gebhart/patrepeval huggingface dataset:
Medical therapy for induction and maintenance of remission in pouchitis: A systematic review (2007)

To determine the effectiveness of medical therapy (including metronidazole, bismuth carbomer enemas, oral probiotic bacteria, butyrate suppositories, and glutamine suppositories) for inducing a response or for maintaining remission in pouchitis. Studies were selected using the MEDLINE data base (1966-December 1997), abstracts from major gastrointestinal meetings, and references from published articles and reviews. Four randomized controlled trials of medical therapy in adult patients with pouchitis were identified: two placebo controlled trials in active chronic pouchitis; one maintenance of remission trial comparing two active agents in chronic pouchitis; and one placebo-controlled maintenance of remission trial for chronic pouchitis. A single patient “n-of-1” trial for active chronic pouchitis was excluded. Data were extracted by three independent observers based on the intention to treat principle. Extracted data were converted to 2 × 2 tables (response versus no response and medical therapy versus placebo or medical therapy versus medical therapy) and an odds ratio with 95% confidence intervals (CI) were determined as described by Cochrane and Mantel and Haenszel. In addition, the absolute risk reduction, relative risk reduction, and number needed to treat were determined. The odds ratios of inducing a response using oral metronidazole or bismuth carbomer foam enemas compared with placebo in active chronic pouchitis were 12.34 (95% CI 2.34-64.95) and 1.00 (95% CI 0.29-3.42), respectively. The odds ratio of maintaining remission in chronic pouchitis for oral probiotic bacteria (VSL-3) compared with placebo was 15.33 (95% CI 4.51-52.14). There was no difference in the odds ratio of inducing symptomatic remission and then maintaining symptomatic remission after discontinuing suppressive medical therapy for chronic pouchitis with glutamine suppositories compared with butyrate suppositories, 2.75 (95% CI 0.48-15.94). Metronidazole is an effective therapy for active chronic pouchitis. Bismuth carbomer foam enemas are not effective therapy for active chronic pouchitis. Oral probiotic therapy with VSL-3 is an effective therapy for maintaining remission in patients with chronic pouchitis in remission. There is no difference in maintenance of symptomatic remission in patients with chronic pouchitis treated with glutamine versus butyrate suppositories, and it is unknown whether glutamine and butyrate are equally effective or ineffective. Additional randomized, double-blind, placebo-controlled, dose-ranging clinical trials are needed to determine the efficacy of empiric medical therapies currently being used in patients with pouchitis.
Mechanism of substrate dephosphorylation in low Mr protein tyrosine phosphatase (1999)

Substrate dephosphorylation by the low molecular weight protein tyrosine phosphatases proceeds via nucleophilic substitution at the phosphorous atom yielding a cysteinyl phosphate intermediate. However, several questions regarding the exact reaction mechanism remain unanswered. Starting from the crystal structure of the enzyme we study the energetics of this reaction, using the empirical valence bond method in combination with molecular dynamics and free energy perturbation simulations. The free energy profiles of two mechanisms corresponding to different protonation states of the reacting groups are examined along stepwise and concerted pathways. The activation barriers calculated relative to the enzyme-substrate complex are very similar for both monoanionic and dianionic substrates, but taking the substrate binding step into account shows that hydrolysis of monoanionic substrates is strongly favored by the enzyme, because a dianionic substrate will not bind when the reacting cysteine is ionized. The calculated activation barrier for dephosphorylation of monoanionic phenyl phosphate according to this novel mechanism is 14 kcal mol−1, which is in good agreement with experimental data. Proteins 1999;36:370–379. © 1999 Wiley-Liss, Inc.
Composition dependence of lattice spacing for low dislocation density undoped liquid encapsulated Czochralski GaAs crystals (1991)

