gebhart/patrepeval huggingface dataset:
The clinical diagnosis of gastritis. II. Aspects of current therapy and drug consumption. (1984)

Patients with a clinical diagnosis of 'gastritis' or non-ulcer dyspepsia were studied as to the extent and pattern of drugs prescribed from October 1978 through September 1981. This was permitted by the Diagnosis and Therapy Survey, an ongoing nationwide sample study, covering all outpatient care in Sweden. In 98% of the consultations a drug was considered to be indicated. Antacids were prescribed in 76%, an anticholinergic drug in 40%, and a histamine-H2-receptor antagonist (cimetidine) in 3%. The latter figure seemed to increase during the 3-year study period, concomitant with a decrease in the prescription rate of anticholinergic drugs. Gastritis was the major indication not only for antacids and anticholinergic drugs but also for cimetidine, accounting for 35% of all cimetidine prescriptions. Total sales of these drugs in 1981 amounted to about SKR 150 million. Antacids comprised 57%, anticholinergic/spasmolytics 22%, and cimetidine 21% of this amount. The extensive drug use is remarkable considering the lack of convincing data from randomized controlled clinical trials supporting a therapeutic effect of any drug regimen in gastritis. More such trials in well-defined patient groups are therefore greatly needed.
A Peptide Fragment of Human DNA Topoisomerase II α Forms a Stable Coiled-coil Structure in Solution (1995)

Results are presented on a peptide fragment (1013-1056) from human DNA topoisomerase II alpha. This was selected using the procedure of Lupas et al. (Lupas, A., Van Dyke, M., and Stock, J. (1991) Science 252, 1162-1164) for its potential to adopt a stable coiled-coil structure. The same theoretical treatment rejected the segment 994-1021 proposed by Zwelling and Perry (Zwelling, L. A., and Perry, W. M. (1989) Mol. Endocrinol. 3, 603-604) as a possible core for leucine-zipper formation. Our experimental studies combine cross-linking and CD analysis. Cross-linking establishes that the 1013-1056 fragment forms a stable homodimer in solution. Effects of increasing peptide concentration on CD spectra confirm that only the 1013-1056 fragment can undergo a coiled-coil stabilization from an isolated alpha-helix. Unfolding experiments further show that the coiled-coil is more stable in guanidium chloride than in urea. Values of -6.8 and -7.4 kcal/mol for the dimerization free energy are determined by thermal and urea unfolding, respectively. These are strikingly similar to the value recently found for the dissociation/reassociation of the entire yeast topoisomerase II from sedimentation equilibrium experiments (Lamhasni, S., Larsen, A. K., Barray, M., Monnot, M., Delain, E., and Fermandjian, S. (1995) Biochemistry 34, 3632-3639), although their significance relatively to topoisomerase II undoubtedly requires further analysis.
CMOS‐based Chemical Sensors (2005)

This chapter contains sections titled: Chemical Sensors Using CMOS Technology for Developing Chemical Sensors CMOS-based Chemical Sensors Acknowledgments References
Heart transplantation: approaching a new century. (1999)

Although cardiac surgeons have gained considerable experience with heart transplantation during the past 30 years, this operation still presents many challenges. The number of transplant candidates continues to exceed the number of available donor hearts, and the shortage is not expected to improve. For patients fortunate enough to receive a donor heart, perioperative mortality is a serious concern. After the 1st postoperative year, the most frequent cause of death is transplant vasculopathy. Other potential complications include renal dysfunction, bleeding, infection, and allograft rejection. Despite these problems, heart transplantation remains the best hope for patients with end-stage heart failure that is unresponsive to conventional therapy. In the future, mechanical cardiac assistance and new medical treatments for end-stage heart disease may offer alternatives to heart transplantation, reducing the competition for scarce donor hearts.
Maxwell Garnett theory for mixtures of anisotropic inclusions: Application to conducting polymers (1997)

