gebhart/patrepeval huggingface dataset:
Comparison of Laser-Welded and Sutured Arteriotomies (1986)

We compared the histologic features, tensile strength, and collagen synthesis of laser-welded and sutured arteriotomies. Four bilateral canine femoral or carotid arteries, 2 cm long, were studied at one through four weeks postoperatively, with one vessel (control) closed with interrupted 6-0 polypropylene sutures and the contralateral vessel (experimental) welded with an argon laser (0.5 W [1417 J/cm2], four-minute exposure per 1-cm length of incision). Histologic examination revealed that laser-welded arteriotomies had less inflammatory reaction, more normal collagen and elastin reorientation, and similar endothelial continuity when compared with the control, sutured wounds. The tensile strength of the one- and two-week laser-welded specimens was less than that of sutured wounds and became approximately equal to sutured repairs at three and four weeks. There were no significant differences in the rate of collagen synthesis. There was no evidence of abnormal healing in the laser-welded specimens, suggesting that argon laser welding may be an alternative to suture repair of arteriotomies.
Bilayer Organic–Inorganic Gate Dielectrics for High‐Performance, Low‐Voltage, Single‐Walled Carbon Nanotube Thin‐Film Transistors, Complementary Logic Gates, and p–n Diodes on Plastic Substrates (2006)

Abstract High‐capacitance bilayer dielectrics based on atomic‐layer‐deposited HfO 2 and spin‐cast epoxy are used with networks of single‐walled carbon nanotubes (SWNTs) to enable low‐voltage, hysteresis‐free, and high‐performance thin‐film transistors (TFTs) on silicon and flexible plastic substrates. These HfO 2 –epoxy dielectrics exhibit excellent properties including mechanical flexibility, large capacitance (up to ca. 330 nF cm –2 ), and low leakage current (ca. 10 –8 A cm –2 ); their low‐temperature (ca. 150 °C) deposition makes them compatible with a range of plastic substrates. Analysis and measurements of these dielectrics as gate insulators in SWNT TFTs illustrate several attractive characteristics for this application. Their compatibility with polymers used for charge‐transfer doping of SWNTs is also demonstrated through the fabrication of n‐channel SWNT TFTs, low‐voltage p–n diodes, and complementary logic gates.
Efficient processing of streaming graphs for evolution-aware clustering (2013)

The clustering of vertices often evolves with time in a streaming graph, where graph update events are given as a stream of edge (vertex) insertions and deletions. Although a sliding window in stream processing naturally captures some cluster evolution, it alone may not be adequate, especially if the window size is large and the clustering within the windowed stream is unstable. Prior graph clustering approaches are mostly insensitive to clustering evolution. In this paper, we present an efficient approach to processing streaming graphs for evolution-aware clustering (EAC) of vertices. We incrementally manage individual connected components as clusters subject to a constraint on the maximal cluster size. For each cluster, we keep the relative recency of edges in a sorted order and favor more recent edges in clustering. We evaluate the effectiveness of EAC and compare it with a previous state-of-the-art evolution-insensitive clustering (EIC) approach. The results show that EAC is both effective and efficient in capturing evolution in a streaming graph. Moreover, we implement EAC as a streaming graph operator on IBM's InfoSphere Streams, a large-scale distributed middleware for stream processing, and show snapshots of the user cluster evolution in a streaming Twitter mention graph.
Current Protocols in Human Genetics (2001)

Much of the experience accumulated from using the positional cloning approach for identifying new disease genes has been brought together in this single volume. This book is a well-organized and comprehensive collection of more than 150 protocols. Although comprehensive, this volume is not complete. The book was designed to be a companion book to the popular `Current Protocols of Molecular Biology`; thus many of the basic techniques are referred to rather than explained. Overall, this book is an excellent research and teaching tool. Genome researchers will find this volume worth its weight.
A simple physical picture for quantum control of wave packet localization (1997)

Based on weak field quantum control theory, a semiclassical approximation relates the characteristic parameters of the tailored light field to corresponding classical dynamical quantities and thus reveals the underlying physical basis of wave packet focusing. A coordinate-dependent two-level-system approximation is employed to further analyze the molecular dynamics induced by short laser pulses, thus leading to a simple interpretation of the observed correlation between the pulse chirp and vibrational focusing and defocusing. Though our study is presented in the context of quantum control, the conclusions are general, providing an intuitive picture of the quantum coherence of light–matter interaction and a guideline for the design of tailored laser fields.
The Kinetics, Substrate, and Inhibitor Specificity of the Monocarboxylate (Lactate) Transporter of Rat Liver Cells Determined Using the Fluorescent Intracellular pH Indicator, 2′,7′-Bis(carboxyethyl)-5(6)-carboxyfluorescein (1996)

