gebhart/patrepeval huggingface dataset:
Adhesion-Dependent Cell Mechanosensitivity (2003)

The conversion of physical signals, such as contractile forces or external mechanical perturbations, into chemical signaling events is a fundamental cellular process that occurs at cell-extracellular matrix contacts, known as focal adhesions. At these sites, transmembrane integrin receptors are associated via their cytoplasmic domains with the actin cytoskeleton. This interaction with actin is mediated by a submembrane plaque, consisting of numerous cytoskeletal and signaling molecules. Application of intrinsic or external forces to these structures dramatically affects their assembly and triggers adhesion-mediated signaling. In this review, we discuss the structure-function relationships of focal adhesions and the possible mode of action of the putative mechanosensor associated with them. We also discuss the general phenomenon of mechanosensitivity, and the approaches used to measure local forces at adhesion sites, the cytoskeleton-mediated regulation of local contractility, and the nature of the signaling networks that both affect contractility and are affected by it.
Betulinic acid triggers CD95 (APO-1/Fas)- and p53-independent apoptosis via activation of caspases in neuroectodermal tumors. (1997)

Betulinic acid (BA), a melanoma-specific cytotoxic agent, induced apoptosis in neuroectodermal tumors, such as neuroblastoma, medulloblastoma, and Ewing's sarcoma, representing the most common solid tumors of childhood. BA triggered an apoptosis pathway different from the one previously identified for standard chemotherapeutic drugs. BA-induced apoptosis was independent of CD95-ligand/receptor interaction and accumulation of wild-type p53 protein, but it critically depended on activation of caspases (interleukin 1beta-converting enzyme/Ced-3-like proteases). FLICE/MACH (caspase-8), considered to be an upstream protease in the caspase cascade, and the downstream caspase CPP32/YAMA/Apopain (caspase-3) were activated, resulting in cleavage of the prototype substrate of caspases PARP. The broad-spectrum peptide inhibitor benzyloxycarbonyl-Val-Ala-Asp-fluoromethylketone, which blocked cleavage of FLICE and PARP, also completely abrogated BA-triggered apoptosis. Cleavage of caspases was preceded by disturbance of mitochondrial membrane potential and by generation of reactive oxygen species. Overexpression of Bcl-2 and Bcl-XL conferred resistance to BA at the level of mitochondrial dysfunction, protease activation, and nuclear fragmentation. This suggested that mitochondrial alterations were involved in BA-induced activation of caspases. Furthermore, Bax and Bcl-xs, two death-promoting proteins of the Bcl-2 family, were up-regulated following BA treatment. Most importantly, neuroblastoma cells resistant to CD95- and doxorubicin-mediated apoptosis were sensitive to treatment with BA, suggesting that BA may bypass some forms of drug resistance. Because BA exhibited significant antitumor activity on patients' derived neuroblastoma cells ex vivo, BA may be a promising new agent for the treatment of neuroectodermal tumors in vivo.
Nitric Oxide-Releasing Fumed Silica Particles:  Synthesis, Characterization, and Biomedical Application (2003)

The preparation, characterization, and preliminary biomedical application of various nitric oxide (NO)-releasing fumed silica particles (0.2-0.3 microm) are reported. The tiny NO-releasing particles are synthesized by first tethering alkylamines onto the surface of the silica using amine-containing silylation reagents. These amine groups are then converted to corresponding N-diazeniumdiolate groups via reaction with NO(g) at high pressure in the presence of methoxide bases (e.g., NaOMe). N-Diazeniumdiolate groups were found to form more readily with secondary amino nitrogens than primary amino nitrogens tethered to the silica. Different alkali metal cations of the methoxide bases, however, have little effect on the degree of N-diazeniumdiolate formation. The N-diazeniumdiolate moieties attached on the silica surface undergo a primarily proton-driven dissociation to NO under physiological conditions, with an "apparent" reaction order somewhat greater than 1 owing to local increases in pH at the surface of the particles as free amine groups are generated. The rates of N-diazeniumdiolate dissociation are further related to the parent amine structures and the pH of the soaking buffer. The N-diazeniumdiolate groups also undergo slow thermal dissociation to NO, with zero-order dissociation observed at both -15 and 23 degrees C. It is further shown that the resulting NO-releasing fumed silica particles can be embedded into polymer films to create coatings that are thromboresistant, via the release of NO at fluxes that mimic healthy endothelial cells (EC). For example a polyurethane coating containing 20 wt % of NO-releasing particles prepared with pendant hexane diamine structure (i.e., Sil-2N[6]-N(2)O(2)Na) is shown to exhibit improved surface thromboresistivity (compared to controls) when used to coat the inner walls of extracorporeal circuits (ECC) employed in a rabbit model for extracorporeal blood circulation.
Ion-beam-deposited polycrystalline diamondlike films (1976)

