gebhart/patrepeval huggingface dataset:
A Parallel Approach to XML Parsing (2006)

A language for semi-structured documents, XML has emerged as the core of the Web services architecture, and is playing crucial roles in messaging systems, databases, and document processing. However, the processing of XML documents has a reputation for poor performance, and a number of optimizations have been developed to address this performance problem from different perspectives, none of which have been entirely satisfactory. In this paper, we present a seemingly quixotic, but novel approach: parallel XML parsing. Parallel XML parsing leverages the growing prevalence of multicore architectures in all sectors of the computer market, and yields significant performance improvements. This paper presents our design and implementation of parallel XML parsing. Our design consists of an initial preparsing phase to determine the structure of the XML document, followed by a full, parallel parse. The results of the preparsing phase are used to help partition the XML document for data parallel processing. Our parallel parsing phase is a modification of the libxml2 in Veillard, D. (2004) XML parser, which shows that our approach applies to real-world, production quality parsers. Our empirical study shows our parallel XML parsing algorithm can improved the XML parsing performance significantly and scales well
A Convenient Method for the Preparation of 4-Aryloxyphenols (1991)

A convenient method for the preparation of 4-aryloxyphenols via the homologation of preformed phenols is described. Condensation of various 4-substituted phenols with either 4-fluorobenzaldehyde (8) or 4-fluoroacetophenone (9) yielded the corresponding 4-aryloxybenzaldehydes, 10, and acetophenones, 11, in 70-93 % yield. Baeyer-Villiger oxidation of these materials with 3-chloroperoxybenzoic acid (MCPBA) yielded the corresponding 4-formyloxy and 4-acetoxyphenyl ethers which were hydrolyzed without purification to the desired 4-aryloxyphenols 12 in 72-94 % yield. Both 4-fluorobenzaldehyde (8) and 4-fluoroacetophenone (9) are synthetically equivalent to the a4 umpoled synthon 6. Extension of this methodology of the preparation of 4,4′-[arylbis(oxy)]bisphenols from aromatic diols is also described. Condensation of various aromatic diols with 8 or 9 yielded the corresponding 4,4′[arylbis(oxy)]bisbenzaldehydes 15 and acetophenones 16 in 71-89 % yield. Baeyer-Villiger oxidation of these compounds with MCPBA yielded the desired 4,4′-[arylbis(oxy)]bisphenyl bisformates 17 and bisacetates 18 in 67-84 % yield. Hydrolysis of these compounds afforded the desired 4,4′-[arylbis(oxy)]bisphenols 19 in 70-91% yield.
Effect of stellar activity on the high precision transit light curve (2015)

Stellar activity features such as spots and plages can create difficulties in determining planetary parameters through spectroscopic and photometric observations. The overlap of a transiting planet and a stellar spot, for instance, can produce anomalies in the transit light curve that may lead to inaccurate estimation of the transit duration, depth, and timing. Such inaccuracies can affect the precise derivation of the planet’s radius. In this talk we will present the results of a quantitative study on the effects of stellar spots on high precision transit light curves. We show that spot anomalies can lead to the estimate of a planet radius that is 4% smaller than the real value. The effects on the transit duration can also be of the order of 4%, longer or shorter. Depending on the size and distribution of spots, anomalies can also produce transit timing variations with significant amplitudes. For instance, TTVs with signal amplitudes of 200 seconds can be produced by spots as large as the largest sunspot. Finally, we examine the impact of active regions on the transit depth measurements in different wavelengths, in order to probe the impact of this effect on transmission spectroscopy measurements. We show that significant (up to 10%) underestimation/overestimation of the planet-to-star radius ratio can be measured, especially in the short wavelength regime.
The role of tyrosine phosphorylation in signal transduction through surface Ig in human B cells. Inhibition of tyrosine phosphorylation prevents intracellular calcium release (1991)

