gebhart/patrepeval huggingface dataset:
Acid secretion and the H,K ATPase of stomach. (1994)

The regulation of acid secretion was clarified by the development of H2-receptor antagonists in the 1970s. It appears that gastrin and acetylcholine exert their effects on acid secretion mainly by stimulation of histamine release from the enterochromaffin-like (ECL) cell of the fundic gastric mucosa. The isolated ECL cell of rat gastric mucosa responds to gastrin/cholecystokinin (CCK), acetylcholine, and epinephrine with histamine release and to somatostatin and R-alpha-methyl histamine by inhibition of histamine release. Histamine and acetylcholine stimulate the parietal cell by elevation of cAMP or [Ca]i by activation of H2 or M3 receptors, respectively. These independent pathways converge to activate the gastric acid pump, the H+,K+ ATPase. Activation is a function of the association of the ATPase with a potassium chloride transport pathway that occurs in the membrane of the secretory canaliculus of the parietal cell. Hence the secretory canaliculus is the site of acid secretion, the acid being pumped into the lumen of the canaliculus. The pump is composed of two subunits, a large catalytic and a smaller glycosylated protein. This final step of acid secretion has become the target of drugs also designed to inhibit acid secretion. The target domain of the benzimidazole class of acid pump inhibitors is the extracytoplasmic domain of the pump that is secreting acid, and the target amino acids are the cysteines present in this domain. The secondary structure of the pump can be analyzed by determining trypsin-sensitive bonds in intact, cytoplasmic-side-out vesicles of the ATPase, and it has been shown that the alpha subunit has at least eight membrane-spanning segments. Omeprazole, the first acid pump inhibitor, forms a disulfide bond with cysteines in the extracytoplasmic loop between the fifth and sixth membrane-spanning segment and to a cysteine in the extracytoplasmic loop between the seventh and eight segments, preventing phosphorylation of the pump by ATP. As a result of the effective and long-lasting inhibition of acid secretion by the acid pump inhibitor, superior clinical results have been found in all forms of acid-related disease.
In-flight performance of the Absolute Scalar Magnetometer vector mode on board the Swarm satellites (2015)

Abstract The role of the Absolute Scalar Magnetometer (ASM) in the European Space Agency (ESA) Swarm mission is to deliver absolute measurements of the magnetic field’s strength for science investigations and in-flight calibration of the Vector Field Magnetometer (VFM). However, the ASM instrument can also simultaneously deliver vector measurements with no impact on the magnetometer’s scalar performance, using a so-called vector mode. This vector mode has been continuously operated since the beginning of the mission, except for short periods of time during commissioning. Since both scalar and vector measurements are perfectly synchronous and spatially coherent, a direct assessment of the ASM vector performance can then be carried out at instrument level without need to correct for the various magnetic perturbations generated by the satellites. After a brief description of the instrument’s operating principles, a thorough analysis of the instrument’s behavior is presented, as well as a characterization of its environment in flight, using an alternative high sampling rate (burst) scalar mode that could be run a few days during commissioning. The ASM vector calibration process is next detailed, with some emphasis on its sensitivity to operational conditions. Finally, the evolution of the instrument’s performance during the first year of the mission is presented and discussed in view of the mission’s performance requirements for vector measurements.
Studies of Gastrointestinal Interactions (1973)

Lagerlöf, H. O., Johansson, C. & Ekelund, K. Studies of gastrointestinal interactions. V. Gastric secretion and duodenal reflux in man after a com-posite meal. The influence of glucose on gastric secretion, emptying and gastric volume. Scand. J. Gastroent. 1973, 8, 735-742.Gastric secretion rate was estimated quantitatively after a fluid meal com-posed of milk protein, fat, and lactose and was found to be moderate. The constant secretion rate was not influenced by addition of 10 per cent glucose to the meal. Correction was made for duodenal reflux. Constant relations were found to exist between gastric volumes, secretion, and emptying for a considerable time in each experiment, with deviations in the beginning and at the end. Addition of 10 per cent glucose slowed the emptying during the first hour after ingestion of the meal, resulting in a slower decrease of gastric volumes.
Analysis of retroviral protease cleavage sites reveals two types of cleavage sites and the structural requirements of the P1 amino acid (1991)

