gebhart/patrepeval huggingface dataset:
Aspirin-Exacerbated Respiratory Disease: Evaluation and Management (2010)

The clinical syndrome of aspirin-exacerbated respiratory disease (AERD) is a condition where inhibition of cyclooxygenase-1 (COX-1) induces attacks of upper and lower airway reactions, including rhinorrhea and varying degrees of bronchospasm and laryngospasm. Although the reaction is not IgE-mediated, patients can also present with anaphylactic hypersensitivity reactions, including hypotension, after exposure to COX-1 inhibiting drugs. All patients with AERD have underlying nasal polyps and intractable sinus disease which may be difficult to treat with standard medical and surgical interventions. This review article focuses on the management of AERD patients with a particular emphasis on aspirin desensitization and continuous treatment with aspirin.
Interpreting oxygenation-based neuroimaging signals: the importance and the challenge of understanding brain oxygen metabolism (2010)

Functional magnetic resonance imaging is widely used to map patterns of brain activation based on blood oxygenation level dependent (BOLD) signal changes associated with changes in neural activity. However, because oxygenation changes depend on the relative changes in cerebral blood flow (CBF) and cerebral metabolic rate of oxygen (CMRO(2)), a quantitative interpretation of BOLD signals, and also other functional neuroimaging signals related to blood or tissue oxygenation, is fundamentally limited until we better understand brain oxygen metabolism and how it is related to blood flow. However, the positive side of the complexity of oxygenation signals is that when combined with dynamic CBF measurements they potentially provide the best tool currently available for investigating the dynamics of CMRO(2). This review focuses on the problem of interpreting oxygenation-based signals, the challenges involved in measuring CMRO(2) in general, and what is needed to put oxygenation-based estimates of CMRO(2) on a firm foundation. The importance of developing a solid theoretical framework is emphasized, both as an essential tool for analyzing oxygenation-based multimodal measurements, and also potentially as a way to better understand the physiological phenomena themselves. The existing data, integrated within a simple theoretical framework of O(2) transport, suggests the hypothesis that an important functional role of the mismatch of CBF and CMRO(2) changes with neural activation is to prevent a fall of tissue pO(2). Future directions for better understanding brain oxygen metabolism are discussed.
In Vitro Production of Short-Chain Fatty Acids by Bacterial Fermentation of Dietary Fiber Compared with Effects of Those Fibers on Hepatic Sterol Synthesis in Rats (1993)

The aim of this study was to determine the effects of fiber feeding on short-chain fatty acid (SCFA) production in laboratory rats and in an in vitro fermentation model using fecal inocula from rats adapted to a high fiber diet. In addition, the effect of fiber intake on endogenous sterol synthesis was evaluated. Twenty male Sprague-Dawley rats were divided into four groups and fed a control or 30% fiber diet (cellulose, pectin or pea fiber) for 4 wk. In vitro fermentation was compared with measurements of cecal SCFA content of fiber-adapted rats. Sterol synthesis in isolated hepatocytes was determined in groups of five to seven rats fed 15% dietary fiber for 4 wk. Cellulose was poorly fermented in both the in vitro and in vivo experiments. Pectin fermentation produced high levels of propionate, whereas pea fiber was associated with notable butyrate production. Adaptation to pectin produced seven times more SCFA in rat cecal contents (515 +/- 78 mumol) in comparison to a fiber-free diet (70.6 +/- 4.9 mumol), with similar results observed in vitro. Sterol synthesis in hepatocytes of rats fed pectin was significantly greater than in those of control or cellulose-fed rats. Despite significantly higher rates of SCFA production in pectin-fed rats, cholesterol synthesis was not inhibited, suggesting that SCFA are not the cholesterol-lowering factor of highly fermentable fiber sources.
Automatic Tractography Segmentation Using a High-Dimensional White Matter Atlas (2007)

