gebhart/patrepeval huggingface dataset:
Immunohistochemical detection and immunochemical analysis of type II collagen degradation in human normal, rheumatoid, and osteoarthritic articular cartilages and in explants of bovine articular cartilage cultured with interleukin 1. (1989)

Articular cartilage destruction and loss of function in arthritic diseases involves proteolytic degradation of the connective tissue matrix. We have investigated the degradation of cartilage collagen by developing immunochemical methods that permit the identification and analysis of type II collagen degradation in situ. Previously, a technique to specifically identify type II collagen degradation in situ in articular cartilage did not exist. These methods utilize a polyclonal antiserum (R181) that specifically reacts with unwound alpha-chains and CNBr-derived peptides, alpha 1(II)CB11 and alpha 1(II)CB8, of human and bovine type II collagens. The experimental approach is based on the fact that when fibrillar collagens are cleaved the helical collagen molecule unwinds, exposing hidden epitopes. Here we demonstrate the use of R181 in studying type II collagen degradation in bovine articular cartilage that has been cultured with or without IL-1 and in human normal, rheumatoid, and osteoarthritic articular cartilages. Compared to cartilages either freshly isolated or cultured without IL-1, bovine cartilage cultured with IL-1 for 3-5 d showed an increase in both pericellular and intercellular immunohistochemical staining. Extracts of these cartilages contained type II collagen alpha chains that were increased in amount after culture with IL-1 for 11 d. In addition, culture with IL-1 resulted in the appearance of alpha chain fragments of lower molecular weight. All human arthritic tissues examined showed areas of pronounced pericellular and territorial staining for collagen degradation as compared with non-diseased tissues, indicating that chondrocytes are responsible in part for this degradation as compared with non-diseased tissues. In most cases rheumatoid cartilage was stained most intensely at the articular surface and in the deep and mid-zones, whereas osteoarthritic cartilage usually stained more in the superficial and mid-zones, but less intensely. Distinct patterns of sites of collagen degradation reflect differences in collagen destruction in these diseases, suggesting possible different sources of chondrocyte activation. These experiments demonstrate the application of immunological methods to detect collagen degradation and demonstrate an increase of collagen degradation in human arthritides and in IL-1-treated viable bovine cartilage.
Molecular cloning of complex chromosomal translocation t(8;14;12)(q24.1;q32.3;q24.1) in a Burkitt lymphoma cell line defines a new gene (BCL7A) with homology to caldesmon (1996)

Chromosome 12q24.1 is a recurrent breakpoint in high-grade B-cell non-Hodgkin lymphoma (B-NHL). To identify the genes involved at 12q24.1, molecular cloning of a three-way translocation t(8;14;12)(q24.1;q32.3;q24.1) in a Burkitt lymphoma cell line (Wien 133) was performed; all four translocation breakpoints were cloned and sequenced. Analysis of clones encompassing the der(12)(12;14)(q24.1;q32.3) breakpoint showed a CpG island from chromosome 12q24.1 juxtaposed in a tail-to-tail configuration with a productively rearranged Ig VH4-DH-JH5 gene. A total of 4.5 kb of genomic DNA including the CpG island was sequenced and analyzed using gene-identification programs; all three programs identified a potential 92-bp exon within the centromeric boundary of the CpG island. Using this as a probe, an RNA transcript of 3.8 kb, expressed at low levels in a wide variety of normal tissues, was detected. Overlapping cDNA clones were isolated and sequenced. The longest open-reading frame predicted a serine-rich protein of 231 amino acids. This protein, termed BCL7A, exhibited no recognizable protein motifs but showed homology with the actin-binding protein, caldesmon. In Wien 133, the BCL7A breakpoint occurred within the first intron and resulted in a MYC-BCL7A fusion transcript, with exon I of BCL7A being replaced by MYC exon I. The normal, untranslocated allele of BCL7A was also expressed without mutation. One of the 11 other B-NHL cell lines examined with 12q24.1 cytogenetic abnormalities, a mediastinal B-NHL cell line (Karpas 1106), showed biallelic rearrangement within the first intron of BCL7A, which was adjacent to the breakpoint observed in Wien 133. Disruption of the amino-terminus of BCL7A defines a new mechanism in the pathogenesis of a subset of high-grade B-NHL.
Quantifying the Smooth Muscle Content of the Prostate Using Double-Immunoenzymatic Staining and Color Assisted Image Analysis (1992)

