gebhart/patrepeval huggingface dataset:
Bismuth-mediated disruption of the glycocalyx- cell wall of Helicobacter pylori:ultrastructural evidence for a mechanism of action for bismuth salts (1999)

The mechanism of bismuth's bactericidal activity against Helicobacter pylori was investigated using transmission electron microscopy (TEM) and analytical electron microscopy (AEM); time-kill kinetic methods evaluated the effect of excess divalent cations. TEM analysis of untreated H. pylori revealed a normal morphology. In contrast, H. pylori exposed to bismuth salts had swollen, distorted cells with membrane-cell wall blebbing and a cytoplasm containing electron-dense, sometimes crystalline aggregates. By AEM, swollen cells contained bismuth at the cell periphery, whereas bacillary forms contained cytoplasmic bismuth localizations. Time-kill studies showed that the bactericidal activity of bismuth could be prevented by pretreatment with divalent cations. The effects of bismuth salts on the glycocalyces-cell walls of H. pylori with reversal of bactericidal activity by divalent cations are identical to those produced by other polycationic agents on various gram-negative bacilli. We conclude that disruption of the glycocalyces-cell walls of H. pylori is one mechanism of action for bismuth salts.
Laser ablation of solid substrates in a water-confined environment (2001)

Laser ablation of Si under a water surface has been investigated. The laser used is a KrF excimer laser, which has a wavelength of 248 nm and a pulse duration of 23 ns. It is found that the laser ablation rate of Si varies with the thickness of the water layer above the Si substrates. The laser ablation rate is the most highly enhanced with a water layer of 1.1 mm. It is assumed that the plasma generated in the water confinement regime with an optimal water layer thickness induces the strongest pressure. This high-pressure, high-temperature plasma results in the highest ablation rate. A wide-band microphone is used to detect the audible acoustic wave generated during the laser ablation. The amplitude of the acoustic wave is closely related to the ablation rate. It is found that the first peak-to-peak amplitude of the acoustic wave is the strongest when the water layer thickness is 1.1 mm above the substrate. Fast Fourier transform analysis of the wave forms shows that there are several frequency components included in the acoustic waves. The dominant frequency component decreases from 10.6 to 3.5 kHz as the water layer thickness varies from 1 to 2.2 mm. Diagnostics of the acoustic wave emission can be used to find the optimal water layer thickness to enhance the laser ablation rate. With proper calibration, acoustic-wave detection can be used as a real-time monitoring of the laser ablation.
Microfilament-associated Protein 7 Increases the Membrane Expression of Transient Receptor Potential Vanilloid 4 (TRPV4) (2003)

The molecular mechanism of the transmission of changes in the shape of the cell surface to ion channels remains obscure. Ca2+ influx induced by cell deformity is inhibited by actin-freezing reagents, suggesting that the actin microfilament couples with an ion channel. Transient receptor potential vanilloid 4 (TRPV4) is a candidate in the calcium-permeable, swelling-activated mechanosensitive channel in heterogeneously expressed cells. To investigate the mechanosensitive molecular complex, we found that microtubule-associated protein 7 (MAP7) is the mouse TRPV4 C-terminal binding protein. MAP7 was coimmunoprecipitated with TRPV4. The results of a pull-down assay demonstrated that the alignment of amino acids 798-809 of TRPV4 was important in this interaction. TRPV4 and MAP7 colocalized in the lung and kidney. The coexpression of these two molecules resulted in the redistribution of TRPV4 toward the membrane and increased its functional expression. The alignment of amino acids 798-809 of TRPV4 was also important in the functional expression. The activated current was abolished by actin-freezing but not by microtubule-freezing reagents. We therefore believe that MAP7 may enhance the membrane expression of TRPV4 and possibly link cytoskeletal microfilaments.
Security Requirements Engineering: A Framework for Representation and Analysis (2008)