Crystals with varied composition were pulled by the As-partial-pressure controlled liquid encapsulated Czochralski method. The dislocation density was found to be as low as 2×103 cm−2 at the cores of the crystals. Lattice spacing (d) was measured with a precision of Δd/d ∼ 5.9 × 10−6 using synchrotron radiation. For a variation of 7×10−5 in the As-atom fraction in the crystals, the lattice spacing varied by less than 1×10−5 Å.
The antipruritic and antiallergic effects of Fuyangning ointment (2008)

Objective To study the antipruritic and antiallergic effects of Fuyangning ointment.Methods The effects of Fuyangning ointment on histamine-induced itch in guinea pigs,the inhibitory actions on histamine-induced increase of capillary permeability in mice,and the effects on 2,4-dinitrochlorobenzol(DNCB)-induced delayed hypersensitivity reaction in mice were observed.Results The application of Fuyangning ointment on the skin of guinea pigs significantly lowered the itch threshold,inhibited the increase of skin capillary permeability in mice induced by histamine.The application of Fuyangning ointment on skin also inhibited the DNCB-induced delayed hypersensitivity reaction in mice.Conclusions Fuyangning ointment could relieve itching,inhibit the increase of capillary permeability caused by phlogogenic substances.It also has significant inhibitory effects on type IV hypersensitivity reactions.
Coordinated Multi-Antenna Processing for Cellular Underlay Device-to-Device Communication (2014)

We propose linear coordinated transmit-receive beamforming methods for spatial underlay direct device-to-device (D2D) communication in cellular networks where the user terminals (UTs) employ multiple antenna elements. For a D2D terminal pair, direct communication is a beneficial alternative compared
Method for reactivating catalysts and a method for recycling supercritical fluids used to reactivate the catalysts (2023)

A method of reactivating a catalyst, such as a solid catalyst or a liquid catalyst. The method comprises providing a catalyst that is at least partially deactivated by fouling agents. The catalyst is contacted with a fluid reactivating agent that is at or above a critical point of the fluid reactivating agent and is of sufficient density to dissolve impurities. The fluid reactivating agent reacts with at least one fouling agent, releasing the at least one fouling agent from the catalyst. The at least one fouling agent becomes dissolved in the fluid reactivating agent and is subsequently separated or removed from the fluid reactivating agent so that the fluid reactivating agent may be reused. A system for reactivating a catalyst is also disclosed.
Modeling of Cell-to-Cell Communication Processes with Petri Nets Using the Example of Quorum Sensing (2011)

The understanding of the molecular mechanism of cell-to-cell communication is fundamental for system biology. Up to now, the main objectives of bioinformatics have been reconstruction, modeling and analysis of metabolic, regulatory and signaling processes, based on data generated from high-throughput technologies. Cell-to-cell communication or quorum sensing (QS), the use of small molecule signals to coordinate complex patterns of behavior in bacteria, has been the focus of many reports over the past decade. Based on the quorum sensing process of the organism Aliivibrio salmonicida, we aim at developing a functional Petri net, which will allow modeling and simulating cell-to-cell communication processes. Using a new editor-controlled information system called VANESA (http://vanesa.sf.net), we present how to combine different fields of studies such as life-science, database consulting, modeling, visualization and simulation for a semi-automatic reconstruction of the complex signaling quorum sensing network. We show how cell-to-cell communication processes and information-flow within a cell and across cell colonies can be modeled using VANESA and how those models can be simulated with Petri net network structures in a sophisticated way.
Interoperability of mobile agents for ubiquitous applications (2007)

Abstract A mobile agent is an important platform for applications for the coming ubiquitous society. Many different kinds of mobile agent platforms have been developed. However, agents from one agent platform are generally not able to migrate into another agent platform. As a solution to this problem, we propose an interoperability concept using an incarnation agent. The concept realizes logical mobility within different kinds of agent platforms. The incarnation agent extracts an agent's procedures and status, compiling them into agent platform independent format and then re‐compiling them to target agent platform format, thus enabling the process to continue. The incarnation agent also has autonomy for interoperability. It manages complex migration for interoperability, so agent's procedure can be described in simple mobile model. Moreover, the incarnation agent modifies agent's procedures as applicable to facilities of target agent platform. This paper also reports an interoperability middle‐ware and its examination. The middle‐ware is a foundation of realizing the Incarnation Agent, and the response time and network traffic overheads by the interoperability middle‐ware has been measured. © 2007 Wiley Periodicals, Inc. Electr Eng Jpn, 161(4): 49–59, 2007; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/eej.20388
Vitamin C protects HL60 and U266 cells from arsenic toxicity (2005)