X-ray and electron beam diffraction analyses have been carried out on thin films deposited from a beam of carbon ions. Results show that the films consist of a polycrystalline background of cubic diamond with a particle size of 50–100 Å with single-crystal regions up to 5 μm in diameter.
Free Radical Activity and Loss of Plasma Antioxidants, Vitamin E, and Sulfhydryl Groups in Patients With Burns: The 1993 Moyer Award (1993)

This study examines the relationship of burn injury and plasma levels of conjugated dienes, total sulfhydryl groups, and vitamin E in patients with thermal injuries. Plasma neopterin levels were determined as an index of macrophage activity and serine elastase as an index of polymorphonuclear cell activation. Thirteen patients with burns, six survivors and seven nonsurvivors, were studied for the first 4 days, then every other day until postburn day 14. Twelve healthy volunteers served as the control group. Survivors had 56% +/- 4% total body surface area burned, and nonsurvivors had 63.9% +/- % total body surface area burned. The patients with burns, compared with the control group, showed elevated plasma levels of the lipid peroxidation products conjugated dienes (0.767 +/- 0.045 vs 0.269 +/- 0.013 Abs at 233 nm) and reduced levels of the natural scavengers of free radicals, vitamin E (196.2 +/- 12.6 vs 841.1 +/- 22.7 micrograms/dl) and total sulfhydryl groups (54.0 +/- 0.4 vs 15.8 +/- 1.0 mumol/dl). The total sulfhydryl groups/conjugated dienes ratio fell at a greater rate (9.8% +/- 3.2% vs 3.2% +/- 0.7%/day) in nonsurvivors than in survivors (p < 0.05 by Mann-Whitney). The levels of elastase were slightly elevated in the patients with burns, but there was no difference between survivors and nonsurvivors. Normal neopterin levels are 3 to 10 nm/L; peak levels were 119 +/- 48 nm/L in nonsurvivors and 37.4 +/- 10 nm/L in survivors. Patients with burns demonstrated evidence of increased oxygen free radical activity and activation of polymorphonuclear cell and macrophages. Nonsurvivors demonstrated increased consumption of antioxidants compared with survivors.(ABSTRACT TRUNCATED AT 250 WORDS)
Ligand- and voltage-gated ion channels (1995)

Voltage-Gated K+ Channel Genes, K.G. Chandy and G.A. Gutman Voltage-Gated Sodium Channels, A.L. Goldin Voltage-Gated Calcium Channels, A. Stea, T. Wah Soong, and T.P. Snutch Nicotinic Acetylcholine Receptors, J. Lindstrom 5-HT3 Receptors, J.J. Lambert, J.A. Peters, and A.G. Hope Ionotropic Glutamate Receptors, R. Sprengel and P.H. Seeburg Gaba Receptors, R.F. Tyndale, R.W. Olsen, and A.J. Tobin Inhibitory Glycine Receptors, D. Langosch Cyclic Nucleotide-Gated Channels, K.-W. Yau and T.-Y. Chen
Reduction of mountain pine beetle (Coleoptera: Scolytidae) attacks by verbenone in lodgepole pine stands in British Columbia (1989)