The effective dielectric function ${\ensuremath{\epsilon}}_{e}$ for a medium of anisotropic inclusions embedded in an isotropic host is calculated using the Maxwell Garnett approximation. For uniaxial inclusions, ${\ensuremath{\epsilon}}_{e}$ depends on how well the inclusions are aligned. We apply this approximation to study ${\ensuremath{\epsilon}}_{e}$ for a model of quasi-one-dimensional organic polymers. The polymer is assumed to be made up of small single crystals embedded in an isotropic host of randomly oriented polymer chains. The host dielectric function is calculated using the effective-medium approximation (EMA). The resulting frequency-dependent ${\ensuremath{\epsilon}}_{e}(\ensuremath{\omega})$ closely resembles experiment. Specifically, $\mathrm{Re}{\ensuremath{\epsilon}}_{e}(\ensuremath{\omega})$ is negative over a wide frequency range, while $\mathrm{Im}{\ensuremath{\epsilon}}_{e}(\ensuremath{\omega})$ exhibits a broad ``surface plasmon'' band at low frequencies, which results from localized electronic excitations within the crystallites. If the host is above the conductivity percolation threshold, $\mathrm{Im}{\ensuremath{\epsilon}}_{e}(\ensuremath{\omega})$ has a low-frequency Drude peak in addition to the surface plasmon band, and $\mathrm{Re}{\ensuremath{\epsilon}}_{e}(\ensuremath{\omega})$ is negative over an even wider frequency range. We also calculate the cubic nonlinear susceptibility ${\ensuremath{\chi}}_{e}(\ensuremath{\omega})$ of the polymer, using a nonlinear EMA. At certain frequencies, ${\ensuremath{\chi}}_{e}(\ensuremath{\omega})$ is found to be strongly enhanced above that of the corresponding single crystals. Our results suggest that the electromagnetic properties of conducting polymers can be understood by viewing the material as randomly inhomogeneous on a small scale such that the quasistatic limit is applicable.
Synthesis and elastic properties of V<sub>2</sub>AlC thin films by magnetron sputtering from elemental targets (2009)

The influence of deposition temperature on phase formation of V2AlC is studied by magnetron sputtering from elemental targets. At substrate temperatures below 750 °C, we observed the formation of AlxVy and V2C using x-ray diffraction (XRD) analysis. At 750 °C, a phase pure polycrystalline V2AlC film on a ∼12 nm thick transition layer has been observed using XRD and transmission electron microscopy. Selected area electron diffraction indicates that the film grown on the transition layer consists of phase pure V2AlC. As the substrate temperature is increased to 850 °C, the formation of V2C in addition to the V2AlC phase is observed. This may be due to desorption of aluminium causing the decomposition of V2AlC into vanadium carbides and aluminium. The V2AlC film is fully dense and polycrystalline and the elastic modulus based on nanoindentation is within the expected error margin consistent with previously reported theoretical calculations and the diamond anvil cell measurement of bulk V2AlC samples.
Structural Requirements for the Substrates of the H<sup>+</sup>/Peptide Cotransporter PEPT2 Determined by Three-Dimensional Quantitative Structure−Activity Relationship Analysis (2006)

The renal type H(+)/peptide cotransporter PEPT2 has a substantial influence on the in vivo disposition of dipeptides and tripeptides as well as peptide-like drugs within the body, particularly in kidney, lung, and the brain. The comparative molecular similarity indices analysis (CoMSIA) method was applied to identify those regions in the substrate structures that are responsible for recognition and for differences in affinity. We have developed a comprehensive 3D quantitative structure-activity relationship (3D-QSAR) model based on 83 compounds that is able to explain and predict the binding affinities of new PEPT2 substrates. This 3D-QSAR model possesses a high predictive power (q(2) = 0.755; r(2) = 0.893). An additional 3D-QSAR model based on the same compounds was generated and correlated with affinity data of the intestinal H(+)/peptide cotransporter PEPT1. By comparing the CoMSIA contour plots, differences in selectivity between the intestinal and the renal type peptide carrier become evident.
[3+2] Cycloaddition Reaction for the Stereoselective Synthesis of a New Spirooxindole Compound Grafted Imidazo[2,1-b]thiazole Scaffold: Crystal Structure and Computational Study (2021)

