interleukin-10 (IL-10), compared with IL-4, to control the production of tumour necrosis factor-alpha (TNF-alpha), IL-1 beta and IL-1 receptor antagonist (IL-1ra) and the expression of major histocompatibility complex (MHC) class II antigens by monocytes/macrophages isolated from synovial fluid of patients with rheumatoid or other forms of chronic inflammatory arthritis. Mononuclear cells were isolated from synovial fluid and peripheral blood and incubated with or without lipopolysaccharide (LPS), and with or without IL-10 (100 U/ml, 10 ng/ml) or IL-4 (10 ng/ml) for 22 hr. TNF-alpha, IL-1 beta and IL-1ra levels were measured by enzyme-linked immunosorbent assay (ELISA) in the culture supernatants, and MHC class II expression was examined on the monocytes/macrophages by flow cytometry. IL-10, unlike IL-4, decreased TNF-alpha production by LPS-stimulated synovial fluid cells to the same extent as by LPS-stimulated peripheral blood cells from the same patients. IL-10 and IL-4 suppressed equally IL-1 beta production by the same cells. However, only IL-4 significantly increased IL-1ra production by synovial fluid mononuclear cells. Synovial fluid cells expressed increased levels of MHC class II antigen, and these levels were not as efficiently suppressed by IL-10 as they were for peripheral blood cells. Because IL-10 and IL-4 differentially regulate TNF-alpha and IL-1ra production by synovial fluid mononuclear cells, selective use of either IL-10 or IL-4 in the treatment of chronic inflammatory conditions will depend on whether TNF-alpha or IL-1, respectively, is established as primarily responsible for the maintenance of the chronic inflammatory condition.
FRET and FRAP imaging: Approaches to characterise tau and stathmin interactions with microtubules in cells (2013)

Microtubules (MTs) are involved in many crucial processes such as cell morphogenesis, mitosis and motility. These dynamic structures resulting from the complex assembly of tubulin are tightly regulated by stabilising MT-associated proteins (MAPs) such as tau and destabilising proteins, notably stathmin. Because of their key role, these MAPs and their interactions have been extensively studied using biochemical and biophysical approaches, particularly in vitro. Nevertheless, numerous questions remain unanswered and the mechanisms of interaction between MT and these proteins are still unclear in cells. Techniques coupling cell imaging and fluorescence methods, such as Förster resonance energy transfer and fluorescence recovery after photobleaching, are excellent tools to study these interactions in situ. After describing these methods, we will present emblematic data from the literature and unpublished experimental results from our laboratory concerning the interactions between MTs, tau and stathmin in cells.
Formation of a Continuous Solid‐Solution Particle and its Application to Rechargeable Lithium Batteries (2012)

Abstract High‐energy electrode materials are under worldwide development for rechargeable lithium batteries to be used in electric vehicles and other energy storage applications. High capacity and energy density are readily achievable using Ni‐rich Li[Ni 1‐ x M x ]O 2 ( x = 0.1–0.2, M = Ni, Co, Mn, and Al) cathodes. Unfortunately, their structural instability is associated with severe capacity fading on cycling, which hinders practical applications. Here, a method is presented for producing a continuous compositional change between Li[Ni 0.8 Co 0.2 ]O 2 (center) and Li[Ni 0.8 Co 0.01 Mn 0.19 ]O 2 (surface) in a spherical particle, resulting in an average composition of Li[Ni 0.8 Co 0.06 Mn 0.14 ]O 2 . The chemical composition in the particle is gradually altered by decreasing the Co concentration while adding Mn content. The Ni content remains fixed. Coin cells with the solid‐solution cathode deliver a specific capacity over 210 mAh g −1 in the voltage range of 2.7–4.3 V vs. Li/Li + with capacity retention of 85% over 100 cycles at 25 and 55 °C. The main exothermic temperature upon heating appears at around 250 °C with relatively low heat generation (810 J g −1 ). The presence of the tetravalent Mn at the particle surface is mainly responsible for the high capacity upon cycling and excellent thermal properties.
The First Structure of Dipeptidyl-peptidase III Provides Insight into the Catalytic Mechanism and Mode of Substrate Binding (2008)