The primary objective of the present study was to develop a method for quantifying the smooth muscle content of the prostate adenoma. A double immunoenzymatic staining technique was coupled with color assisted image analysis to determine the area density of the smooth muscle within the prostate adenoma. Eight males with symptomatic BPH underwent transrectal biopsy of the prostate. Four micron thick tissue sections were used for the double immunoenzymatic staining process. Rabbit anti-desmin and mouse anti-human prostatic acid phosphatase antibodies were used to selectively bind smooth muscle and prostatic epithelium, respectively. The two different tissue antigens were identified with peroxidase-antiperoxidase (PAP) and alkaline phosphatase-antialkaline phosphatase techniques. The alkaline phosphatase activity and peroxidase activity were developed with fast red and DAB chromogens. The BQ MEG IV Vista color system image analysis was used to discriminate color differences from the stained tissue sections. The thresholds were set to identify smooth muscle (dark brown), epithelium (red), fibrous tissue (pale brown), and glandular lumina (colorless). The mean area density of smooth muscle, fibrous tissue, glandular epithelium, and glandular lumina was 22%, 54%, 16%, and 9%, respectively. The present study suggests that a significant component of the prostate adenoma is smooth muscle. The application of this technique will be utilized to provide further insights into the role of smooth muscle in the pathogenesis and therapy of BPH.
Robot Learning Control Based on Neural Network Prediction (2012)

Learning feedforward control based on the available dynamic/kinematic system model and sensor information is generally effective for reducing the repeatable errors of a learned trajectory. For new trajectories, however, the system cannot benefit from previous learning data and it has to go through the learning process again to regain its performance. In industrial applications, this means production line has to stop for learning, and the overall productivity of the process is compromised. To solve this problem, this paper proposes a learning control scheme based on neural network (NN) prediction. Learning/training is performed for the neural networks for a set of trajectories in advance. Then the feedforward compensation torque for any trajectory in the set can be calculated according to the predicted error from multiple neural networks managed with expert logic. Experimental study on a 6-DOF industrial robot has shown the superior performance of the proposed NN based learning scheme in the position tracking as well as the residual vibration reduction, without any further learning or end-effector sensors during operation after completion learning/training of motion trajectories in advance.© 2012 ASME
Initiation of DNA Fragmentation during Apoptosis Induces Phosphorylation of H2AX Histone at Serine 139 (2000)

Histone H2AX is a ubiquitous member of the H2A histone family that differs from the other H2A histones by the presence of an evolutionarily conserved C-terminal motif, -KKATQASQEY. The serine residue in this motif becomes rapidly phosphorylated in cells and animals when DNA double-stranded breaks are introduced into their chromatin by various physical and chemical means. In the present communication we show that this phosphorylated form of H2AX, referred to as gamma-H2AX, appears during apoptosis concurrently with the initial appearance of high molecular weight DNA fragments. gamma-H2AX forms before the appearance of internucleosomal DNA fragments and the externalization of phosphatidylserine to the outer membrane leaflet. gamma-H2AX formation is inhibited by N-benzyloxycarbonyl-Val-Ala-Asp-fluoromethyl ketone and the inhibitor of caspase-activated DNase, and it is induced when DNase I and restriction enzymes are introduced into cells, suggesting that any apoptotic endonuclease is sufficient to induce gamma-H2AX formation. These results indicate that gamma-H2AX formation is an early chromatin modification following initiation of DNA fragmentation during apoptosis.
Impedance Analysis of Silicon Nanowire Lithium Ion Battery Anodes (2009)