A new spirooxindole hybrid engrafted imidazo[2,1-b]thiazole core structure was designed and achieved via [3+2] cycloaddition reaction approach. One multi-component reaction between the ethylene derivative based imidazo[2,1-b]thiazole scaffold with 6-Cl-isatin and the secondary amine under heat conditions afforded the desired compound in a stereoselective manner. The relative absolute configuration was assigned based on single-crystal X-ray diffraction analysis. Hirshfeld calculations for 4 revealed the importance of the H…H (36.8%), H…C (22.9%), Cl…H (10.4%) and S…H (6.6%), as well as the O…H (4.7%), N…H (5.3%), Cl…C (1.6%), Cl…O (1.0%) and N…O (0.5%) contacts in the crystal stability. DFT calculations showed excellent straight-line correlations (R2 = 0.9776–0.9962) between the calculated and experimental geometric parameters. The compound has polar nature (3.1664 Debye). TD-DFT and GIAO calculations were used to assign and correlate the experimental UV-Vis and NMR spectra, respectively.
Chemical‐Assisted Thermal Disproportionation of Porous Silicon Monoxide into Silicon‐Based Multicomponent Systems (2012)

Under the surface: Ag nanoparticles are deposited onto the surface of commercially available SiO particles, and subsequent chemical etching results in the formation of nanoporous SiO without changing the chemical and physical properties of the original SiO. Moreover, chemical-assisted thermal annealing produces a shape-preserving Si-based multicomponent system, which exhibits high-performance electrochemical properties.
Purification, Characterization, and Crystallization of Monoamine Oxidase from<i>Escherichia coli</i>K-12 (1994)

The gene for monoamine oxidase (MAO) was cloned from an Escherichia coli genomic library and MAO was overproduced in the periplasmic space. The enzyme was purified to homogeneity by preparation of a periplasmic fraction, followed by ammonium sulfate fractionation and DEAE-cellulose column chromatography. Crystals were obtained by the hanging drop method using sodium citrate as a precipitant. The enzyme was found to be a dimer of identical subunits with a molecular weight of 80,000, and showed the highest activity at pH 7.5 and 45 degrees C. The enzyme was inhibited by a MAO specific inhibitor, hydroxylamine, hydrazine, phenelzine, isoniazid, and tranycpromine. The enzyme oxidized tyramine, phenethylamine, and tryptamine at higher rates, but not oxidized diamine and polyamines such as putrescine and spermine. The antibody against E. coli MAO cross-reacted with purified MAO A from Klebsiella aerogenes.
Vitamin A status affects chromatin structure. (1986)

We have examined RNA synthesis by nuclei isolated from testes of rats of varying vitamin A status. Nuclei from retinol-deficient animals showed substantially decreased RNA synthesis by polymerase II when compared to nuclei from normal animals. Within 4 hours after oral administration of retinyl acetate (as the source of retinol) to deficient animals, RNA synthesis by polymerase II had significantly increased. Administration of retinoic acid had a similar but lesser effect. Nucleoside analysis after alkaline hydrolysis of the RNA synthesized by the endogenous polymerase II suggested that the increased activity was due to a greater number of actively transcribing polymerase II molecules on the DNA. Further, when the template capacity of testicular chromatin isolated from deficient and retinyl acetate refed animals was compared, the number of sites recognized by E. coli RNA polymerase was increased twofold after retinyl acetate administration. We conclude that these retinol-induced changes in transcription are due at least in part to changes in chromatin structure.
Measurements of slider-disk contacts during dynamic load-unload (1991)

The laser Doppler vibrometer (LDV) and acoustic emission (AE) have been used to investigate the slider dynamics and to detect possible slider-disk contacts during dynamic load-unload. One of the puzzling aspects of previous work has been the AE indication of contacts at an LDV measured spacing of about 8 mu m. The procedure of LDV spacing measurement for load-unload is investigated, and three sources of possible error are found and verified by experiment. First is the deviation between single shot and average measurements. Second is the disk motion that occurs during loading. Third is the elevation difference at the measured point and the closest point during loading, which depends on the unloaded pitch and roll angles. It is found that the jump in the velocity signal of single shot LDV measurement gives a good indicator of contacts. The electrical resistance method is applied to the detection of contacts during dynamic load-unload and compared with the results obtained by the LDV and AE. Its contact signal is in good agreement with the jump in the LDV velocity signal and more distinguishable than the AE signal.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
The Behavioral Approach to Open and Interconnected Systems (2007)