This paper presents a framework for security requirements elicitation and analysis. The framework is based on constructing a context for the system, representing security requirements as constraints, and developing satisfaction arguments for the security requirements. The system context is described using a problem-oriented notation, then is validated against the security requirements through construction of a satisfaction argument. The satisfaction argument consists of two parts: a formal argument that the system can meet its security requirements and a structured informal argument supporting the assumptions expressed in the formal argument. The construction of the satisfaction argument may fail, revealing either that the security requirement cannot be satisfied in the context or that the context does not contain sufficient information to develop the argument. In this case, designers and architects are asked to provide additional design information to resolve the problems. We evaluate the framework by applying it to a security requirements analysis within an air traffic control technology evaluation project.
Can software reliability outperform hardware reliability on high performance interconnects? (2008)

An important part of modern supercomputing platforms is the network interconnect. As the number of computing nodes in clusters have increased, the role of the interconnect has become more important. Modern interconnects, such as InfiniBand, Quadrics, and Myrinet have become popular due to their low latency and increased performance over traditional Ethernet. As these interconnects become more widely used and clusters continue to scale, design choices such as where data reliability should be provided are an important issue. In this work we address the issue of network reliability design using InfiniBand as a case study. Unlike other high-performance interconnects, InfiniBand exposes both reliable and unreliable APIs. As part of our study we implement the Message Passing Interface (MPI) over the Unreliable Connection (UC) transport and compare with the Reliable Connection (RC) and Unreliable Datagram (UD) transports for MPI. We detail the costs of reliability for different message patterns and show that providing reliability in software instead of hardware can increase performance up to 25% in a molecular dynamics application (NAMD) on a 512-core InfiniBand cluster.
Bacterial stimuli activate nitric oxide colonic mucosal production in diverticular disease. Protective effects of <i>L. casei DG</i> ® (<i>Lactobacillus paracasei</i> CNCM I‐1572) (2016)

Colonic mucosa of patients with DD is characterized by a different reactivity toward pathogenic stimuli. LCDG plays a role in counteracting the pro-inflammatory effects exerted by EIEC, suggesting a beneficial role of this probiotic in DD.
[Amelioration of insulin resistance after scald by c-Jun N-terminal kinase inhibitor in rat]. (2006)

SP600125 can partially ameliorate insulin resistance after scald by inhibition of JNK activation, and decrease the level of IRS-1 phospho-serine307.
Contractile elements in the regulation of macromolecular permeability. (1986)

The leakage of macromolecules from the vasculature to the interstitium is greatly accentuated by mediators of edema such as histamine and bradykinin. The mechanism for this effect is not well delineated although many agents that affect smooth muscle tone may also affect macromolecular leakage. Leakage occurs primarily from the small venules. The demonstration that mediators of edema produce interendothelial gaps in the venules as well as changes in the shape of the endothelial nuclei has led to the hypothesis that a contraction of a vascular wall component may be responsible for the observed leakage of macromolecules. This component does not appear to be the vascular smooth muscle itself. Two other elements of the vascular wall, the endothelium and the pericytes, have been shown to contain many of the same elements of the contractile machinery present in smooth muscle. Most recent studies have presumed that endothelial cell contraction is responsible for the formation of the interendothelial gaps through which the macromolecules move. However, endothelial contraction has been difficult to demonstrate experimentally. Alternatively, inasmuch as pericytic processes can end near endothelial junctions and there is an abundance of fibronectin between the pericytes and the endothelium, it may be a pericytic contraction that causes the interendothelial gap formation.
11. Model Reduction Using Krylov Methods (2005)

In this chapter, we turn our attention to the third use of the Krylov iteration as described at the beginning of the previous chapter (page 314), that is, approximation by moment matching. If the to-be-approximated system Σ is described in state space terms (4.13), this problem can be solved iteratively and in a numerically efficient manner by means of the Arnoldi and Lanczos factorizations. There is an extended literature on this topic. First, the paper by Gragg and Lindquist [146] discusses many connections between system theory and the realization problem on the one hand and numerical analysis, Padé approximation, and Lanczos methods on the other. See also the course notes of Van Dooren [333], the work of Gutknecht [161], and the book of Komzsik [209], as well as [154], [132], [236], [37]. Approximation by moment matching A linear discrete- or continuous-time system defined by a convolution sum or integral is uniquely determined by its impulse response h. Equivalently, the Laplace transform of the impulse response H, called the transfer function of the system, can be used. For the systems considered here, H is a rational function. In this case, the complexity of the system turns out to be the rank of the Hankel operator ℋ defined in section 5.4, or the McMillan degree of H (see page 96). Therefore, one way to approximate a system is to approximate its transfer function H by a rational function of lower degree. This can be done by matching some terms of the Laurent series expansion of H at various points of the complex plane. Often, the expansion around infinity is used: H(s)= ∑ i≥0 hi s−i . The coefficients ht are known as Markov parameters of the system.
Surface-Enhanced Raman Spectroscopy for Rapid and Cost-Effective Quantification of Amines in Sour Water (2015)

