gebhart/patrepeval huggingface dataset:
Manipulation of cytokines in the management of patients with inflammatory bowel disease (2000)

In recent years, new concepts have been formulated for the therapeutic management of the intractable forms of Crohn's disease and ulcerative colitis, the two major forms of inflammatory bowel disease. These advances are based largely on new insights into the immune-inflammatory events occurring in the gut of these patients. Analysis of the types of immune response ongoing in the inflamed intestine has revealed that in Crohn's disease there is predominantly a T-helper cell type 1 response, with exaggerated production of interleukin (IL)-12 and interferon (IFN)-gamma, whereas in ulcerative colitis the lesion seems more of an antibody-mediated hypersensitivity reaction. Despite these differences, downstream inflammatory events are the same in both conditions. In both Crohn's disease and ulcerative colitis mucosa, IL-1gamma, IL-6, IL-8 and tumour necrosis factor (TNF)-alpha are produced in excess, and the production of free radicals accompanying the influx of nonspecific inflammatory cells into the mucosa is above the normal range. Strategies aimed at inhibiting T-cell responses are therefore more relevant in Crohn's disease, whereas, in theory at least, inhibition of downstream inflammatory processes should be therapeutic in both Crohn's disease and ulcerative colitis. This review seeks to summarize studies in which anticytokine antibodies, cytokines or cytokine-modifying agents have been used in the treatment of either Crohn's disease or ulcerative colitis.
Identification of an UP element consensus sequence for bacterial promoters (1998)

The UP element, a component of bacterial promoters located upstream of the -35 hexamer, increases transcription by interacting with the RNA polymerase alpha-subunit. By using a modification of the SELEX procedure for identification of protein-binding sites, we selected in vitro and subsequently screened in vivo for sequences that greatly increased promoter activity when situated upstream of the Escherichia coli rrnB P1 core promoter. A set of 31 of these upstream sequences increased transcription from 136- to 326-fold in vivo, considerably more than the natural rrnB P1 UP element, and was used to derive a consensus sequence: -59 nnAAA(A/T)(A/T)T(A/T)TTTTnnAAAAnnn -38. The most active selected sequence contained the derived consensus, displayed all of the properties of an UP element, and the interaction of this sequence with the alpha C-terminal domain was similar to that of previously characterized UP elements. The identification of the UP element consensus should facilitate a detailed understanding of the alpha-DNA interaction. Based on the evolutionary conservation of the residues in alpha responsible for interaction with UP elements, we suggest that the UP element consensus sequence should be applicable throughout eubacteria, should generally facilitate promoter prediction, and may be of use for biotechnological applications.
Tutorial: Integrated-photonic switching structures (2018)

Recent developments in waveguided 2 × 2 and N × M photonic switches are reviewed, including both broadband and narrowband resonant devices for the Si, InP, and AlN platforms. Practical actuation of switches by electro-optical and thermo-optical techniques is discussed. Present datacom-and-computing applications are reviewed, and potential applications are proposed for chip-scale photonic and optoelectronic integrated switching networks. Potential is found in the reconfigurable, programmable “mesh” switches that enable a promising group of applications in new areas beyond those in data centers and cloud servers. Many important matrix switches use gated semiconductor optical amplifiers. The family of broadband, directional-coupler 2 × 2 switches featuring two or three side-coupled waveguides deserves future experimentation, including devices that employ phase-change materials. The newer 2 × 2 resonant switches include standing-wave resonators, different from the micro-ring traveling-wave resonators. The resonant devices comprise nanobeam interferometers, complex-Bragg interferometers, and asymmetric contra-directional couplers. Although the fast, resonant devices offer ultralow switching energy, ∼1 fJ/bit, they have limitations. They require several trade-offs when deployed, but they do have practical application.
The Myeloid Leukemia-associated Protein SET Is a Potent Inhibitor of Protein Phosphatase 2A (1996)