In this article we have presented an approach to the mathematical description of dynamical systems. The central notion is the behavior, which consists of the set of time trajectories that are declared possible by the model of a dynamical system. Often, the behavior is defined as the set of solutions of a system of differential equations. Models that specify a behavior usually involve latent variables in addition to the manifest variables the model aims at. We have also described a methodology for modeling interconnected systems, called tearing, zooming, and linking. The underlying mathematical language consists of terminals, modules, the interconnection graph, the module embedding, and the manifest variable assignment. The combination of module equations, interconnection constraints, and manifest variable assignment leads to a latent-variable representation for the behavior of the manifest variables the model aims. This methodology of tearing, zooming, and linking offers a systematic procedure for modeling interconnected systems that is much better adapted to the physics of interconnected systems than input/output-modeling procedures such as, for example, Simulink. The methodology of tearing, zooming, and linking has many things in common with bond graphs.
Removing Biofilms from Microstructured Titanium Ex Vivo: A Novel Approach Using Atmospheric Plasma Technology (2011)

The removal of biofilms from microstructured titanium used for dental implants is a still unresolved challenge. This experimental study investigated disinfection and removal of in situ formed biofilms from microstructured titanium using cold atmospheric plasma in combination with air/water spray. Titanium discs (roughness (Ra): 1.96 µm) were exposed to human oral cavities for 24 and 72 hours (n = 149 each) to produce biofilms. Biofilm thickness was determined using confocal laser scanning microscopy (n = 5 each). Plasma treatment of biofilms was carried out ex vivo using a microwave-driven pulsed plasma source working at temperatures from 39 to 43°C. Following plasma treatment, one group was air/water spray treated before re-treatment by second plasma pulses. Vital microorganisms on the titanium surfaces were identified by contact culture (Rodac agar plates). Biofilm presence and bacterial viability were quantified by fluorescence microscopy. Morphology of titanium surfaces and attached biofilms was visualized by scanning electron microscopy (SEM). Total protein amounts of biofilms were colorimetrically quantified. Untreated and air/water treated biofilms served as controls. Cold plasma treatment of native biofilms with a mean thickness of 19 µm (24 h) to 91 µm (72 h) covering the microstructure of the titanium surface caused inactivation of biofilm bacteria and significant reduction of protein amounts. Total removal of biofilms, however, required additional application of air/water spray, and a second series of plasma treatment. Importantly, the microstructure of the titanium discs was not altered by plasma treatment. The combination of atmospheric plasma and non-abrasive air/water spray is applicable for complete elimination of oral biofilms from microstructured titanium used for dental implants and may enable new routes for the therapy of periimplant disease.
Color Kinetic Nanoparticles (2008)

Eu3+ doped LaF3 nanoparticles functionalized with a 3-4 formylphenyl benzoic acid ligand were synthesized. Excitation energy-dependent energy transfer from the ligand to Eu3+ yields color tunability from the red to greenish-blue as a function of excitation wavelengths. This synthetic approach provides large shifts in the resultant chromaticity with an excitation wavelength including the generation of white light.
Measuring the accuracy of ROM reciprocal tables (2002)

It is proved that a conventional ROM reciprocal table construction algorithm generates tables that minimize the relative error. The worst case relative errors realized for such optimally computed k-bits-in, m-bits-out ROM reciprocal tables are then determined for all table sizes 3 /spl les/ k, m /spl les/ 12. It is then proved that the table construction algorithm always generates a k-bits-in, k-bits-out table with relative errors never any greater than 3(2/sup -k/)/4 for any k, and, more generally with g guard bits, that for (k + g)-bits-out the relative error is never any greater than 2/sup -(k+1)/(1 + 1/(2/sup g+1/)). To provide for determining test data without prior construction of a full ROM reciprocal table, a procedure that requires generation and searching of only a small portion of such a table to determine regions containing input data yielding the worst case relative errors is described.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Molecular Characterization of the NCoA‐1–STAT 6 Interaction (2008)

