gebhart/patrepeval huggingface dataset:
Characterization of 14-3-3sigma Dimerization Determinants: Requirement of Homodimerization for Inhibition of Cell Proliferation (2006)

The seven highly conserved 14-3-3 proteins expressed in mammalian cells form a complex pattern of homo- and hetero-dimers, which is poorly characterized. Among the 14-3-3 proteins 14-3-3sigma is unique as it has tumor suppressive properties. Expression of 14-3-3sigma is induced by DNA damage in a p53-dependent manner and mediates a cell cycle arrest. Here we show that the 14-3-3sigma protein exclusively forms homodimers when it is ectopically expressed at high levels, whereas ectopic 14-3-3zeta formed heterodimers with the five other 14-3-3 isoforms. The x-ray structure of 14-3-3sigma revealed five residues (Ser5, Glu20, Phe25, Q55, Glu80) as candidate determinants of dimerization specificity. Here we converted these amino-acids to residues present in 14-3-3zeta at the analogous positions. Thereby, Ser5, Glu20 and Glu80 were identified as key residues responsible for the selective homodimerization of 14-3-3sigma. Conversion of all five candidate residues was sufficient to switch the dimerization pattern of 14-3-3sigma to a pattern which is very similar to that of 14-3-3zeta. In contrast to wildtype 14-3-3sigma this 14-3-3sigma variant and 14-3-3zeta were unable to mediate inhibition of cell proliferation. Therefore, homodimerization by 14-3-3sigma is required for its unique functions among the seven mammalian 14-3-3 proteins. As inactivation of 14-3-3sigma sensitizes to DNA-damaging drugs, substances designed to interfere with 14-3-3sigma homodimerization may be used to inactivate 14-3-3sigma function for cancer therapeutic purposes.
Computer Image Generation for Flight Simulation (1981)

Visual simulation seems to imply image realism-though visual simulation systems can produce realistic images, their main goal Is training effectiveness.
A photonic wavelength-division switching system using tunable laser diode filters (1990)

A photonic wavelength-division switching system using semiconductor tunable wavelength filters is proposed. A switching system using wavelength switches and multistage switching networks is discussed. A crucial point in developing this switching system is to achieve a large number of wavelength-division channels. The potential of 100 wavelength-division channels in such switching systems is estimated, based on InP optical integrated circuits. A wavelength network synchronization which permits the network to utilize such a large number of wavelength-division channels without wavelength misalignment and drift is proposed. An eight-channel wavelength-division switching experiment, using phase-shift-controlled distributed feedback laser diodes as tunable wavelength filters, is reported.
Amphotropic Retrovirus Vector System for Human Cell Gene Transfer (1984)

Retroviral vectors have been constructed for gene transfer in mammalian and avian cells, however most retroviral vector systems are complicated by the spread of a replication-competent helper virus. This problem has been circumvented by segregating the viral genome into cis- and trans-acting components. By establishing helper cell lines that produce the trans-acting viral gene products, one can propagate the cis-acting component in them and harvest defective viral particles that contain only the cis-acting component. The cis-acting component can provide a useful vehicle for the highly efficient transfer of genes into target cells. The defective vector systems described to date, however, are restricted in host range to murine, avian, rat, and dog cells. We describe a helper-free vector system based entirely on an amphotropic murine virus with a wide mammalian host range, including the ability to carry out efficient gene transfer into human cells. We also describe a double mutation constructed in the trans-acting genome which reduces the frequency of replication-competent recombinant viruses to undetectable levels.
Antianginal effects of hydroxyfasudil, a Rho‐kinase inhibitor, in a canine model of effort angina (2001)