We propose a new white matter atlas creation method that learns a model of the common white matter structures present in a group of subjects. We demonstrate that our atlas creation method, which is based on group spectral clustering of tractography, discovers structures corresponding to expected white matter anatomy such as the corpus callosum, uncinate fasciculus, cingulum bundles, arcuate fasciculus, and corona radiata. The white matter clusters are augmented with expert anatomical labels and stored in a new type of atlas that we call a high-dimensional white matter atlas. We then show how to perform automatic segmentation of tractography from novel subjects by extending the spectral clustering solution, stored in the atlas, using the Nystrom method. We present results regarding the stability of our method and parameter choices. Finally we give results from an atlas creation and automatic segmentation experiment. We demonstrate that our automatic tractography segmentation identifies corresponding white matter regions across hemispheres and across subjects, enabling group comparison of white matter anatomy.
Decontamination of surgical instruments from prion proteins: in vitro studies on the detachment, destabilization and degradation of PrPSc bound to steel surfaces (2004)

Effective reprocessing of surgical instruments ensuring elimination of inadvertent contamination with infectious agents causing transmissible spongiform encephalopathies (TSEs) is essential for the prevention of iatrogenic transmission of Creutzfeldt-Jakob disease (CJD) or its new variant (vCJD) from asymptomatic carriers. In a search for effective yet instrument-friendly and routinely applicable reprocessing procedures, we used an in vitro carrier assay to assess the decontamination activity exerted by different reagents on pathological prion protein (PrP(Sc)), the biochemical marker for TSE infectivity, attached to steel surfaces. In this assay, steel wires were contaminated with 263K scrapie brain homogenate and reprocessed for decontamination by exposure to several different test reagents. Residual contamination with PrP(Sc) and its protease-resistant core PrP27-30, still present after reprocessing on the wire surface or in the cleaning solution, was monitored by sensitive Western blot detection without or after proteinase K digestion. Using this approach, various reagents and processing conditions were screened for both their efficacy of decontamination and their active principles, such as detachment, destabilization or degradation of surface-bound prion protein. This revealed that, under appropriate conditions, relatively mild reagents such as 0.2 % SDS/0.3 % NaOH (pH 12.8), a commercially available alkaline cleaner (pH 11.9-12.2), a disinfectant containing 0.2 % peracetic acid and low concentrations of NaOH (pH 8.9) or 5 % SDS (pH 7.1) exert potent decontaminating activities on PrP(Sc)/PrP27-30 attached to steel surfaces. For in vivo validation, wires reprocessed in these reagents have been implanted into reporter animals in ongoing experiments.
Geometry of self-propulsion at low Reynolds number (1989)

The problem of swimming at low Reynolds number is formulated in terms of a gauge field on the space of shapes. Effective methods for computing this field, by solving a linear boundary-value problem, are described. We employ conformal-mapping techniques to calculate swimming motions for cylinders with a variety of crosssections. We also determine the net translationl motion due to arbitrary infinitesimal deformations of a sphere.
Lattice vibrations and the bonding nature of boron carbide (1996)

The vibrations of boron carbide have been studied by the valence force model. There have been so far several ambiguities in the interpretation of experimental spectra, which made theoretical study difficult. This paper solves the main difficulties, that is, characterization of the highest band and most of the Raman bands, providing reasonable interpretations for low-frequency modes. The band is ascribed to the anti-symmetric stretching of the linear chain. The necessity of large angle-bending forces of carbon atom arose for better fitting, which fact can be regarded as evidence for formation of strong covalent bonds around this atom. The present analysis also throws a new light on the Longuet-Higgins interpretation of the role of carbon incorporation. The coexistence of the strong covalent bonds of carbon atoms and the relatively weak icosahedral bonds results in such a balance of bonding that the intra-icosahedral and rhombohedral bonds are further weakened, and the covalent bonds of the carbon chain are instead reinforced.
Persistence of Perchlorate and the Relative Numbers of Perchlorate- and Chlorate-Respiring Microorganisms in Natural Waters, Soils, and Wastewater (2001)