The kinetics of transport of L-lactate, pyruvate, ketone bodies, and other monocarboxylates into isolated hepatocytes from starved rats were measured at 25 degrees C using the intracellular pH-sensitive dye, 2',7'-bis(carboxyethyl)- 5(6)-carboxyfluorescein, to detect the associated proton influx. Transport kinetics were similar, but not identical, to those determined using the same technique for the monocarboxylate transporter (MCT) of Ehrlich Lettré tumor cells (MCT1) (Carpenter, L., and Halestrap, A. P. (1994) Biochem. J. 304, 751-760). Km values for L-lactate (4.7 mM), D-lactate (27 mM), D,L-2-hydroxybutyrate (3.3 mM), L-3-hydroxybutyrate (12.7 mM), and acetoacetate (6.1 mM) were very similar in both cell types, whereas in hepatocytes the Km values were higher than MCT1 for pyruvate (1.3 mM, cf. 0.72 mM), D-3-hydroxybutyrate (24.7 mM, cf. 10.1 mM), D-2-chloropropionate (1.3 mM, cf. 0.8 mM), 4-hydroxybutyrate (18.1 mM, cf. 7.7 mM), and acetate (5.4 mM, cf. 3.7 mM). In contrast, the hepatocyte carrier had lower Km values than MCT1 for glycolate, chloroacetate, dichloroacetate, and 2-hydroxy-2-methylpropionate. Differences in stereoselectivity were also detected; both carriers showed a lower Km for L-lactate than D-lactate, while hepatocyte MCT exhibited a lower Km for D- than L-2-chloropropionate and for L- than D-3-hydroxybutyrate; this is not the case for MCT1. A range of inhibitors of MCT1, including alpha-cyanocinnamate derivatives, phloretin, and niflumic acid, inhibited hepatocyte MCT with K0.5 values significantly higher than for tumor cell MCT1, while stilbene disulfonate derivatives and p-chloromercuribenzene sulfonate had similar K0.5 values in both cell types. The branched chain ketoacids alpha-ketoisocaproate and alpha-ketoisovalerate were also potent inhibitors of hepatocyte MCT with K0.5 values of 270 and 340 microM, respectively. The activation energy of L-lactate transport into hepatocytes was 58 kJ mol-1, and measured rates of transport at 37 degrees C were considerably greater than those required for maximal rates of gluconeogenesis. The properties of the hepatocyte monocarboxylate transporter are consistent with the presence of a distinct isoform of MCT in liver cells as suggested by the cloning and sequencing of MCT2 from hamster liver (Garcia, C. K., Brown, M. S., Pathak, R. K., and Goldstein, J. L. (1995) J. Biol. Chem. 270, 1843-1849).
Therapy of rheumatoid arthritis with mycophenolate mofetil. (1993)

Mycophenolate mofetil, a pro-drug for mycophenolic acid, is an investigational immunosuppressive compound that is being developed for the treatment of rheumatoid arthritis (RA). The drug and its primary metabolite, mycophenolic acid, inhibit the de novo pathway of purine biosynthesis and have greater anti-proliferative effects on lymphocytes than on other rapidly dividing cells. Significant clinical improvement has been seen in many mycophenolate mofetil-treated RA patients who have been refractory to treatment with a variety of disease-modifying anti-rheumatic drugs (DMARDs). Treatment with mycophenolate mofetil reduces rheumatoid factor titres, immunoglobulin (IgG, IgM, and IgA) levels, and the total number of T cells (CD2) in RA patient peripheral blood; in addition, lymphocyte mitogen responses are inhibited and delayed hypersensitivity skin test reactivity is decreased. A dose of 2 g daily is more effective than lower doses, including several pulsing regimens. The most frequent adverse events reported by patients on mycophenolate mofetil are gastrointestinal, mainly nausea, vomiting, abdominal pain, and diarrhea. RA studies have demonstrated no clinically significant nephrotoxicity, hepatotoxicity, or bone marrow toxicity attributable to mycophenolate mofetil.
Dual frequency wire antennas (1996)

