gebhart/patrepeval huggingface dataset:
Selective Induction of Prostaglandin G/H Synthase I by Stem Cell Factor and Dexamethasone in Mast Cells (1995)

This study examines the regulatory effects of two cytokines, stem cell factor (SCF) and interleukin-3, and a glucocorticoid, dexamethasone, on lipid mediator generation in mouse bone marrow-derived mast cells (BMMC). Treatment of BMMC with SCF induced a modest, dose-dependent increase in three eicosanoids, thromboxane B2, prostaglandin D2, and leukotriene B4. These increases were accompanied by a marked elevation in cytosolic PLA2 (cPLA2). Dexamethasone blocked the induction of cPLA2 levels and the elevation in leukotriene B4 induced by SCF. By contrast, the combination of SCF and dexamethasone dramatically increased (5-8-fold) the capacity by BMMC to produce prostanoid products. This increase in prostanoid products was mirrored by an increase in prostaglandin G/H synthase I (PGHS-I) levels. Dexamethasone, alone, had no effect on PGHS-I, cPLA2, or prostanoid levels. Moreover, neither SCF or dexamethasone, alone or in combination, influenced prostaglandin G/H synthase II (PGHS-II) levels. In contrast to SCF, interleukin-3 alone or in combination with dexamethasone had no effect on prostanoid synthesis or PGHS-I or II levels. To better understand the SCF and dexamethasone effect, PGHS-I and PGHS-II mRNA expression were examined by Northern analysis. PGHS-I mRNA was markedly induced (maximal levels at 5 h) by the combination of SCF and dexamethasone. PGHS-II mRNA was undetectable in either control or SCF/dexamethasone-treated BMMC. Neither SCF or dexamethasone, alone, altered mRNA for either PGHS isotype. Taken together, these studies reveal that PGHS-I may be critical to prostanoid formation in mast cells exposed to cytokines and glucocorticoids. Moreover, they suggest that synergistic induction of PGHS-I could represent a novel mechanism for the anti-inflammatory action of glucocorticoids.
From Fernand Widal rhinitis syndrome and chronic sinusitis to total muco-ciliary disease. (1988)

It is claimed that 25% of the total population show symptoms of a muco-ciliary chronic sinusitis, presenting as a posterior catharrh that can be confirmed by computerized tomography and by prolonged sinuso-nasal saccharine clearance. This manifestation of the mucus ciliary transport syndrome may be associated with other disorders (rhinitis, otitis, bronchitis, irritable colon, sterility and dextrocardia). The role of aspirin and intolerance to other drugs or chemicals especially anti-inflammatory drugs, has been implicated. Acid air pollution may play a part, as the respiratory mucus does not tolerate an acid pH. Alkaline aerosols and theophyllin which activates cilia mobility, usually increase mucus fluidity and facilitate its clearance from the sinuses.
Deep Learning in Drug Design: Protein-Ligand Binding Affinity Prediction (2020)

Computational drug design relies on the calculation of binding strength between two biological counterparts especially a chemical compound, i.e., a ligand, and a protein. Predicting the affinity of protein-ligand binding with reasonable accuracy is crucial for drug discovery, and enables the optimization of compounds to achieve better interaction with their target protein. In this paper, we propose a data-driven framework named DeepAtom to accurately predict the protein-ligand binding affinity. With 3D Convolutional Neural Network (3D-CNN) architecture, DeepAtom could automatically extract binding related atomic interaction patterns from the voxelized complex structure. Compared with the other CNN based approaches, our light-weight model design effectively improves the model representational capacity, even with the limited available training data. We carried out validation experiments on the PDBbind v.2016 benchmark and the independent Astex Diverse Set. We demonstrate that the less feature engineering dependent DeepAtom approach consistently outperforms the other baseline scoring methods. We also compile and propose a new benchmark dataset to further improve the model performances. With the new dataset as training input, DeepAtom achieves Pearson's R=0.83 and RMSE=1.23 pK units on the PDBbind v.2016 core set. The promising results demonstrate that DeepAtom models can be potentially adopted in computational drug development protocols such as molecular docking and virtual screening.
Hybrid electrical energy storage systems (2010)

Electrical energy is a high quality form of energy that can be easily converted to other forms of energy with high efficiency and, even more importantly, it can be used to control lower grades of energy quality with ease. However, building a cost-effective electrical energy storage (EES) system is a challenging task despite steady advances in the design and manufacturing of EES elements including various battery and supercapacitor technologies. As of today, no single type of EES element fulfills high energy density, high power delivery capacity, low cost per unit of storage, long cycle life, low leakage, and so on at the same time.
Physiologically based modelling of inhibition of metabolism and assessment of the relative potency of drug and metabolite: dextromethorphan <i>vs</i>. dextrorphan using quinidine inhibition (2003)

