gebhart/patrepeval huggingface dataset:
Productive and efficient computational science through domain-specific abstractions (2014)

In an ideal world, scientific applications are computationally efficient, maintainable and composable and allow scientists to work very productively. We argue that these goals are achievable for a specific application field by choosing suitable domain-specific abstractions that encapsulate domain knowledge with a high degree of expressiveness. This thesis demonstrates the design and composition of domain-specific abstractions by abstracting the stages a scientist goes through in formulating a problem of numerically solving a partial differential equation. Domain knowledge is used to transform this problem into a different, lower level representation and decompose it into parts which can be solved using existing tools. A system for the portable solution of partial differential equations using the finite element method on unstructured meshes is formulated, in which contributions from different scientific communities are composed to solve sophisticated problems. The concrete implementations of these domain-specific abstractions are Firedrake and PyOP2. Firedrake allows scientists to describe variational forms and discretisations for linear and non-linear finite element problems symbolically, in a notation very close to their mathematical models. PyOP2 abstracts the performance-portable parallel execution of local computations over the mesh on a range of hardware architectures, targeting multi-core CPUs, GPUs and accelerators. Thereby, a separation of concerns is achieved, in which Firedrake encapsulates domain knowledge about the finite element method separately from its efficient parallel execution in PyOP2, which in turn is completely agnostic to the higher abstraction layer. As a consequence of the composability of those abstractions, optimised implementations for different hardware architectures can be automatically generated without any changes to a single high-level source. Performance matches or exceeds what is realistically attainable by hand-written code. Firedrake and PyOP2 are combined to form a tool chain that is demonstrated to be competitive with or faster than available alternatives on a wide range of different finite element problems.
Characteristic pore sizes and transport in porous media (1987)

Analytic calculations of \ensuremath{\Lambda}, a pore-size parameter which characterizes surface effects on transport in porous media, are carried out using two distinct approximations: (1) effective-medium theory and (2) percolation ideas recently applied by Katz and Thompson to the permeability of sedimentary rocks. Our calculations suggest that \ensuremath{\Lambda} may be determined by mercury injection experiments. We also study the phenomenon of electrical surface conduction using both approximations.
How useful are non-blocking loads, stream buffers and speculative execution in multiple issue processors? (2002)

We investigate the relative performance impact of non-blocking loads, stream buffers, and speculative execution both used individually and in conjunction with each other. We have simulated the SPEC92 benchmarks on a statically scheduled quad-issue processor model, running code from the Multiflow compiler. Non-blocking loads and stream buffers both provide a significant performance advantage, and their combination performs significantly better than either alone. For example, with a 64-byte, 2-way set associative cache with 32 cycle fetch latency, non-blocking loads reduce the run-time by 21% while stream-buffers reduce it by 26%, and the combined use of the two yields a 47% reduction. The addition of speculative execution further improves the performance of the systems that we have simulated, with or without non-blocking loads and stream buffers, by an additional 20% to 4O%. We expect that the use of all three of these techniques will be important in future generations of microprocessors.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
The effect of prostaglandins and thromboxane A2 on coronary vessel tone--mechanisms of action and therapeutic implications. (1993)

Prostaglandins (PGI2, PGE2, PGF2 alpha) and thromboxane (TX) A2 are vasoactive, cell membrane-derived lipid mediators that are formed in response to stimulation of vascular smooth muscle cells by a variety of chemical agonists. Different receptor subtypes mediate the contractile and relaxing effects of prostaglandins and TXA2 on coronary vascular smooth muscle: a high-affinity (kD: > or = 1 nM) PGH2/TXA2 receptor mediates the contractile actions of TXA2; a low-affinity (kD 100-200 nM) receptor mediates the contractile actions of other prostaglandins ('primary prostaglandin receptor') and a PGI2 receptor (kD > or = 20 nM) mediates vessel relaxation. These receptors are coupled to intracellular signal transduction pathways via different G-proteins and modify muscle tone by control of cytosolic Cai++. Ca(++)- and ATP-dependent K-channels are regulated by PGI2 (opening) and TXA2 (closure) and are involved in the setting of coronary smooth muscle tone. There is experimental and clinical evidence for enhanced local TXA2 levels, an increased number of platelet TXA2 receptors and a reduced number of PGI2 receptors in acute myocardial infarction. There is also experimental evidence for increased synthesis of PGF2 alpha-receptors in vascular smooth muscle that may mediate smooth muscle proliferation. The interference of both TXA2 and PGI2 with K(+)-channels in coronary arteries may have important implications for coronary vasospasm and ischaemia-related cardiac hypoperfusion.
Monoclonal antibodies to purified muscarinic receptor display agonist-like activity. (1984)