Abstract Organic amines are corrosion control agents that increase pH and scavenge corrosive contaminants. Their presence in sour water can lead to the formation of heat-stable salts, resulting in potentially corrosive deposits. The measurement and monitoring of amines in sour water requires chromatographic techniques, with corresponding complexity, training, and expense. A rapid, field-deployable method to measure amines in refinery process waters would speed testing time, increase the temporal data resolution, and allow for immediate response and process adjustment. We present a new approach to amine measurement using Surface-Enhanced Raman Spectroscopy. By mixing a pH-adjusted sample with gold nanoparticles, a strong amine signal is obtained with a potential for sub-100-ppb detection. An optimized approach for ppm-level detection reports 27.8±3.9-ppm and 76.4±5.1-ppm for ~25-ppm and ~75-ppm samples, respectively, with more than one-hundred tests per sample over a three-month period. This method is at least as accurate, sensitive, and repeatable as ion chromatography, yet can be performed in the field in under five minutes.
Structure of the Carboxyl-terminal Src Kinase, Csk (2002)

The carboxyl-terminal Src kinase (Csk) is an indispensable negative regulator for the Src family tyrosine kinases (SFKs) that play pivotal roles in various cell signalings. To understand the molecular basis of the Csk-mediated regulation of SFKs, we elucidated the crystal structure of full-length Csk. The Csk crystal consists of six molecules classified as active or inactive states according to the coordinations of catalytic residues. Csk assembles the SH2 and SH3 domains differently from inactive SFKs, and their binding pockets are oriented outward enabling the intermolecular interaction. In active molecules, the SH2-kinase and SH2-SH3 linkers are tightly stuck to the N-lobe of the kinase domain to stabilize the active conformation, and there is a direct linkage between the SH2 and the kinase domains. In inactive molecules, the SH2 domains are rotated destroying the linkage to the kinase domain. Cross-correlation matrices for the active molecules reveal that the SH2 domain and the N-lobe of the kinase domain move as a unit. These observations suggest that Csk can be regulated through coupling of the SH2 and kinase domains and that Csk provides a novel built-in activation mechanism for cytoplasmic tyrosine kinases.
Blue noise sampling with controlled aliasing (2013)

In this article we revisit the problem of blue noise sampling with a strong focus on the spectral properties of the sampling patterns. Starting from the observation that oscillations in the power spectrum of a sampling pattern can cause aliasing artifacts in the resulting images, we synthesize two new types of blue noise patterns: step blue noise with a power spectrum in the form of a step function and single-peak blue noise with a wide zero-region and no oscillations except for a single peak. We study the mathematical relationship of the radial power spectrum to a spatial statistic known as the radial distribution function to determine which power spectra can actually be realized and to construct the corresponding point sets. Finally, we show that both proposed sampling patterns effectively prevent structured aliasing at low sampling rates and perform well at high sampling rates.
Cercospora chenopodii en el cultivo de la quinua en Cuba (2002)

El cultivo de la quinua (Chenopodium quinua Willd.) es tipico de America del Sur. Se desarrolla fundamentalmente en ecuador, Argentina, Peru y Bolivia. En la decada del ochenta y como resultado de un programa de Cultivos Andinos del INIAP en Ecuador, fue seleccionado como cultivo prioritario de estudio y promocion, debido a su amplio rango de adaptacion y calidad nutritiva de la planta.
Intracellular Calcium and Control of Burst Generation in Neurons of Guinea‐Pig Neocortex <i>in Vitro</i> (1989)