Physiologically based PK modelling with perturbation of metabolism using an inhibitor allowed evaluation of the antitussive potency of DOR without the need for separate administration of DOR.
How expert systems can support network diagnostics, management and control (1988)

The purpose of this paper is to: briefly review the typical networking situation and related problems and consequences that have to be considered in network management environments; give an insight into the characteristics and the functionality that can be derived from using expert systems, how they can help and support networking operations, and how they differ from conventional systems; show specifically how expert systems can most effectively be applied to improve network diagnostic, management and support capabilities; provide practical examples on the strategic options that might be available to most effectively improve network operational capabilities; resolving a considerable range of support problems which include both trivial and complex diagnostic issues, online and remote problem determination to identify immediate and potential problems, down to a component, line and sub-component level; and indicate the costs, benefits and the conclusions that can be drawn from considering the use of expert systems to support network management and control.
Phase III Study of Fluorouracil, Leucovorin, and Levamisole in High-Risk Stage II and III Colon Cancer: Final Report of Intergroup 0089 (2005)

The 6- to 8-month regimens of LDLV and HDLV without levamisole used in this trial, rather than the previous standard regimen of 12 months of LEV, have become widely used. INT-0089 has long-term follow-up of the largest clinical trial of patients with high-risk colon cancer, documenting not only the durability of the treatment effects, but also the natural history of patients with high-risk colon cancer, and analyses of treatment based on age, race, and comorbid conditions such as obesity, diabetes, and second primary cancers.
Development of New Hole-Type Avalanche Detectors and the First Results of Their Applications (2008)

We have developed a new detector of photons and charged particles-a hole-type structure with electrodes made of a double layered resistive material: a thin low resistive layer coated with a layer having much higher resistivity. One of the unique features of this detector is its capability to operate at high gas gains (up to ) in air or in gas mixtures with air. They can also operate in a cascaded mode or be combined with other detectors, for example with GEM. This opens new avenues in their applications. Several prototypes based on this new detector and oriented to practical applications were developed and successfully tested: a detector of soft X-rays and alpha particles, a flame sensor, a detector of dangerous gases. All of these devices could operate stably even in humid air and/or in dusty conditions. The main advantages of these devices are their simplicity, low cost, and high sensitivity. For example, due to the avalanche multiplication, the detectors of flames and dangerous gases have a sensitivity of 10-100 times higher than commercial devices. We therefore believe that new detectors will have a great future.
Stratification of Hepatocellular Carcinoma Patients Based on Acetate Utilization (2015)

Hepatocellular carcinoma (HCC) is a deadly form of liver cancer that is increasingly prevalent. We analyzed global gene expression profiling of 361 HCC tumors and 49 adjacent noncancerous liver samples by means of combinatorial network-based analysis. We investigated the correlation between transcriptome and proteome of HCC and reconstructed a functional genome-scale metabolic model (GEM) for HCC. We identified fundamental metabolic processes required for cell proliferation using the network centric view provided by the GEM. Our analysis revealed tight regulation of fatty acid biosynthesis (FAB) and highly significant deregulation of fatty acid oxidation in HCC. We predicted mitochondrial acetate as an emerging substrate for FAB through upregulation of mitochondrial acetyl-CoA synthetase (ACSS1) in HCC. We analyzed heterogeneous expression of ACSS1 and ACSS2 between HCC patients stratified by high and low ACSS1 and ACSS2 expression and revealed that ACSS1 is associated with tumor growth and malignancy under hypoxic conditions in human HCC.
The Burden of Gastrointestinal and Liver Diseases, 2006 (2006)

Gastrointestinal and liver diseases are significant contributors to the morbidity, mortality, and health-care expenditures of the U.S. population.
Reformatsky reaction: carboxymethylenation of cyclic anhydrides and reactions of products thereof (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTReformatsky reaction: carboxymethylenation of cyclic anhydrides and reactions of products thereofBanavara L. Mylari and William J. ZembrowskiCite this: J. Org. Chem. 1991, 56, 7, 2587–2589Publication Date (Print):March 1, 1991Publication History Published online1 May 2002Published inissue 1 March 1991https://pubs.acs.org/doi/10.1021/jo00007a061https://doi.org/10.1021/jo00007a061research-articleACS PublicationsRequest reuse permissionsArticle Views240Altmetric-Citations9LEARN 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 Get e-Alerts
Proofreading and Aminoacylation of tRNAs Before Export from the Nucleus (1998)

After synthesis and processing in the nucleus, mature transfer RNAs (tRNAs) are exported to the cytoplasm in a Ran.guanosine triphosphate-dependent manner. Export of defective or immature tRNAs is avoided by monitoring both structure and function of tRNAs in the nucleus, and only tRNAs with mature 5' and 3' ends are exported. All tRNAs examined can be aminoacylated in nuclei of Xenopus oocytes, thereby providing a possible mechanism for functional proofreading of newly made tRNAs. Inhibition of aminoacylation of a specific tRNA retards its appearance in the cytoplasm, indicating that nuclear aminoacylation promotes efficient export.
Efficacy and irritancy of enhancers on the in-vitro and in-vivo percutaneous absorption of curcumin (2003)

