gebhart/patrepeval huggingface dataset:
Sulindac sulfone inhibits azoxymethane-induced colon carcinogenesis in rats without reducing prostaglandin levels. (1997)

Nonsteroidal anti-inflammatory drugs (NSAIDs), such as sulindac, have cancer chemopreventive properties by a mechanism that has been suggested to involve cyclooxygenase inhibition and reduction of prostaglandin (PGE2) levels in the target tissue. To test this hypothesis, we studied the effect of dietary sulindac sulfone (500-2000 ppm), a metabolite of sulindac reported to lack cyclooxygenase inhibitory activity, on tumor formation and PGE2 levels in the azoxymethane model of colon carcinogenesis. Rats treated with sulindac at 400 ppm and piroxicam at 150 ppm were used as positive controls. Rats received two s.c. injections of azoxymethane (15 mg/kg) for 2 weeks and were fed either experimental or control diets until necropsy. After 31 weeks of sulfone treatment, a dose-related increase in sulfone levels in both serum and cecal contents was measured; there was no evidence of metabolic conversion to sulindac or other metabolites. Rats treated with sulfone at 1000 and 2000 ppm, sulindac, and piroxicam had significantly fewer colonic adenomas and carcinomas compared with rats fed control diet as measured by tumor incidence, multiplicity, and tumor burden. Sulfone-treated rats also showed a dose-response relationship for inhibiting all tumor parameters. Colons from rats treated with sulindac or piroxicam contained PGE2 levels that ranged from approximately 16-49% of control levels. PGE2 levels in rats treated with sulfone up to 2000 ppm ranged from 78-118% of control levels. Moreover, the effects of sulindac sulfone on various enzymes responsible for regulating prostaglandin levels were evaluated. No significant inhibitory effects were observed for cyclooxygenase, lipoxygenase, or phospholipase A2. These results suggest that reduction of prostaglandin levels in the target tissue may not be necessary for the chemopreventive properties of sulindac.
An operation and maintenance process model for energy management (1999)

A main focus in many management solutions today is the collection of information. Technical solutions using open systems and protocols have accomplished this. In energy management systems an impressive amount of information about alarm status, currents, voltages and other values are forwarded. The use of this information may vary a lot depening on the organisation using the management system and the purpose of using it. Support to identify the right process model to handle this information is critical. Not until this is accomplished will the full use of the management system be reached. The work to find the right "operation and maintenance" process model for a network of energy equipment involves several areas in the operation and maintenance organisation. By addressing a couple of key areas, for which full support is offered by the management system, a model to start with can be found rather easily. A process model is discussed in this paper, using a standard energy management tool. Parts of this work can be adapted smoothly to any other support and maintenance organisation handling energy equipment.
MODELS FOR INTERPRETING SCANNING CAPACITANCE MICROSCOPE MEASUREMENTS (1998)

Theoretical high-frequency capacitance-versusvoltage curves have been calculated for silicon in order to correlate scanning capacitance microscope (SCM) measurements with semiconductor dopant profiles. For twodimensional cases, the linear finite-element method is used to solve Poisson’s equation in the semiconductor region and Laplace’s equation in the oxide and the ambient regions. For three-dimensional cases, the collocation method is used in the semiconductor region, and the linear finite-element method is used outside this region. For a given oxide thickness, probe shape, and probe-tip size, the capacitance is calculated for a series of cases of uniform doping, and a few example solutions are found for a model graded doping profile. For the case of uniform doping, the theory can be used to form a database for rapid interpretation of SCM measurement data.
[Planning of actions for liquidation of medical-and-sanitary consequences after railway accidents with hazardous cargo]. (2011)

On the basis of analysis of experience of eliminate the consequences of derailing train accidents given the classification of emergency situations, set the features predict the expected health loss under the explosion of various damaging factors. The recommendations concerning the planning of medical consequences control after railway accidents with hazardous cargo are given.
Failure of pauling's bond energy equation (1968)