Cross-linking surface Ig on human B cells, or the TCR complex on T cells leads to the rapid appearance of newly tyrosine phosphorylated proteins. This is associated with inositol phospholipid turnover and a rise in intracellular calcium. Incubation of human B or T lymphocytes with the tyrosine kinase inhibitors, herbimycin and genistein, inhibits new tyrosine phosphorylation after receptor-linked activation. This is associated with complete abrogation of the increase in intracellular calcium in these lymphocytes and inhibition of inositol phospholipid turnover. Herbimycin- and genistein-treated lymphocytes are nevertheless still capable of responding to aluminum fluoride with a rise in intracellular calcium. These data support the contention that a B cell-associated protein tyrosine kinase regulates signal transduction via phospholipase C. CD45, the membrane associated protein tyrosine phosphatase, and PMA that activates protein kinase C, both inhibit the calcium response in B lymphocytes induced by receptor cross-linking. PMA and cross-linking CD45 both induced the appearance of tyrosine phosphorylated proteins in human B cells, although the pattern is quite distinct from that seen when surface lg is cross-linked. However, the induction of new tyrosine phosphorylation by anti-mu does not appear to be affected by these reagents. Although this may reflect an insensitivity of the tyrosine phosphorylation assay, it could indicate that regulation of the calcium response and regulation of the tyrosine kinase can be independent processes.
Real Time Monitoring of Permeability, Elastic Moduli and Strength in Sands and Shales Using Digital Rock Physics (2003)

Abstract The Digital Rock Physics (DRP) technology is based on a rigorous numerical simulation of physical experiments in a realistic pore space, at the pore-scale level. The output is usually a macroscopic property conventionally measured in the lab. For example, single-phase viscous fluid flow simulation through a digitized pore space provides absolute permeability. A simulation of electrical current provides conductivity, and a simulation of the stress field provides the elastic moduli and strength. DRP complements lab measurements and, at the same time, enormously enhances the geoscientist's capabilities because digital experiments can be conducted in real time and on small fragments of rock, such as drill cuttings. In this paper, results of a feasibility study on DRP technology is reported using for the first time the drill cutting samples in obtaining petrophysical properties including permeability and porosity of formations. This real-time technology may become very beneficial to the industry once it is established that the results are reliable. The 3D digital pore space needed for numerical simulation has been recreated from 2D images by means of statistical simulation. An example is also presented where the 3D digital pore space was obtained by direct CT scanning of drill cutting. The resulting macroscopic rock properties have been compared to independently obtained core data from laboratory measurements and log data from the same interval where cuttings are obtained.
PREPARE: Predictive Performance Anomaly Prevention for Virtualized Cloud Systems (2012)

Virtualized cloud systems are prone to performance anomalies due to various reasons such as resource contentions, software bugs, and hardware failures. In this paper, we present a novel Predictive Performance Anomaly Prevention (PREPARE) system that provides automatic performance anomaly prevention for virtualized cloud computing infrastructures. PREPARE integrates online anomaly prediction, learning-based cause inference, and predictive prevention actuation to minimize the performance anomaly penalty without human intervention. We have implemented PREPARE on top of the Xen platform and tested it on the NCSU's Virtual Computing Lab using a commercial data stream processing system (IBM System S) and an online auction benchmark (RUBiS). The experimental results show that PREPARE can effectively prevent performance anomalies while imposing low overhead to the cloud infrastructure.
Formation of oxygen vacancies and Ti3+ state in TiO2 thin film and enhanced optical properties by air plasma treatment (2016)

This is the first time we report that simply air plasma treatment can also enhances the optical absorbance and absorption region of titanium oxide (TiO2) films, while keeping them transparent. TiO2 thin films having moderate doping of Fe and Co exhibit significant enhancement in the aforementioned optical properties upon air plasma treatment. The moderate doping could facilitate the formation of charge trap centers or avoid the formation of charge recombination centers. Variation in surface species viz. Ti(3+), Ti(4+), O(2-), oxygen vacancies, OH group and optical properties was studied using X-ray photon spectroscopy (XPS) and UV-Vis spectroscopy. The air plasma treatment caused enhanced optical absorbance and optical absorption region as revealed by the formation of Ti(3+) and oxygen vacancies in the band gap of TiO2 films. The samples were treated in plasma with varying treatment time from 0 to 60 seconds. With the increasing treatment time, Ti(3+) and oxygen vacancies increased in the Fe and Co doped TiO2 films leading to increased absorbance; however, the increase in optical absorption region/red shift (from 3.22 to 3.00 eV) was observed in Fe doped TiO2 films, on the contrary Co doped TiO2 films exhibited blue shift (from 3.36 to 3.62 eV) due to Burstein Moss shift.
A Live Attenuated Equine H3N8 Influenza Vaccine Is Highly Immunogenic and Efficacious in Mice and Ferrets (2014)