Monoclonal antibody M-35, which immunoprecipitates native calf brain acetylcholine muscarinic receptor, mimics agonist stimulation of the intact guinea pig myometrium: the antibody, just like carbamoylcholine hydrochloride, causes a rise in intracellular cyclic GMP content, an inhibition of cyclic AMP accumulation due to prostacyclin, and induces uterine contractions. Another antibody, M-23, which reacts with the denatured muscarinic receptor, is devoid of agonist-like activity at the cyclic nucleotide level but is still able to induce contractions of both rat and guinea pig myometrium. The cyclic nucleotide changes caused by both carbamoylcholine and antibody M-35 are inhibited by atropine; this antagonist, which blocks carbamoylcholine-mediated contractions, fails however, to prevent contractions induced by antibodies M-35 and M-23. These results suggest that the information necessary to transmit muscarinic signals is entirely contained in the receptor and that ligands only act to trigger the biological response. The data also imply that the muscarinic receptors of the myometrium are coupled to multiple effector systems.
Role of a<i>Candida albicans</i>P1-Type ATPase in Resistance to Copper and Silver Ion Toxicity (2000)

Copper ion homeostasis is complicated in that copper is an essential element needed for a variety of cellular processes but is toxic at excess levels. To identify Candida albicans genes that are involved in resistance to copper ion toxicity, a library containing inserts of C. albicans genomic DNA was used to complement the copper sensitivity phenotype of a Saccharomyces cerevisiae cup1Delta strain that is unable to produce Cup1p, a metallothionein (MT) responsible for high-level copper ion resistance. A P1-type ATPase (CPx type) that is closely related to the human Menkes and Wilson disease proteins was cloned. The gene encoding this pump was termed CRD1 (for copper resistance determinant). A gene encoding a 76-amino-acid MT similar to higher eukaryotic MTs in structure was also cloned, and the gene was termed CRD2. Transcription of the CRD1 gene was found to increase upon growth with increasing copper levels, while the CRD2 mRNA was expressed at a constant level. Strains with the CRD1 gene disrupted were extremely sensitive to exogenous copper and failed to grow in medium containing 100 microM CuSO(4). These crd1 strains also exhibited increased sensitivity to silver and cadmium, indicating that Crd1p is somewhat promiscuous with respect to metal ion transport. Although strains with the CRD2 gene disrupted showed reduced growth rate with increasing copper concentration, the crd2 mutants eventually attained wild-type levels of growth, demonstrating that CRD2 is less important for resistance to copper ion toxicity. Crd1p is the first example of a eukaryotic copper pump that provides the primary source of cellular copper resistance, and its ability to confer silver resistance may enhance the prevalence of C. albicans as a nosocomial pathogen.
Oxygen-Bridged Borate Anions from Tris(pentafluorophenyl)borane:  Synthesis, NMR Characterization, and Reactivity (2005)

