gebhart/patrepeval huggingface dataset:
Flexible Docking and Design (1995)

Docking and design are the major computational steps toward understanding and affecting receptor-ligand interactions. The flexibility of many ligands makes these calculations difficult and requires the development and use of special methods. The need for such tools is illustrated by two examples: the design of protease inhibitors and the analysis and design of peptide antigens binding to specific MHC receptors. We review the computational concepts that have been extended from rigid-body to flexible docking, as well as the following important strategies for flexible docking and design: (a) Monte Carlo/molecular dynamics docking, (b) in-site combinatorial search, (c) ligand build-up, and (d) site mapping and fragment assembly. The use of empirical free energy as a target function is discussed. Due to the rapid development of the methodology, most new methods have been tested on only a limited number of applications and are likely to improve results obtained by more traditional computational or graphic tools.
Refractive beam shaping optics for high-power laser systems and applications (2011)

Performance of high-power lasers and applications is improved by refractive field mapping beam shapers providing flattop intensity profile; their unique features, like lossless profile transformation, saving beam divergence, bring flexibility in building various optical systems.
Dermaseptins from Phyllomedusa oreades andPhyllomedusa distincta (2002)

Amphibian skin secretions are known as a rich source of biologically active molecules, most of which are alkaloids, biogenic amines, and peptides. Dermaseptins are a class of antimicrobial peptides present in tree frogs of the Phyllomedusa genus. They are cationic molecules of 28-34 residues that permeabilize the membrane of Gram-positive and Gram-negative bacteria, yeasts, and filamentous fungi, showing little or no hemolytic activity. This work reports the isolation, molecular mass analysis, primary structure determination, biological activities, and potential therapeutic applications of an antimicrobial peptide found in the skin secretion of Phyllomedusa oreades, which is a newly described amphibian species endemic of the Brazilian savanna. DS 01 is a 29-residue-long peptide with a molecular mass of 2793.39 Da showing antibacterial properties against Gram-positive and Gram-negative bacteria in the range of 3-25 microm. Anti-protozoan activity was investigated using T. cruzi in its trypomatigote and epimastigote forms cultivated in both cell culture and blood media. Within 2 h after incubation with DS 01 at a final concentration of approximately 6 microm, no protozoan cells were detected. Two synthetic dermaseptins, described previously by our group and named dermadistinctins K and L (DD K and DD L), also had their anti-Trypanosoma cruzi activity investigated and demonstrated similar properties. Toxicity of DS 01 to mouse erythrocytes and white blood cells was evaluated by means of atomic force microscopy and flow cytometry. No morphological alterations were observed at a lytic concentration of DS 01, suggesting its therapeutic value especially as an anti-T. cruzi agent to prevent infections during blood transfusion.
Performance of Corrosion Prevention Methods – 18 Year Study (2009)

Abstract Over the last 30 years, a variety of approaches have been taken to delay the start of corrosion of reinforcement in concrete. While short term and accelerated performance data is readily available in the literature, it is difficult to find long term laboratory data performed under control conditions. This report intends on filling that gap in the knowledge base of the performance of the various products evaluated. The long term laboratory performance of specimens with 1.75 inches (4.4 cm) of concrete cover exposed to 3 wt% NaCl at 72° F (22 °C) and 64% humidity is presented. Specimens were made with corrosion inhibitors, concrete penetrant sealers, coated rebar, galvanized rebar, and supplementary cementitious materials of various types and quantities.
Immunogenetics of pemphigus: An update (2006)