Retroviruses encode a protease which cleaves the viral Gag and Gag/Pol protein precursors into mature products. To understand the target sequence specificity of the viral protease, the amino acid sequences from 46 known processing sites from 10 diverse retroviruses were compared. Sequence preference was evident in positions P4 through P3' when compared to flanking sequences. Approximately 80% of all cleavage site sequences could be grouped into two classes based on the sequence composition flanking the scissile bond. The sequences at the amino-terminal cleavage site of the major capsid protein of Gag is always a member of one of the two classes while the carboxyl-terminal cleavage site is of the other class, suggesting a biological role for the two classes. Known processing site sequences proved useful in a motif searching strategy to identify processing sites in retroviral protein sequences, particularly in Gag. In all known cleavage sites, the P1 amino acid is hydrophobic and unbranched at the beta-carbon. The sequence requirements of the P1 position were tested by site-directed mutagenesis of the P1 Phe codon in an HIV-1 Pol cleavage site. Mutations were tested for protease-mediated cleavage of the Pol precursor expressed in Escherichia coli.
Understanding and Controlling the Microstructure of Complex Foods (2007)

Part 1 Microstructural elements and their interactions: Polysaccharides: their role in food microstructure Proteins in food microstructure formation Structure and function of fat crystals and their role in microstructure formation in complex foods Effects of water distribution and transport on food microstructure Structure and function of emulsifiers and their role in microstructure formation in complex foods Colloidal systems in foods containing droplets and bubbles Ingredient interactions in complex foods: aggregation and phase separation. Part 2 Novel methods to study food microstructure: Atomic force microscopy (AFM) techniques for characterizing food structure Confocal fluorescence microscopy (CLSM) for food structure characterization Advances in image analysis for the study of food microstructure Food characterisation using scattering methods Acoustic techniques to characterize food microstructure Modelling and computer simulation of food structures. Part 3 Microstructural-based approaches to design of functionality in foods: Creation of novel microstructures through processing: structure formation in (semi-) solid food materials Influence of food microstructure on food rheology Influence of food microstructure on flavour interactions Relating food microstructure to sensory quality Physicochemical and structural aspects of lipid digestion Nanoscale liquid self-assembled dispersions in foods and the delivery of functional ingredients. Part 4 Microstructural approaches to improving food product quality: Structure-engineering of ice-cream and foam-based foods The texture and microstructure of spreads Microstructural approaches to the study and improvement of cheese and yogurt products Microstructural aspects of protein-based drinks The microstructure of chocolate Bubble formation and stabilisation in bread dough Food microstructure and shelf-life of emulsion and gel-based products.
Use of an α<sub>1</sub>-Blocker, YM-12617, in Micturition Difficulty (1987)

The adrenergic alpha 1-blocker has been clinically used for the treatment of patients who have micturition difficulty. However, one of its remarkable adverse reactions is orthostatic hypotension, which prevents this kind of drug from being widely used. In the present study a newly synthesized alpha 1-blocker, YM-12617, was tried and evaluated in 77 male patients with mild benign prostatic hyperplasia and in 5 women with micturition difficulties of unknown origin. Both 0.2- and 0.4-mg doses relieved the difficulty in about 80% of the patients, subjectively and objectively. A statistically significant decrease in residual urine volume (RUV) and an increase in average flow rate (Qave) and maximum flow rate (Qmax) were observed, especially in the group of patients who received 0.4 mg of this drug, but the maximum urethral closure pressure (UCPmax), maximum bladder capacity (Vmax) and premicturition pressure were unchanged. Neither orthostatic hypotension nor a fall in blood pressure were noted, and adverse reactions were negligible. Hence, the use of this drug seems to be worthwhile for the treatment of patients with mild micturition difficulty.
Synthesis of the main metabolite (OL-17) of cyclosporin A (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis of the main metabolite (OL-17) of cyclosporin AMarcel K. Eberle and Francois NuningerCite this: J. Org. Chem. 1992, 57, 9, 2689–2691Publication Date (Print):April 1, 1992Publication History Published online1 May 2002Published inissue 1 April 1992https://pubs.acs.org/doi/10.1021/jo00035a027https://doi.org/10.1021/jo00035a027research-articleACS PublicationsRequest reuse permissionsArticle Views254Altmetric-Citations18LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
A Novel cis-Acting Element in a Liver Cytochrome P450 3A Gene Confers Synergistic Induction by Glucocorticoids plus Antiglucocorticoids (1995)