Two potent heat-stable protein phosphatase 2A (PP2A) inhibitor proteins designated I1PP2A and I2PP2A have been purified to apparent homogeneity from extracts of bovine kidney (Li, M., Guo, H., and Damuni, Z. (1995) Biochemistry 34, 1988-1996). N-terminal and internal amino acid sequencing indicated that I2PP2A was a truncated form of SET, a largely nuclear protein that is fused to nucleoporin Nup214 in acute non-lymphocytic myeloid leukemia. Experiments using purified preparations of recombinant human SET confirmed that this protein inhibited PP2A. Half-maximal inhibition of the phosphatase occurred at about 2 nM SET. By contrast, SET (up to 20 nM) did not affect the activities of purified preparations of protein phosphatases 1, 2B, and 2C. The results indicate that SET is a potent and specific inhibitor of PP2A and suggest that impaired regulation of PP2A may contribute to acute myeloid leukemogenesis.
Synthesis and characterization of phosphorescent cyclometalated iridium complexes containing 2,5‐diphenylpyridine based ligands (2005)

Abstract A series of phosphorescent cyclometalated iridium complexes with 2,5‐diphenylpyridine‐based ligands has been synthesized and characterized to investigate the effect of the simple ligand modification on photophysics, thermostability and electrochemistry. The complexes have the general structure (C ∧ N) 2 Ir(acac), where C ∧ N is a monoanionic cyclometalating ligand [e.g. 2,5‐diphenylpyridyl (dppy), 2,5‐di(4‐methoxyphenyl)pyridyl (dmoppy), 2,5‐di(4‐ethoxyphenyl)pyridyl (deoppy) and 2,5‐di(4‐ethylphenyl)pyridyl (deppy)]. The absorption, emission, cyclic voltammetry and thermostability of the complexes were systematically investigated. The (dppy) 2 Ir(acac) has been characterized using X‐ray crystallography. Calculation on the electronic ground state of (dppy) 2 Ir(acac) was carried out using B3LYP density functional theory. The highest occupied molecular orbital (HOMO) level is a mixture of Ir and ligand orbitals, while the lowest occupied molecular orbital (LUMO) is predominantly dppy ligand‐based. Electrochemical studies showed the oxidation potentials of (dmoppy) 2 Ir(acac), (deoppy) 2 Ir(acac), (deppy) 2 Ir(acac) were smaller than that of (ppy) 2 Ir(acac), while the oxidation potential of (dppy) 2 Ir(acac) was larger relative to (ppy) 2 Ir(acac). The 10% weight reduction temperatures of these complexes were above that of (ppy) 2 Ir(acac). All complexes exhibited intense green photoluminescence, which has been attributed to MLCT triplet emission. The maximum emission wavelengths in CH 2 Cl 2 at room temperature were in the range 531–544 nm, which is more red‐shifted than that of (ppy) 2 Ir(acac). Copyright © 2005 John Wiley &amp; Sons, Ltd.
Restenosis after coronary angioplasty. Potential biologic determinants and role of intimal hyperplasia. (1989)

Restenosis after successful PTCA remains a major problem limiting the efficacy of the procedure. The pathophysiologic mechanism of restenosis has been enigmatic so far, but accumulated evidence strongly suggests that intimal hyperplasia is the major mechanism. Based on current understanding of the process of intimal hyperplasia, one unifying concept may be that there are at least two major local biologic determinants influencing this process, lesion characteristics and regional flow dynamics. Lesion characteristics include the plaque structure and the quantity of smooth muscle. These may provide the anatomic substrate that determines the extent of injury and the degree of smooth muscle cell proliferation. The amount of smooth muscle cells in the stenotic lesion activated by injury to undergo proliferation may determine the eventual bulk of the restenotic lesion. In addition, low wall shear stress could promote intimal hyperplasia and cause structural change of vessels to decrease the lumen, whereas high wall shear stress exerts the opposite effects. Intimal hyperplasia after balloon injury is a complex process involving platelets, growth factors, endothelial cells, smooth muscle cells, mechanical injury, wall shear stress, and probably other unknown factors. Platelets not only contribute growth factors such as PDGF but also cause organized thrombus. Different growth factors may be involved in initiating smooth muscle cell proliferation and may come from many different sources, including smooth muscle cells, endothelial cells, and macrophages. Intact confluent endothelial cells may produce heparin sulfates and inhibit intimal proliferation; however, regenerating endothelial cells may have the opposite effect. Thus, the proliferative potential of smooth muscle cells, endothelial recovery, extent of injury, wall shear stress, and other unknown factors may all influence this process. Based on these concepts concerning the biology of restenosis, some research directions concerning potential forms of therapy are proposed.
Histo-chemical studies on the anti-ulcer effect of bamboo grass in rats. (1990)