Pemphigus are rare but informative models of organ-specific autoimmune diseases, resulting from the interplay of environmental, genetic and stochastic factors. There are many arguments to consider that pemphigus have a genetic basis involving, as many other autoimmune diseases, several different genes with additive or synergistic effects. So far, the unique strategy used to identify the contributive loci has been direct analysis of candidate genes through conventional case-control association studies. The major histocompatibility complex in particular the class II locus was demonstrated to be associated with pemphigus with a high rate of replicability. The progresses in the understanding of pemphigus physiopathology and the development of new molecular tools offer new perspectives to unveiled the genetic basis of this group of autoimmune blistering diseases, as shown by recent studies of candidate genes expressed at different levels of the autoimmune process.
Effect of premixing length and flameholder design on NO(x) emissions (1997)

A flame-tube study was performed to determine the effects of premixing length and flameholder design on NO(x) emissions with premixed, prevaporized Jet-A fuel. Two premixing lengths and two flameholder designs were studied with greater than 99 percent combustion efficiency at 755-866 K inlet temperature and 10 to 15 atm inlet pressure. An operating window was defined with over 99 percent combustion efficiency, together with flameholder pressure drops to prevent autoignition and flashback in the premixing, prevaporized combustion system. (Author)
Bcl-2 down-regulates the activity of transcription factor NF-kappaB induced upon apoptosis. (1996)

Among the many target genes of the transcription factor NF-kappaB are p53 and c-myc, both of which are involved in apoptosis. This prompted us to investigate the role of NF-kappaB in this process. We report that NF-kappaB is potently activated upon serum starvation, a condition leading to apoptosis in 293 cells. Similar to Bcl-2, a transdominant-negative mutant of the NF-kappaB p65 subunit partially inhibited apoptosis, indicating a direct involvement of the transcription factor in induction of cell death. As expected, the p65 mutant suppresses kappaB-dependent gene expression. Surprisingly, transiently or stably overexpressed Bcl-2 had the same effect. The transcription inhibitory activity of the two proteins correlated with their cell death protective potential. Like Bcl-2, the related protein Bcl-xL but not Bcl-xS was able to suppress kB-dependent transcription. Bcl-2 inhibited NF-kappaB activity by an unusual mechanism. It did not prevent the release of IkappaB in the cytoplasm but down-modulated the transactivating potential of nuclear p65. These data show that NF-kappaB can participate in apoptosis. We suggest that at least part of the anti-apoptotic potential of Bcl-2 may be explained from a hitherto undiscovered activity of Bcl-2 in controlling nuclear gene expression.
Kinetics and Mechanism of the Etching of CoSi2 in HF‐based Solutions (1996)

The wet etching behavior of films in HF‐based solutions is investigated for a wide range of experimental conditions. It is established that the etching rate of depends on the concentrations of ions and on the initial concentration of HF . Interaction of and HF with the occurs in the adsorption layer. The concentration of adsorbed particles is described by the equation of the Freundlich adsorption isotherm. The kinetic equation of the etching rate is , where kR ≈ 2.5 ⋅ 107 exp (−10500/RT) nm/s (0.416 at 293 K), and . It is shown that the induction period increases in the etching process of in diluted HF, which is attributed to the presence of a thin surface layer on top of the .
Preface (1995)

ADVERTISEMENT RETURN TO BOOKPREVPrefaceNEXTPrefaceJUDD O. NELSONJUDD O. NELSONUniversity of Maryland College Park, MD 20742More by JUDD O. NELSON, ALEXANDER E. KARUALEXANDER E. KARUUniversity of California Berkeley, CA 94720More by ALEXANDER E. KARU, and ROSIE B. WONGROSIE B. WONGAmerican Cyanamid Agricultural Research Division Princeton, NJ 08543More by ROSIE B. WONGDOI: 10.1021/bk-1995-0586.pr001 This publication is free to access through this site. Learn MorePublication Date (Print):March 23, 1995Publication History Published online23 July 2009Published inprint 23 March 1995Request reuse permissions Copyright © 1995 American Chemical Society. This publication is available under these Terms of Use. Immunoanalysis of Agrochemicalspp ix-xiACS Symposium SeriesVol. 586ISBN13: 9780841231498eISBN: 9780841215115Chapter Views118Citations-LEARN ABOUT THESE METRICSChapter 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. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail PDF (319 KB) Get e-Alerts
Antimicrobial Resistance in Swine Fecal Specimens Across Different Farm Management Systems (2020)

