gebhart/patrepeval huggingface dataset:
Enhanced macrophage degradation of low density lipoprotein previously incubated with cultured endothelial cells: recognition by receptors for acetylated low density lipoproteins. (1981)

Human low density lipoprotein (LDL) was incubated with an established line of rabbit aortic endothelial cells. Density gradient fractionation showed a time-, concentration-, and temperature-dependent increase in the average density of the LDL (from about 1.036 to as high as 1.070 g/ml). Incubation without cells or with other types of cultured cells (fibroblasts, hepatocytes, 3T3-L1 cells) caused no significant change in density. 125I-Labeled LDL (125I-LDL) recovered after incubation with endothelial cells (EC-modified LDL) was taken up and degraded 3 to 4 times more rapidly than control LDL by resident mouse peritoneal macrophages and by an established tumor line of mouse macrophages (J774 cells). Macrophage degradation of EC-modified 125I-LDL exhibited saturation kinetics (greater than 85% inhibited by excess unlabeled EC-modified LDL). Degradation was also inhibited by unlabeled acetylated LDL and, conversely, unlabeled EC-modified LDL inhibited degradation of acetylated 125I-LDL. Incubation of LDL with conditioned medium-removed from endothelial cell cultures modified neither its density nor its rate of degradation by macrophages. These studies show that endothelial cells have the potential to metabolically modify the LDL molecule, generating a form that is more rapidly degraded by macrophages and that is recognized by the macrophage receptor for acetylated LDL. This process may play a significant role in the pathogenesis of atherosclerosis.
Natural and Engineered Photoactivated Nucleotidyl Cyclases for Optogenetic Applications (2010)

Cyclic nucleotides, cAMP and cGMP, are ubiquitous second messengers that regulate metabolic and behavioral responses in diverse organisms. We describe purification, engineering, and characterization of photoactivated nucleotidyl cyclases that can be used to manipulate cAMP and cGMP levels in vivo. We identified the blaC gene encoding a putative photoactivated adenylyl cyclase in the Beggiatoa sp. PS genome. BlaC contains a BLUF domain involved in blue-light sensing using FAD and a nucleotidyl cyclase domain. The blaC gene was overexpressed in Escherichia coli, and its product was purified. Irradiation of BlaC in vitro resulted in a small red shift in flavin absorbance, typical of BLUF photoreceptors. BlaC had adenylyl cyclase activity that was negligible in the dark and up-regulated by light by 2 orders of magnitude. To convert BlaC into a guanylyl cyclase, we constructed a model of the nucleotidyl cyclase domain and mutagenized several residues predicted to be involved in substrate binding. One triple mutant, designated BlgC, was found to have photoactivated guanylyl cyclase in vitro. Irradiation with blue light of the E. coli cya mutant expressing BlaC or BlgC resulted in the significant increases in cAMP or cGMP synthesis, respectively. BlaC, but not BlgC, restored cAMP-dependent growth of the mutant in the presence of light. Small protein sizes, negligible activities in the dark, high light-to-dark activation ratios, functionality at broad temperature range and physiological pH, as well as utilization of the naturally occurring flavins as chromophores make BlaC and BlgC attractive for optogenetic applications in various animal and microbial models.
A Small-Molecule Inhibitor of T. gondii Motility Induces the Posttranslational Modification of Myosin Light Chain-1 and Inhibits Myosin Motor Activity (2010)

Toxoplasma gondii is an obligate intracellular parasite that enters cells by a process of active penetration. Host cell penetration and parasite motility are driven by a myosin motor complex consisting of four known proteins: TgMyoA, an unconventional Class XIV myosin; TgMLC1, a myosin light chain; and two membrane-associated proteins, TgGAP45 and TgGAP50. Little is known about how the activity of the myosin motor complex is regulated. Here, we show that treatment of parasites with a recently identified small-molecule inhibitor of invasion and motility results in a rapid and irreversible change in the electrophoretic mobility of TgMLC1. While the precise nature of the TgMLC1 modification has not yet been established, it was mapped to the peptide Val46-Arg59. To determine if the TgMLC1 modification is responsible for the motility defect observed in parasites after compound treatment, the activity of myosin motor complexes from control and compound-treated parasites was compared in an in vitro motility assay. TgMyoA motor complexes containing the modified TgMLC1 showed significantly decreased motor activity compared to control complexes. This change in motor activity likely accounts for the motility defects seen in the parasites after compound treatment and provides the first evidence, in any species, that the mechanical activity of Class XIV myosins can be modulated by posttranslational modifications to their associated light chains.
Self-aligned complementary bipolar technology for low-power dissipation and ultra-high-speed LSIs (1995)