Dipeptidyl-peptidases III (DPP III) are zinc-dependent enzymes that specifically cleave the first two amino acids from the N terminus of different length peptides. In mammals, DPP III is associated with important physiological functions and is a potential biomarker for certain types of cancer. Here, we present the 1.95-A crystal structure of yeast DPP III representing the prototype for the M49 family of metallopeptidases. It shows a novel fold with two domains forming a wide cleft containing the catalytic metal ion. DPP III exhibits no overall similarity to other metallopeptidases, such as thermolysin and neprilysin, but zinc coordination and catalytically important residues are structurally conserved. Substrate recognition is accomplished by a binding site for the N terminus of the peptide at an appropriate distance from the metal center and by a series of conserved arginine residues anchoring the C termini of different length substrates.
Serum Markers of Liver Fibrosis: Combining the BIPED Classification and the Neo-Epitope Approach in the Development of New Biomarkers (2010)

Background: Fibrosis is a central histological feature of chronic liver diseases and is characterized by the accumulation and reorganization of the extracellular matrix. The gold standard for assessment of fibrosis is histological evaluation of a percutaneous liver biopsy. Albeit a considerable effort have been invested in finding alternative non-invasive approaches, these have not been sufficiently succesfull to replace biopsy assessment. Aim: To identify the extracellular matrix proteins of interest, that as protein degradation fragments produced during extracellular matrix metabolism neo-epitopes, may be targeted for novel biochemical marker development in fibrosis. We used the recently proposed BIPED system ( B urden of disease, I nvestigative, P rognostic, E fficacy and D iagnostic) to characterise present serological markers. Methods: Pubmed was search for keywords; Liver fibrosis, neo-epitopes, biomarkers, clinical trail, extra cellular matrix, protease, degradation, fragment. Results and Conclusion: Implementation of BIPED categorization in the development and validation of fibrosis biomarkers to simplify and standardize the use of existing and future biomarkers seems advantageous. In addition, a systematic use of the neo-epitope approach, i.e. the quantification of peptide epitopes generated from enzymatic cleavage of proteins during extracellular remodeling, may prove productive in the quest to find new markers of liver fibrosis.
Implications of Amphetamine-Induced Stereotyped Behavior as a Model for Tardive Dyskinesias (1972)

Amphetamine-induced stereotyped behavior in animals and tardive dyskinesias in humans are both related to the activity of dopamine at striatal dopamine receptors. Antichlinergic agents potentiate the stereotyped behavior induced by amphetamines. Anticholinergic agents, as well as prolonged chlorpromazie pretreatment, decrease the threshold for ampheramine-induced stereotyped behavior. These observations have several implications for tardive dydkinesias in man. Anticholinergic medications should worsen tardive dyskinesias. Anticholinergics may also decrease the threshold for tardive dyskinesias, thereby increasing the incidence of the disorder. Patients who have a subclinical abnormality of the dopaminergic receptors may manifest this movement disorder only when given anticholinergic medication. It is suggested that patients on long-term neuroleptic therapy not be routinely given anticholinergic agents, since these drugs worsen tardive duskinesias in patients who have this disorder and may increase the incidence of tardive dyskinesias in patients receiving neuroleptics.
Development of an animal model for ovotoxicity using 4‐vinylcyclohexene: a case study (2007)

This article provides an overview of the questions asked and the approaches taken in studying VCH and VCD to support these conclusions.
A matched-resolution wide aspect-ratio HDTV system (1988)

A fully NTSC-compatible two-channel wide-aspect-ratio high-definition television (HDTV) system with equal vertical and horizontal resolutions is described. The wideband Y, I, Q components are spectrally split into low-frequency and high-frequency bands. However, only the low-frequency components are spatially split into center and edge segments. The low-frequency edge signals are NTSC encoded and decoded using the existing hardware for the compatible center signals. The proposed system produces minimal crossluminance and crosschrominance, and provides equal edge and center resolutions.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Role of CSBP/p38/RK stress response kinase in LPS and cytokine signaling mechanisms (1996)