R. G. Pearson, Chem. Commun. (London), 1968, 65 DOI: 10.1039/C19680000065
Mass Spectrometric Profiling of Intact Biological Tissue by Using Desorption Electrospray Ionization (2005)

Direct chemical profiling of biological tissues, including metastatic human-liver adenocarcinoma, was carried out by using mass spectrometry under ambient conditions. Desorption electrospray ionization revealed enhanced signals from sphingolipids and increased unsaturation levels of the phospholipids in the tumor region of the tissue (see picture).
Double Click Reaction for the Acquisition of a Highly Potent and Selective mPTPB Inhibitor (2010)

Tuberculosis (TB), which is caused by Mycobacterium tuberculosis (Mtb), is a major worldwide threat to public health. Mycobacterium protein tyrosine phosphatase B (mPTPB) is a virulent phosphatase secreted by Mtb, which is essential for the survival and persistence of the bacterium in the host. Consequently, small-molecule inhibitors of mPTPB are expected to serve as anti-TB agents with a novel mode of action. Herein, we report the discovery of highly potent and selective mPTPB inhibitors using a novel, double Click chemistry strategy. The most potent mPTPB inhibitor from this approach possesses a K(i) value of 160 nM and a >25-fold selectivity for mPTPB over 19 other protein tyrosine phosphatases (PTBs). Molecular docking study of the enzyme-inhibitor complex provides a rationale for the high potency and selectivity of the lead compound and reveals an unusual binding mode, which may guide further optimization effort.
A probabilistic definition of item similarity (2011)

In item-based collaborative filtering, a critical intermediate step to personalized recommendations is the definition of an item-similarity metric. Existing algorithms compute the item-similarity using the user-to-item ratings (cosine, Pearson, Jaccard, etc.). When computing the similarity between two items A and B many of these algorithms divide the actual number of co-occurring users by some "difficulty" of co-occurrence. We refine this approach by defining item similarity as the ratio of the actual number of co-occurrences to the number of co-occurrences that would be expected if user choices were random. In the final step of our method to compute personalized recommendations we apply the usage history of a user to the item similarity matrix. The well defined probabilistic meaning of our similarities allows us to further improve this final step. We measured the quality of our algorithm on a large real-world data-set. As part of Comcast's efforts to improve its personalized recommendations of movies and TV shows, several top recommender companies were invited to apply their algorithms to one year of Video-on-Demand usage data. Our algorithm tied for first place. This paper includes a MapReduce pseudo code implementation of our algorithm.
Vacuum Pack Technique of Temporary Abdominal Closure: A 7-Year Experience with 112 Patients (2000)

The vacuum pack is the temporary abdominal wound closure of choice in patients undergoing open abdominal management at our institution. Primary closure is achieved in the majority of patients with a low rate of complication. The technique is simple and easily mastered. Technical complications are rare and easily repaired.
Dissolution and Degradation of Bacillus thuringiensis δ-Endotoxin by Gut Juice Protease of the Silkworm Bombyx mori (1983)

The dissolution and degradation of dagger-endotoxin (crystal) of Bacillus thuringiensis subsp. kurstaki strain HD-1 were investigated. Crystals were dissolved in 0.1 M phosphate-carbonate-NaOH buffer at pH > 12. Swelling of crystals occurred in the buffer between pH 10 and 11, and crystals dissolved in the same buffer supplemented with gut juice protease of the silkworm Bombyx mori. The proteolytic dissolution of crystals occurred after a time lag of several minutes in 0.1 M carbonate-NaOH buffer, pH 10.2. The time lag was not observed when crystals were suspended in the buffer for 30 min before the addition of protease. After the dissolution of the crystals and further degradation of the solubilized protein, the appearance of a toxic protein with a molecular weight of 59,000, designated P-59, was observed. Lower-molecular-weight peptides (less than 40,000) showed no toxicity to the silkworm larvae on feeding. Digestion of the 120,000-dalton subunit of the crystal by gut juice protease also produced P-59. These observations suggest the occurrence of a similar process in vivo, i.e., the swelling of crystals due to the alkalinity of gut juice and the production of P-59, dependent on the hydrolysis of swollen crystals by gut juice protease.
An Insight on the Leading HIV Entry Inhibitors (2006)