1. The effects of Rho-kinase inhibitor, fasudil, and of a more specific Rho-kinase inhibitor, hydroxyfasudil, on pacing-induced myocardial ischaemia were determined in anaesthetized open-chest dogs. 2. The dogs were subjected to left anterior descending coronary artery (LAD) stenosis producing a sufficient ischaemia as measured by ST-segment depression on electrocardiograms only when the hearts were paced 60 beats min(-1) above the baseline. After a recovery (nonpacing) period, drugs or saline were infused intravenously over 30 min. The animals were again subjected to 5 min of pacing 25 min after the initiation of the treatment. 3. Hydroxyfasudil (0.1 and 0.3 mg kg(-1)) and fasudil (0.3 mg kg(-1)) suppressed the ST-segment depression. Hydroxyfasudil and fasudil also increased the regional blood flow of the LAD perfused endomyocardium region in the canine model of effort angina. 4. To determine the flow profile for hydroxyfasudil in dogs, blood flow in three vascular beds was measured. Hydroxyfasudil (0.3 mg kg(-1) for 30 min) significantly increased coronary blood flow and vertebral blood flow, without significantly changing the femoral blood flow. 5. Hydroxyfasudil had no inotropic or chronotropic effect on the isolated hearts of guinea-pigs. Hydroxyfasudil (2 mg kg(-1) for 20 min) did not affect the PR or QTc interval in anaesthetized dogs. 6. Inhibition of Rho-kinase appears to protect myocardium subjected to pacing-induced ischaemia through the increase in the regional myocardial blood flow. Hydroxyfasudil may be categorized as a novel type of anti-anginal drug, without any inotropic or chronotropic effects.
The effect of botulinum toxin type A injection for intrinsic rhinitis (1998)

Botulinum toxin type A (BTA) is known to inhibit the release of acetylcholine from cholinergic nerve endings. Owing to the characteristics of BTA, we thought that it could be used for the treatment of intrinsic rhinitis acting as an anticholinergic drug. In a double-blind placebo-controlled study four units of BTA were injected into the middle turbinate (two units) and inferior turbinate (two units) in each nasal cavity. Rhinorrhoea, nasal obstruction, and sneezing were recorded in a symptom diary on the basis of a scale of 5 and the number of paper tissues used per day was also recorded for 24 weeks. Rhinorrhoea was significantly diminished in severity (24.1-41.5 per cent reduction) and paper tissue use (54.3 per cent reduction) in the BTA group compared with the placebo group. This effect could be maintained for four weeks. Sneezing and nasal stuffiness were not affected by BTA. These results suggest that BTA can be used to treat rhinorrhoea in intrinsic rhinitis patients, however, the effective period is short.
The molecular biology of leaf senescence (1997)

Senescence is a complex, highly regulated, developmental phase in the life of a leaf that results in the co-ordinated degradation of macromolecules and the subsequent mobilization of components to other parts of the plant. The application of molecular biology techniques to the study of leaf senescence has, in the last few years, enabled the isolation and characterization of a large range of cDNA clones representing genes that show increased expression in senescing leaves. The analysis of these genes and identification of the function of the encoded proteins will allow a picture of the complex processes that take place during senescence to be assembled. To date, genes encoding degradative enzymes such as proteases and nucleases, enzymes involved in lipid and carbohydrate metabolism and enzymes involved in nitrogen mobilization have all been identified as senescence-enhanced genes. A variety of other genes of no obvious senescence-related function have also been identified; their role in senescence may be less predictable and, possibly, more interesting. The combined action of several internal and external signals may be involved in the induction of senescence. Analysis of the regulatory mechanisms controlling the expression of senescence-induced genes will allow the signalling pathways that are involved in the regulation of senescence to be elucidated. Experiments with transgenic plants and mutants are already shedding light on the role played by cytokinins and ethylene in regulating senescence in leaves.
Electron microscopy and biochemical properties of polyamine-compacted DNA (1987)

We have obtained polyamine-compacted DNA and analyzed it by electron microscopy employing the method described by Dubochet, suitable for the study of complexes in which the main interactions are of ionic character. In addition, we have developed a simple biochemical method, based on the action of pancreatic DNase I, to demonstrate the condensation of DNA with spermidine. DNA-spermidine complexes are resistant to the action of DNase I, and there is a strong correlation between the presence of condensed DNA forms, both as toroids and as cylinders, and the insensitivity to DNase I activity. We have also shown that pBR322 DNA-spermidine complexes are transcriptionally active in the presence of Escherichia coli RNA polymerase. This supports the data concerning the biological activity of spermidine-condensed DNA.
A microstructure semiconductor thermocouple for microwave power sensors (2002)

By using standard silicon planar process, combined with an anisotropically etch technology, a microstructure Si-Ta/sub 2/N thermocouple for microwave power sensors has been fabricated. The sensor has a sensitivity as high as 200 /spl mu/V/mW over a frequency range of 10 MHz to 18 GHz at a power level from 1 /spl mu/W to 100 mW.
Bone morphogenetic protein-4 inhibits proliferation and induces apoptosis of multiple myeloma cells (2001)

