gebhart/patrepeval huggingface dataset:
Host–microbe interactions in distal airways: relevance to chronic airway diseases (2015)

This article is the summary of a workshop, which took place in November 2013, on the roles of microorganisms in chronic respiratory diseases. Until recently, it was assumed that lower airways were sterile in healthy individuals. However, it has long been acknowledged that microorganisms could be identified in distal airway secretions from patients with various respiratory diseases, including cystic fibrosis (CF) and non-CF bronchiectasis, chronic obstructive pulmonary disease, asthma and other chronic airway diseases (e.g. post-transplantation bronchiolitis obliterans). These microorganisms were sometimes considered as infectious agents that triggered host immune responses and contributed to disease onset and/or progression; alternatively, microorganisms were often considered as colonisers, which were considered unlikely to play roles in disease pathophysiology. These concepts were developed at a time when the identification of microorganisms relied on culture-based methods. Importantly, the majority of microorganisms cannot be cultured using conventional methods, and the use of novel culture-independent methods that rely on the identification of microorganism genomes has revealed that healthy distal airways display a complex flora called the airway microbiota. The present article reviews some aspects of current literature on host-microbe (mostly bacteria and viruses) interactions in healthy and diseased airways, with a special focus on distal airways.
Efficient Induction of Logic Programs (1990)

Abstract A new research area, Inductive Logic Programming, is presently emerging. While inheriting various positive characteristics of the parent subjects of Logic Programming and Machine Learning, it is hoped that the new area will overcome many of the limitations of its forebears. The background to present developments within this area is discussed and various goals and aspirations for the increasing body of researchers are identified. Inductive Logic Programming needs to be based on sound principles from both Logic and Statistics. On the side of statistical justification ofhypotheses we discuss the possible relationship be-tween Algorithmic Complexity theory and Probably-Approximately-Correct (PAC) Learning. In terms of logic we provide a unifying framework for Muggleton and Buntine&amp;apos;s Inverse Resolution (IR) and Plotkin&amp;apos;s Relative Least General Generali-sation (RLGG) by rederiving RLGG in terms of IR. This leads to a discussion of the feasibility of extending the RLGG framework to allow for the invention of new predicates, previously discussed only within the cor~text of IR.
Triggered Self-Assembly of Simple Dynamic Covalent Surfactants (2009)

A prototype surfactant system was developed with the unique feature that it can be switched between an aggregated, amphiphilic state and a nonaggregated, nonamphiphilic state using external stimuli. This switchable surfactant system uses the reversible formation of a dynamic covalent bond for pH- and temperature-triggered on/off self-assembly of micellar aggregates by reversible displacement of the equilibrium between nonamphiphilic building blocks and their amphiphilic counterparts. The potential for application in controlled-release systems is shown by reversible uptake and release of an organic dye in aqueous media.
A safety and efficacy study of a resorbable hydrogel for reduction of post-operative adhesions following myomectomy (2008)

This 71-patient study provides the first clinical evidence of the safety and efficacy of Hydrogel for the reduction of adhesions following myomectomy. The ClinicalTrials.gov Identifier is NCT00562471.
Nasal drug delivery of sumatriptan succinate. (2005)

The purpose of this work was to increase the nasal absorption of sumatriptan succinate by using bile salts. A rat in situ nasal perfusion technique was used to examine the rate and extent of absorption of sumatriptan succinate. In vitro enzymatic drug degradation studies were carried out with rat nasal washings. Various experimental conditions such as nasal perfusion rate, pH of the perfusion medium and concentrations of absorption enhancers such as sodium deoxycholate, sodium caprate, sodium tauroglycocholate and EDTA were optimized. In vivo studies were carried out for the optimized formulation in rabbits and the pharmacokinetics parameters of nasal solution were compared with marketed nasal solutions. Nasal absorption of sumatriptan succinate was pH dependent. It was found maximum at pH 5.5 and decreased at higher pH values. In in vitro enzymatic degradation studies, no measurable degradation was observed during the first week. The extent of drug absorption was increased by absorption enhancers. Sodium deoxycholate appeared to be more effective for enhancing the nasal absorption of sumatriptan succinate than the other absorption enhancers. The order of increasing absorption of sumatriptan succinate caused by theenhancers was sodium deoxycholate > sodium caprate > sodium tauroglycocholate > EDTA.
Prolonged Infusion of Gemcitabine: Clinical and Pharmacodynamic Studies During a Phase I Trial in Relapsed Acute Myelogenous Leukemia (2002)