Oral administration of a hot-water extract (Folin) of bamboo grass (Sasa albomarginata Makino & Shibata) significantly reduced the incidence of water-immersion and restraint stress-, ethanol-induced and indomethacin-induced gastric ulcers in rats. Histological examination of the Folin-treated gastric mucosa showed that microscopic blood clots overlaid the superficial epithelium, maintaining the cellular integrity of gastric mucosa, especially against stress ulcer. In addition, Folin suppressed the incidence of hyperaemia and a decline of acid mucopolysaccharides in the ethanol-induced ulcer. Folin suppressed a release of histamine from rat mast cells, and stabilized erythrocytes and accelerated their agglutination under acid conditions. These results suggest that a microscopic haemostatic effect of Folin reinforced by a membrane-stabilizing effect might be responsible for the prevention of the gastric lesions.
A Convenient Procedure for the Palladium‐Catalyzed Cyanation of Aryl Halides (2003)

A useful source of cyanide for the palladium-catalyzed cyanation of aryl halides is acetone cyanohydrin (see scheme; dpppe=1,5-bis(diphenylphosphanyl)pentane, tmeda=N,N,N′,N′-tetramethylethylenediamine). The key to the success of the reaction is the slow dosage of the cyanation reagent to the reaction mixture to prevent the deactivation of the palladium catalyst caused by excess cyanide ions in solution.
Mass Spectrometric Characterization of Microscale Enzyme Catalyzed Reactions of Surface-Bound Peptides and Proteins (1987)

Many important biomolecules occur in nature only in very low abundance. Ever more sensitive analytical tools are thus required for the elucidation of their structure and chemical behavior. We have recently demonstrated (1,2) a new mass spectrometric method for investigating microscale chemical reactions of both gas and condensed phase reagents with the surface of organic solids. Here we report the results of an investigation of the utility of this new method for measuring enzyme catalyzed reactions of surface-bound peptides and proteins.
Optical properties of high-delta air–silica microstructure optical fibers (2000)

We analyze the waveguide properties of microstructure optical fibers consisting of a silica core surrounded by a single ring of large air holes. Although the fibers can support numerous transverse spatial modes, coupling between these modes even in the presence of large perturbations is prevented for small core dimensions, owing to a large wave-vector mismatch between the lowest-order modes. The result is an optical fiber that can appear single mode with propagation properties that can be achieved only in multimode waveguides.
Surface structure of silicon carbide irradiated with helium ions with monoenergy and continuous energy distributions (1982)

Silicon carbide was irradiated at room temperature and 600 °C with helium ions with monoenergy (3–100 keV) and continuous energy distribution ranging from 0.5 keV to 20 keV up to a total dose of 1×1019 ions/cm2 using an ion accelerator controlled by a microcomputer. For room temperature irradiation, porous structures appear on the surface of samples irradiated to dose of ∼5×1018 ions/cm2, and the damaged layer is easily removed from underlying undamaged layer by ultrasonic vibrations. On the other hand, for target temperature of 600 °C, such porous surface structures are not observed, which is due to thermal annealing. It has been shown that the surface deformation depends strongly not only on the implantation profile, but also on irradiation modes of helium ions. Flaking is completely avoided by prebombardment of helium ions with continuous energy distribution, which deliberately produces a pathway for gas release. In order to simulate wall erosion due to helium bombardment, silicon carbide was also irradiated with a Maxwellian distribution. No blistering or flaking is observed for an average energy of 3 keV.
Substituted 1,3,4-thiadiazoles with anticonvulsant activity. 2. Aminoalkyl derivatives (1986)