The effect of the aggregation-inhibiting pheromone verbenone on mountain pine beetle attacks in lodgepole pine stands was assessed by affixing verbenone release devices on trees on a 10 × 10 m grid. In one experiment, aggregation to trees baited with an attractive combination of trans-verbenol, exo-brevicomin, and myrcene was reduced in verbenone-treated blocks compared with control blocks (attractive baits only). The mean number of trees with mass attacks (≥31.3 attacks/m 2 ), mean percentage of available trees mass attacked, and mean total number of trees infested were reduced by 74.3, 66.7, and 58.5%, respectively. The ratio of 1987 attacks to 1986 attacks was reduced from 14.0 to 2.6. In a second experiment, using no attractive baits, verbenone caused similar but nonsignificant reductions. The mean number of trees with mass attacks, mean percentage of available trees mass attacked, and mean total number of trees infested were reduced by 75.2, 53.5, and 62.1%, respectively. The 1987 to 1986 attack ratio was reduced from 13.2 in control blocks to 0.2 in the verbenone-treated blocks, and the percentage of trees that were infested but not mass attacked was significantly increased, from 45.7% in the control blocks to 63.2% in the verbenone-treated blocks. We conclude that verbenone shows promise as a management tool for controlling the mountain pine beetle.
A 4-Methoxybenzoate O-Demethylase from Pseudomonas putida. A New Type of Monooxygenase System (1975)

A strain of Pseudomonas putida grown on 4-methoxybenzoate as sole carbon source contains an enzyme system for the O-demethylation of this substrate. The enzyme system is purifiable and can be separated into two components: an NADH-dependent reductase and an iron-containing and acid-labile-sulfur-containing monooxygenase. The reductase, of molecular weight 42000 and containing two chromophores, an FMN and an iron-sulfur complex (EPR at g = 1.95), reduces both one-electron and two-electron acceptors (i.e., ferricyanide, 2,6-dichloroindophenol, cytochrome c, and cytochrome b5) at an optimum pH of 8.0. Increasing ionic strength affects these activities differently. The absolute spectrum of the oxidized displays distinct absorption peaks at 409 and 463 nm and a small shoulder between 538 and 554 nm. Treatment with dithionite or NADH reduces the absorbance throughout the visible range, yielding a spectrum with small maxima at 402 and 538 nm. Spectroscopic characteristics of the reductase indicate a tight coupling between its two chromophores. The iron-containing and acid-labile-sulfur-containing monooxygenase, which has a molecular weight of about 120000, contains an iron-sulfur chromophore with an EPR signal at g = 1.90. This protein is a dimer whose subunits each have a molecular weight of about 50000 and are perhaps identical. The optical absorption properties are somewhat unusual. In contrast to other iron-sulfur proteins, there is no significant peak near 415 nm in the absorption spectrum of the oxidized protein, but rather one at 455 nm. The presence of the substrate 4-methoxybenzoate increases both the NADH-dependent reductase. Hydroxylation can be achieved by the monooxygenase also in absence of the reductase with artifical reductants. This enzyme opens a new group of oxygenases within the classification scheme, i.e., iron-containing and labile-sulfur-containing monooxygenases. From the reported data, a scheme for the interaction of the isolated pigments and their relationship to various acceptors is proposed.
Cloning and characterization of the gene for rabbit C-reactive protein (1986)

C-reactive protein (CRP), an acute-phase plasma protein of hepatic origin in man and rabbit, is a cyclic pentamer composed of five identical nonglycosylated Mr 22 500 subunits. We have isolated both cDNA and genomic clones for rabbit CRP. These clones were used as probes to demonstrate that when CRP synthesis is increased following an acute inflammatory stimulus, there is a corresponding increase in the level of accumulated CRP mRNA. The rabbit CRP gene is 2.6 kilobases in length containing a single intron of 252 base pairs (bp) which interrupts the codon for amino acid 2 in the protein. The mRNA for CRP contains a 5'-nontranslated region of 113 bp and a 3'-nontranslated region of 1550 bp. Sequencing of the protein-coding region of the gene indicates that the primary translation product contains a 20 amino acid N-terminal signal peptide. The deduced amino acid sequence is in general agreement with the published sequence [Wang, C. M., Nguyen, N. Y., Yonaha, K., Robey, F., & Liu, T.-Y. (1982) J. Biol. Chem. 257, 13610-13615] except in the region between amino acids 63 and 73. In this region, the sequence of both cDNA and genomic clones indicates the presence of 28 amino acids not previously reported. This alteration may be the result of genetic heterogeneity or an error in the reported protein sequence.
Unleashing the Power of JumpStart: A New Technique for Disaster Recovery, Cloning, or Snapshotting a Solaris System (2000)