The previously known anion [(C6F5)3B(mu-OH)B(C6F5)3]- (2) has been prepared by a two-step procedure, involving deprotonation of (C6F5)3BOH2 to give [B(C6F5)3OH]- (1), followed by addition of B(C6F5)3. The solution structure and the dynamics of 2 have been investigated by 1H and 19F NMR spectroscopy. The reaction of [NHEt3]2 with NEt3 resulted in the formation of [NHEt3]+ [(C6F5)3BOH]-, [NHEt3]+ [(C6F5)3BH]-, and (C6F5)3B- (CH2CH=N+ Et2). This indicates that in the presence of a nucleophile anion 2 can dissociate to B(C6F5)3 and 1. The reaction of [HDMAN]2 with 1,8-bis(dimethylamino)naphthalene (DMAN) confirmed this trend. In the presence of water, 2 transformed into the adduct [(C6F5)3BO(H)H...O(H)B(C6F5)3]- (3), containing the borate 1 hydrogen-bonded to a water molecule coordinated to B(C6F5)3. The same compound is formed by treating (C6F5)3BOH2 with 0.5 equiv of a base. A competition study established that for 1 the Lewis acid-base interaction with B(C6F5)3 is about 5 times preferred over H-bonding to (C6F5)3BOH2. The X-ray single-crystal analysis of [2-methyl-3H-indolium]3 provided the first experimental observation of an asymmetric H-bond in the [H3O2]- moiety, the measured O-H and H...O bond distances being significantly different [1.14(2) vs 1.26(2) A]. The reaction of NEt3 with an equimolar mixture of B(C6F5)3 and bis(pentafluorophenyl)borinic acid, (C6F5)2BOH, afforded the novel borinatoborate salt [NHEt3]+ [(C6F5)3BOB(C6F5)2]- ([NHEt3]4). X-ray diffraction showed that the B-O bond distances are significantly shorter than in [(C6F5)3B(mu-OH)B(C6F5)3]-. Variable-temperature 19F NMR revealed high mobility of the five aryl rings, at variance with the more crowded anion 2. 2D NMR correlation experiments showed that in CD2Cl2 the two anions [(C6F5)3BOH]- and [(C6F5)3BH]- form tight ion pairs with [NHEt3]+, in which the NH proton establishes a conventional (BO...HN) or an unconventional (BH...HN), respectively, hydrogen bond with the anion. The diborate anions 2-4, on the contrary, gave loose ion pairs with the ammonium cation, due both to the delocalized anionic charge and to the more sterically encumbered position of the oxygen atoms that should act as H-bond acceptors.
MBE Growth and Optical Properties of Novel Corrugated-Interface Quantum Wells (1988)

We have systematically studied MBE growth and properties of novel corrugated-interface quantum wells, where the GaAs well thickness is modulated with the average period of 32 Å–324 Å along the interface for possible formation of quantum wire states. The modulation is attempted by the alternate deposition of fractional monolayer of GaAs and AlAs on (001) flat and slightly misoriented substrates. Although the 2-dimensional nucleation is dominant in the growth of AlAs at a lower substrate temperature ( T s <600°C) and prevents the formation of modulation, the growth mode on the most misoriented planes is transformed to step flow at a higher T s (≧640°C) under the appropriate growth rate and V/III flux ratio, leading to the formation of quasi-periodic GaAs/AlAs or Al x A Ga 1- x A As/Al x B Ga 1- x B As modulated structures. Measured photoluminescence energies are compared with the theory to demonstrate the composition modulation and the laterally confined quasi-one-dimensional electronic states along the interfaces and also to estimate the periodicity fluctuation and the compositional mixing in GaAs-AlAs modulated structures.
Systemic delivery of human microdystrophin to regenerating mouse dystrophic muscle by muscle progenitor cells (2004)

Cell-based therapy for Duchenne muscular dystrophy patients and mdx mice has proven to be a safe but ineffective form of treatment. Recently, a group of cells called muscle side population (SP) cells have been isolated based on their ability to efflux the DNA-binding dye Hoechst. To understand the potential of skeletal muscle SP cells to serve as precursors for muscle, SP cells from the two mice strains mdx(5cv) and C57BL/6N were isolated, transduced, and transplanted. Under coculture conditions with myogenic cells, some cells within the SP cell population can give rise to early Pax7-positive satellite cells and other later stage myogenic cells. Transduced SP cells were transplanted via the tail vein and were shown to successfully deliver enhanced GFP and human microdystrophin to the skeletal muscle of nonirradiated mdx(5cv) mice, thus demonstrating their ability to travel through the capillaries and enter into damaged muscle. These results demonstrate that i.v. delivery of genes via SP cells is possible and that these SP cells are capable of recapitulating the myogenic lineage. Because this approach shows definitive engraftment by using autologous transplantation of noninjured recipients, our data may have substantial implications for therapy of muscular dystrophy.
Role of Thymosin β4 on Skeletal Myoblast Migration, Proliferation, and Survival (2012)