A new type of dual frequency antenna is introduced by combining a helical and a monopole antenna. The antenna configuration is shown to operate at two discrete frequencies, i.e. ~900 and 1800 MHz. The size of the antenna configuration can be decreased at the cost of the bandwidth. The bandwidth is shown to increase by adding a reactive matching network to the antenna.
A Unified Artificial Neural Network Architecture for Active Power Filters (2007)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> In this paper, an efficient and reliable neural active power filter (APF) to estimate and compensate for harmonic distortions from an AC line is proposed. The proposed filter is completely based on Adaline neural networks which are organized in different independent blocks. We introduce a neural method based on Adalines for the online extraction of the voltage components to recover a balanced and equilibrated voltage system, and three different methods for harmonic filtering. These three methods efficiently separate the fundamental harmonic from the distortion harmonics of the measured currents. According to either the Instantaneous Power Theory or to the Fourier series analysis of the currents, each of these methods are based on a specific decomposition. The original decomposition of the currents or of the powers then allows defining the architecture and the inputs of Adaline neural networks. Different learning schemes are then used to control the inverter to inject elaborated reference currents in the power system. Results obtained by simulation and their real-time validation in experiments are presented to compare the compensation methods. By their learning capabilities, artificial neural networks are able to take into account time-varying parameters, and thus appreciably improve the performance of traditional compensating methods. The effectiveness of the algorithms is demonstrated in their application to harmonics compensation in power systems. </para>
Analysis of swine leukocyte antigen class I gene profiles and porcine endogenous retrovirus viremia level in a transgenic porcine herd inbred for xenotransplantation research (2018)

Molecular characterization of swine leukocyte antigen (<i>SLA</i>) genes is important for elucidating the immune responses between swine-donor and human-recipient in xenotransplantation. Examination of associations between alleles of <i>SLA</i> class I genes, type of pig genetic modification, porcine endogenous retrovirus (PERV) viral titer, and PERV subtypes may shed light on the nature of xenograft acceptance or rejection and the safety of xenotransplantation. No significant difference in PERV <i>gag</i> RNA level between transgenic and non-transgenic pigs was noted; likewise, the type of applied transgene had no impact on PERV viremia. <i>SLA-1</i> gene profile type may correspond with PERV level in blood and thereby influence infectiveness. Screening of pigs should provide selection of animals with low PERV expression and exclusion of specimens with PERV-C in the genome due to possible recombination between A and C subtypes, which may lead to autoinfection. Presence of PERV-C integrated in the genome was detected in 31.25% of specimens, but statistically significant increased viremia in specimens with PERV-C was not observed. There is a need for multidirectional molecular characterization (<i>SLA</i> typing, viremia estimation, and PERV subtype screening) of animals intended for xenotransplantation research in the interest of xeno-recipient safety.
Recombinant Ig-Like Transcript 3-Fc Modulates T Cell Responses via Induction of Th Anergy and Differentiation of CD8+ T Suppressor Cells (2006)

The Ig-like transcript (ILT)3 is crucial to the tolerogenic activity acquired by dendritic cells exposed to allospecific T suppressor (Ts) cells. We have explored the immunomodulatory property of the extracellular region of ILT3 using a cytoplasmic deletion mutant of ILT3 (ILT3delta), expressed as membrane-bound ILT3 on KG1 cells, and a rILT3-Fc fusion protein. We found that both membrane-bound and soluble ILT3 inhibited T cell proliferation in primary and secondary MLC inducing anergy in CD4+ Th cells and suppressing the differentiation of IFN-gamma-producing CD8+ CTL. Furthermore, membrane-bound and soluble ILT3 induced the differentiation of CD8+ FOXP3+ Ts cells in primary 7-day MLC. The suppressive activity of these CD8+ Ts cells is alloantigen specific and mediated by their capacity to induce the up-regulation of ILT3 and down-regulation of costimulatory molecules such as CD86 in APC from the stimulator used for priming, but not on control HLA-mismatched APC. Our finding that ILT3-Fc has potent immunosuppressive activity in vitro and that it acts on T cells only upon activation suggests the possibility that this agent may be of use for specific suppression of the immune response in autoimmunity or transplantation.
A Next-Generation Guide Extension System for Percutaneous Coronary Intervention (2020)

The CrossLiner is a next generation guide extension system that may offer advantages over first generation devices. Further clinical evaluation will be required to assess the role of this new device in PCI.
Sensitivity and Specificity of Metal Surface-Immobilized “Molecular Beacon” Biosensors (2005)