Fully symmetrical complementary bipolar transistors for low power-dissipation and ultra-high-speed LSIs have been integrated in the same chip using a 0.3-/spl mu/m SPOTEC process. Reducing the surface concentration of the boron by oxidation at the surface of the boron diffusion layer suppressed the upward diffusion of boron from the subcollector of the pnp transistor during epitaxial growth. This enabled thin epitaxial layer growth for both npn and pnp transistors simultaneously. Cutoff frequencies of 30 and 32 GHz were obtained in npn and pnp transistors, respectively. Simulated results showed that the power dissipation is reduced to 1/5 in a complementary active pull-down circuit compared with an ECL circuit.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Binding of collagen to Staphylococcus aureus Cowan 1 (1986)

Collagen binds to a receptor protein present on the surfaces of Staphylococcus aureus cells. Binding of 125I-labeled type II collagen to its bacterial receptor is reversible, and Scatchard plot analysis indicates the presence of one class of receptor that occurs on an average of 3 X 10(4) copies per cell and binds type II collagen with a Kd of 10(-7) M. Studies on the specificity of collagen cell binding indicate that the receptor does not recognize noncollagenous proteins but binds all of the different collagen types tested (types I to VI). Furthermore, isolated collagen alpha chains and peptides generated by cyanogen bromide cleavage of type I collagen alpha chains are recognized by the receptor as indicated by the ability of these polypeptides to inhibit binding of 125I-labeled type II collagen to staphylococcal cells. Synthetic collagen analogs were tested as inhibitors of type II collagen binding to bacterial cells. The peptides (Pro-Gly-Pro)n, (Pro-Pro-Gly)10, and (Pro-OH-Pro-Gly)10 were recognized by the receptor, whereas the peptides (Pro-Ala-Gly)n and polyproline showed no inhibitory activity.
Surface ocean circulation in the Norwegian Sea 15,000 B.P. to present (1985)

Quantitative studies of foraminifera and radiolaria, semi‐quantitative analyses of diatoms and coccoliths, and the distribution of ice‐rafted sediments have been performed on cores from the southeastern Norwegian Sea. The results document large variations in sea‐surface temperatures and ocean circulation, showing a strong correlation between oceanic data and palaeoclimatic data from the neighbouring coastal areas of Norway. For the first time the Allerød – Younger Dryas climatic fluctuations and the Holocene climatic optimum are shown in records from the Norwegian Sea. Starting at about 13,000 B.P. the sea surface became seasonally ice‐free with productive seasons. During the Allerød a narrow wedge of temperate Atlantic water flowed into the southeastern Norwegian Sea. In Younger Dryas time the surface waters cooled by several degrees. Holocene surface conditions were relatively constant, with somewhat higher temperatures in a period possibly corresponding with Atlantic time.
Exoglycosidase purity and linkage specificity: assessment using oligosaccharide substrates and high-pH anion-exchange chromatography with pulsed amperometric detection (1996)

Simplified HPLC protocols to determine the activity and linkage specificity and to detect the most commonly-encountered contaminants in available exoglycosidase preparations (Jacob and Scudder, Methods Enzymol., 230, 280-300, 1994) were developed. Monosaccharides and oligosaccharides were analyzed in a single chromatographic step using high-pH anion-exchange chromatography with pulsed amperometric detection. All analyses were performed with underivatized oligosaccharide substrates and by direct injection of unprocessed, diluted enzyme digests into the chromatograph. The sialidase from Newcastle disease virus was found to release both alpha (2-->3)- and alpha (2-->6)-linked Neu5Ac from a triantennary, lactosamine-type oligosaccharide. The activity of alpha-galactosidase from green coffee beans was assayed using Gal alpha(1-->3)[Fuc-alpha(1ar2)]Gal by detection of Gal and Fuc alpha(1-->3)Gal. The linkage specificities of beta-galactosidases from Streptococcus pneumoniae and bovine testis were assessed using Gal beta(1-->3 or 4)GlcNAc beta(1-->3)beta(1-->4)Glc as substrates. Contaminating beta-N-acetylhexosaminidase activity in the beta-galactosidase preparation was assayed using an agalactobiantennary oligosaccharide. The alpha(1-->3 or 4) linkage specificity of fucosidase III from almond meal was confirmed (Scudder et al., J. Biol. Chem. 265, 16472-16477, 1990) by its inactivity against a biantennary oligosaccharide with all Fuc residues linked alpha(1-->6). An alpha-fucosidase from chicken liver was found to cleave alpha(1-->2,3 or 6)-linked Fuc residues from oligosaccharides. The activity of jack bean (Canavalia ensiformis) alpha-mannosidase was assayed with a relatively resistant substrate, Man alpha(1-->3)- Man beta(1-->4)GlcNAc. A GlcNAc beta(1-->4)-terminated triantennary oligosaccharide was used to assay for contaminating beta-N-acetylhexosaminidase activity in alpha-mannosidase preparations and to determine the linkage and branch specificity of beta-N-acetylhexosaminidase at different enzyme concentrations.
Astrocytes and neurons regulate the expression of the neural recognition molecule janusin by cultured oligodendrocytes (1993)