The impedance behavior of silicon nanowire electrodes has been investigated to understand the electrochemical process kinetics that influences the performance when used as a high-capacity anode in a lithium ion battery. The ac response was measured by using impedance spectroscopy in equilibrium conditions at different lithium compositions and during several cycles of charge and discharge in a half cell vs. metallic lithium. The impedance analysis shows the contribution of both surface resistance and solid state diffusion through the bulk of the nanowires. The surface process is dominated by a solid electrolyte layer (SEI) consisting of an inner, inorganic insoluble part and several organic compounds at the outer interface, as seen by XPS analysis. The surface resistivity, which seems to be correlated with the Coulombic efficiency of the electrode, grows at very high lithium contents due to an increase in the inorganic SEI thickness. We estimate the diffusion coefficient of about 2 × 10 -10 cm 2/s for lithium diffusion in silicon. A large increase in the electrode impedance was observed at very low lithium compositions, probably due to a different mechanism for lithium diffusion inside the wires. Restricting the discharge voltage to 0.7 V prevents this large impedance and improves the electrode lifetime. Cells cycled between 0.07 and 0.70 V vs. metallic lithium at a current density of 0.84 A/g (C/5) showed good Coulombic efficiency (about 99%) and maintained a capacity of about 2000 mAh/g after 80 cycles. © 2009 American Chemical Society.
A Helper-Independent Adenovirus Vector with E1, E3, and Fiber Deleted: Structure and Infectivity of Fiberless Particles (1999)

The adenovirus (Ad) fiber protein largely determines viral tropism through interaction with specific cell surface receptors. This molecule may also be involved in virion assembly or maturation, as some previously characterized fiber mutants were defective for processing of viral structural proteins. We previously described packaging cell lines that express Ad type 5 (Ad5) fiber and can complement the temperature-sensitive Ad fiber mutant H5ts142. We have now used these packaging cells to construct a new adenoviral vector (Ad5.betagal.DeltaF) with E1, E3, and L5 (fiber) deleted and analyzed the fiber null phenotype. Ad5.betagal.DeltaF growth was completely helper independent, and fiberless particles were produced by a single final round of growth in 293 cells. Cryoelectron microscopic studies and sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis showed that the structure and composition of these particles was nearly identical to those of first-generation Ad vectors. As expected, fiberless particles had reduced infectivity on epithelial cells, but they retained the ability to infect monocytic cells via an integrin-dependent pathway. These studies provide a novel approach to developing retargeted Ad gene therapy vectors.
Synthesis and ring-opening metathesis polymerization (ROMP) of new N-fluoro-phenylnorbornene dicarboximides by 2nd generation ruthenium alkylidene catalysts (2007)

Ring-opening metathesis polymerization (ROMP) of norbornene dicarboximides with linear aliphatic and aromatic substituents has been described We recently proceeded with the synthesis of new polynorbornene dicarboximides by ROMP of exo-N-(1-adamantyl)-norbornene-5,6-dicarboximide and exo-endo-N-cyclohexyl-(cyclopentyl)-norbornene-5,6-dicarboximides using well-defined ruthenium alkylidene (vinylidene) catalysts The carboximide functionalized polynorbornenes showed high T g 's, good mechanical properties and high thermal resistance The membranes prepared from these polymers exhibit rather high permselectivity for the separation of hydrogen from nitrogen, carbon monoxide, methane and ethylene
Intensified and protective CD4+ T cell immunity in mice with anti–dendritic cell HIV gag fusion antibody vaccine (2006)

Current human immunodeficiency virus (HIV) vaccine approaches emphasize prime boost strategies comprising multiple doses of DNA vaccine and recombinant viral vectors. We are developing a protein-based approach that directly harnesses principles for generating T cell immunity. Vaccine is delivered to maturing dendritic cells in lymphoid tissue by engineering protein antigen into an antibody to DEC-205, a receptor for antigen presentation. Here we characterize the CD4+ T cell immune response to HIV gag and compare efficacy with other vaccine strategies in a single dose. DEC-205-targeted HIV gag p24 or p41 induces stronger CD4+ T cell immunity relative to high doses of gag protein, HIV gag plasmid DNA, or recombinant adenovirus-gag. High frequencies of interferon (IFN)-gamma- and interleukin 2-producing CD4+ T cells are elicited, including double cytokine-producing cells. In addition, the response is broad because the primed mice respond to an array of peptides in different major histocompatibility complex haplotypes. Long-lived T cell memory is observed. After subcutaneous vaccination, CD4+ and IFN-gamma-dependent protection develops to a challenge with recombinant vaccinia-gag virus at a mucosal surface, the airway. We suggest that a DEC-targeted vaccine, in part because of an unusually strong and protective CD4+ T cell response, will improve vaccine efficacy as a stand-alone approach or with other modalities.
Two-dimensional atomic crystals (2005)