The separate developments of microarray patterning of DNA oligonucleotides, and of DNA hairpins as sensitive probes for oligonucleotide identification in solution, have had a tremendous impact on basic biological research and clinical applications. We have combined these two approaches to develop arrayable and label-free biological sensors based on fluorescence unquenching of DNA hairpins immobilized on metal surfaces. The thermodynamic and kinetic response of these sensors, and the factors important in hybridization efficiency, were investigated. Hybridization efficiency was found to be sensitive to hairpin secondary structure, as well as to the surface distribution of DNA hairpins on the substrate. The identity of the bases used in the hairpin stem as well as the overall loop length significantly affected sensitivity and selectivity. Surface-immobilized hairpins discriminated between two sequences with a single base-pair mismatch with high sensitivity (over an order of magnitude difference in signal) under identical assay conditions (no change in stringency). This represents a significant improvement over other microarray-based techniques.
Strand Invasion of Extended, Mixed-Sequence B-DNA by γPNAs (2009)

In this communication, we show that peptide nucleic acids (PNAs) with lengths of 15-20 nucleotides, when preorganized into a right-handed helix, can invade mixed-sequence double-helical B-form DNA (B-DNA). Strand invasion occurs in a highly sequence-specific manner through direct Watson-Crick base pairing. Unlike the previously developed double-duplex invasion strategy, which requires simultaneous binding of two strands of pseudocomplementary PNAs to DNA, only a single strand of gammaPNA is required for invasion in this case, and no nucleobase substitution is needed.
PAK4: a pluripotent kinase that regulates prostate cancer cell adhesion (2010)

Hepatocyte growth factor (HGF) is associated with tumour progression and increases the invasiveness of prostate carcinoma cells. Migration and invasion require coordinated reorganisation of the actin cytoskeleton and regulation of cell-adhesion dynamics. Rho-family GTPases orchestrate both of these cellular processes. p21-activated kinase 4 (PAK4), a specific effector of the Rho GTPase Cdc42, is activated by HGF, and we have previously shown that activated PAK4 induces a loss of both actin stress fibres and focal adhesions. We now report that DU145 human prostate cancer cells with reduced levels of PAK4 expression are unable to successfully migrate in response to HGF, have prominent actin stress fibres, and an increase in the size and number of focal adhesions. Moreover, these cells have a concomitant reduction in cell-adhesion turnover rates. We find that PAK4 is localised at focal adhesions, is immunoprecipitated with paxillin and phosphorylates paxillin on serine 272. Furthermore, we demonstrate that PAK4 can regulate RhoA activity via GEF-H1. Our results suggest that PAK4 is a pluripotent kinase that can regulate both actin cytoskeletal rearrangement and focal-adhesion dynamics.
Acetylcholine receptor metabolism in a nonfusing muscle cell line. (1977)

The development and turnover of acetylcholine receptors in a nonfusing muscle cell line has been investigated using iodinated alpha-bungarotoxin as a probe for acetylcholine receptor. logarithmically growing cells do not bind toxin, while cells that have ceased cell division bind toxin at a site which has the pharmacological characteristics of an acetylcholine receptor. These binding sites are removed from the cell surface at a rate equal to 8.9 +/- 0.5% of the total surface binding sites/h and appear at a rate equal to 8.3 +/- 1.5% of the total surface binding sites/h. Appearance of new binding sites can occur for a period of 1 1/2 h in the presence of cycloheximide, during which time 15% of the surface receptors can be replaced. There is a hidden population of receptors which is not accessible to toxin without disrupting the cell. This population amounts to 35% of the Triton-extractable receptors in the cell and is composed of two classes. One class, termed a precursor receptor, appears to move from the hidden population to the cell surface, and composes about 40% of the total hidden receptor population. The second class of hidden receptors does not appear to function as a surface precursor and is neither depleted nor enriched by any of the procedures we employed. Surface receptors and hidden receptors are distinguishable on the basis of their sedimentation coefficient about 0.5 to 0.6 S lower than surface receptors. We were unable to distinguish between precursor and non-precursor hidden receptors on the basis of cursor and nonprecursor hidden receptors on the basis of their sedimentation coefficients.
Stem cell factor and leukemia inhibitory factor promote primordial germ cell survival by suppressing programmed cell death (apoptosis) (1993)