A new member of the mitogen-activated protein kinase family, alternatively termed CSBP, p38, or RK, has been identified independently by several laboratories recently. Activation of this novel protein kinase via dual phosphorylation has been observed in different cell systems upon stimulation by a wide spectrum of stimuli, such as physicochemical stress and treatment with lipopolysaccharide or proinflammatory cytokines such as interleukin-1 and tumor necrosis factor. Furthermore, CSAID cytokine biosynthesis inhibitors have now been determined to be potent and selective inhibitors of CSBP/p38/RK kinase activity. These inhibitors will help to dissect signaling pathways involved in inflammatory responses. In particular, for the first time a definitive signal transduction pathway can be prescribed to the action of lipopolysaccharide in cytokine production in macrophages.
Ultrastructure of Picosecond Laser Intrastromal Photodisruption (1996)

Intrastromal photodisruption with a Nd:YLF picosecond laser induced no thermal necrosis or coagulative change in the region of tissue interaction. Lamellar intrastromal photodisruption demonstrated both tissue loss and lamellar separation when performed with the current treatment parameters, possibly limiting ablation efficiency and predictability.
Hybrid sol-gel materials for integration of optoelectronic components (2001)

We report on the integration of the Bragg filters with 1/spl times/8 multimode interference (MMI) power splitters on silicon substrate, and the demonstration of 1/spl times/8 external cavity distributed Bragg reflector (DBR) lasers. Hybrid organic-inorganic material is developed based on the sol-gel synthesis of an organically modified silicon alkoxide. The sol-gel material is spin coated on grating SiO/sub 2/-Si wafers, and the designed components (splitters and filters) are UV imprinted and developed using solvent assisted photolithography. The Bragg reflectors show filtering up to 98% with a bandwidth of about 0.8 nm consistent with their theoretical prediction. Integrated reflectors and MMI splitters are then used as feedback resonators for DBR lasers. Single-mode lasing with sidemode suppressions of up to 40 dB and a linewidth of about 400 kHz is observed. At 1550- nm wavelength, the loss and power uniformity in the MMI splitters, designed on the basis of lowest loss, are, respectively, 0.13 dB and 0.03 dB poorer than their theoretical calculations.
The up‐regulation of proteasome subunits and lysosomal proteases in hepatocellular carcinomas of the HBx gene knockin transgenic mice (2005)

Chronic infection of hepatitis virus B (HBV) has been proven to be one of the most important risk factors of hepatocellular carcinoma (HCC). HBx has been shown to function in the viral life cycle and the development of HCC. Recently, we have reported that HBx transgenic mice (p21-HBx), generated by gene knockin, develop HCC at the age of 18 months. To further study the function of HBx during the development of HCC in vivo, we performed proteomic analysis of the transgenic and wild-type control mice. The combination of 2-DE and MALDI-TOF MS revealed that proteasome subunits (PSMA6, PSMB4, PSMC2 and PSMD12) were up-regulated in tumor tissues of the p21-HBx transgenic mice. Cathepsin B, ubiquinol-cytochrome C reductase core protein 1 and an ATP-dependent caseinolytic protease, which were involved in the cellular proteolytic process, were also found increased in tumors. The results were confirmed in tumors of transgenic mice and HCCs of human using RT-PCR. All these results suggested that the strengthened ubiquitin-proteasome and lysosomal pathway might contribute to the development of HBx-related HCC.
Surface modification by nonthermal plasma induced by using magnetic-field-assisted gliding arc discharge (2012)

The authors report on the introduction of a magnetic field to gliding arc discharge (GD) in order to enhance surface modification by nonthermal plasma at atmospheric-pressure. The GD is induced between two wire electrodes by using a pulse high-voltage power supply with peak-to-peak voltage of 5 kV. When a magnetic field of 0.25 T is applied, the GD enlarged and a 19-cm-long stretch of plasma is excited. The surface treatment of polyethylene terephthalate and polytetrafluoroethylene films is performed. The adhesion improved by up to ∼30 times due to the enhanced chemical activity in the films.
An activator stimulating the enzymic hydrolysis of sphingoglycolipids. (1976)