Bone morphogenetic proteins (BMPs) can be isolated from organic bone matrix and are able to initiate de novo cartilage and bone formation. Here it is shown that BMP-4 inhibited DNA synthesis in a dose-dependent manner in 3 IL-6-dependent multiple myeloma (MM) cell lines (OH-2, IH-1, and ANBL-6). In contrast, no effect on DNA synthesis was observed in 3 IL-6-independent MM cell lines (JJN-3, U266, and RPMI 8226). BMP-4 induced cell cycle growth arrest in the G(0)/G(1) phase in OH-2 and ANBL-6 cells but not in IH-1 cells. BMP-4 induced apoptosis in OH-2 and IH-1 cells, but not significantly in ANBL-6 cells. Furthermore, BMP-4 induced apoptosis in freshly isolated MM cells from 4 of 13 patients. In the OH-2 and ANBL-6 cell lines and in a patient sample, immunoblotting showed that BMP-4 down-regulated IL-6-induced tyrosine phosphorylation of Stat3, suggesting a mechanism for the apparent antagonism between IL-6 and BMP-4. BMP-4 or analogues may be attractive therapeutic agents in MM because of possible beneficial effects on both tumor burden and bone disease.
Effect of various concentrations of antibiotics on osteogenic cell viability and activity (2011)

Infection is a common complication of open fractures. Systemic antibiotics often cause adverse events before eradication of infected bone occurs. The local delivery of antibiotics and the use of implants that deliver both growth factors and antimicrobials are ways to circumvent systemic toxicity while decreasing infection and to reach extremely high levels required to treat bacterial biofilms. When choosing an antibiotic for a local delivery system, one should consider the effect that the antibiotic has on cell viability and osteogenic activity. To address this concern, osteoblasts were treated with 21 different antibiotics over 8 concentrations from 0 to 5000 µg/ml. Osteoblast deoxyribonucleic acid content and alkaline phosphatase activity (ALP) were measured to determine cell number and osteogenic activity, respectively. Antibiotics that caused the greatest decrement include rifampin, minocycline, doxycycline, nafcillin, penicillin, ciprofloxacin, colistin methanesulfonate, and gentamicin; their cell number and ALP were significantly less than control at drug concentrations ≤ 200 µg/ml. Conversely, amikacin, tobramycin, and vancomycin were the least cytotoxic and did not appreciably affect cell number and ALP until very high concentrations were used. This comprehensive evaluation of numerous antibiotics' effects on osteoblast viability and activity will enable clinicians and researchers to choose the optimal antibiotic for treatment of infection and maintenance of healthy host bone.
Facile Synthesis of Silver(I)−Carbene Complexes. Useful Carbene Transfer Agents (1998)

[Ag(Et2-Bimy)2][AgBr2] (1; Et2-Bimy = diethylbenzimidazol-2-ylidene) was obtained readily from the reaction of [Et2-BimyH]Br with Ag2O. Compound 2, [Ag(Et2-Bimy)2]PF6, was prepared by the reaction of [Et2-Bimy]PF6 with Ag2O under basic phase transfer catalysis conditions. Both compounds 1 and 2 are good carbene transfer agents. Thus, Pd(Et2-Bimy)2Cl2, Au(Et2-Bimy)Br, and [Au(Et2-Bimy)2]PF6 were obtained in high yields using 1 and 2 as carbene sources. The byproduct AgBr or AgCl can be reused to generate 1 under basic phase transfer catalysis conditions. The crystal structure of compound 1 revealed that linear [Ag(Et2-Bimy)2]+ and [AgBr2]- groups were associated through a short AgI−AgI contact (2.956 Å). FAB/mass spectrometry and molar conductivity measurements indicate the existence of ligand-unsupported AgI−AgI interactions in the gas phase and acetonitrile solution. 13C NMR studies suggest that the two Bimy ligands in 1 are fluxional in solution.
A new process of cancer prevention mediated through inhibition of tumor necrosis factor alpha expression. (1996)