Although there is no compelling evidence that vitamin C has antitumor activity in humans, clinical trials are testing the hypothesis that ascorbic acid (AA) will enhance the efficacy of arsenic trioxide (As2O3) in myeloma. In vitro, AA cytotoxicity depends on its interaction with free transition metal ions in culture media leading to the generation of H2O2 and other reactive oxygen species (ROSs). Therefore, to circumvent the extracellular in vitro pro-oxidant effects of AA, we loaded HL60, U266, and RPMI-8226 cells with vitamin C by incubation with dehydroascorbic acid (DHA). Loading cells in this manner resulted in prominent, dose-dependent protection of As2O3-treated cells as measured by viability, colony formation, and apoptosis assays. Glutathione depletion enhanced cell sensitivity to the cytotoxic effects of As2O3 and vitamin C loading provided protection. AA was found to generate cytotoxic concentrations of H2O2 in culture medium without cells and copper/iron chelators inhibited this reaction. However, AA did not generate H2O2 in simple buffer or human plasma. Direct incubation with AA resulted in increased intracellular ROSs, whereas DHA incubation decreased it. These results clarify an apparent paradox and indicate that vitamin C loading in HL60, U266, and RPMI-8226 cells ameliorates As2O3 cytotoxicity.
Electrocatalytic Oxidation Reactions at (100) Facetted Platinum Films (2011)

Abstract not Available.
A Measurement Device to Assist Amputee Prothetic Fitting (1994)

SANDERS, JOAN E. Ph. D.; DALY, COLIN H. Ph. D.; CUMMINGS, WILLIAM R.; REED, RUSSELL D.; MARKS, ROBERT J. II Ph. D. Author Information
Prolyl isomerase Pin1 enhances osteoblast differentiation through Runx2 regulation (2013)

Peptidyl-prolyl isomerase 1 (Pin1) is the only enzyme known to catalyze isomerization of the pSer/Thr-Pro peptide bond. Pin1 induces conformational change of substrates and subsequently regulates diverse cellular processes. However, its role in osteoblast differentiation is not well understood. Here we show that Pin1 enhances osteoblast differentiation. Pin1 interacts and affects the protein stability and transcriptional activity of an important osteogenic transcriptional factor Runx2. Our results indicate that this regulation is likely due to suppression of poly-ubiquitination-mediated proteasomal degradation of Runx2. Our current finding suggests that Pin1 is a novel regulator of osteoblast differentiation that acts through the regulation of Runx2 function.
Grand challenges in the field of stem cell research (2014)

SPECIALTY GRAND CHALLENGE article Front. Cell Dev. Biol., 13 February 2014Sec. Stem Cell Research Volume 2 - 2014 | https://doi.org/10.3389/fcell.2014.00002
S100A8/A9 Proteins Mediate Neutrophilic Inflammation and Lung Pathology during Tuberculosis (2013)