Cell numbers of perchlorate (PRM)- and chlorate (CRM)-reducing microorganisms and the persistence of perchlorate were determined in samples of soils, natural waters, and wastewater incubated under laboratory conditions. Complete perchlorate reduction in raw wastewater and creek water was achieved in 4 to 7 days and 8 to 29 days, respectively, depending on the individual growth substrate (acetate, lactate, citric acid, or molasses) employed. Perchlorate persisted in most mixed cultures developed with 2 g of “pristine” soil, but declined in mixed cultures developed with 100 g of soil. Less than seven days were required to completely reduce perchlorate in cultures started with 10 g of a perchlorate-contaminated soil obtained from a site in Texas. The concentration of PRM was estimated using a 5-tube most probable number (MPN) procedure. To account for discrepancies due to differences in the total number of bacteria (per mass of sample) in the samples, difficulty in removing bacteria from soil samples, and the lack of an unequivocal method to measure total viable cells in these different systems, we normalized our MPN results on the basis of 106 or 109 total bacteria counted using acridine orange direct counts (AODC). There were more PRM in wastewater samples on a per-cell basis (15 to 350 PRM/106-AODC) than in water samples (0.02 to 0.4 PRM/106-AODC). There were also more PRM in soils from sites exhibiting direct evidence of perchlorate contamination (100 to 200 PRM/109-AODC) than from other sites (nondetectable to 0.77 PRM/109-AODC). These results demonstrate that perchlorate-reducing bacteria are present at perchlorate-contaminated sites, and that perchlorate can be degraded by these microorganisms through the addition of different electron donors, such as acetate and lactate.
Corrosion protection of epoxy-coated steel using different silane coupling agents (1999)

To suppress steel corrosion at elevated temperature and in humid condition, silane coupling agents N-β-aminoethyl aminopropyltrimethoxysilane (AAPS), γ-glycidoxypropyltrimethoxysilane (GPS), and bis[3-(trimethoxysilyl)-1-phenylpropyl]tetrasulfide (RC-2) were introduced as primers into an epoxy/steel system. Silane coupling agents and epoxy were coated onto the steel surface using the solution casting method. The polymer degradation and steel corrosion formation after heat and humid treatment were investigated by Fourier transform infrared reflection and absorption spectroscopy (FTIR–RAS) and scanning electron microscopy (SEM). Compared to various silane treated epoxy/steel systems, the AAPS-treated epoxy/steel (AAPS/epoxy = 6 : 4) system suppressed steel corrosion at 400°C for 10 min in air and for 5 days at 60°C in 100% relative humidity. This is due to the formation of SiOSi linkage and FeOSi bond on steel surface, which are resistant to water diffusion and thermally stable at elevated temperature. The relationship between chemical bonding at the steel–epoxy interface and corrosion protection on the steel surface was also investigated. © 1999 John Wiley & Sons, Inc. J Appl Polym Sci 71: 585–593, 1999
Managing Pressure Drilling with Continous Circulation, A Summary of Eni Experience (2011)

Abstract Drilling exploration wells may be challenging due to uncertainties related to several factors like well downhole pressure, pore and fracture pressures, etc. As a result, a well may fail to reach its target depth. Managed Pressure Drilling (MPD) is a useful technique in challenging conditions. It allows pore and fracture pressures to be accurately calculated while drilling, and the mud weight adjusted accordingly. Besides, it reduces the chance of human errors as it is an automatic device managed by specific software. Eni's distinctive MPD system is the e-nbd™ (Eni Near Balance Drilling). This system consists of an innovative drilling process that maintains constant bottom hole annular pressure at all times. The system does not require that mud circulation be stopped and compensated with a back up pressure. The e-nbd™ is assisted by a proprietary system for continuous circulation that is called e-cd™ (Eni Circulating Device). The e-cd™ system is composed of special subs that are positioned on top of each drilling stand. The number of required subs is defined by the length of the open hole section that is to be drilled with continuous circulation. The system is completed by a dedicated manifold that is positioned on the rig floor that automatically diverts mud flow from the Stand Pipe Manifold to the subs. e-nbd™ through the e-cd™ System ensures a continuous MPD process, without any "transient" time. This paper presents this innovative system and the achieved results. It reports a summary of the applications performed to date, including some offshore applications from floaters, as well as the major benefits of the system.
GaAs on Si epitaxy by aspect ratio trapping: Analysis and reduction of defects propagating along the trench direction (2015)