Mechanisms of cancer prevention were studied using structurally different cancer-preventive agents, sarcophytol A, canventol, (-)-epigallo-catechin gallate, and tamoxifen, based on our evidence that tumor necrosis factor alpha (TNF-alpha) acts as an endogenous tumor promoter relevant to human carcinogenesis. Pretreatment with the four preventive agents commonly inhibited TNF-alpha mRNA expression and TNF-alpha release in BALB/3T3 cells induced by a tumor promoter, okadaic acid, whereas the expression of early response genes (c-jun, junB, c-fos, and fosB) was enhanced. These results strongly suggest that inhibition of TNF-alpha mRNA expression and its release is a new process of cancer prevention.
Exploring the outcome of genetic modifications of glycosylation in cultured cell lines by concurrent isolation of the major classes of vertebrate glycans (2000)

In the preceding article (Manzi,A.E., Norgard-Sumnicht,K., Argade,S., Marth,J.D., van Halbeek,H. and Varki.A. [2000] GLYCOBIOLOGY:, 10, 669-688), we reported a comprehensive approach for the extraction, fractionation, and isolation of all of the major classes of sugar chains (glycans) from vertebrate tissues. Here we apply this "Glycan Isolation Protocol" to a variety of cultured mammalian cell lines, including two wild-type Chinese hamster ovary (CHO) cell lines and some of their genetically modified variants that were predicted or known to have defined abnormalities in the biosynthesis of one or more classes of glycans. We also use this approach to characterize clone 489, a new derivative of the GAG-deficient CHO clone pgsA-745, in which sulfation has been restored by transfection of a wild-type CHO cDNA library. By metabolically labeling the cell lines with [6-(3)H]glucosamine we were able to monitor the recovery of all major classes of glycans. The results allow us to reach several conclusions: first, the protocol described in the preceding paper is further validated by finding good recovery of total radioactivity and appropriate distribution of label in the correct glycan classes in the fractions from a variety of cell lines; second, the amount of radioactivity recovered in free glycosylphosphatidylinositol (GPI) lipids is remarkably high when compared to that found in GPI anchors, with the former being the dominant form in some cells; third, cells with known genetic mutations in specific glycosylation pathways are shown to have the expected changes in the distribution of recovered radioactivity in the appropriate fractions; fourth, the N- and O- glycans recovered via the protocol are of adequate quality to demonstrate marked differences in their structural profiles and/or content; fifth, the protocol can pick up unexpected differences of glycan classes not predicted to be affected by the primary defect; finally, the reappearance of sulfation in the novel clone 489 is not due to restoration of GAG sulfation, but rather due to the new expression of sulfation in the fraction enriched in N- and O-linked glycopeptides. These results demonstrate the power of this comprehensive approach for the concurrent exploration and profiling of the different major classes of glycans in cells.
Simple vector microprocessors for multimedia applications (1998)

In anticipation of the emergence of multimedia applications as an important workload, microprocessor companies have augmented their instruction-set architectures with short vector extensions, thus adding basic vector hardware to state-of-the-art superscalar processors. Although a vector architecture may be a good match for multimedia applications, there is growing evidence that the control logic for increasingly complex superscalar processors is difficult to implement, Rather than combining a complex superscalar core with short wide vector hardware, we propose using a much simpler processor design that is similar to traditional vector computers with long vectors and simple control logic for instruction issue. Such a design would use the bulk of its transistors and die area for datapath and registers, and thus lessen the time required to design, implement, and verify control. In this paper we present data that quantifies this trading of control transistors for datapath and register transistors. We demonstrate that a 2-way, in-order vector processor with a vector length of 64 and a vector width of 8 requires no more die area, and possibly significantly less area, than a 4-way, out-of-order superscalar processor with short vector extensions. Furthermore, we show that the simple long vector processor is, on average, 2.7 times faster executing multimedia applications than the superscalar processor; and 1.6 times faster than one with short vector extensions. To explain the reasons for the higher performance, we analyze execution time in terms of dynamic operation count and cycles per operation (CPO). A vector processor executes fewer operations by using vector instructions to stripmine a loop. Moreover, a long vector processor achieves a lower CPO by effectively using parallelism at both the operation and the instruction levels. Thus by reducing both terms of the CPO equation, the simple long vector processor achieves greater performance.
B Cell-Activating Factor Belonging to the TNF Family Acts through Separate Receptors to Support B Cell Survival and T Cell-Independent Antibody Formation (2004)