Abstract Rationale A hallmark of pulmonary tuberculosis (TB) is the formation of granulomas. However, the immune factors that drive the formation of a protective granuloma during latent TB, and the factors that drive the formation of inflammatory granulomas during active TB, are not well defined. Objectives The objective of this study was to identify the underlying immune mechanisms involved in formation of inflammatory granulomas seen during active TB. Methods The immune mediators involved in inflammatory granuloma formation during TB were assessed using human samples and experimental models of Mycobacterium tuberculosis infection, using molecular and immunologic techniques. Measurements and Main Results We demonstrate that in human patients with active TB and in nonhuman primate models of M. tuberculosis infection, neutrophils producing S100 proteins are dominant within the inflammatory lung granulomas seen during active TB. Using the mouse model of TB, we demonstrate that the exacerbated lung inflammation seen as a result of neutrophilic accumulation is dependent on S100A8/A9 proteins. S100A8/A9 proteins promote neutrophil accumulation by inducing production of proinflammatory chemokines and cytokines, and influencing leukocyte trafficking. Importantly, serum levels of S100A8/A9 proteins along with neutrophil-associated chemokines, such as keratinocyte chemoattractant, can be used as potential surrogate biomarkers to assess lung inflammation and disease severity in human TB. Conclusions Our results thus show a major pathologic role for S100A8/A9 proteins in mediating neutrophil accumulation and inflammation associated with TB. Thus, targeting specific molecules, such as S100A8/A9 proteins, has the potential to decrease lung tissue damage without impacting protective immunity against TB.
Effect of Stent Duration on Ureteral Healing Following Endoureterotomy in an Animal Model (1993)

Ureteral strictures were created in 18 minipigs. Six weeks after stricture inducement, endourologic incision with a balloon cutting device was performed and a 7 F internal polyurethane stent was placed. After this step, 14 pigs remained in the study and were randomized into three different groups depending upon the time when the stent was removed: 1, 3 or 6 weeks. Twelve weeks after stricture incision, the pigs were killed, the status of the incised ureteral segment was evaluated histologically, and a healing score was determined. There were no statistically significant overall differences among the mean values of the overall healing score throughout the three different groups. However, when the one-week and the six-week groups (p < .05) were compared with respect to strictures requiring more than one incision due to stricture length greater than 2 centimeters, a more favorable outcome occurred in the 1 week group. Based on these findings it may be reasonable to remove ureteral stents as early as 1 week after endoureterotomy and endopyelotomy.
Curie-Weiss law for almost localized itinerant-electron ferromagnets (2000)

Two mechanisms of the Curie-Weiss law for itinerant-electron ferromagnets are examined by the $1/d$ expansion theory, with d being the spatial dimensionality. One is the temperature dependence of a novel exchange interaction, which is caused by the virtual exchange of pair excitations of quasiparticles in spin channels. It corresponds to that of Weiss' magnetic mean fields, and it is of leading order in $1/d.$ The other is that of the mode-mode coupling between intersite spin fluctuations, and it is of higher order in $1/d.$ When the density of states is almost constant around the Fermi level, the mode-mode coupling is responsible for the Curie-Weiss law as it is in Murata and Doniach's theory or the so-called self-consistent renormalization theory. When the Fermi level is in the vicinity of a sharp peak in the density of states for quasiparticles, on the other hand, Weiss' magnetic mean fields are responsible for the Curie-Weiss law; the mode-mode coupling suppresses the Curie-Weiss law. Unless $T\ensuremath{\ll}{T}_{K},$ with ${T}_{K}$ being the Kondo temperature, local thermal spin fluctuations, which are of leading order in $1/d,$ also contribute to the Curie-Weiss law.
Demonstration of optical heterodyne detection using a mode locked semiconductor laser broad-band coherent probe system (2005)

The experimental results of optical heterodyne detection based on injection locking technique, using two independently modelocked semiconductor laser oscillators are presented. A signal-to-noise ratio of over 60 dB/Hz has been achieved in a demultiplexed channel.
Tuning Energy Levels of Electron‐Transport Materials by Nitrogen Orientation for Electrophosphorescent Devices with an ‘Ideal’ Operating Voltage (2010)

A series of 1,3,5-triazine-core-containing electron-transport materials (ETMs) are reported as an undoped electron-transport layer (ETL), whose energy levels can be tuned by introducing pyridine rings on the periphery of the molecule and also orientation of nitrogen. An unprecedented low operating voltage of 2.42 V, corresponding to the emitting photon energy (hv), was achieved for the fac-tris(2-phenylpyridine) iridium (Ir(PPy)3) based green phosphorescent OLEDs at 100 cd m−2 without consumption of their efficiency. Moreover, the threshold voltage for electroluminescence can be even 0.1 ∼ 0.2 V lower than the minimum value of hv/e. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Unique poly(dA) poly(dT) B'-conformation in cellular and synthetic DNAs (1987)