Response properties of neurons in brain slices of guinea pig parietal neocortex were examined following intracellular injection of the Ca2+ chelators, EGTA and BAPTA. Although chelator injection did not cause any consistent change in passive membrane properties, it did induce 81% of neurons encountered at all sub-pial depths to become 'bursters', in that just-threshold depolarizing current pulses triggered all-or-none bursts of 2 - 5 fast action potentials. Transition to 'burstiness' was associated with disappearance of an AHP and appearance of a DAP. Although chelator caused a slight increase in steady-state firing rate, marked accommodation persisted. Extracellular Co2+ or Mn2+ had an effect on steady-state firing rate similar to that of the intracellular chelators; however, exposure to these Ca2+ channel blockers also caused steady state depolarization, increased resting input resistance and time constant, and profound spike broadening. This treatment never induced transition to 'burstiness'. Chelator-injected neurons ceased to generate bursts when Ca2+ was replaced by Mn2+ in the Ringer's solution. During exposure to 10-6 M TTX and 20 mM TEA, 50 - 200 msec Ca2+ spikes followed brief depolarizing pulses. As chelator was injected into the cell, there was progressive prolongation of the Ca2+ plateaus, which was associated with slowing of the rate at which membrane resistance gradually recovered following the initial increase in conductance. These findings indicate that under normal conditions, activity-related increases in intracellular Ca2+ activate processes which prevent most neocortical neurons from being bursters. These processes probably include Ca2+-dependent K+ currents, and Ca2+-dependent Ca2+ channel inactivation.
Are your isolation precautions up-to-date? (2009)

In Brief Are your isolation precautions up-to-date? Find out about the recommendations in the latest CDC guideline, which addresses severe acute respiratory syndrome, avian influenza, and community-associated methicillin-resistant Staphylococcus aureus.
Effects of Chinese herb medicine Radix Scrophulariae on ventricular remodeling. (2010)

The effects and mechanism of the extract of Radix Scrophulariae (ERS), a traditional Chinese herb, on experimental ventricular remodeling in rats was studied. Rats were separated randomly into 5 groups: sham, model, captopril (40 mg x kg(-1)) and ERS (8, 16 g x kg(-1)). The experimental ventricular remodeling was induced with ligating the left anterior descending branch of the coronary artery of the rats. The sham group was conducted the same procedure without ligation. After 4 weeks treatment with intragastric administration of the corresponding drugs, the left ventricular weight index (LVWI) and heart weight index (HWI) were determined. The concentrations of angiotensin II (Ang II) and hydroxyproline (Hyp) in myocardium were detected. Myocardium tissue was stained with HE and picric acid/Sirius red for cardiocyte cross-section area and collagen content measurements. Real-time RT-PCR was used to detect the gene expressions of AT1R, TNF-alpha and TGF-beta1 mRNA. ERS could significantly reduce the LVWI, HWI, decrease the content of Ang II, Hyp, diminish cardiocyte cross-section area and ameliorate collagen deposition. In addition, ERS could down regulate the gene expressions of AT1R, TNF-alpha and TGF-beta1 mRNA in myocardium. ERS has beneficial effect against ventricular remodeling. The mechanism may be related to decreasing the level of Ang II and cardiac fibrosis, modulating some gene expressions associated with cardiac hypertrophy.
Clinical and Biochemical Parameters of Androgen Action in Normal Healthy Caucasian<i>Versus</i>Chinese Subjects (1991)