Many protein-protein interactions involved in cell signalling, cell adhesion and regulation of transcription are mediated by short alpha-helical recognition motifs with the sequence Leu-Xaa-Xaa-Leu-Leu (LXXLL, where Xaa is any amino acid). Originally observed in cofactors that interact with hormone-activated nuclear receptors, LXXLL motifs are now known to occur in many transcription factors, including the STAT family, which transmit signals from activated cytokine receptors at the cell surface to target genes in the nucleus. STAT 6 becomes activated in response to IL-4 and IL-13, which regulate immune and anti-inflammatory responses. Structural studies have revealed how an LXXLL motif located in 2.5 turns of an alpha-helical peptide derived from STAT 6 provide contacts through the leucine side chains to the coactivator of transcription, NCoA-1. However, since many protein-protein interactions are mediated by LXXLL motifs, it is important to understand how specificity is achieved in this and other signalling pathways. Here, we show that energetically important contacts between STAT 6 and NCoA-1 are made in residues that flank the LXXLL motif, including the underlined residues in the sequence LLPPTEQDLTKLL. We also demonstrate how the affinity for NCoA-1 of peptides derived from this region of STAT 6 can be significantly improved by optimising knobs-into-holes contacts on the surface of the protein. The results provide important new insights into the origins of binding specificity, and might be of practical value in the design of novel small-molecule inhibitors of this important protein-protein interaction.
Effect of simultaneous application of heat and pressure on the survival of bacterial spores (1991)

The effect of simultaneous application of moderate hydrostatic pressure (10-300 atm) and heat on the survival of the Bacillus stearothermophilus spores in a flow-through system was investigated. A high heterogeneity of the sensitization of spores to heat by pressure was found. A higher degree of reduction of heat resistance was observed at the low than at the high temperatures tested. The simultaneous application of moderate pressure and heat can not be applied for the preservation of liquid foods due to the extreme heterogeneity of spore sensitization to heat by pressure.
High-Mobility Group Chromatin Proteins 1 and 2 Functionally Interact with Steroid Hormone Receptors To Enhance Their DNA Binding In Vitro and Transcriptional Activity in Mammalian Cells (1998)

We previously reported that the chromatin high-mobility group protein 1 (HMG-1) enhances the sequence-specific DNA binding activity of progesterone receptor (PR) in vitro, thus providing the first evidence that HMG-1 may have a coregulatory role in steroid receptor-mediated gene transcription. Here we show that HMG-1 and the highly related HMG-2 stimulate DNA binding by other steroid receptors, including estrogen, androgen, and glucocorticoid receptors, but have no effect on DNA binding by several nonsteroid nuclear receptors, including retinoid acid receptor (RAR), retinoic X receptor (RXR), and vitamin D receptor (VDR). As highly purified recombinant full-length proteins, all steroid receptors tested exhibited weak binding affinity for their optimal palindromic hormone response elements (HREs), and the addition of purified HMG-1 or -2 substantially increased their affinity for HREs. Purified RAR, RXR, and VDR also exhibited little to no detectable binding to their cognate direct repeat HREs but, in contrast to results with steroid receptors, the addition of HMG-1 or HMG-2 had no stimulatory effect. Instead, the addition of purified RXR enhanced RAR and VDR DNA binding through a heterodimerization mechanism and HMG-1 or HMG-2 had no further effect on DNA binding by RXR-RAR or RXR-VDR heterodimers. HMG-1 and HMG-2 (HMG-1/-2) themselves do not bind to progesterone response elements, but in the presence of PR they were detected as part of an HMG-PR-DNA ternary complex. HMG-1/-2 can also interact transiently in vitro with PR in the absence of DNA; however, no direct protein interaction was detected with VDR. These results, taken together with the fact that PR can bend its target DNA and that HMG-1/-2 are non-sequence-specific DNA binding proteins that recognize DNA structure, suggest that HMG-1/-2 are recruited to the PR-DNA complex by the combined effect of transient protein interaction and DNA bending. In transient-transfection assays, coexpression of HMG-1 or HMG-2 increased PR-mediated transcription in mammalian cells by as much as 7- to 10-fold without altering the basal promoter activity of target reporter genes. This increase in PR-mediated gene activation by coexpression of HMG-1/-2 was observed in different cell types and with different target promoters, suggesting a generality to the functional interaction between HMG-1/-2 and PR in vivo. Cotransfection of HMG-1 also increased reporter gene activation mediated by other steroid receptors, including glucocorticoid and androgen receptors, but it had a minimal influence on VDR-dependent transcription in vivo. These results support the conclusion that HMG-1/-2 are coregulatory proteins that increase the DNA binding and transcriptional activity of the steroid hormone class of receptors but that do not functionally interact with certain nonsteroid classes of nuclear receptors.