An activator stimulating the enzymic hydrolysis of sphingoglycolipids has been purified from human liver. The purity of the activator, as examined by disc gel electrophoresis, showed one major band stained with both amido black and periodate-Schiff reagent. Chemical analyses identify the activator as a glycoprotein. The physical properties of the activator are: heat-stable, nondialyzable; molecular weight, about 21,000; isoelectric point (pI), 4.1. The purified activator stimulates the hydrolysis of GM1 by beta-galactosidase, GM2 by beta-hexosaminidase, as well as ceramide trihexoside by alpha-galactosidase A or B. The hydrolysis by glycosidases depends upon the amount of activator added. An antibody against the activator was developed from rabbits. The specificity of the antibody to the activator has been established. The antibody was used to make the affinity column for isolation of the activator. It was also used to develop a sensitive immunodiffusion method to detect the activator.
Prognostic importance of prostate-specific antigen for monitoring patients with stages B2 to D1 prostate cancer. (1985)

To evaluate the prognostic value of prostate-specific antigen (PA) for detection of tumor growth after definitive therapy, 602 sera from 70 patients with stages B2 to D1 prostate cancer (26 of whom recurred) were analyzed in a blind study. Using Cox's proportional-hazards model, a highly significant association was found between serially measured PA and disease-free survival time (p = 0.0002). A positive predictive value of 100% was found for some markedly elevated PA levels and confirmed recurrence of disease. In fact, this study suggested that once a PA level of 88 ng/ml was reached, there was an average time of less than 2 months before a recurrence was clinically confirmed. Tumor growth in patients who recurred was indicated by a PA elevation before recurrence in 92% (24 of 26) as opposed to 20% (9 of 44) in disease-free patients. Additionally, in these 24 of 26 patients, levels of PA were elevated 12 months (mean lead time) before a confirmed disease recurrence. In patients who were still disease free, serial PA appeared to increase concurrently with putative tumor growth as shown by the initial surgical stage. Generally, the greater the PA level the more advanced was the stage of disease (B2 to D1). These data suggest that PA may be a useful adjuvant marker for monitoring tumor growth in patients with regionally confined prostate cancer.
Azithromycin Blocks Neutrophil Recruitment in Pseudomonas Endobronchial Infection (2004)

Macrolides exert their effects on the host by modulation of immune responses. In this study, we assessed the therapeutic efficacy of azithromycin in a murine model of mucoid Pseudomonas aeruginosa endobronchial infection. The clearance of Pseudomonas from the airway of mice treated with the macrolide azithromycin was not different than untreated mice challenged with Pseudomonas beads. However, the azithromycin-treated mice showed a remarkable reduction in lung cellular infiltrate in response to Pseudomonas beads, as compared with untreated mice. This effect was associated with significant decreases in lung levels of tumor necrosis factor-alpha and keratinocyte-derived chemokine in azithromycin-treated mice compared with untreated mice. Furthermore, there was a significant reduction in the response of both mouse and human neutrophils to chemokine-dependent and -independent chemoattractants when studied in vitro. Inhibition of chemotaxis correlated with azithromycin-mediated inhibition of extracellular signal-regulated kinase-1 and -2 activation. This study indicates that the azithromycin treatment in vivo results in significant reduction in airway-specific inflammation, which occurs in part by inhibition of neutrophil recruitment to the lung through reduction in proinflammatory cytokine expression and inhibition of neutrophil migration via the extracellular signal-regulated kinase-1 and -2 signal transduction pathway.
Pulse Charging of Capacitor Bank by Explosive-Driven Shock Wave Ferroelectric Generator (2006)

Ultracompact explosive-driven shock wave ferroelectric generators (FEGs) were used as autonomous primary power sources for charging capacitor banks of different capacitance. The FEGs utilized longitudinal (when the shock wave propagates along the polarization vector P) shock wave depolarization of Pb(Zr <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">52</sub> Ti <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">48</sub> )O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> (PZT) polycrystalline ferroelectric ceramic. PZT disks having diameters ranging from 25 to 27 mm and three different thicknesses: 0.65, 2.1, and 5.1 mm. It was experimentally shown that during the charging process the FEGs were capable of producing pulsed power with peak amplitudes up to 0.3 MW. Results for charging voltage, electric charge transfer and energy transfer from the FEGs to the capacitor banks of capacitances CL = 2.25, 4.5, 9.0, 18.0, and 36.0 nF are presented. Analysis of the experimental data shows that the maximum energy transfer from the FEG to the capacitor bank differs for each type of ferroelectric energy-carrying element, and is dependent upon the capacitance of the capacitor banks.