The induction by dexamethasone of rat liver CYP3A1 differs from classical glucocorticoid gene regulation in part because both glucocorticoids and antiglucocorticoids such as pregnenolone 16 alpha-carbonitrile (PCN) induce CYP3A1 through transcriptional gene activation. In the present study, we transiently expressed in primary cultures of rat hepatocytes plasmids consisting of CYP3A1 5'-flanking sequences fused to a chloramphenicol acetyltransferase reporter plasmid. Deletional analysis identified a 78-base pair (bp) element located approximately 135 bp upstream of the transcriptional start site that was inducible by treatment of the cultures with dexamethasone or PCN and was induced synergistically by dexamethasone plus PCN. Nuclear extract from control rat liver protected two regions within the 78-bp sequence against digestion with DNase I. The same two regions were protected when nuclear extracts from dexamethasone-treated animals were used. Analysis of both of the "footprints" (FP1 and FP2) failed to reveal a classical sequence for the glucocorticoid-responsive element. A 33-bp element that includes FP1 sequences inserted into the chloramphenicol acetyltransferase reporter plasmid and transiently expressed in rat hepatocytes conferred a profile of dexamethasone and PCN induction similar to that of the 78-bp element. However, an Escherichia coli expressed glucocorticoid receptor protein failed to protect sequences within FP1 in DNase I footprinting experiments and failed to change its mobility in gel shift assays. Moreover, as judged by the gel shift assay, the specific protein binding to this fragment was the same whether nuclear extracts from the liver of untreated or dexamethasone-treated rats were used. We conclude that the activation of CYP3A1 gene transcription by glucocorticoids may involve proteins already bound to the controlling element in the CYP3A1 gene through a mechanism in which GR in the presence of hormone does not bind directly to CYP3A1 DNA.
A new SVD-based optimal inverse filter design for ultrasonic applications (1993)

A new approach for the design of optimal pseudoinverse filter for ultrasonic applications is presented. The filter is derived from the spatio-temporal impulse response of the US system at scatterer locations (assumed to be on a uniform grid) in the region of interest (ROI). We provide a derivation for the filter coefficients based linear formulation of the pulse propagation from the scatterers to the transducer. In this paper, we show the frequency response of the derived filter using experimental data and we demonstrate that the new formulation does indeed behave as an inverse filter (i.e., it provides spectral inversion in the passband of the original system). However, for coded-excitation systems, the pseudoinverse can be derived for 2D and 3D imaging. This approach will provide the opportunity for simultaneous acquisition of many image lines upon each transmit. Thus, it can be used to increase the frame rate of ultrasound imaging systems
An Oligomeric Signaling Platform Formed by the Toll-like Receptor Signal Transducers MyD88 and IRAK-4 (2009)

Toll-like receptors (TLRs) mediate responses to pathogen-associated molecules as part of the vertebrate innate immune response to infection. Receptor dimerization is coupled to downstream signal transduction by the recruitment of a post-receptor complex containing the adaptor protein MyD88 and the IRAK protein kinases. In this work, we show that the death domains of human MyD88 and IRAK-4 assemble into closed complexes having unusual stoichiometries of 7:4 and 8:4, the Myddosome. Formation of the Myddosome is likely to be a key event for TLR4 signaling in vivo as we show here that pathway activation requires that the receptors cluster into lipid rafts. Taken together, these findings indicate that TLR activation causes the formation of a highly oligomeric signaling platform analogous to the death-inducing signaling complex of the Fas receptor pathway.
Relevance of apple consumption for protection against oxidative damage induced by hydrogen peroxide in human lymphocytes (2007)