Antimicrobial use in agricultural animals is known to be associated with increases in antimicrobial resistance. Most prior studies have utilized culture and susceptibility testing of select organisms to document these phenomena. In this study we aimed to detect 66 antimicrobial resistance (AMR) genes for 10 antimicrobial agent classes directly in swine fecal samples using our previously developed antimicrobial resistance TaqMan array card (AMR-TAC) across three different swine farm management systems. This included 38 extensive antimicrobial use (both in treatment and feed), 30 limited antimicrobial use (treatment only), and 30 no antimicrobial use farms. The number of resistance genes detected in extensive antimicrobial use farms was higher than in limited and no antimicrobial use farms (28.2 genes ± 4.2 vs. 24.0 genes ± 4.1 and 22.8 genes ± 3.6, respectively, <i>p</i> < 0.05). A principal component analysis and hierarchical clustering of the AMR gene data showed the extensive use farm samples were disparate from the limited and no antimicrobial use farms. The prevalence of resistance genes in extensive use farms was significantly higher than the other farm categories for 18 resistance genes including <i>bla</i> <sub>SHV</sub>, <i>bla</i> <sub>CTX-M1</sub> group, <i>bla</i> <sub>CTX-M9</sub> group, <i>bla</i> <sub>VEB</sub>, <i>bla</i> <sub>CMY2-LAT,</sub> <i>aac(6')-lb-cr</i>, <i>qnrB1</i>, <i>gyrA</i>83L-<i>E. coli</i>, <i>armA</i>, <i>rmtB</i>, <i>aac(3)-IIa, mphA</i>, 23S <i>rRNA</i> 2075G-<i>Campylobacter</i> spp., <i>mcr-1</i>, <i>catA1</i>, <i>floR</i>, <i>dfrA5-14</i>, and <i>dfrA17</i>. These genotypic findings were supported by phenotypic susceptibility results on fecal <i>E. coli</i> isolates. To examine the timing of AMR gene abundance in swine farms, we also performed a longitudinal study in pigs. The results showed that AMR prevalence occurred both early, presumably from mothers, as well as after weaning, presumably from the environment. In summary, detection of AMR genes directly in fecal samples can be used to qualitatively and quantitatively monitor AMR in swine farms.
Increased risk of preterm birth and low birthweight with very high number of oocytes following IVF: an analysis of 65 868 singleton live birth outcomes (2015)

No funding was obtained. There are no competing interests to declare.
<i>Alnus</i> peptides modify membrane porosity and induce the release of nitrogen-rich metabolites from nitrogen-fixing <i>Frankia</i> (2015)

Actinorhizal plant growth in pioneer ecosystems depends on the symbiosis with the nitrogen-fixing actinobacterium Frankia cells that are housed in special root organs called nodules. Nitrogen fixation occurs in differentiated Frankia cells known as vesicles. Vesicles lack a pathway for assimilating ammonia beyond the glutamine stage and are supposed to transfer reduced nitrogen to the plant host cells. However, a mechanism for the transfer of nitrogen-fixation products to the plant cells remains elusive. Here, new elements for this metabolic exchange are described. We show that Alnus glutinosa nodules express defensin-like peptides, and one of these, Ag5, was found to target Frankia vesicles. In vitro and in vivo analyses showed that Ag5 induces drastic physiological changes in Frankia, including an increased permeability of vesicle membranes. A significant release of nitrogen-containing metabolites, mainly glutamine and glutamate, was found in N2-fixing cultures treated with Ag5. This work demonstrates that the Ag5 peptide is central for Frankia physiology in nodules and uncovers a novel cellular function for this large and widespread defensin peptide family.
LES PONTS METALLIQUES A LA SNCF: LE PATRIMOINE, LES REPARATIONS, LA RECONSTRUCTION ET LA CONSTRUCTION (1986)