The main strategies nowadays to fight AIDS rely on chemical therapy to inhibit the reverse transcriptase or protease of HIV. However, a synthetic 36 amino-acids peptide that blocks the entry of the virus in the target cells (enfuvirtide) has recently reached approval for clinical application. This molecule may probably be just the leader of a new generation of drugs that is about to emerge to interrupt the first step in the HIV life cycle, i.e. preventing the virus from actually entering cells. This paper reviews the enfuvirtide path from clinical trials to the attempts to detail its molecular-level mode of action. It is commonly accepted that this peptide would block the fusion between viral and cell plasma membrane through binding to the N-terminal heptad repeat (NHR) region of the viral protein gp41. However, there has been growing evidence that this model of action may be unrealistic, the action of enfuvirtide being more complex and diverse than initially thought. Membrane-assisted local concentration increase and interference with gp120/co-receptor docking may also contribute for the inhibitory action of the peptide. Selected HIV-entry inhibitors on clinical trials are presented to characterize the future drugs in the market in this class.
Optoelectronic Properties of Nanostructured Ensembles Controlled by Biomolecular Logic Systems (2008)

A nanostructured system composed of enzyme-functionalized silica microparticles, ca. 74 microm, and gold-coated magnetic nanoparticles, 18 +/- 3 nm, modified with pH-sensitive organic shells was used to process biochemical signals and transduce the output signal into the changes of the optoelectronic properties of the assembly. The enzymes (glucose oxidase, invertase, esterase) covalently bound to the silica microparticles performed Boolean logic operations AND/OR processing biochemical information received in the form of chemical input signals resulting in changes of the solution pH value. Dissociation state of the organic shells on the gold-coated magnetic nanoparticles was controlled by pH changes generated in situ by the enzyme logic systems. The charge variation on the organic shells upon the reversible protonation/dissociation process resulted in the changes of the gold layer localized surface plasmon resonance energy (LSPR), thus producing optical changes in the system. The proton transfer process allowed the functional coupling of the information processing enzyme systems with the signal transducing gold-coated magnetic nanoparticles providing their cooperative performance. Magnetic properties of the gold-coated magnetic nanoparticles allowed separation of the signal-transducing nanoparticles from the enzyme-modified signal processing silica microparticles. The reversible system operation was achieved by the Reset function, returning the pH value and optical properties of the system to the initial state. This process was biocatalyzed by another immobilized enzyme (urease) activated with a biochemical signal. The studied approach opens the way to novel optical biosensors logically processing multiple biochemical signals and "smart" multisignal responsive materials with logically switchable optical properties.
Inactivation of Escherichia coli by Carbon Dioxide under Pressure (1996)

ABSTRACT Thermal inactivation of Escherichia coli was studied under CO 2 pressures of 1.2, 2.5, and 5 MPa at 25, 35, and 45°C. Two phases were observed in the destruction curves. The earlier stage was characterized by a slow rate of inactivation, which increased sharply at the later stage. An increase of pressure and/or temperature enhanced the antimicrobial effects of CO 2 under pressure. The effects on cell structure were studied by scanning electron microscopy and the specific mechanism of action appeared to be related to enzyme inactivation.
Continuous Fluorescence Monitoring of Rapid Cycle DNA Amplification (2013)