PURPOSE: To determine the maximum tolerated duration of infusions at the fixed gemcitabine dose rate of 10 mg/m 2 /min and to analyze the pharmacodynamic actions in leukemia blasts during gemcitabine therapy. PATIENTS AND METHODS: The study was conducted in a phase I trial by escalating the duration of gemcitabine infusion at a fixed-dose rate of 10 mg/m 2 /min. Patients with relapsed or refractory acute myelogenous leukemia (AML) received gemcitabine for 8.0 (n = 3), 10.0 (n = 3), 12.5 (n = 8), 15.5 (n = 3), or 18.0 hours (n = 2). Pharmacokinetic and pharmacodynamic investigations were undertaken in circulating AML blasts. RESULTS: Gemcitabine was infused for up to 18 hours at the fixed-dose rate. Four patients had grade 3 toxicities at longer infusion schedules. One patient had a partial remission; two others had a reduction in blasts and concomitant rise in neutrophils. Gemcitabine triphosphate was detectable in AML cells even at 1 hour after the start of infusion in eight patients. The concentration ranged from 130 to 900 μmol/L at the end of the infusion. Consistently, there was a rapid decline in DNA synthesis, which remained suppressed at 85% to 95% during and for at least 10 hours after the end of the infusion. Compared with levels in cells measured before therapy, at 8 hours after the start of the infusion, there was a decline in the cellular purine deoxynucleotide pools. CONCLUSION: At the fixed-dose rate of 10 mg/m 2 /min, gemcitabine could be administered for longer than 12 hours without untoward toxicity. The favorable toxicity profile and pharmacokinetic and pharmacodynamic features warrant combination with DNA-damaging agents.
Role of Cytokines in Allograft Rejection (2001)

This review examines the evidence, both from experimental models and numerous clinical settings, that has suggested that suppression of acute allograft rejection correlates with a relative decrease in type-1 cytokine production and an increase in type-2 cytokine production. This correlation has spurred studies on cytokine gene polymorphisms, to assess evidence that certain cytokine-producing genotypes are associated with increased incidence of transplant rejection, and also an interest in the value of monitoring cytokine profiles post-transplantation in long-term follow-up of transplant patients. An appraisal is given of the potential for cytokine gene therapy in transplantation, using both dendritic cells (DC) and graft tissue itself as target cells. Along the same lines, gene-targeting of DCs to increase or decrease expression of molecules (CD40/CD80/CD86/CD200) believed to control the polarization of T cell development (and cytokine production) is discussed. The review concludes with consideration of the possibility that one future goal of the pharmaceutical industry will be to develop novel immunosuppressants with selective inhibitory action on the production of distinct cytokines.
Burn wound closure with cultured autologous keratinocytes and fibroblasts attached to a collagen-glycosaminoglycan substrate (1989)

Improved survival of patients with extensive burn injuries requires the development of better techniques for timely and permanent closure of the full-thickness wound. We developed procedures for establishing confluent, stratified layers of cultured, autologous keratinocytes on the surface of a modified collagen-glycosaminoglycan membrane that contains autologous fibroblasts. We transferred the composite grafts onto limited areas of excised full-thickness burn wounds of four patients with extensive burn injuries. Our results indicate that this composite graft material has acceptable "take," with formation of a basement membrane within 9 days of graft placement. Use of this technique for major wound coverage may offer a significant advance in the care of extensively burned patients and also may be useful for providing skin for reconstructive surgery. (<i>JAMA</i>. 1989;262:2125-2130)
Inhibition of cholesteryl ester transfer protein activity by monoclonal antibody. Effects on cholesteryl ester formation and neutral lipid mass transfer in human plasma. (1989)

We have employed a neutralizing monoclonal antibody, prepared against the Mr 74,000 cholesteryl ester transfer protein (CETP), to investigate the regulation of lecithin:cholesterol acyltransferase (LCAT) activity by cholesteryl ester (CE) transfer, and also to determine which lipoproteins are substrates for LCAT in human plasma. The incubation of normolipidemic plasma led to transfer of CE from HDL to VLDL, and of triglycerides from VLDL to LDL and HDL. This net mass transfer of neutral lipids between the lipoproteins was eliminated by the monoclonal antibody. However, CE transfer inhibition had no effect on the rate of plasma cholesterol esterification in plasma incubated from 10 min to 24 h at 37 degrees C. In the absence of CE transfer, HDL and LDL exhibited cholesterol esterification activity, whereas VLDL did not. The rate of CE formation in HDL was three to four times greater than in LDL during the first hour of incubation, but CE formation in HDL decreased after 6-8 h, while that in LDL continued. Thus, (a) the Mr 74,000 CETP is responsible for all neutral lipid mass transfer in incubated human plasma, (b) the rate of CE formation in plasma is not regulated by CE transfer from HDL to other lipoproteins, and (c) HDL is the major initial substrate for LCAT; LDL assumes a more significant role only after prolonged incubation of plasma.
Anti-patched-1 antibodies suppress hedgehog signaling pathway and pancreatic cancer proliferation. (2007)