Janusin (formerly designated J1-160/180) is an extracellular matrix glycoprotein highly homologous to tenascin, consisting of two major molecular forms of 160 and 180 kD expressed by oligodendrocytes and in myelin. Janusin expression is upregulated during myelination and in the adult it remains expressed at lower levels. It is also present at the node of Ranvier, where myelin, axon, and astrocytic process are in close contact. To gain an understanding of the regulatory mechanisms which may underlie expression of janusin, the differentiation stage-dependent expression of janusin was studied in cultures enriched in mouse oligodendrocytes and their precursor cells. Expression of janusin by these cells was highest on both A2B5+ and O4+/O1- oligodendroglial precursor cells and a subset of myelin associated glycoprotein-positive (MAG+) oligodendrocytes. Hardly any of the more differentiated O1+ or O10+ oligodendrocytes expressed janusin. Expression of janusin was influenced by co-culture with astrocytes or neurons. Astrocytes or astrocytic-conditioned culture supernatants elevated the expression of janusin by the more differentiated oligodendrocytes (O1+ or MAG+ cells), while its expression by oligodendroglial precursor cells was relatively unchanged. Platelet-derived growth factor, but not basic fibroblast growth factor, also elevated the expression of janusin by O1+ or O10+ oligodendrocytes. In contrast, co-culture with neurons originating from dorsal root ganglia or spinal cord decreased the expression of cell-bound janusin by oligodendrocytes and their precursor cells. These observations indicate that expression of janusin on these cells in culture is susceptible to opposing regulatory influences from astrocytes and neurons. Such influences may modulate the temporal and spatial distribution of janusin in the developing and adult central nervous system.
The Challenge of Viral Reservoirs in HIV-1 Infection (2002)

A viral reservoir is a cell type or anatomical site in association with which a replication-competent form of the virus accumulates and persists with more stable kinetic properties than the main pool of actively replicating virus. This article reviews several cell types and anatomical sites proposed as potential reservoirs for HIV-1. It is now clear that HIV-1 persists in a small reservoir of latently infected resting memory CD4(+) T cells, which shows minimal decay even in patients on highly active antiretroviral therapy (HAART). The persistence of virus in this reservoir is consistent with the biology of these cells and the long-term persistence of immunologic memory. The viral replication that continues in patients on suppressive HAART may also contribute to the stability of this reservoir. There may be other reservoirs, but the latent reservoir in resting CD4(+) T cells appears to be sufficient to guarantee lifetime persistence of HIV-1 in the majority of patients on current HAART regimens, and unless new approaches are developed, eradication will not be possible. The clinical implications of this and other HIV-1 reservoirs are discussed.
Sleep disorders as core symptoms of depression (2008)

Links between sleep and depression are strong. About three quarters of depressed patients have insomnia symptoms, and hypersomnia is present in about 40% of young depressed adults and 10% of older patients, with a preponderance in females. The symptoms cause huge distress, have a major impact on quality of life, and are a strong risk factor for suicide. As well as the subjective experience of sleep symptoms, there are well-documented changes in objective sleep architecture in depression. Mechanisms of sleep regulation and how they might be disturbed in depression are discussed. The sleep symptoms are often unresolved by treatment, and confer a greater risk of relapse and recurrence. Epidemiological studies have pointed out that insomnia in nondepressed subjects is a risk factor for later development of depression. There is therefore a need for more successful management of sleep disturbance in depression, in order to improve quality of life in these patients and reduce an important factor in depressive relapse and recurrence.
Server-based maintenance approach for computer classroom workstations (2000)