Rapid cycle DNA amplification was continuously monitored by three different fluorescence techniques. Fluorescence was monitored by (i) the double-strand-specific dye SYBR Green I, (ii) a decrease in fluorescein quenching by rhodamine after exonuclease cleavage of a dual-labeled hydrolysis probe and (iii) resonance energy transfer of fluorescein to Cy5 by adjacent hybridization probes. Fluorescence data acquired once per cycle provides rapid absolute quantification of initial template copy number. The sensitivity of SYBR Green I detection is limited by nonspecific product formation. Use of a single exonuclease hydrolysis probe or two adjacent hybridization probes offers increasing levels of specificity. In contrast to fluorescence measurement once per cycle, continuous monitoring throughout each cycle monitors the temperature dependence of fluorescence. The cumulative, irreversible signal of hydrolysis probes can be distinguished easily from the temperature-dependent, reversible signal of hybridization probes. By using SYBR Green I, product denaturation, annealing and extension can be followed within each cycle. Substantial product-to-product annealing occurs during later amplification cycles, suggesting that product annealing is a major cause of the plateau effect. Continuous within-cycle monitoring allows rapid optimization of amplification conditions and should be particularly useful in developing new, standardized clinical assays.
Activation of human monocytes by granulocyte-macrophage colony- stimulating factor: increased urokinase-type plasminogen activator activity (1991)

Granulocyte-macrophage colony-stimulating factor (GM-CSF) raised the plasminogen activator (PA) activity of cultured human monocytes. This activity was characterized to be urokinase-PA (u-PA) by incubation with specific IgG and by sodium dodecyl sulfate-polyacrylamide gel electrophoresis zymography. Increased u-PA activity reflected GM-CSF- induction of u-PA mRNA levels. The stimulatory properties of GM-CSF for monocyte PA activity differed from those of interleukin-4, which induced monocyte tissue-type PA (t-PA) activity, and of interferon- gamma (IFN-gamma), which alone was not stimulatory but augmented lipopolysaccharide-induced t-PA activity. GM-CSF alone did not stimulate detectable monocyte t-PA activity but combined with IFN-gamma to promote this activity. Plasmin formation arising from GM-CSF-induced u-PA in monocytes may contribute to the matrix turnover involved in, eg, cell migration and inflammation, and may explain some of the pathology seen in GM-CSF transgenic mice.
Interleukin-18 production and pulmonary function in COPD (2007)

Interleukin (IL)-18 production and pulmonary function were evaluated in patients with chronic obstructive pulmonary disease (COPD) in order to determine the role of IL-18 in COPD. Immunohistochemical techniques were used to examine IL-18 production in the lungs of patients with very severe COPD (Global Initiative for Chronic Obstructive Lung Disease (GOLD) stage IV, n = 16), smokers (n = 27) and nonsmokers (n = 23). Serum cytokine levels and pulmonary function were analysed in patients with GOLD stage I-IV COPD (n = 62), smokers (n = 34) and nonsmokers (n = 47). Persistent and severe small airway inflammation was observed in the lungs of ex-smokers with very severe COPD. IL-18 proteins were strongly expressed in alveolar macrophages, CD8+ T-cells, and both the bronchiolar and alveolar epithelia in the lungs of COPD patients. Serum levels of IL-18 in COPD patients and smokers were significantly higher than those in nonsmokers. Moreover, serum levels of IL-18 in patients with GOLD stage III and IV COPD were significantly higher than in smokers and nonsmokers. There was a significant negative correlation between serum IL-18 level and the predicted forced expiratory volume in one second in patients with COPD. In contrast, serum levels of IL-4, IL-13 and interferon-gamma were not significantly increased in any of the three groups. In conclusion, overproduction of interleukin-18 in the lungs may be involved in the pathogenesis of chronic obstructive pulmonary disease.
CRX ChIP-seq reveals the cis-regulatory architecture of mouse photoreceptors (2010)