Proliferating primordial germ cells (PGCs) isolated from mouse embryos soon after their arrival in the genital ridges would only survive in vitro at temperature of less than 30 degrees C (De Felici, M. and McLaren, A. (1983). Exp. Cell. Res. 144, 417-427; Wabik-Sliz, B. and McLaren, A. (1984). Exp. Cell. Res. 154, 530-536) or when co-cultured on cell feeder layers (Donovan, P. J., Stott, D., Godin, I., Heasman, J. and Wylie, C. C. (1986). Cell 44, 831-838; De Felici, M. and Dolci, S. (1991). Dev. Biol. 147, 281-284). In the present paper we report that mouse PGC death in vitro occurs with all the hallmarks of programmed cell death or apoptosis. We found that after 4-5 hours in culture many PGCs isolated from 12.5 dpc fetal gonads assumed a nuclear morphology and produced membrane bound fragments (apoptotic bodies) typical of apoptotic cells. In addition, PGCs in culture accumulated high level of tissue transglutaminase (tTGase; an enzyme that is induced and activated during apoptosis) and showed extensive degradation of DNA to oligonucleosomal fragments, which is characteristic of apoptosis. The physiological relevance of this mechanism of PGC death is supported by the finding that some PGCs undergoing apoptosis, as revealed by the high level of tTGase expression, were detected in the embryo. Most importantly, we show that the addition of stem cell factor (SCF) or leukemia inhibitory factor (LIF) to the culture medium, two cytokines known to favour PGC survival and/or proliferation in vitro, markedly reduced the occurrence of apoptosis in PGCs during the first hours in culture.(ABSTRACT TRUNCATED AT 250 WORDS)
Enteral nutrient intake level determines intestinal protein synthesis and accretion rates in neonatal pigs (2000)

Our objective was to determine the minimum enteral intake level necessary to increase the protein accretion rate (PAR) in the neonatal small intestine. Seven-day-old piglets received an equal total daily intake of an elemental diet, with different proportions given enterally (0, 10%, 20%, 40%, 60%, 80%, and 100%). After 7 days, piglets were infused intravenously with [(2)H(3)]leucine for 6 h, and the fractional protein synthesis rate (FSR) was measured in the proximal (PJ) and distal jejunum (DJ) and the proximal (PI) and distal ileum (DI). The jejunal FSR increased from 45%/day to 130%/day between 0 and 60% enteral intake, whereas the FSR in the ileum was less sensitive to enteral intake level. At 0% enteral intake, PAR was significantly negative in the PJ, DJ, and PI (range -70 to -43 mg/day) and positive in the DI (49 mg/day), whereas intestinal protein balance occurred at 20% enteral intake. At 100% enteral intake, the PAR was greatest in the DI, even though the rates of protein turnover were 50% lower than in the PJ. We conclude that there is net intestinal protein loss at 0% enteral intake, protein balance at 20% enteral intake, and maximal intestinal protein accretion at 60% enteral intake.
Antibodies against transforming growth factor-beta 1 suppress intimal hyperplasia in a rat model. (1994)

Intimal hyperplasia is induced by therapeutic vascular interventions and often results in clinically important narrowing of the vascular lumen. Examination of the role of TGF-beta 1 in a rat carotid artery injury model confirmed the presence of a previously reported increase in TGF-beta 1 mRNA in the media of injured arteries. Administration of neutralizing anti- TGF-beta 1 antibodies significantly (P < 0.05) reduced the size of the intimal lesions that developed after carotid balloon injury. A control antibody had no effect. The intimal/medial area ratio was also reduced in the anti-TGF-beta 1 group relative to controls (P < 0.01). Immunohistochemical staining showed that two TGF-beta 1-induced extracellular matrix components, EDA + fibronectin and versican, were greatly increased in the untreated neointimal lesions, but were almost completely absent from the lesions of the anti-TGF-beta 1-treated animals. We conclude that TGF-beta 1 is causally involved in the development of intimal hyperplasia, and that anti-TGF-beta 1 agents may be useful in achieving at least partial control of this condition.
Fluorescence-lifetime-based tomography for turbid media (2005)

We derive a novel algorithm to recover the in vivo distributions of fluorophores based on an asymptotic life-time analysis of time-domain fluorescence measurements with turbid tissue. We experimentally demonstrate the advantage offered by this method in localizing fluorophores with distinct lifetimes. This algorithm has wide applicability for diagnostic fluorescence imaging in the presence of several-centimeter-thick biological tissue, since fluorescence lifetime is a sensitive indicator of local tissue environment and interactions at the molecular level.