In a single-dosing crossover study, we investigated the ability of apple fruit consumption to protect human lymphocytes against peroxide-induced damage to DNA. Six healthy, non-smoking male volunteers were placed for 2d on an antioxidant-poor (AP) diet. After 48h of AP diet, the volunteers were required to consume a homogenate obtained from 600g of red delicious unpeeled apples or water (500 ml); blood samples were collected 0, 3, 6 and 24 h post-consumption. To evaluate whether the apple intake was sufficient to restore resistance of DNA to oxidative damage, for each subject at any time point the plasma total antioxidant activity, reactive oxygen species (ROS) formation and induction of micronuclei (MN) in isolated lymphocytes following hydrogen peroxide (H2O2) treatment were measured. Results indicated a significant inhibition (58%, P <0.05) of H2O2-induced MN frequency in the plasma samples collected at 3 h after apple consumption, as compared with plasma samples collected at 0 h (4.17 (SD 1.83) v. 9.85 (SD 1.87) MN/1000 binucleated (BN) cells, respectively). A gradual return towards the value observed at 0 h was recorded starting from 6 to 24 h. MN frequency induced by H2O2 was significantly influenced by plasma total antioxidant activity (r = -0.95, P <0.05) and by the increase of intracellular ROS formation (r = 0.88, P <0.05). These findings suggest that the consumption of whole apple provides a useful dietary source of active scavengers to protect cells and tissue from oxidative stress and related DNA injury.
Atomic layer deposition (ALD) of tantalum-based materials for zero thickness copper barrier applications (2001)

A metalorganic atomic layer deposition (ALD) process has been demonstrated for advanced 'zero thickness' copper barrier applications. This process, which is carried out at substrate temperatures below 450/spl deg/C on commercial ALD reactor, employs TBTDET and NH/sub 3/ as the tantalum and nitrogen sources, respectively. Fundamental ALD functionality data is presented, including work performed on low-k dielectric substrates. The chemical, microstructural, and electrical performance of these films is presented, in addition to their conformality over high aspect ratio patterned structures, and implications for applications in advanced microelectronics processing will be discussed.
Dendritic Cells and Anergic Type I NKT Cells Play a Crucial Role in Sulfatide-Mediated Immune Regulation in Experimental Autoimmune Encephalomyelitis (2014)

CD1d-restricted NKT cells can be divided into two groups: type I NKT cells use a semi-invariant TCR, whereas type II express a relatively diverse set of TCRs. A major subset of type II NKT cells recognizes myelin-derived sulfatides and is selectively enriched in the CNS tissue during experimental autoimmune encephalomyelitis (EAE). We have shown that activation of sulfatide-reactive type II NKT cells by sulfatide prevents induction of EAE. In this article, we have addressed the mechanism of regulation, as well as whether a single immunodominant form of synthetic sulfatide can treat ongoing chronic and relapsing EAE in SJL/J mice. We have shown that the activation of sulfatide-reactive type II NKT cells leads to a significant reduction in the frequency and effector function of myelin proteolipid proteins 139-151/I-A(s)-tetramer(+) cells in lymphoid and CNS tissues. In addition, type I NKT cells and dendritic cells (DCs) in the periphery, as well as CNS-resident microglia, are inactivated after sulfatide administration, and mice deficient in type I NKT cells are not protected from disease. Moreover, tolerized DCs from sulfatide-treated animals can adoptively transfer protection into naive mice. Treatment of SJL/J mice with a synthetic cis-tetracosenoyl sulfatide, but not α-galactosylceramide, reverses ongoing chronic and relapsing EAE. Our data highlight a novel immune-regulatory pathway involving NKT subset interactions leading to inactivation of type I NKT cells, DCs, and microglial cells in suppression of autoimmunity. Because CD1 molecules are nonpolymorphic, the sulfatide-mediated immune-regulatory pathway can be targeted for development of non-HLA-dependent therapeutic approaches to T cell-mediated autoimmune diseases.
Evidence for leucine zipper motif in lactose repressor protein (1991)