Approximately 98% of mammalian DNA is noncoding, yet we understand relatively little about the function of this enigmatic portion of the genome. The cis-regulatory elements that control gene expression reside in noncoding regions and can be identified by mapping the binding sites of tissue-specific transcription factors. Cone-rod homeobox (CRX) is a key transcription factor in photoreceptor differentiation and survival, but its in vivo targets are largely unknown. Here, we used chromatin immunoprecipitation with massively parallel sequencing (ChIP-seq) on CRX to identify thousands of cis-regulatory regions around photoreceptor genes in adult mouse retina. CRX directly regulates downstream photoreceptor transcription factors and their target genes via a network of spatially distributed regulatory elements around each locus. CRX-bound regions act in a synergistic fashion to activate transcription and contain multiple CRX binding sites which interact in a spacing- and orientation-dependent manner to fine-tune transcript levels. CRX ChIP-seq was also performed on Nrl(-/-) retinas, which represent an enriched source of cone photoreceptors. Comparison with the wild-type ChIP-seq data set identified numerous rod- and cone-specific CRX-bound regions as well as many shared elements. Thus, CRX combinatorially orchestrates the transcriptional networks of both rods and cones by coordinating the expression of photoreceptor genes including most retinal disease genes. In addition, this study pinpoints thousands of noncoding regions of relevance to both Mendelian and complex retinal disease.
Spider Silk:  Ancient Ideas for New Biomaterials (2006)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSpider Silk: Ancient Ideas for New BiomaterialsRandolph V. LewisView Author Information Department of Molecular Biology, University of Wyoming, Laramie, Wyoming 82071-3944 Cite this: Chem. Rev. 2006, 106, 9, 3762–3774Publication Date (Web):June 15, 2006Publication History Received12 August 2005Published online15 June 2006Published inissue 1 September 2006https://doi.org/10.1021/cr010194gCopyright © 2006 American Chemical SocietyRIGHTS & PERMISSIONSArticle Views6064Altmetric-Citations296LEARN 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 InReddit Read OnlinePDF (2 MB) Get e-AlertsSUBJECTS:Biomimetic materials,Fibers,Monomers,Peptides and proteins,Protein structure Get e-Alerts
Long-range intramolecular electron transfer in azurins. (1989)

The Cu(II) sites of azurins, the blue single copper proteins, isolated from Pseudomonas aeruginosa and Alcaligenes spp. (Iwasaki) are reduced by CO2- radicals, produced by pulse radiolysis, in two distinct reaction steps: (i) a fast bimolecular phase, at the rates (5.0 +/- 0.8) x 10(8) M-1.s-1 (P. aeruginosa) and (6.0 +/- 1.0) x 10(8) M-1.s-1 (Alcaligenes); (ii) a slow unimolecular phase with specific rates of 44 +/- 7 s-1 in the former and 8.5 +/- 1.5 s-1 for the latter (all at 298 K, 0.1 M ionic strength). Concomitant with the fast reduction of Cu(II), the single disulfide bridge linking cysteine-3 to -26 in these proteins is reduced to the RSSR- radical ion as evidenced by its characteristic absorption band centered at 410 nm. This radical ion decays in a unimolecular process with a rate identical to that of the slow Cu(II) reduction phase in the respective protein, thus clearly suggesting that a long-range intramolecular electron transfer occurs between the RSSR- radicals and the Cu(II) site. The temperature dependence of the internal electron transfer process in both proteins was measured over the 4 degrees C to 42 degrees C range. The activation parameters derived are delta H* = 47.5 +/- 4.0 and 16.7 +/- 1.5 kJ.mol-1; and delta S not equal to = -56.5 +/- 7.0 and -171 +/- 18 J.K-1.mol-1, respectively. Using the Marcus theory, we found that the intramolecular electron transfer rates and their activation parameters observed for the two azurins correlate well with the distances between the reactive sites, their redox potential, and the nature of the separating medium. Thus, azurins with distinct structural and reactivity characteristics isolated from different bacteria or modified by site-directed mutagenesis can be used in comparing long-range electron transfer process between their conserved disulfide bridge and the Cu(II) sites.
Efficacy of Repeat Pulmonary Vein Isolation Procedures in Patients with Recurrent Atrial Fibrillation (2004)

Recurrent AF following selective PV isolation is overwhelmingly associated with PV electrical reconnection. Repeat PV isolation without linear ablation provides effective treatment for recurrent AF in patients in whom an initial PV isolation procedure failed, independent of clinical characteristics.