We report free-standing atomic crystals that are strictly 2D and can be viewed as individual atomic planes pulled out of bulk crystals or as unrolled single-wall nanotubes. By using micromechanical cleavage, we have prepared and studied a variety of 2D crystals including single layers of boron nitride, graphite, several dichalcogenides, and complex oxides. These atomically thin sheets (essentially gigantic 2D molecules unprotected from the immediate environment) are stable under ambient conditions, exhibit high crystal quality, and are continuous on a macroscopic scale.
Evidence Linking Chondrocyte Lipid Peroxidation to Cartilage Matrix Protein Degradation (2000)

Reactive oxygen species (ROS) are implicated in both cartilage aging and the pathogenesis of osteoarthritis. We developed an in vitro model to study the role of chondrocyte-derived ROS in cartilage matrix protein degradation. Matrix proteins in cultured primary articular chondrocytes were labeled with [(3)H]proline, and the washed cell matrix was returned to a serum-free balanced salt solution. Exposure to hydrogen peroxide resulted in oxidative damage to the cell matrix as established by monitoring the release of labeled material into the medium. Calcium ionophore treatment of chondrocytes, in a dose-dependent manner, significantly enhanced the release of labeled matrix, suggesting a chondrocyte-dependent mechanism of matrix degradation. Antioxidant enzymes such as catalase or superoxide dismutase did not influence matrix release by the calcium ionophore-activated chondrocytes. However, vitamin E, at physiological concentrations, significantly diminished the release of labeled matrix by activated chondrocytes. The fact that vitamin E is a chain-breaking antioxidant indicates that the mechanism of matrix degradation and release is mediated by the lipid peroxidation process. Lipid peroxidation was measured in chondrocytes loaded with cis-parinaric acid. Both resting and activated cells showed constitutive and enhanced levels of lipid peroxidation activity, which were significantly reduced in the presence of vitamin E. In an immunoblot analysis, malondialdehyde and hydroxynonenal adducts were observed in chondrocyte-matrix extracts, and the amount of adducts increased with calcium ionophore treatment. Furthermore, vitamin E diminished aldehyde-protein adduct formation in activated extracts, which suggests that vitamin E has an antioxidant role in preventing protein oxidation. This study provides in vitro evidence linking chondrocyte lipid peroxidation to cartilage matrix protein (collagen) oxidation and degradation and suggests that vitamin E has a preventive role. These observations indicate that chondrocyte lipid peroxidation may have a role in the pathogenesis of cartilage aging and osteoarthritis.
Formation and properties of surface-anchored polymer assemblies with tunable physico-chemical characteristics (2003)

We describe two new methodologies leading to the formation of novel surface-anchored polymer assemblies on solid substrates. While the main goal is to understand the fundamentals pertaining to the preparation and properties of the surface-bound polymer assemblies (including neutral and chargeable polymers), several examples also are mentioned throughout the Thesis that point out to practical applications of such structures.\n\nThe first method is based on generating assemblies comprising anchored polymers with a gradual variation of grafting densities on solid substrates. These structures are prepared by first covering the substrate with a molecular gradient of the polymerization initiator, followed by polymerization from these substrate-bound initiator centers ("grafting from"). We apply this technique to prepare grafting density gradients of poly(acryl amide) (PAAm) and poly(acrylic acid) (PAA) on silica-covered substrates. We show that using the grafting density gradient geometry, the characteristics of surface-anchored polymers in both the low grafting density ("mushroom") regime as well as the high grafting density ("brush") regime can be accessed conveniently on a single sample. We use a battery of experimental methods, including Fourier transform infrared spectroscopy (FTIR), Near-edge absorption fine structure spectroscopy (NEXAFS), contact angle, ellipsometry, to study the characteristics of the surface-bound polymer layers. We also probe the scaling laws of neutral polymer as a function of grafting density, and for weak polyelectrolyte, in addition to the grafting density, we study the affect of solution ionic strength and pH values.\n\nIn the second novel method, which we coined as "mechanically assisted polymer assembly" (MAPA), we form surface anchored polymers by "grafting from" polymerization initiators deposited on elastic surfaces that have been previously extended uniaxially by a certain length increment, &amp;#923;x. Upon releasing the strain in the substrate after completion of polymerization, we show the grafting density of the polymers grafted to flexible substrates can be tuned as a function of &amp;#923;x.
Introduction to Infrared Fiber Optics (2010)