Amino acid sequence homology between the carboxyl-terminal segment of the lac repressor and eukaryotic proteins containing the leucine zipper motif with associated basic DNA binding region (bZIP) has been identified. Based on the sequence comparisons, site-specific mutations have been generated at two sites predicted to participate in oligomer formation based on the three-leucine heptad repeat at positions 342, 349, and 356. Leu342----Ala, Leu349----Ala, and Leu349----Pro have been isolated and their oligomeric state and ligand binding properties evaluated. These mutant proteins do not form tetramers but exist as stable dimers with inducer binding comparable with the wild-type protein. Apparent operator affinities for lac repressor proteins with mutations in the proposed bZIP domain were significantly lower than the corresponding wild-type values. For these dimeric mutant proteins, the monomer-dimer equilibrium is linked to the apparent operator binding constant. The values for the monomer-monomer binding constant and for the intrinsic operator binding constant for the dimer cannot be resolved from measurements of the observed Kd for operator DNA. Further studies on these proteins are in progress.
Photodynamic Treatment with Benzoporphyrin Derivative Monoacid Ring A Produces Protein Tyrosine Phosphorylation Events and DNA Fragmentation in Murine P815 Cells (1998)

Treatment with benzoporphyrin derivative monoacid ring A (BPD-MA, verteporfin) and broad-spectrum fluorescent light rapidly produced apoptosis in murine P815 mastocytoma cells. Fragmentation of DNA, a fundamental characteristic of cells undergoing apoptosis, was evident within 3 h following the photodynamic treatment. Western immunoblot analysis using the specific antiphosphotyrosine monoclonal antibody 4G10 indicated that molecular species of >200 kDa were phosphorylated on tyrosine residues during or immediately following the irradiation of cells loaded with BPD-MA. Increased tyrosine phosphorylation of a 15 kDa protein was evident by 15 min postirradiation. In the absence of light, BPD-MA did not affect the status of cellular protein tyrosine phosphorylation or cause DNA fragmentation. The protein kinase inhibitor staurosporine prevented tyrosine phosphorylation of the >200 kDa species but did not affect tyrosine phosphorylation of the 15 kDa protein or the level of DNA fragmentation produced by the photo-dynamic treatment. The protein tyrosine phosphorylation events observed for P815 cells treated with cytotoxic levels of BPD-MA and light may not be directly related to the induction of the apoptotic cell death pathway.
Cat-qubits for quantum computation (2016)

The development of quantum Josephson circuits has created a strong expectation for reliable processing of quantum information. While this progress has already led to various proof-of-principle experiments on small-scale quantum systems, a major scaling step is required towards many-qubit protocols. Fault-tolerant computation with protected logical qubits usually comes at the expense of a significant overhead in the hardware. Each of the involved physical qubits still needs to satisfy the best achieved properties (coherence times, coupling strengths and tunability). Here, and in the aim of addressing alternative approaches to deal with these obstacles, I overview a series of recent theoretical proposals, and the experimental developments following these proposals, to enable a hardware-efficient paradigm for quantum memory protection and universal quantum computation.
The complete nucleotide sequence of the adenylate cyclase gene ofEscherichia coli (1984)

The complete nucleotide sequence of the cya gene from E. coli was determined. The gene encodes a polypeptide consisting of 848 amino acid residues with a calculated molecular weight of 97,542. The deduced protein structure reveals that cyclase is comprised of two domains, an amino-terminal region exhibiting catalytic activity and a carboxy-terminal region possibly carrying regulatory function. The frequent appearance of rare codons in the beginning of the gene as well as the sequence duplication in the promoter-initiator region suggest possible regulation(s) at the translational level. An unknown gene (cyaX) which seems to code for a very hydrophobic protein was found following the cya gene. Sequence analysis suggests that the cyax is a part of the cya operon.