Due to the demand of 24x7 coverage by present day data centers, the need for a proven disaster recovery plan is a must. To assist in providing disaster recovery for systems running Sun Microsystems' Solaris 2.x (SunOS 5.x) operating system, a tool was developed which captures the image of the system to one or more volumes of optical media with the first volume being bootable. The optical media used by this tool is CD (Compact Disc) with hooks put in place for DVD (Digital Video Disc or Digital Versatile Disc).This tool was developed with the following objectives in mind: (1) no magnetic media; (2) bootable media; (3) minimal user interaction; (4) handle multiple volume sets; (5) handle environments that do not use a Network Information Service (NIS or NIS+); and, (6) handle environments that do not use Network File System (NFS). The power of this tool is made possible by utilizing two special features present in the Solaris operating system, namely the installboot utility and the JumpStart mechanism (as implemented on the Solaris 2.x Install CD).The complete process of capturing and restoring a Solaris system's image to bootable optical media involves five phases: (1) pre-imaging preparation; (2) setup of target host; (3) capture image of target host; (4) burn image to media; and, (5) restore image to target host. Each of these phases is controlled by one master Bourne shell script. The overall tool is implemented in 26 Bourne shell scripts controlled by the 5 master scripts. This tool, known as the (Capture And Recovery Tool), was placed on a mobile cart and consisted of the following components: UltraSparc 10, internal CD-ROM drive, internal floppy drive, 256 MB memory, 2 network interface cards (NIC), keyboard, mouse, monitor, external SCSI 18 GB disk drive, external SCSI CD-RW, and external SCSI DLT.This tool provides the following functions: (1) bare-metal recovery; (2) capture a snapshot of a system to optical media; (3) cloning a system; and, (4) rollout multiple clones of a system via optical media. Using the principles discussed in this paper and creating additional Bourne shell scripts, the CART has been modified to provide the following additional outputs: (1) make copies of the Solaris Install CD; (2) make customized Solaris Install CD (essentially a customized JumpStart from CD); and, (3) a specialized bootable CD for disaster recovery that assists third party Backup and Recovery utilities (Legato Networker and Veritas NetBackup).
Cytotoxicity of Carbon Nanomaterials:  Single-Wall Nanotube, Multi-Wall Nanotube, and Fullerene (2005)

A cytotoxicity test protocol for single-wall nanotubes (SWNTs), multi-wall nanotubes (with diameters ranging from 10 to 20 nm, MWNT10), and fullerene (C60) was tested. Profound cytotoxicity of SWNTs was observed in alveolar macrophage (AM) after a 6-h exposure in vitro. The cytotoxicity increases by as high as approximately 35% when the dosage of SWNTs was increased by 11.30 microg/cm2. No significant toxicity was observed for C60 up to a dose of 226.00 microg/cm2. The cytotoxicity apparently follows a sequence order on a mass basis: SWNTs > MWNT10 > quartz > C60. SWNTs significantly impaired phagocytosis of AM at the low dose of 0.38 microg/cm2, whereas MWNT10 and C60 induced injury only at the high dose of 3.06 microg/cm2. The macrophages exposed to SWNTs or MWNT10 of 3.06 microg/cm2 showed characteristic features of necrosis and degeneration. A sign of apoptotic cell death likely existed. Carbon nanomaterials with different geometric structures exhibit quite different cytotoxicity and bioactivity in vitro, although they may not be accurately reflected in the comparative toxicity in vivo.
Laser Based and Air Coupled Ultrasound as Noncontact and Remote Techniques for Testing of Railroad Tracks (2002)

Laser based and air coupled ultrasound test methods are used for testing for internal and surface breaking cracks in railroad tracks. Signals were generated with an infrared pulse laser and detected with a confocal Fabry-Perot interferometer (CFPI) or a micromachined capacitive air coupled transducer. The experiments demonstrate the flexibility and capability of this hybrid technique to detect cracks that are undetectable with current testing techniques. Cracks of different orientations and locations on the rail head, web and base were interrogated, in addition to other common discontinuities in the rail track. The noncontact and remote nature of these techniques renders them suitable for inservice applications.
The Human Arp2/3 Complex Is Composed of Evolutionarily Conserved Subunits and Is Localized to Cellular Regions of Dynamic Actin Filament Assembly (1997)