The role of membrane fluidity in the process of signal transduction after binding of Interleukin-2 (Il-2) to its specific cell-surface receptor was investigated in lymphocytes from normal donors and patients with Chronic Lymphocytic Leukemia (CLL). Membrane fluidity was assessed by fluorescence polarization analysis of the apolar fluorophor 1,6-diphenyl-1, 3, 5-hexatrien (DPH) incorporated in the lipid core of the cell membrane. Phytohemagglutinin (PHA) stimulation of lymphocytes for 72h disclosed marked membrane fluidization in normal lymphocytes without affecting lipid phase separation lacking in leukemic cells. Binding of Il-2 induced a significant decrease of the thermotropic transition temperature and overall membrane fluidization within 1h. These effects were not observed in CLL lymphocytes. Results are discussed in terms of defective transmembrane signalling in leukemic cells and pathogenetic implications for uncoupling from proliferation and differentiation signals in the development of leukemia.
Annotation Tools and Knowledge Representation for a Text-To-Scene System (2012)

Text-to-scene conversion requires knowledge about how actions and locations are expressed in language and realized in the world. To provide this knowlege, we are creating a lexical resource (VigNet) that extends FrameNet by creating a set of intermediate frames (vignettes) that bridge between the high-level semantics of FrameNet frames and a new set of low-level primitive graphical frames. Vignettes can be thought of as a link between function and form – between what a scene means and what it looks like. In this paper, we describe the set of primitive graphical frames and the functional properties of 3D objects (affordances) we use in this decomposition. We examine the methods and tools we have developed to populate VigNet with a large number of action and location vignettes.
The Biophysics of Passive Convective Cooling During Catheter Ablation with Gold versus Platinum Electrodes and Multielectrode Phased Radiofrequency Energy Delivery (2015)

Passive convective cooling during RF ablation is more efficient with gold compared to platinum electrodes, particularly when ablations are temperature limited. Using temperature feedback power control, deeper lesions can be reliably achieved with gold electrodes.
Coronary Artery Stenosis in High-risk Patients: 64–Section CT and Coronary Angiography—Prospective Study and Analysis of Discordance (2009)

Despite excellent sensitivity and negative likelihood ratios in a per-patient or per-vessel analysis, some coronary artery stenosis remained misdiagnosed with 64-section CT, resulting in limited sensitivity on a per-segment basis owing to anatomic discordance and failure to accurately quantify intermediate stenosis.
Clearance of phenylalanine ammonia-lyase from normal and tumor-bearing mice. (1977)

Yeast phenylalanine ammonia-lyase was administered i.p. to normal and tumor-bearing mice, and its clearance from plasma was studied. Single and multiple weekly injections at dosages of 10,20,50 and 100 units/kg were administered to C57BL female, C57BL X DBA/2F1 male, and A/J female mice. L5178Y murine lymphoblastic leukemia, B16 melanoma, BW10232 adenocarcinoma, and 15091A anaplastic carcinoma were implanted 7 to 11 days prior to enzyme injection in the appropriate host. After a single injection, the average plasma half-lives of phenylalanine ammonia-lyase were 18 to 24 hr in all groups studied. While the other tumors had no effect on the plasma level of phenylalanine ammonia-lyase after a single injection, L5178Y murine lymphoblastic leukemia and 15091A anaplastic carcinoma significantly depressed the maximal level of phenylalanine ammonia-lyase attained in the plasma. After repeated injections of phenylalanine ammonia-lyase, the initial plasma enzyme level was significantly reduced when 20 units/kg were administered, and the clearance of the enzyme from the plasma was greatly accelerated regardless of the amount administered. Furthermore, in tumor-bearing mice, the rate of clearance was significantly more rapid than in the appropriate non-tumor-bearing control.
Role of interleukin-6 in the paraneoplastic inflammatory syndrome associated with renal-cell carcinoma (1997)