This paper describes the synthesis and pharmacological evaluation of a number evaluation of a number of substituted 1,3,4-thiadiazoles. The first member of the series, 2-(aminomethyl)-5-(2-biphenylyl)-1,3,4-thiadiazole (7) was found to possess potent anticonvulsant properties in rats and mice and compared favorably with the standard anticonvulsant drugs phenytoin, phenobarbital, and carbamazepine in a number of test situations. The potency of compound 7 was maintained on alkylation of the side-chain nitrogen atom; however, aryl substitution or chain lengthening caused a drop in potency. Replacement of the 2-biphenylyl group by phenyl or benzyl also lead to inactive compounds.
Assembly and Function of Type III Secretory Systems (2000)

Type III secretion systems allow Yersinia spp., Salmonella spp., Shigella spp., Bordetella spp., and Pseudomonas aeruginosa and enteropathogenic Escherichia coli adhering at the surface of a eukaryotic cell to inject bacterial proteins across the two bacterial membranes and the eukaryotic cell membrane to destroy or subvert the target cell. These systems consist of a secretion apparatus, made of approximately 25 proteins, and an array of proteins released by this apparatus. Some of these released proteins are "effectors," which are delivered into the cytosol of the target cell, whereas the others are "translocators," which help the effectors to cross the membrane of the eukaryotic cell. Most of the effectors act on the cytoskeleton or on intracellular-signaling cascades. A protein injected by the enteropathogenic E. coli serves as a membrane receptor for the docking of the bacterium itself at the surface of the cell. Type III secretion systems also occur in plant pathogens where they are involved both in causing disease in susceptible hosts and in eliciting the so-called hypersensitive response in resistant or nonhost plants. They consist of 15-20 Hrp proteins building a secretion apparatus and two groups of effectors: harpins and avirulence proteins. Harpins are presumably secreted in the extracellular compartment, whereas avirulence proteins are thought to be targeted into plant cells. Although a coherent picture is clearly emerging, basic questions remain to be answered. In particular, little is known about how the type III apparatus fits together to deliver proteins in animal cells. It is even more mysterious for plant cells where a thick wall has to be crossed. In spite of these haunting questions, type III secretion appears as a fascinating trans-kingdom communication device.
Predicting Thread Discourse Structure over Technical Web Forums (2011)

Online discussion forums are a valuable means for users to resolve specific information needs, both interactively for the participants and statically for users who search/browse over historical thread data. However, the complex structure of forum threads can make it difficult for users to extract relevant information. The discourse structure of web forum threads, the form of labelled dependency relationships between posts, has the potential to greatly improve information access over web forum archives. In this paper, we present the task of parsing user forum threads to determine the labelled dependencies between posts. Three methods, including a dependency parsing approach, are proposed to jointly classify the links (relationships) between posts and the dialogue act (type) of each link. The proposed methods significantly surpass an informed baseline. We also experiment with in situ classification of evolving threads, and establish that our best methods are able to perform equivalently well over partial threads as complete threads.
Primate betaherpesviruses (2007)

The last few years have witnessed significant expansion of the simian cytomegalovirus (CMV) model of human CMV (HCMV) infection. Progress in the utilization of the simian CMV models has been highlighted by a better understanding of natural history, development of species-specific reagents and techniques, sequencing of several viral genomes, and generation of a bacterial artificial chromosome (BAC) containing a full-length CMV genome. This work has demonstrated that, not only is there strong conservation of genomic organization and coding content, but also that the simian CMV exhibit significant parallels to HCMV in the course of viral infection in both immunocompetent hosts and those without a fully functional immune system. A wide range of experimental approaches into the molecular biology of HCMV, mechanisms of HCMV persistence and pathogenesis, and the design of novel treatment and prevention strategies are now possible in different non-human primate (NHP) models.
Visualisation of HIFU lesions using elastography of the human prostate in vivo: preliminary results (2003)

An imaging system was developed for prostate elastography in vivo using a transrectal ultrasound (US) probe to guide high-intensity focused US (HIFU) therapy of prostate cancer. Uniform compression was applied using a balloon, while a sector image was acquired. Strain was calculated from the gradient of the displacements obtained from the ultrasonic signal using the cross-correlation technique. Elastograms were acquired on a total of 31 patients undergoing HIFU therapy for localised prostate cancer. For two patients, only part of the prostate was treated and posttherapy magnetic resonance imaging (MRI) confirmed the size and position of the HIFU lesions seen in the elastograms as low strain areas, with a strain contrast ratio between 1.6 and 3.2. The whole prostate was treated for the next 29 patients. After treatment, the whole prostate appeared to be stiff in the elastograms and a 40% to 60% (mean 50%) decrease in average strain was observed when compared to strains measured before HIFU application. Tumours identified by biopsies and sonograms could occasionally be seen in the preoperative elastograms. Decorrelation effects occurred mainly because of low sonographic signal-to-noise ratio (SNR) and of out-of-plane motion induced by respiration.
A mobility-based framework for adaptive clustering in wireless ad hoc networks (1999)