Massive cell death associated with poor donor cell survival was a limiting factor in the success of myoblast transfer therapy (MTT). The current study is aimed to determine the effects of thymosin & β 4 on human skeletal myoblast (hSkM) migration, proliferation and survival under hypoxia. hSkM was cultured in basal medium (BM, M199 medium with 10% fetal bovine serum) supplemented with various concentrations of thymosin & β 4. Supernatant was collected to test the toxicity of thymosin & β 4 towards hSkM. Cell number was quantified using CyQuant cell proliferation assay kit. Cell viability was determined by calculating the lactate dehydrogenase (LDH) in the supernatant. hSkM migration was determined using cell culture insert. No significant toxicity of thymosin & β 4 towards hSkM was found when thymosin & β 4 was increased up to 600ng/ml. Thymosin & β increased hSkM proliferation rate by 35.4+13.4% at 600ng/ml. It enhanced hSkM viability (cell injury =10.9±1.7%) as compared with control (cell injury = 24.6%, p < 0.05) under hypoxia (5% CO2+ 94% N2+1% O2) for 48 hours (hrs). Increased migration rate (164.5+15/well, p < 0.05 vs control) was achieved with thymosin & β 4 at 100ng/ml concentration. Thymosin & β 4 increased the activities of PI3K and AKT, and reduced the activities of caspases 3 and 8. We conclude that thymosin & β 4 increased hSkM migration and proliferation. It enhanced hSkM viability under hypoxia, providing a new strategy to improve hSkM survival in MTT. Furthermore, recent patents on thymosin & β 4 and skeletal myoblasts as therapeutic agents will be discussed.
Investigation of domain structure in urethan elastomers by X-Ray and thermal methods (1973)

Abstract Wide- and small-angle X-ray diffraction and differential scanning calorimetry have been used to gain some understanding of the extent of domain formation in polyurethans of varying urethan content. The process by which these hard domains and the rubbery polyester (or polyether) chains orient or crystallize upon stretching has been examined. It is shown that the hard-segment domains undergo continuous “restructuration” under stress, especially at elevated temperatures. This leads, in some cases, to extensive stress relaxation but results in highly oriented samples which have extremely high maximum tensile strengths.
Nabumetone: A “Nonacidic” Nonsteroidal Antiinflammatory Drug (1993)

Nabumetone is a prodrug metabolized to an active metabolite structurally related to naproxen. Studies have demonstrated the efficacy of nabumetone, but no advantages over the many other NSAIDs now available.
Recent developments in amperometric detection for microchip capillary electrophoresis (2002)

The interest in microfluidic devices has increased considerably over the past decade due to the numerous advantages of working within a miniature, microfabricated format. This review focuses on recent advances in coupling amperometric detection with microchip capillary electrophoresis (CE). Advances in electrochemical cell design, isolation of the detector from the separation field, and integration of both pre- and postseparation reaction chambers are discussed. The use of microchip CE with amperometric detection for enzyme/immunoassays, clinical and environmental assays, and the determination of neurotransmitters is described.
Study of the origin of bending induced by bimetallic effect on microcantilever (2007)

An analytical model for predicting the deflection and force of a bimaterialcantilever is presented. We introduce the clamping effect characterised by an axial loadupon temperature changes. This new approach predicts a non linear thermal dependence ofcantilever strain. A profilometry technique was used to measure the thermal strain.Comparison with experimental results is used to verify the model. The concordance of theanalytical model presented with experimental measurements is better than 10.
Chemometric Analysis of Nuclear Magnetic Resonance Spectroscopy Data (2000)

Chemometric analysis of nuclear magnetic resonance (NMR) spectroscopy has increased dramatically in recent years. A variety of different chemometric techniques have been applied to a wide range of problems in food, agricultural, medical, process and industrial systems. This article gives a brief review of chemometric analysis of NMR spectral data, including a summary of the types of mixtures and experiments analyzed with chemometric techniques. Common experimental problems encountered during the chemometric analysis of NMR data are also discussed.
An Eigen-Analysis of Compact Antenna Arrays and Its Application to Port Decoupling (2008)