The Aspect Ratio Trapping technique has been extensively evaluated for improving the quality of III-V heteroepitaxial films grown on Si, due to the potential for terminating defects at the sidewalls of SiO2 patterned trenches that enclose the growth region. However, defects propagating along the trench direction cannot be effectively confined with this technique. We studied the effect of the trench bottom geometry on the density of defects of GaAs fins, grown by metal-organic chemical vapor deposition on 300 mm Si (001) wafers inside narrow (&lt;90 nm wide) trenches. Plan view and cross sectional Scanning Electron Microscopy and Transmission Electron Microscopy, together with High Resolution X-Ray Diffraction, were used to evaluate the crystal quality of GaAs. The prevalent defects that reach the top surface of GaAs fins are {111} twin planes propagating along the trench direction. The lowest density of twin planes, ∼8 × 108 cm−2, was achieved on “V” shaped bottom trenches, where GaAs nucleation occurs only on {111} Si planes, minimizing the interfacial energy and preventing the formation of antiphase boundaries.
Efficient RF Frequency Down-Conversion Using Coupled Quantum-Well Optical Phase Modulator (2011)

Frequency down-conversion is important to radar front-end. In this work, we achieve efficient RF frequency down-conversion using a coupled quantum-well optical phase modulator fabricated on an indium phosphide material platform. When used in conjunction with an optical phase-locked loop-based linear phase demodulator, a 1-mm-long device exhibits a down-conversion loss of ~2.6 dB and a spurious-free dynamic range of ~125 dB·Hz <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2/3</sup> in the photodetector shot-noise limit. Furthermore, the phase modulator has a very low optical propagation loss (<;0.2 dB/mm). This allows for a longer modulator device capable of achieving even higher performance.
APPENDIX (2015)

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Critical Factors Affecting the Wettability of α‐Alumina by Molten Aluminum (2004)

The wetting behaviors of α‐Al 2 O 3 single crystals with three different faces—R(01 1 2), A(011 2 0), and C(0001)—and polycrystals (PC) by molten aluminum were studied over a wide temperature range using both a conventional and an improved sessile‐drop method. The critical factors affecting the wettability, such as temperature, atmosphere, substrate surface roughness, and crystallographic orientation, and the influence from the experimental technique, were thoroughly investigated. The results show that the aluminum surface oxidation and the thickness of the oxide film have a pronounced effect on the wettability, especially at low temperatures. To eliminate this effect, the experimental temperature must be over a critical value. Vacuum favors lowering this value compared with atmosphere, and the improved sessile‐drop method, particularly using an impingement‐dropping mode (I‐mode), helps to weaken this effect by mechanical disruption and removal of the oxide film. However, the dropping distance and the dropping force must be controlled to prevent an overspreading of the drop. The effects of the substrate surface roughness and temperature are not significant in the case of a clean aluminum surface and a fine‐prepared alumina surface. On the other hand, the effect of the alumina surface crystallographic orientation is noticeable and the wettability is in the order of R > A > PC > C. The intrinsic contact angles of the Al/α‐Al 2 O 3 system in the temperature range of 1000°–1500°C were estimated to be 76°–85° for the R and A faces, 88°–100° for the C face, and 77°–90° for the polycrystal, depending on the temperature.
Virulence of a mouse-adapted Semliki Forest virus strain is associated with reduced susceptibility to interferon (2007)