Equine influenza viruses have crossed the species barrier to infect other mammals such as dogs, pigs, and camels and therefore may also pose a threat to humans. We believe that it is important to develop vaccines against equine influenza viruses in the event that an EIV evolves, adapts, and spreads in humans, causing disease. We generated a live attenuated H3N8 vaccine candidate and demonstrated that the vaccine was immunogenic and protected mice and ferrets against homologous and heterologous EIV.
Inflammasome-Dependent Release of the Alarmin HMGB1 in Endotoxemia (2010)

Endotoxin administration recapitulates many of the host responses to sepsis. Inhibitors of the cysteine protease caspase 1 have long been sought as a therapeutic because mice lacking caspase 1 are resistant to LPS-induced endotoxic shock. According to current thinking, caspase 1-mediated shock requires the proinflammatory caspase 1 substrates IL-1β and IL-18. We show, however, that mice lacking both IL-1β and IL-18 are normally susceptible to LPS-induced splenocyte apoptosis and endotoxic shock. This finding indicates the existence of another caspase 1-dependent mediator of endotoxemia. Reduced serum high mobility group box 1 (HMGB1) levels in caspase 1-deficient mice correlated with their resistance to LPS. A critical role for HMGB1 in endotoxemia was confirmed when mice deficient for IL-1β and IL-18 were protected from a lethal dose of LPS by pretreatment with HMGB1-neutralizing Abs. We found that HMGB1 secretion from LPS-primed macrophages required the inflammasome components apoptotic speck protein containing a caspase activation and recruitment domain (ASC), caspase 1 and Nalp3, whereas HMGB1 secretion from macrophages infected in vitro with Salmonella typhimurium was dependent on caspase 1 and Ipaf. Thus, HMGB1 secretion, which is critical for endotoxemia, occurs downstream of inflammasome assembly and caspase 1 activation.
Regulation of connective tissue growth factor gene expression in human skin fibroblasts and during wound repair. (1993)

Connective tissue growth factor (CTGF) is a cysteine-rich peptide that exhibits platelet-derived growth factor (PDGF)-like biological and immunological activities. CTGF is a member of a family of peptides that include serum-induced immediate early gene products, a v-src-induced peptide, and a putative avian transforming gene, nov. In the present study, we demonstrate that human foreskin fibroblasts produce high levels of CTGF mRNA and protein after activation with transforming growth factor beta (TGF-beta) but not other growth factors including PDGF, epidermal growth factor, and basic fibroblast growth factor. Because of the high level selective induction of CTGF by TGF-beta, it appears that CTGF is a major autocrine growth factor produced by TGF-beta-treated human skin fibroblasts. Cycloheximide did not block the large TGF-beta stimulation of CTGF gene expression, indicating that it is directly regulated by TGF-beta. Similar regulatory mechanisms appear to function in vivo during wound repair where there is a coordinate expression of TGF-beta 1 before CTGF in regenerating tissue, suggesting a cascade process for control of tissue regeneration and repair.
Enhanced pneumonia resolution by inhalation of nitric oxide? (1993)

We present a patient with severe bacteraemic pneumococcal pneumonia associated with severe hypoxaemia, where nitric oxide (NO) 15-40 ppm was added to the inspired gas. Nitric oxide therapy improved gas exchange, reduced pulmonary vasoconstriction and peak airway pressure. The patient survived. We observed an unexpected rapid and complete disappearance of bilateral pulmonary infiltrates during the first 120 h of the 7-day NO inhalation period.
Effects of calcitonin gene-related peptide on normal and atheromatous vessels and on resistance vessels in the coronary circulation in humans. (1991)

These data indicate that CGRP has little effect in humans at rest on coronary resistance vessels in nonischemic myocardium but causes marked dilatation of normal arteries and variable dilatation of atheromatous epicardial arteries.
Improved peak detection in mass spectrum by incorporating continuous wavelet transform-based pattern matching (2006)

The algorithm is implemented in R and will be included as an open source module in the Bioconductor project.
[Antitumor effect of human lactoferrin against newly established human pancreatic cancer cell line SPA]. (1998)