We investigated the possible causative role of interleukin 6 (IL-6) in the paraneoplastic inflammatory syndrome and in paraneoplastic cholestasis (Stauffer syndrome) associated with renal-cell carcinoma in a series of 119 patients with metastases. IL-6 levels were found significantly higher in patients with paraneoplastic fever and weight loss. Patients with detectable serum IL-6 (n = 90, 76%) had significantly higher serum CRP, haptoglobin, and serum alkaline-phosphatase and gammaglutamyl-transferase levels. Platelets, polymorphonuclear neutrophil (PMN) and monocyte counts were also significantly higher in patients with detectable serum IL-6; in contrast, hemoglobin levels were significantly lower in patients with serum IL-6 over 80 pg/ml. Three of these patients were included in a phase-II trial of an anti-IL-6 monoclonal antibody given daily during 21 days. Reductions of CRP, haptoglobin and serum alkalin phosphatases were observed in all 3 patients during anti-IL-6 administration, with a subsequent increase up to or above pre-treatment levels after the end of anti-IL-6. Decrease of platelets, PMN and monocyte counts were also observed in the 3 patients during anti-IL-6 administration, with a normalization of cell counts in a patient with increased platelets, PMN and monocyte counts. Hemoglobin concentration, serum albumin concentration and lymphocyte counts remained stable in the 3 patients during and after anti-IL-6 administration. Serum IL-6, as evaluated by IRMA, decreased in the 3 patients during anti-IL-6 administration, but increased above pre-treatment levels after the end of anti-IL-6 administration. These results demonstrate that IL-6 is involved in the physiopathology of paraneoplastic syndromes observed in patients with metastatic renal-cell carcinoma, in particular CRP and haptoglobin increase, paraneoplastic cholestasis, also paraneoplastic thrombocytosis, neutrophilia and monocytosis.
Dielectric-lined cylindrical metallic THz waveguides: mode structure and dispersion (2010)

Thin dielectric layers deposited on the inner surface of hollow cylindrical metallic waveguides for Terahertz (THz) waves reduce transmission losses below 1 dB/m. Impact of the dielectric layer on the waveguide dispersion is experimentally investigated by near-field mapping of guided short THz pulses at the input and the output of the waveguide. We obtain dispersion characteristics for the low-loss waveguide modes, the linearly-polarized HE(11) mode and the TE(01) mode, and compare the experimental results to the metallic waveguide dispersion. The additional dispersion due to the dielectric layer is found to be small for the HE(11) mode and the phase velocity is primarily determined by the waveguide radius.
Parametric integer programming (1988)

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An Even More Physiological Pacing: Changing the Sequence of Ventricular Activation (1983)

Physiological pacing includes preservation of A -V sequential stimulation and adaptation of heart rate to body requirements. However the sequence of ventricular activation (VA) is also important. In four patients with aortic valvular disease, LBBB and HV ~ 70 msec a Medtronic Versatrax DDD pacemaker was implanted at the time of aortic valve surgery. The ventricular electrode was placed in the free wall of the LV. With ditTerents pulse generator A-V intervals (PG-A V), we obtained: A) LBBB morphology when PG-AV was > A-V conducted interval (C-AV); B) “RBBB” morphology when PG-A V < C-A V, and C) intermediate (“fusion”) morphology when PG-A V ⋍ CAV. A mean delay of 70 ± 5 msec between beginning of the spontaneous activation of RV and arrival of stimulation to ventricular electrode in LV favoured these fusion beats. The sequence of mechanical ventricular emptying was non-invasively assessed by radioisotopic (Tc-99 m Pyp labelled red blood cells) study of the “wave of emptying” and of phase histograms, using the Fourier’s analysis. The most “normal” pattern was found in C. LV ejection fraction (radioisotopic cineangiogram) was 0.59 ± 0.035 in C versus 0.51 ± 0.047 in B (p < 0.001) and 0.47 ± 0.045 in A (p < 0.001). We conclude than an appropriate placement of ventricular electrode besides a correct programation of A-V delay in DDD pacemakers allows for a more synergistic ventricular activation in patients with LBBB, improving their ventricular performance.
The SAM domain of polyhomeotic forms a helical polymer. (2002)

The polycomb group (PcG) proteins are important in the maintenance of stable repression patterns during development. Several PcG members contain a protein protein interaction module called a SAM domain (also known as SPM, PNT and HLH). Here we report the high-resolution structure of the SAM domain of polyhomeotic (Ph). Ph-SAM forms a helical polymer structure, providing a likely mechanism for the extension of PcG complexes. The structure of the polymer resembles that formed by the SAM domain of another transcriptional repressor, TEL. The formation of these polymer structures by SAM domains in two divergent repressors suggests a conserved mode of repression involving a higher order chromatin structure.