The TNF-related ligand, B cell-activating factor belonging to the TNF family (BAFF), is necessary for normal B cell development and survival, and specifically binds the receptors transmembrane activator and calcium-modulator and cyclophilin ligand interactor (TACI), B cell maturation Ag (BCMA), and BAFF-R. Similarities between mice completely lacking BAFF and A/WySnJ strain mice that express a naturally occurring mutant form of BAFF-R suggest that BAFF acts primarily through BAFF-R. However, the nearly full-length BAFF-R protein expressed by A/WySnJ mice makes unambiguous interpretation of receptor function in these animals impossible. Using homologous recombination we created mice completely lacking BAFF-R and compared them directly to A/WySnJ mice and to mice lacking BAFF. BAFF-R-null mice exhibit loss of mature B cells similar to that observed in BAFF(-/-) and A/WySnJ mice. Also, mice lacking both TACI and BCMA simultaneously exhibit no B cell loss, thus confirming that BAFF-R is the primary receptor for transmitting the BAFF-dependent B cell survival signal. However, while BAFF-R-null mice cannot carry out T cell-dependent Ab formation, they differ from BAFF-deficient mice in generating normal levels of Ab to at least some T cell-independent Ags. These studies clearly demonstrate that BAFF regulates Ab responses in vivo through receptors in addition to BAFF-R.
Importance of size and sulfation of heparin in release of basic fibroblast growth factor from the vascular endothelium and extracellular matrix (1992)

We have characterized the importance of size, sulfation, and anticoagulant activity of heparin in release of basic fibroblast growth factor (bFGF) from the subendothelial extracellular matrix (ECM) and the luminal surface of the vascular endothelium. For this purpose, 125I-bFGF was first incubated with ECM and confluent endothelial cell cultures, or administered as a bolus into the blood of rats, the immobilized 125I-bFGF was then subjected to release by various chemically modified species of heparin and size-homogeneous oligosaccharides derived from depolymerized heparin. Both totally desulfated and N-desulfated heparin failed to release the ECM-bound bFGF. Likewise, substitution of N-sulfate groups of heparin and low molecular weight heparin (fragmin) by acetyl or hexanoyl residues resulted in an almost complete inhibition of bFGF release by these polysaccharides. The presence of O-sulfate groups in heparin increased but was not critical for release of ECM-bound bFGF. Similar structural requirements were identified for release of 125I-bFGF bound to low-affinity sites on the surface of vascular endothelial cells. Oligosaccharides derived from depolymerized heparin and containing as little as 8-10 sugar units were, on a weight basis, equivalent to whole heparin in their ability to release bFGF from ECM. Low-sulfate oligosaccharides were less effective releasers of bFGF as compared to medium- and high-sulfate fractions of the same size oligosaccharides. Heparin fractions with high and low affinity to antithrombin III exhibited a similar high bFGF-releasing activity despite a 200-fold difference in their anticoagulant activities.(ABSTRACT TRUNCATED AT 250 WORDS)
Type II collagen peptides for measuring cartilage degradation. (2004)

This paper describes two new immunoassays for a peptide of the triple helix of type II collagen (Coll 2-1) and its nitrated form (Coll 2-1 NO(2)). In healthy subjects aged between 20 and 65 years old, Coll 2-1 and Coll 2-1 NO(2) levels in serum were in means 125.13+/-3.71 and 0.16+/-0.08 nmol/l, respectively. These levels did not significantly vary with age. However, up to 45 years of age, Coll 2-1 NO(2) levels in women were significantly higher than in men. In patients with knee osteoarthritis (OA), Coll 2-1 in serum was found to be elevated compared to healthy controls (267.45+/-26.42 nmol/l vs 126.78+/-6.61 nmol/l). Further, we have demonstrated that an increase of the urinary levels of Coll 2-1 or Coll 2-1 NO(2) over 1 year was predictive of joint space narrowing progression in OA patients. In conclusion, these preliminary results indicate that Coll 2-1 could be a predictive marker of knee OA progression.
The β-Adrenergic Receptors (2006)

β-Adrenergic receptors (β-ARs) are members of the superfamily of G protein-coupled receptors that are stimulated by the catecholamines epinephrine and norepinephine (1). As part of the sympathetic nervous system, β-ARs have important roles in cardiovascular, respiratory, metabolic, central nervous system, and reproductive functions. Mice lacking one or more of the three β-AR subtype genes (β1, β2, and β3) have been generated to elucidate the physiological role of individual subtypes. Moreover, cells and tissues extracted from these mice have been utilized as tools to understand the molecular and cellular basis of subtype-specific receptor function. These studies are summarized in this chapter.