These results provide a new strategy for controling Hh dependent development of pancreatic cancer and other Hh related carcinomas.
Laser diode wavelength-modulation spectroscopy for simultaneous measurement of temperature, pressure, and velocity in shock-heated oxygen flows (1993)

Wavelength modulation at 10 MHz of an AlGaAs laser diode, superposed on repetitive linear scans of wavelength, is applied to measure second-harmonic absorption line shapes of oxygen in the A band. Theoretical expressions of the harmonic line shapes, including the effect of laser amplitude modulation and varying modulation depth, are presented. A least-squares fit of the experimental line shapes to theoretical second-harmonic line shapes permits simultaneous determination of the temperature and the pressure. The use of high-repetition-rate (10-kHz) linear scans of the studied wavelength region permits application of the technique to high-speed unidimensional transient flows generated in a shock tube; velocity is derived from the Doppler shift of the absorption profiles.
Terrestrial Gross Carbon Dioxide Uptake: Global Distribution and Covariation with Climate (2010)

Terrestrial gross primary production (GPP) is the largest global CO(2) flux driving several ecosystem functions. We provide an observation-based estimate of this flux at 123 +/- 8 petagrams of carbon per year (Pg C year(-1)) using eddy covariance flux data and various diagnostic models. Tropical forests and savannahs account for 60%. GPP over 40% of the vegetated land is associated with precipitation. State-of-the-art process-oriented biosphere models used for climate predictions exhibit a large between-model variation of GPP's latitudinal patterns and show higher spatial correlations between GPP and precipitation, suggesting the existence of missing processes or feedback mechanisms which attenuate the vegetation response to climate. Our estimates of spatially distributed GPP and its covariation with climate can help improve coupled climate-carbon cycle process models.
Simulation of algae growth in a bench‐scale bubble column reactor (2002)

The growth of the marine red microalga Porphyridium sp. in a bubble-column photobioreactor was simulated. The proposed model constitutes a dynamic integration of the kinetics of photosynthesis and photoinhibition with the fluid dynamics of the bubble column, including the effects of shear stress on the kinetics of growth. The kinetic data used in the model were obtained in independent experiments run in a thin-film photobioreactor with defined light/dark cycles. The maintenance term was modified to take into account the effects of liquid flow in the bioreactor on the growth rate. A hybrid method proposed for the approximate solution of the equations gave an appreciable reduction of the calculation time. Extrapolations of the model indicated the possibility of predicting the optimal diameter for an assembly of bubble column photobioreactors. Satisfactory fit was found with the experimental results of biomass growth in a 13-liter bubble column.
Stochastic rotation dynamics: A Galilean-invariant mesoscopic model for fluid flow (2001)

A recently introduced stochastic model for fluid dynamics with continuous velocities and efficient multiparticle collisions is investigated, and it is shown how full Galilean-invariance can be achieved for arbitrary Mach numbers. Analytic expressions for the viscosity and diffusion constant are also derived and compared with simulation results. Long-time tails in the velocity and stress autocorrelation functions are measured.
Time-Dependent Density Functional Theory Predictions of the Vertical Excitation Energies of Silanones as Models for the Excitation Process in Porous Silicon (2005)

Time-dependent density functional theory calculations with a proper treatment of the asymptotic form of the exchange-correlation potential have been performed on R(R')Si=O to predict vertical excitation energies. The species R(R')Si=O is used as a model for the binding of the -(R)Si=O chromophore to a porous silicon surface. The calculated vertical excitation energies are substantially lower than those determined previously and show that vertical excitation of the lone chromophore is possible for all types of substituents including electronegative ones with KrF laser excitation in contrast to other predictions. If the substituents are electropositive, the chromophore can also be excited by a nitrogen laser. These results, in concert with the effect of the porous silicon surface on the R(R')Si=O excited states, confirm our previous explanation of the photoluminescence of porous silicon as being due to the presence of Si=O chromophores and provide new insights into the photoexcitation process. The results show that the differences in the vertical and adiabatic excitation energies are strongly dependent on whether the substituents are electronegative or electropositive with the former leading to larger differences and the latter leading to smaller differences. The results for the energy differences are explained in terms of the changes in the Si=O bond length on vertical excitation and on the changes in bond angles, which are related to the ability of the Si center in the excited state to undergo an inversion process.
The Orphan G Protein-coupled Receptor GPR40 Is Activated by Medium and Long Chain Fatty Acids (2003)