Stimulation of androgen-sensitive hair follicles is mediated by dihydrotestosterone (DHT), which is formed in these tissues by 5 alpha-reduction of testosterone. A possible mechanism for increased body hair in some human populations might, therefore, be an increase in 5 alpha-reductase activity, resulting in elevated tissue levels of DHT. If present, this finding could have other important clinical implications, since the 5 alpha-reductase enzyme is pivotal in the pathophysiology of prostatic disease. To explore differences in clinical and biochemical parameters of androgen action, we conducted a study of 184 caucasian and Chinese subjects in whom we evaluated chest hair density and serum levels of androgen precursors and 5 alpha-reduced androgen metabolites. Differences in chest hair density were most notable in the men, in whom comparative mean chest hair scores (using a scale of 0-4) were 3.0 vs. 0.8 (P less than 0.0001), caucasian vs. Chinese. Levels of 5 alpha-reduced androgen products were also strikingly higher in the caucasian vs. Chinese subjects. Serum 3 alpha-androstanediol glucuronide levels (nanomoles per L) were 34.7 +/- 2.4 vs. 19.7 +/- 0.9 (P less than 0.001) for the men and 21.5 +/- 3.2 vs. 9.4 +/- 0.6 (P less than 0.001) for the women, and serum levels of androsterone glucuronide (nanomoles per L) were 179 +/- 26 vs. 107 +/- 7 (P less than 0.01) for the caucasian vs. Chinese men and 173 +/- 23 vs. 81 +/- 9 (P less than 0.001) for the women. Serum levels of total and bioavailable testosterone did not differ between the racial groups, but serum levels of the precursor androgens, dehydroepiandrosterone sulfate and androstenedione, were significantly higher in the caucasian vs. Chinese men, but not in the women. We conclude that increased serum levels of 5 alpha-reduced androgen metabolites in caucasians vs. Chinese subjects provide circumstantial evidence for a racial difference in 5 alpha-reductase activity and suggest a mechanism for the increased body hair observed in the caucasian men. Increased levels of precursor androgens may also play a role.
Synthesis and Characterization of Strontium Titanate Nanoparticles as Potential High Temperature Oxygen Sensor Material (2006)

We present a simple and highly reproductive method for the preparation of thin films consisting of strontium titanate nanoparticles. The films are produced by spin coating of a sol on silicon targets and subsequent annealing under ambient conditions. Analysis by atomic force microscopy shows particles with typical sizes between 10 nm and 50 nm. X‐ray photoelectron spectroscopy displays a stoichiometry of the films as anticipated from preliminary experiments with strontium titanate single crystals. Metastable‐induced electron spectroscopy and ultraviolet photoelectron spectroscopy are used as tools to give evidence to the similar electronic properties of nanoparticle film and single crystal. These results support the prospect for an application of the nanoparticle films as high temperature oxygen sensor with superior properties.
A Novel Biquad Filter Circuit for Continuous-Time Sigma-Delta Modulators (2006)

A novel biquad circuit is presented that allows the loop filter of a high-order continuous-time sigma-delta modulator to be implemented by cascading low-order biquad sections, considerably easing the design and implementation of the high-order continuous-time sigma-delta modulator. Experiment on a 4th-order bandpass continuous-time sigma- delta modulator is conducted successfully and the results are presented.
Eliminating conditional branches for enhancing instruction level parallelism in VLIW compiler (2002)

In VLIW (Very Long Installation Word) compilers, one of the most important issues is how to handle conditional branches, because control dependences are caused by conditional branches and limit the scope of scheduling. This paper proposes the efficient method of eliminating conditional branches. We use SSA (Static Single Assignment) information for preserving semantics. By using our methods, global scheduling techniques can be processed more efficiently and simply. We utilize /spl phi/-functions aggressively, thus computations for code motion are not required. We don't need complex hardware support. Our scheme also makes the performance independent on the result of branch outcomes.
Strike-slip deformation in the Confidence Hills, southern Death Valley fault zone, eastern California, USA (1996)

The Confidence Hills form a well exposed, composite, positive flower structure developed in Pliocene to Recent lacustrine and alluvial fan sediments. The structure has developed along the current trace of the southern Death Valley dextral strike-slip fault zone. California, USA. NW–SE-striking fault zones bound the Confidence Hills. In 3D, these fault segments are inferred to link at depth to a common basal fault system. The flower structure is formed by doubly plunging anticlines that roughly parallel the bounding fault segments. Fold development was aided by: (a) the presence of a basal salt deposit and numerous detachment horizons within the sedimentary pile and (b) buttressing and uplift along and against the bounding oblique-slip reverse faults. Structural and palaeomagnetic evidence indicates that the anticlines developed with axial surfaces parallel and sub-parallel to the trace of both fault zones. Folding appears to have initially developed adjacent to and above the southeastern fault segment and then propagated outwards and to the northwest. The latest displacements along the current southern Death Valley fault zone are probably only in the orders of hundreds of metres and as young as 0.9 Ma to Recent. This young fault zone is highly segmented along the length of the floor of southern Death Valley: the high proportion of oblique-slip faulting consistent with the strike-slip zone being immature. The Confidence Hills structure displays close geometric similarities with other natural examples of positive flower structures and to the features found in scaled. analogue sandbox experiments of strike-slip faulting.