Type I interferons (IFNs) are essential components of the innate immune system. This study characterized the distinct IFN sensitivities of two closely related Semliki Forest virus (SFV) strains in cell culture. The virulent L10 strain was derived from the original virus isolate by propagation in mice. In contrast, the avirulent SFV strain, designated V42, was derived from an earlier passage of the original virus isolated from mosquitoes. The virulent L10 strain produced a cytopathic effect (CPE) in IFN-treated cells and the production of infectious virus was only two orders of magnitude lower compared with untreated cells. In contrast, the avirulent V42 exerted no CPE in IFN-treated cells and production of infectious virus was four orders of magnitude lower compared with untreated cells. The reduced CPE in IFN-treated cells infected with the avirulent V42 strain was due to inhibition of productive infection and not to reduced cell death. The virulent L10 strain synthesized less genomic RNA but more non-structural proteins than the avirulent V42 strain, suggesting more efficient translation of the L10 genomic RNA. Using a cell line unable to produce IFN, it was shown that the reduced susceptibility of the L10 strain to the action of IFN was not due to reduced IFN induction. Hence, the reduced susceptibility of the virulent L10 strain to the action of IFN allows it to overcome the established IFN-induced antiviral state of the cell, thereby increasing its virulence.
New guidelines for newborn resuscitation (2007)

The new guidelines for newborn resuscitation are more evidence-based than previously ones. However, still there is a need for further research and modifications.
Mapping Tumor Hypoxia In Vivo Using Pattern Recognition of Dynamic Contrast-enhanced MRI Data (2012)

In solid tumors, hypoxia contributes significantly to radiation and chemotherapy resistance and to poor outcomes. The "gold standard" pO(2) electrode measurements of hypoxia in vivo are unsatisfactory because they are invasive and have limited spatial coverage. Here, we present an approach to identify areas of tumor hypoxia using the signal versus time curves of dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) data as a surrogate marker of hypoxia. We apply an unsupervised pattern recognition (PR) technique to determine the differential signal versus time curves associated with different tumor microenvironmental characteristics in DCE-MRI data of a preclinical cancer model. Well-perfused tumor areas are identified by rapid contrast uptake followed by rapid washout; hypoxic areas, which are regions of reduced vascularization, are identified by delayed contrast signal buildup and washout; and necrotic areas exhibit slow or no contrast uptake and no discernible washout over the experimental observation. The strength of the PR concept is that it captures the pixel-enhancing behavior in its entirety-during both contrast agent uptake and washout-and thus, subtleties in the temporal behavior of contrast enhancement related to features of the tumor microenvironment (driven by vascular changes) may be detected. The assignment of the tumor compartments/microenvironment to well vascularized, hypoxic, and necrotic is validated by comparison to data previously obtained using complementary imaging modalities. The proposed novel analysis approach has the advantage that it can be readily translated to the clinic, as DCE-MRI is used routinely for the identification of tumors in patients, is widely available, and easily implemented on any clinical magnet.
In vitro inhibition studies of tolbutamide hydroxylase activity of human liver microsomes by azoles, sulphonamides and quinolines. (1988)

1. A number of compounds have been examined for their ability to inhibit tolbutamide hydroxylase activity in human liver microsomes (control value at a substrate concentration of 150 microM being 0.27 +/- 0.12 nmol min-1 mg-1 protein; mean +/- s.d.; n = 7). 2. IC50 (concentration of inhibitor producing 50% inhibition) values were determined for a range of sulphonamides, imidazoles and aminoquinoline compounds. The most potent inhibition was evident with the 1-substituted imidazole antimycotic drugs ketoconazole, clotrimazole and miconazole and the sulphonamide sulphaphenazole (IC50 values of 16.5, 2.5, 0.85 and 0.5 microM respectively). A number of compounds showed little or no inhibition of tolbutamide hydroxylase as judged by an IC50 of greater than or equal to 500 microM. 3. The Km value for tolbutamide hydroxylase was 125 microM and Vmax, 0.44 nmol min-1 mg-1 protein. All the substituted imidazoles examined in kinetic studies 1v vs 1s, Line-weaver-Burk plots) produced either non-competitive or mixed inhibition. The sulphonamides exhibited competitive inhibition, the Ki for sulphaphenazole being 0.22 microM. Primaquine showed mixed inhibition. Dixon plots confirmed the type of inhibition produced. 4. Although the competitive inhibition between some sulphonamides and tolbutamide is consistent with metabolism by the same isozyme of cytochrome P-450 it does not prove it and further studies with purified enzymes will be necessary to confirm this.