Curcumin is a predominant compound derived from the rhizomes of Curcuma longa L., and shows antibacterial, anti-inflammatory and antineoplastic activity. The in-vitro and in-vivo skin absorption of curcumin was investigated after application of enhancers using Wistar rat as an animal model. The enhancers selected in this study included terpenes, flavonoids and cholestanol. The irritant profiles of these enhancers were also established by transepidermal water loss (TEWL) and histological observations. Cyclic monoterpenes generally showed stronger enhancement of curcumin permeation than the other enhancers. Modulation of concentration and pretreatment duration of enhancers possibly indicated that the enhancers have varied ability and mechanisms to enhance curcumin permeation. Terpineol produced the highest TEWL values among the enhancers tested, whereas ketocholestanol produced no, or only a negligible, increase in TEWL as compared with control. The results showed that skin disruption and inflammation did not necessarily correspond to the enhancing efficiency of the enhancers.
Constraining Credential Usage in Logic-Based Access Control (2010)

Authorization logics allow concise specification of flexible access-control policies, and are the basis for logic-based access-control systems. In such systems, resource owners issue credentials to specify policies, and the consequences of these policies are derived using logical inference rules. Proofs in authorization logics can serve as capabilities for gaining access to resources. Because a proof is derived from a set of credentials possibly issued by different parties, the issuer of a specific credential may not be aware of all the proofs that her credential may make possible. From this credential issuer's standpoint, the policy expressed in her credential may thus have unexpected consequences. To solve this general problem, we propose a system in which credentials can specify constraints on how they are to be used. We show how to modularly extend wellstudied authorization logics to support the specification and enforcement of such constraints. A novelty of our design is that we allow the constraints to be arbitrary well-behaved functions over authorization proofs. Since all the information about an access is contained in the proofs, this makes it possible to express many interesting constraints. We study the formal properties of such a system, and give examples of constraints.
Nuclear dna content of thirteen turfgrass species by flow cytometry (1999)

Knowledge of nuclear DNA content will facilitate future molecular studies of turfgrasses. The objective of this study was to determine genome size of 12 turfgrass species and an interspecific hybrid by means of flow cytometry and to compare genome size of warm and cool‐season grasses. The seven species and an interspecific hybrid of warm‐season turfgrasses had genome sizes ranging from 0.86 to 1.95 pg/2C, while the genome sizes of five cool‐season grasses ranged from 5.65 to 15.59 pg/2C. Ploidy levels of the samples were also determined. The observation of the distinct genome sizes of the warm and cool‐season turfgrasses agrees with previous reports regarding genome sizes of tropical and temperate species in certain angiosperm families including Gramineae.
Engineering Increased Stability into Self‐Assembled Protein Fibers (2006)

Abstract Two stages in the rational redesign of a peptide‐based, self‐assembling fiber (SAF) are described. The SAF system comprises two peptides designed to form an offset α‐helical coiled‐coil heterodimer. The “sticky‐ends” are complementary and promote longitudinal assembly. Alone, the two peptides are unstructured, but co‐assemble upon mixing to form α‐helical fibrils, which bundle to form fibers 40–50 nm wide and tens of micrometers long. Assembly is controllable and occurs at pH 7 in water, making SAFs a potential scaffold for 3D cell culture. The purposes of the redesigns were 1) to investigate the fiber‐thickening process, and 2) to increase fiber stability for potential biological and biomedical applications. First, mutations were made to the original peptide designs to increase fibril–fibril interactions and so produce thicker and more‐stable fibers. The second iteration aimed to increase the primary peptide–peptide interactions by increasing the overlap in the offset dimer and so promote the initial step in fiber formation. As judged by circular dichroism spectroscopy and transmission electron microscopy, both iterations improved fiber assembly and stability: the critical peptide concentration for assembly improved from 60 μ M to 4 μ M ; the midpoint of thermal unfolding increased from 22 °C to 65 °C; and the salt tolerance improved from 75 m M to greater than 250 m M KCl. These improvements bring closer applications of the SAF system under physiological conditions, for example as a biocompatible material for 3D cell culture. In addition, ordered surface features were observed in the second‐ and third‐generation fibers compared with the original design. This indicates improved internal order in the redesigned fibers. In turn, this suggests a molecular mechanism for the improved stability and sheds light on the fiber‐assembly process.
DNA Strands Attached Inside Single Conical Nanopores: Ionic Pore Characteristics and Insight into DNA Biophysics (2010)