Poly(dA).poly(dT), but not B-form DNA, is specifically recognized by experimentally induced anti-kinetoplast or anti-poly(dA).poly(dT) immunoglobulins. Antibody binding is completely competed by poly(dA).poly(dT) and poly(dA).poly(dU) but not by other single- or double-stranded DNA sequences in a right-handed B-form. Antibody interaction with poly(dA).poly(dT) depends on immunoglobulin concentration, incubation time and temperature, and is sensitive to elevated ionic strengths. Similar conformations, for example, (dA)4-6 X (dT)4-6, in the kinetoplast DNA of the parasite Leishmania tarentolae are also immunogenic and induce specific anti-poly(dA).poly(dT) antibodies. These antibody probes specifically recognize nuclear and kinetoplast DNA in fixed flagellated kinetoplastid cells as evidenced by immunofluorescence microscopy. Anti-poly(dA).poly(dT) immunofluorescence is DNase-sensitive and competed by poly(dA).poly(dT), but not other classical double-stranded B-DNAs. Thus, these unique cellular B'-DNA helices are immunogenic and structurally similar to synthetic poly(dA).poly(dT) helices in solution.
Evaluation of the functional properties of cryopreserved buffy coat–derived monocytes for monocyte monolayer assay (2018)

Monocytes from pooled cryopreserved BC PBMNCs can be used reliably to evaluate phagocytic responses of sensitized RBCs and to assess clinical significance of RBC alloantibodies.
The influence of the crankshaft offset on the piston position, the indicated specific fuel economy and the emissions of a direct-injection diesel engine (2014)

The effect of offsetting the crankshaft from the cylinder centre-line by 20 mm towards the thrust side was investigated. The effect on the piston top-dead-centre and bottom-dead-centre positions, the valve timing requirements, the indicated performance and the emissions was examined. The investigation was carried out on a common-rail direct-injection diesel engine. The compression ratio was maintained constant, but the piston’s top-dead-centre position and the piston’s bottom-dead-centre position occur 5.5° crank angle later and 10.5° crank angle later respectively than for the zero-offset case. Camshaft position changes were used to retain either the same valve overlap or the same inlet and exhaust valve opening times as for the zero-offset case. The results show that the indicated performance changes are small and that the direction of change can vary with the operating condition. The largest changes in the nitrogen oxide emissions were consistently increases; the largest changes in the carbon monoxide emissions and the filter smoke number were consistently reductions. Small increases in the indicated specific fuel consumption occurred in the low-load cases and a larger reduction occurred in one of the high-load cases. The indicated mean effective pressure fell in the low-load condition and increased or was unchanged in the high-load condition. Overall, the effect of the offset on the indicated performance is minor and secondary to the effect on the rubbing friction; the results are similar when either the valve overlap or the valve opening time was maintained when the crankshaft was offset.
<title>Extension of tailored design method: illumination with a collimated annular source</title> (1999)

Many commercially available sources can be modeled as collimated, annular sources. We use a tailored central-ray method to concentrate light from such a source onto a cylindrical target. The design method is a straightforward extension of methods previously describing for point sources. The device was developed and is now being used for a commercial application.
Introduction of a New Carrier System for Collective Die-to-Wafer Hybrid Bonding and Laser-Assisted Die Transfer (2020)

Current roadblocks within the collective die-to-wafer bonding flow, limiting die-transfer yield and throughput, are identified and discussed. Based on the obtained assessment a new carrier system is introduced. The use of the ultra-soft and highly-UV-transparent BrewerBOND <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">®</sup> C1301 material and its compatibility with BrewerBOND <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">®</sup> 701 laser release material, which is coated on top of ultra-thin dies, allows for a room temperature, ultra-low force collective bonding with laser-assisted die transfer sequence.