This paper presents a novel framework for dynamically organizing mobile nodes in wireless ad hoc networks into clusters in which the probability of path availability can be bounded. The purpose of the (/spl alpha/, t) cluster is to help minimize the far-reaching effects of topological changes while balancing the need to support more optimal routing. A mobility model for ad hoc networks is developed and is used to derive expressions for the probability of path availability as a function of time. It is shown how this model provides the basis for dynamically grouping nodes into clusters using an efficient distributed clustering algorithm. Since the criteria for cluster organization depends directly upon path availability, the structure of the cluster topology is adaptive with respect to node mobility. Consequently, this framework supports an adaptive hybrid routing architecture that can be more responsive and effective when mobility rates are low and more efficient when mobility rates are high.
Replacement of Glycine with Dicarbonyl and Related Moieties in Analogues of the C-Terminal Pentapeptide of Cholecystokinin: CCK2Agonists Displaying a Novel Binding Mode (2000)

Recent advances in the field of cholecystokinin have indicated the possible occurrence of multiple affinity states of the CCK(2) receptor. Besides, numerous pharmacological experiments performed "in vitro" and "in vivo" support the eventuality of different pharmacological profiles associated to CCK(2) ligands. Indeed, some agonists are essentially anxiogenic and uneffective in memory tests, whereas others are not anxiogenic and appear as able to reinforce memory. The reference compound for the latter profile is the CCK-8 analogue BC 264 (Boc-Tyr(SO(3)H)-gNle-mGly-Trp-(NMe)Nle-Asp-Phe-NH(2)). However, although tetrapeptide ligands based on CCK-4 (Trp-Met-Asp-Phe-NH(2)) are known to possess sufficient structural features for CCK(2) recognition, none shares the properties of BC 264. Hence we have developed new short peptidic or pseudo-peptidic derivatives containing the C-terminal tetrapeptide of BC 264. Our results indicate that some compounds characterized by the presence of two carbonyl groups at the N-terminus, as in 2b (HO(2)C-CH(2)-CONH-Trp-(NMe)Nle-Asp-Phe-NH(2)), are likely to show a BC 264-like profile, bind to the CCK(2) receptor in a specific way, and display remarkable affinities (2b: 0.28 nM on guinea-pig cortex membrane preparations). This original binding mode is discussed and further enlightened by NMR and molecular modeling studies.
Dendrimers Designed for Functions: From Physical, Photophysical, and Supramolecular Properties to Applications in Sensing, Catalysis, Molecular Electronics, Photonics, and Nanomedicine (2010)

ADVERTISEMENT RETURN TO ISSUEPREVReviewNEXTDendrimers Designed for Functions: From Physical, Photophysical, and Supramolecular Properties to Applications in Sensing, Catalysis, Molecular Electronics, Photonics, and NanomedicineDidier Astruc*, Elodie Boisselier, and Cátia OrnelasView Author Information ISM, UMR CNRS No. 5255, Université Bordeaux 1, 33405 Talence Cedex, France* To whom correspondence should be addressed. E-mail: [email protected]Cite this: Chem. Rev. 2010, 110, 4, 1857–1959Publication Date (Web):March 31, 2010Publication History Received30 September 2009Published online31 March 2010Published inissue 14 April 2010https://pubs.acs.org/doi/10.1021/cr900327dhttps://doi.org/10.1021/cr900327dreview-articleACS PublicationsCopyright © 2010 American Chemical SocietyRequest reuse permissionsArticle Views37461Altmetric-Citations1651LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Catalysts,Dendrons,Encapsulation,Fluorescence,Toxicity Get e-Alerts