Infrared (IR) optical fibers may be defined as fiber optics that transmit radiation with wavelengths greater than approximately 2 Î¼m. The first IR fibers were fabricated in the mid-1960s from a rather special class of IR transparent glasses called chalcogenide glasses. It had been known for some time that blending chalcogen elements such as arsenic and sulfur can form a dark red-colored glass that is transparent well beyond 2 Î¼m. Being an excellent glass former, arsenic trisulfide (As2S3) was a logical choice to be drawn into crude fiber using a simple fiber drawing apparatus. Kapany et al. reported on these first IR fibers in 1965, but the losses were very high. In fact, the losses were an untenable 10 dBâm over the IR spectrum from 2 to 8 Î¼m. A loss of 10 dBâm means that a mere 1-m length of As2S3 fiber would transmit only 10% of the incident light apart from reflection losses from the fiber end faces. The reflection losses would amount to an additional 31%, as this glass has a high refractive index of about 2.3. On top of these problems, their As2S3 fiber was quite brittle. During the mid-1970s, the interest in developing an efficient and reliable IR fiber for short-haul applications increased, partly in response to the need for a fiber to link broadband, long-wavelength radiation to remote photodetectors in military sensor applications. In 1975, Hughes Research Laboratories (HRL) researchers in Malibu, CA, began to search for an IR fiber that could be used in a satellite application to link IR radiation in the 3- to 5-Î¼m, 8- to 12-Î¼m, and longer wavelength bands, which was incident on a surveillance satellite, to an interior IR detector array. The basic fiber/detector system as envisioned by HRL is shown schematically in Fig. 1.1. The idea was simple: Take an array of IR fibers and position them so that they would each intercept a large field of view, and then transmit that signal through an IR fiber for a distance of no more than about 50 cm to a mosaic IR detector array. This particular U.S. Army-funded program, called Mosaic Infrared Sensor Technology (MIST), would ultimately require a fiber array consisting of several hundred fibers, each interfaced with one detector element in the detector array. Initially the investigators at HRL experimented with the chalcogenide fibers, but they found the loss too high and the fibers too brittle for their application. Another unfortunate feature of chalcogenide fibers is that they are made from toxic materials.
Magnetic resonance angiography. (1986)

Pulse sequences that permit selective detection of moving spins in a magnetic resonance image have been developed. Experiments were performed by the authors to produce projected angiographic data without the use of contrast agents, with the intensity of each image pixel determined by the macroscopic velocity of the detected spins. With this method, suppression of nonmoving spins is essentially complete, yielding a high dynamic range in signal intensity for detected vessels. Selective detection of moving spins is not dependent on pulsatile flow. Consequently, not only arterial structures, but also venous structures can easily be visualized. High-resolution angiographic images can be obtained by combining the flow experiment with surface coil techniques.
New Aspects of Physiological and Pathophysiological Functions of Adenosine A2AReceptor in Basal Ganglia (2001)

There is now growing interest in the functional role of adenosine A2A receptors. Their distribution within the brain is restricted in the basal ganglia, particularly abundant in the striatum, which are thought to play a crucial role in the control of motor behavior. Indeed, newly developed A2A receptor selective antagonists have a profound influence on motor functions, with anti-Parkinsonian activities in several animal models. Striatal spiny neurons serve as a major anatomical locus for the relay of cortical information flow through the basal ganglia. The GABA releasing projection neurons represent the A2A receptor-mediated main target of adenosine. The GABAergic synaptic neurotransmission is regulated by adenosine via A2A receptors on the presynaptic terminals. Blockade of this modulatory function by A2A antagonists could repair striatopallidal abnormal neuronal activities provoked by striatal dopamine depletion in the Parkinsonian state. A2A receptor antagonists provide a novel therapeutic potential for the treatment of Parkinson's disease.