The Arp2/3 protein complex has been implicated in the control of actin polymerization in cells. The human complex consists of seven subunits which include the actin related proteins Arp2 and Arp3, and five others referred to as p41-Arc, p34-Arc, p21-Arc, p20-Arc, and p16-Arc (p omplex). We have determined the predicted amino acid sequence of all seven subunits. Each has homologues in diverse eukaryotes, implying that the structure and function of the complex has been conserved through evolution. Human Arp2 and Arp3 are very similar to family members from other species. p41-Arc is a new member of the Sop2 family of WD (tryptophan and aspartate) repeat-containing proteins and may be posttranslationally modified, suggesting that it may be involved in regulating the activity and/or localization of the complex. p34-Arc, p21-Arc, p20-Arc, and p16-Arc define novel protein families. We sought to evaluate the function of the Arp2/3 complex in cells by determining its intracellular distribution. Arp3, p34-Arc, and p21-Arc were localized to the lamellipodia of stationary and locomoting fibroblasts, as well to Listeria monocytogenes assembled actin tails. They were not detected in cellular bundles of actin filaments. Taken together with the ability of the Arp2/3 complex to induce actin polymerization, these observations suggest that the complex promotes actin assembly in lamellipodia and may participate in lamellipodial protrusion.
Propagation and interaction of two collinear finite amplitude sound beams (1990)

Propagation and interaction of two collinear finite amplitude sound beams is investigated using Fourier series expansions and numerical methods to solve the nonlinear parabolic equation. The analysis extends to ranges beyond the shock formation distance. Propagation curves and beam patterns for various components of the acoustic field (harmonics and combination frequencies) are shown. Wave profiles at various ranges are also presented. In order to fully appreciate the importance of nonlinear effects on the parametric generation of sound, the results obtained from the fully nonlinear model are compared with those obtained for sources operating at moderate intensity (linear/quasilinear theory) for various source levels, downshift ratios, and absorption lengths. Also discussed is the possibility of matching the solutions of the nonlinear parabolic equation and of the spherical Burgers equation in the far field. The numerical results are compared with some earlier experimental observations by other authors.
An investigation on the property and fast implementation of a ray-driven method for inversion of the attenuated Radon transform with variable focusing fan-beam collimators (2003)

Single photon emission computed tomography (SPECT) is based on the measurement of radiation emitted by a radiotracer injected into the patient. Because of photoelectric absorption and Compton scatter, the gamma photons are attenuated inside the body before arriving at the detector. A quantitative reconstruction must consider the attenuation, which is usually non-uniform. Novikov had derived an explicit inversion formula for the non-uniformly attenuated Radon transform for SPECT reconstruction of parallel-beam collimated projections. In our previous work, we extended his work to variable focusing fan-beam (VFF) collimators. A ray-driven analytical inversion formula for VFF reconstruction with non-uniform attenuation was derived. The drawback of ray-driven based reconstruction is time consuming. In this work, we proposed a fast implementation method. Based on the property of ray-driven strategy, we calculated the reconstruction contribution of every ray for every reconstruction point in advance and saved them into database. When performing the reconstruction, we loaded the saved database, multiplied it by the corresponding rays and added the contributions of all rays together. The final image is then obtained efficiently by computing a divergence equation from the contributions. In addition to the software optimization, we utilized the texture mapping architecture of PC graphics/video card to accelerate the speed of the image reconstruction. We further investigated the property of the associated artifacts in the analytical inversion of the attenuated Radon transform. The artifacts were remarkably reduced when more projections were sampled to mitigate the problem of wide bandwidth of discrete Hilbert transform.
Improving ICE Service Selection in a P2P System using the Gradient Topology (2007)

Internet connectivity establishment (ICE) is becoming increasingly important for P2P systems on the open Internet, as it enables NAT-bound peers to provide accessible services. A problem for P2P systems that provide ICE services is how peers discover good quality ICE servers for NAT traversal, that is, the TURN and STUN servers that provide relaying and hole-punching services, respectively. Skype provides a P2P-based solution to this problem, where super-peers provide ICE services. However, experimental analysis of Skype indicates that peers perform a random walk of super-peers to find one with an acceptable round-trip latency. In this paper, we discuss a self-organizing approach to discovering good quality ICE servers in a P2P system based the walk topology. The walk topology uses information about each peer's ability to provide ICE services (open IP address, available bandwidth and expected session times) to construct a topology where the "better" peers for providing ICE services cluster in the center of the topology; this adaptation of the super-peer search space reduces the problem of finding a good quality ICE server from a random walk to a gradient ascent search.