GPR40 is a member of a subfamily of homologous G protein-coupled receptors that include GPR41 and GPR43 and that have no current function or ligand ascribed. Ligand fishing experiments in HEK293 cells expressing human GPR40 revealed that a range of saturated and unsaturated carboxylic acids with carbon chain lengths greater than six were able to induce an elevation of [Ca(2+)](i), measured using a fluorometric imaging plate reader. 5,8,11-Eicosatriynoic acid was the most potent fatty acid tested, with a pEC(50) of 5.7. G protein coupling of GPR40 was examined in Chinese hamster ovary cells expressing the G alpha(q/i)-responsive Gal4-Elk1 reporter system. Expression of human GPR40 led to a constitutive induction of luciferase activity, which was further increased by exposure of the cells to eicosatriynoic acid. Neither the constitutive nor ligand-mediated luciferase induction was inhibited by pertussis toxin treatment, suggesting that GPR40 was coupled to G alpha(q/11.) Expression analysis by quantitative reverse transcription-PCR showed that GPR40 was specifically expressed in brain and pancreas, with expression in rodent pancreas being localized to insulin-producing beta-cells. These data suggest that some of the physiological effects of fatty acids in pancreatic islets and brain may be mediated through a cell-surface receptor.
Kinetic studies of the transfer of esterified cholesterol between human plasma low and high density lipoproteins. (1980)

In vitro incubations (6 hr at 37 degrees C) of human low density lipoproteins (LDL), high density lipoproteins (HDL), and lipoprotein-free plasma revealed no significant net mass transfers of esterified cholesterol from either lipoprotein fraction to the other. Transfers of esterified [3H]cholesterol from LDL to HDL must therefore have represented a process of molecular exchange between the two fractions. In molar terms, the exchange increased with increasing incubation concentrations of LDL regardless of whether the HDL was increased in parallel, decreased, or kept constant. In direct contrast, with LDL kept constant, an increase in the concentration of HDL resulted in a decrease in the molar rate of exchange of esterified cholesterol between LDL and HDL. The data were then fitted to a mathematical model describing a physical model in which an esterified cholesterol transfer protein circulates in the plasma, interacting with lipoprotein particles into which it deposits and from which it picks up esterified cholesterol molecules. According to this model, to which the experimental data fit extremely well, the transfer protein had a much greater affinity for HDL than for LDL in a transfer process that was readily saturable by HDL but not by LDL.
Placebo-Controlled Phase III Trial of Immunologic Therapy with Sipuleucel-T (APC8015) in Patients with Metastatic, Asymptomatic Hormone Refractory Prostate Cancer (2006)

While the improvement in the primary end point TTP did not achieve statistical significance, this study suggests that sipuleucel-T may provide a survival advantage to asymptomatic HRPC patients. Supportive studies are underway.
Introduction to the Cell multiprocessor (2005)

This paper provides an introductory overview of the Cell multiprocessor. Cell represents a revolutionary extension of conventional microprocessor architecture and organization. The paper discusses the history of the project, the program objectives and challenges, the design concept, the architecture and programming models, and the implementation.
Carboplatin dosing in overweight and obese patients with normal renal function, does weight matter? (2008)

These results suggest that in overweight and obese patients, with a normal renal function, a flat carboplatin dose should be administered, based on the population carboplatin clearance (8.38 l/h = 140 mL/min). Thus, in case an AUC of 5 mg min/mL is desired, the appropriate dose for carboplatin would be 5 x 140 = 700 mg.
The future impact of the microprocessor on total transport system control functions (2002)

The explosive growth of microprocessor use in all varieties of control equipment has led to exceptional versatility for typical system supervision. More functions in less space, combined with distributed decision control logic, has resulted in increased opportunities and responsibilities for system operators. This is valid for both equipment procurement (software, firmware and hardware) and day-to-day utilization. The author discusses the applicability of these microprocessor-based control systems to rail transportation systems. An example of distributed remote control (a motor starter) is discussed as are data acquisition and security considerations.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Successful Virtual Screening for Novel Inhibitors of Human Carbonic Anhydrase:  Strategy and Experimental Confirmation (2002)

Virtual screening of compound libraries is an alternative and complementary approach to high-throughput screening in the lead discovery process. A new strategy is described to search for possible leads of human carbonic anhydrase II, applying a protocol of several consecutive hierarchical filters involving a preselection based on functional group requirements and fast pharmacophore matching. A suitable pharmacophore is derived by a sophisticated "hot spot" analysis of the binding site to detect regions favorable for protein-ligand interactions. In subsequent steps, molecular similarity with known reference ligands is used to rerank the hits from the pharmacophore matching. Finally the best scored candidates are docked flexibly into the protein binding pocket. After examination of the affinity predictions, 13 compounds were selected for experimental testing. Of these 13, three could be shown to be subnanomolar, one is nanomolar, while a further seven are micromolar inhibitors. The binding mode of two hits could be confirmed by crystal structure analysis. The novelty of the discovered leads is best supported by the fact that a search in the patent literature showed the newly discovered subnanomolar compounds to comprise scaffolds not yet covered by existing patents.