Single nanopores attract a great deal of scientific interest as a basis for biosensors and as a system to study the interactions and behavior of molecules in a confined volume. Tuning the geometry and surface chemistry of nanopores helps create devices that control transport of ions and molecules in solution. Here, we present single conically shaped nanopores whose narrow opening of 8 or 12 nm is modified with single-stranded DNA molecules. We find that the DNA occludes the narrow opening of nanopores and that the blockade extent decreases with the ionic strength of the background electrolyte. The results are explained by the ionic strength dependence of the persistence length of DNA. At low KCl concentrations (10 mM) the molecules assume an extended and rigid conformation, thereby blocking the pore lumen and reducing the flow of ionic current to a greater extent than compacted DNA at high salt concentrations. Attaching flexible polymers to the pore walls hence creates a system with tunable opening diameters in order to regulate transport of both neutral and charged species.
A Fourier transform cavity ring down spectrometer (1996)

We present a pulsed multiplex absorption spectrometer in which the sensitivity of the cavity ring down absorption detection technique is combined with the multiplex advantage of a Fourier Transform spectrometer. A description of the Fourier transform cavity ring down (CRD) spectrometer—substantiated with first experimental results on the atmospheric band of molecular oxygen—is given. It is shown that as in the case of normal CRD spectroscopy, the measurement is independent of light intensity fluctuations provided the spectral intensity distribution of the light source is known and is constant during the measurement.
Non-Starch Polysaccharide-Degrading Enzymes Increase the Performance of Broiler Chickens Fed Wheat of Low Apparent Metabolizable Energy (1995)

The effect of a commercial glycanase product (Avizyme TX) on the performance of 4-wk-old broiler chickens fed wheats with low and normal apparent metabolizable energy values was studied. Controls were fed a corn-based diet. Supplementation with the enzyme product significantly (P < 0.01) increased the apparent metabolizable energy of the low metabolizable energy wheat from 12.02 to 14.94 MJ/kg dry matter. The apparent metabolizable energy value of the normal wheat was increased from 14.52 to 14.83 MJ/kg dry matter; this was, however, not significant. Birds fed the low metabolizable energy wheat diet had significantly (P < 0.01) higher digesta viscosity and lower small intestinal starch and protein digestibilities than birds fed the normal wheat diet. Chickens fed the low metabolizable energy wheat tended to grow less than those fed the normal wheat diet. When the low metabolizable energy wheat+enzyme diet was fed, digesta viscosity was significantly (P < 0.01) lower (20.28 vs. 10.36 mPa.s), and small intestinal digestibility coefficient of starch was significantly (P < 0.01) greater (0.584 vs. 0.861) relative to values in birds fed the low metabolizable energy wheat diet alone. Although the protein digestibility coefficient also increased from 0.689 to 0.745, the difference was not significant. Weight gain and feed efficiency of birds fed the low metabolizable energy wheat+enzyme equaled those of controls. The enzyme product significantly (P < 0.01) increased the solubilization of non-starch polysaccharides within the gastrointestinal tract of birds fed both types of wheat diets.(ABSTRACT TRUNCATED AT 250 WORDS)
Performance of high-area-ratio annular dump diffuser using suction-stabilized-vortex flow control (1977)

A short annular dump diffuser having a geometry conductive to formation of suction stabilized toroidal vortices in the region of abrupt area change was tested. The overall diffuser area ratio was 4.0 and the length to inlet height ratio was 2.0. Performance data were obtained at near ambient temperature and pressure for inlet Mach numbers of 0.18 and 0.30 with suction rates ranging from 0 to 18 percent of total inlet mass flowrate. Results show that the exit velocity profile could be readily biased toward either wall by adjustment of inner and outer wall suction rates. Symmetric exit velocity profiles were inherently unstable with a tendency to revert to a hub or tip bias. Diffuser effectiveness was increased from about 38 percent without suction to over 85 percent at a total suction rate of 10 to 12 percent. At the same time diffuser total pressure loss was reduced from 3.1 percent to 1.1 percent at an inlet Mach number of 0.3.
Design and Implementation of Digital Right Management in aCollaborative Peer-To-Peer Network (2007)

P2P (peer-to-peer) applications have enormous successes in information sharing, although there exist illegal distributions of copyright-protected works and anonymous malicious attacks. A P2P research network prototype, called vuCRN, was developed collaboratively by IT professionals using JXTA technology. It allows its peers freely download shared files with upload permissions being monitored and controlled by decentralized-user authentication using local LDAP (lightweight directory access protocol) servers. This paper presents the second-stage implementation of the vuCRN in digital right management (DRM). Two types of licenses can be issued by a authorized team in the vuCRN system. Eight open content licenses with one license for personal use only. According to the legal requirements, the IT team incorporates these licenses into the vuCRN via metadata data management. The step-by-step design and implementation of DRM for sharing PDF files in the vuCRN are detailed in this paper.