This paper describes the antitumor effect of human lactoferrin against the human pancreatic cancer cell line SPA, which was newly established in our laboratory from a metastatic liver tumor of pancreatic origin. In tissue culture, the cancer cells proliferated rapidly at 16 hours of doubling time, and produced tumor markers into the culture medium at a high concentration. Subcutaneous and intraperitoneal transplantation of these neoplastic cells into nude mice resulted in tumor formation and carcinomatous peritonitis. The inhibitory effect of human lactoferrin on the cell growth of SPA was found both in vivo and in vitro. There was significant inhibition of cell growth in vivo at the concentration of 1 microgram/ml of hLf in the culture medium. And in the in vivo assay, hLf delayed the growth of subcutaneously transplanted tumors into BALB/c nude mice, and the effect was retained for two weeks. These results indicate the possibility that hLf will become one of the new drugs for adjuvant therapy against pancreatic cancer.
The Relationship Between Charge Movements Associated with I Ca and I Na-Ca in Cardiac Myocyte (1990)

Ventricular myocytes exhibit a nifedipine-sensitive inward calcium current (ICa) and contracture when they are voltage clamped from -40 to 0 millivolt in the presence of caffeine and in the absence of extracellular sodium. However, upon repolarization they fail to relax because neither the sarcoplasmic reticulum nor the sodium-calcium exchange can reduce intracellular calcium. Sudden application of extracellular sodium during the contracture (but after repolarization) causes immediate relaxation and activates a transient inward sodium-calcium exchange current (INa-Ca), whose peak slightly precedes mechanical relaxation. The total charge carried by the nifedipine-sensitive ICa is twice the total charge carried by the transient inward INa-Ca. Assuming an exchange stoichiometry of three sodium to one calcium, these results indicate that all the calcium entering the cell during the initial depolarization is extruded by the sodium-calcium exchange.
Cell-free biosynthesis of surfactin, a cyclic lipopeptide produced by Bacillus subtilis (1991)

The lipopeptide antibiotic surfactin is a potent extracellular biosurfactant produced by various Bacillus subtilis strains. Biosynthesis of surfactin was studied in a cell-free system prepared from B. subtilis ATCC 21332 and OKB 105, which is a transformant producing surfactin in high yield [Nakano, M. M., Marahiel, M. A., & Zuber, P. (1988) J. Bacteriol. 170, 5662-5668]. Cell material was disintegrated by treatment with lysozyme and French press. A cell-free extract was prepared by ammonium sulfate fractionation, which catalyzed the formation of surfactin at the expense of ATP. Lipopeptide biosynthesis required the L-amino acid components of surfactin and D-3-hydroxytetradecanoyl-coenzyme A thioester. D-Leucine which is present in surfactin was not utilized but inhibited the biosynthetic process. The structure of surfactin, synthesized enzymatically in vitro, was confirmed by chromatographic comparison with the authentic compound and by amino acid analyses. An enzyme fraction was prepared by gel permeation chromatography which catalyzed ATP/pyrophosphate exchange reactions dependent on the component amino acids of surfactin. This enzyme fraction was capable of binding substrate amino acids covalently, probably via thioester linkages. The formation of these intermediates was inhibited by various thiol blocking reagents and phenylmethanesulfonyl fluoride. De novo synthesis of the lipopeptide was not observed with this partially purified enzyme fraction most likely due to the lack of an acyltransferase activity required for linking the beta-hydroxy fatty acid to the peptide moiety.
Hepatic Autophagy in Uncontrolled Experimental Diabetes and Its Relationships to Insulin and Glucagon (1974)

Exogenous glucagon is known to increase hepatic lysosomes, but the relationships between endogenous glucagon and insulin levels and hepatic lysosomes have not been examined. To determine if the hormones of the pancreatic islets influence the development of these organelles glycogenosomes, dense bodies, and autophagosomes were morphometrically quantitated in normal rats, in rats with mild streptozotocin diabetes with normal hormone levels, and in rats with severe streptozotocin diabetes with hyperglucagonemia, hypo-insulinemia, and clinical evidence of uncontrolled diabetes and ketoacidosis. In the latter volume density of lysosomes averaged 222.8x10(-4) (SEM +/-19.8x10(-4)), significantly above the control value of 75x10(-4) (SEM +/-7.0x10(-4)) (P<0.0005); glycogenosomes were absent in the diabetics, the increase being largely the result of increased autophagosomes. Insulin treatment corrected the hyperglucagonemia, hypoinsulinemia, and other manifestations of uncontrolled diabetes and reduced the volume density of lysosomes to 37.4x10(-4) (SEM +/-2.0x10(-4)), significantly below both the untreated diabetic rats and the nondiabetic controls (P<0.0025). In mild streptozotocin diabetes, in which hyperglucagonemia, hypoinsulinemia, and other evidence of uncontrolled diabetes were absent, lysosomes averaged 77.6x10(-4) (SEM +/-5.5x10(-4)), not different from the controls. A statistically significant correlation between all measurements of lysosomal volume density and plasma glucagon was observed (r=0.79; P<0.001). It is concluded that uncontrolled streptozotocin diabetes in rats is accompanied by hepatic autophagy which may be related to the increased plasma glucagon level and/or the decreased insulin and which is corrected by insulin therapy.
Topography of Polymer Chains Grafted on a Polymer Surface Underwater (1997)