Placing the radiators of antenna arrays closer than aggravates the problem of power mismatch. Based on efficiency considerations, a general analysis of this effect is presented, putting forward a simple tool to quantify, compare, and optimize the performance of antenna arrays. This analysis is not restricted with respect to the number of radiators or the degree of compactness. In order to improve power matching, a systematic approach for the design of lossless decoupling and matching networks based on 180 directional couplers is suggested for up to eight radiators. Implications of network losses, which have not yet received appropriate attention by researchers in the past, will be analyzed and discussed by means of a manufactured three-element prototype array.
<title>High-power diode laser marking and engraving of building materials</title> (1997)

A Diomed 60W-cw high power diode laser (HPDL) has been used for the marking and engraving of various building materials, including; marble, granite, clay tiles, ceramic tiles, roof tiles, ordinary Portland cement (OPC) and clay bricks. Morphological and microstructural characteristics have been investigated. The basic mechanism of marking/engraving and the characteristics of the beam absorption are discussed. The effects of material texture, color and laser processing parameters are reported. The work shows that engraving depths of over 2 mm (0.75 mm for a single pass) can be achieved on marble substrates by thermal disintegration of CaCO<SUB>3</SUB> into loose CaO powder and CO<SUB>2</SUB> gas. Uniform amorphous glazed lines (1 - 3 mm line width) of a color different from the untreated materials can be generated on clay tiles, ceramic tiles, roof tiles, clay bricks and OPC by solidification phase formation after laser melting of these materials. Effects of atmospheric conditions, for instance using O<SUB>2</SUB> and Ar gas shrouds, have been examined, with different colored marks being observed when different shroud gases are used. To demonstrate the practical worth of the process a UMIST crest has been marked on a ceramic tile using the system. Laser beam reflectivity is found to depend not only on material composition but also its color. Reflectivity has been found to range between 12% to 18% for the various construction materials used in the experiment, except for marble (grey) which showed over 27% reflectivity. Since the HPDL is a portable device, on-site application of these processing techniques can be realized, which would be either impossible or difficult when using other types of lasers.
Physical characteristics and performance of synthetic wound dressings. (1975)

From these studies it is concluded that: 1) Physical characteristics of wound dressings can be quantified and evaluated for their contribution to in vivo performance. 2) A total performance scoring system can be reliably used to quantitatively separate series of wound dressings by their in vivo performances. 3) The physical characteristics most determinate of good perfprmance in these 5 series of dressings were undersurface texture and water vapor transmission.
Amniotic fluid thyrotropin (TSH) following maternal administration of thyrotropin releasing hormone (1985)

Cord blood and amniotic fluid thyrotropin (TSH), T4, T3, and rT3 concentrations were measured in 49 women who received 400 micrograms thyrotropin releasing hormone (TRH) iv during labor and in 16 control women who received saline. Cord blood serum TSH concentrations were elevated for as long as 4 hours after TRH administration and peak values (38.0 +/- 4.2 microU/ml) were observed from 61-120 minutes after TSH as compared to control values of 5.0 +/- 0.3 microU/ml. The elevations in fetal TSH concentration stimulated the fetal thyroid, resulting in a progressive increase in cord blood T4 and T3 but not rT3 concentrations. These TRH induced elevations in fetal cord blood TSH concentrations were not accompanied by increases in unconcentrated and 4 fold concentrated amniotic fluid TSH concentrations which were almost always below 0.6 microU/ml, the limit of assay sensitivity. Unconcentrated amniotic fluid T4 concentrations were barely detectable and no variation was observed between the TRH treated and saline treated mothers; amniotic fluid T3 was not detectable in any of the groups; and amniotic fluid rT3 concentrations ranged between 46.4 and 55.6 ng/dl and did not differ between groups. These findings suggest that term amniotic fluid TSH values do not reflect transient but marked elevations in fetal serum TSH concentrations and that amniotic fluid TSH determination is probably not useful in the detection of primary fetal hypothyroidism. It is possible, but unlikely, that long-term and even greater elevations in fetal serum TSH concentrations would result in increased amniotic fluid TSH concentrations.(ABSTRACT TRUNCATED AT 250 WORDS)
Akt activation and localisation correlate with tumour invasion and oncogene expression in thyroid cancer (2004)

These data suggest an important role for nuclear activation of Akt 1 in thyroid cancer progression.