The topography of water-soluble polymer chains immobilized on a rigid polymer surface underwater was studied using atomic force microscopy (AFM). As the substrate polymer a smooth poly(ethylene terephthalate) (PET) film was employed and polymer chains of various lengths were chemically immobilized by surface graft polymerization of 2-(dimethylamino)ethyl methacrylate onto the film using the UV-induced graft polymerization method. The degree of polymerization (N) of graft chains ranged from 28 to 960. Except for the shortest chains (N = 28) the graft polymer chains were found to stretch out on the substrate underwater, forming a brush structure. The graft layers exhibited inhomogeneous structure, that is, clusters. This cluster formation was ascribed to substantially poor solvency of water for the graft polymer chain. AFM scanning performed at varying loads from 0.25 to 10 nN underwater revealed that, with the increasing graft chain length, AFM images underwater exhibited deformation (tilting) of the clusters at loads higher than 2.5 nN, unlike those in air. When a fixed area of the grafted surface was subjected to cyclic scanning, the tilting direction of clusters was completely in accordance with the scanning direction, and the image of tilting clusters was reproducible. This suggests that the tilting of clusters is reversible, recovering to the previous unperturbed shape as soon as the loading tip has been taken away. The lateral structure of the polymer chains grafted onto the smooth surface underwater was compared with that predicted by brush theories.
Dietary α‐linolenic acid alters tissue fatty acid composition, but not blood lipids, lipoproteins or coagulation status in humans (1993)

We examined the effect of dietary alpha-linolenic acid (ALA) on the indices of lipid and coagulation status and on the fatty acid composition of serum and peripheral blood mononuclear cell (PBMNC) lipids in ten healthy men (age 21-37 yr) who consumed all their meals at the Western Human Nutrition Research Center for 126 d. There was a stabilization period of 14 d at the start when all 10 subjects consumed the basal diet (BD) containing 23.4 energy percent (en%) fat and two intervention periods of 56 d each. During the first intervention period, 5 subjects consumed the BD containing 23.4 en% fat, and 5 subjects consumed a diet providing 6.3% calories from alpha-linolenic acid [flaxseed oil (FSO) diet containing 28.8 en% fat]. Diets were crossed over between the two groups during the second intervention period. Feeding the FSO diet did not significantly alter serum triglycerides, cholesterol, high-density lipoproteins, low-density lipoproteins, apoprotein A-I and apoprotein B when compared to the corresponding values in the subjects fed the BD, nor was there any effect of the FSO diet on the bleeding time, prothrombin time and partial prothrombin time for these subjects. Feeding the ALA-containing diet did cause a significant increase in ALA concentration in serum (P < 0.001) and PBMNC lipids (P < 0.05). It also caused a significant increase (P < 0.05) in the eicosapentaenoic and docosapentaenoic acid contents of PBMNC lipids, and a decrease (P < 0.01) in linoleic and eicosatrienoic acid contents of serum lipids.(ABSTRACT TRUNCATED AT 250 WORDS)
Ambipolar Field‐Effect Transistor (FET) and Redox Characteristics of a π‐Conjugated Thiophene/1,3,4‐Thiadiazole CT‐Type Copolymer (2005)

Abstract Summary: A π ‐conjugated charge transfer‐type copolymer consisting of an electron‐donating thiophene and an electron‐accepting 1,3,4‐thiadiazole, P(ThdzTh), underwent facile electrochemical p ‐ and n ‐doping, as revealed by cyclic voltammetry. The copolymer gave a new ambipolar field‐effect transistor (FET), which showed typical I DS (source–drain current)– V DS (source–drain voltage) curves in both a p ‐type working mode and an n ‐type working mode. In the n ‐type working mode, the polymer showed a carrier mobility of about 5 × 10 −3 cm 2 · V −1 · s −1 and an on/off ratio of about 3 × 10 4 . n ‐Channel field‐effect transistor characteristics of P(ThdzTh). magnified image n ‐Channel field‐effect transistor characteristics of P(ThdzTh).