LA CONSTRUCTION DES LIGNES PRINCIPALES DU RESEAU DES CHEMINS DE FER FRANCAIS AYANT EU LIEU SURTOUT ENTRE 1842 ET 1875 ENVIRON, UN GRAND NOMBRE D'OUVRAGES D'ART METALLIQUES DE CETTE EPOQUE SONT TOUJOURS EN SERVICE. L'ARTICLE DONNE UN BREF APERCU DU PATRIMOINE CONSISTUE PAR CES PONTS, DE LEURS REPARATIONS, DE LEUR RECONSTRUCTION, AINSI QUE DE LA CONSTRUCTION DES PONTS METALLIQUES NOUVEAUX (A).
How Toll-like receptors and Nod-like receptors contribute to innate immunity in mammals (2005)

Innate immune detection of pathogens relies on specific classes of microbial sensors called pattern-recognition molecules (PRM). In mammals, such PRM include Toll-like receptors (TLRs) and the intracellular proteins NOD1 and NOD2, which belong to the family of Nod-like receptors (NLRs). Over the last decade as these molecules were discovered, a function in innate immunity has been assigned for the majority of them and, for most, the microbial motifs that these molecules detect were identified. One of the next challenges in innate immunity is to establish a better understanding of the complex interplay between signaling pathways induced simultaneously by distinct PRMs and how this affects tailoring first-line responses and the induction of adaptive immunity to a given pathogen.
Graphene: Integrating Water‐Soluble Graphene into Porphyrin Nanohybrids (Adv. Mater. 6/2012) (2012)

Dirk Guldi and co-workers demonstrate on page 800 the realization of high-quality graphene flakes by means of solution processing with tightly interacting constituents to which a porphyrin has been self-assembled. These were integrated into novel photo-electrodes by means of layer-by-layer deposition that give rise to appreciable photocurrents.
Role of Hemocyte‐Derived Granular Components in Invertebrate Defense<sup><i>a</i></sup> (1994)

Figure 2 illustrates an outline of the cellular and humoral defense systems in limulus. On the basis of the knowledge described above, it is suggested that granular components present in L and S granules in the hemocytes play a decisive role in the biological defense for this animal. The isolated L granules contain at least three clotting factors plus coagulogen as the major component. The known anti-LPS factor and a number of additional unknown protein components are also present in the L granules. On the other hand, the isolated S granules contain antimicrobial tachyplesins as the major component, in addition to six unidentified proteins. We speculate that the L-granule-derived protein components, which probably contain all the factors essential for the Limulus clotting system participate, in immobilizing invading microbes, and that the S-granule-derived tachyplesins contribute to a self-defense system against invaders. Although we have not mentioned hemolymph plasma components, there are many humoral factors, such as proteinase inhibitors, alpha 2-macroglobulin, various lectins, C-reactive protein, and polyphemin, all of which are important for antimicrobial defense. Furthermore, Liu and colleagues have reported several endotoxin-binding proteins and a cell-adhesion protein found in the Limulus hemocytes. Although the exact functions of these substances are unknown, they may act in concert with other components to provide biological defense for the animal. Nevertheless, compared to our knowledge of mammalian blood cells, much less remains to be learned of biological/physiological events in horseshoe crab hemocytes.
Band or Polaron: The Hole Conduction Mechanism in the <i>p</i> ‐Type Spinel <scp> <scp> Rh <sub>2</sub> ZnO <sub>4</sub> </scp> </scp> (2011)

Given the emerging role of oxide spinels as hole conductors, we discuss in this article the traditional vs. new methodologies of determining the type of conduction mechanism at play––localized polaronic vs. band‐like transport. Applying (i) traditional small polaron analysis to our in‐situ high temperature four‐point conductivity and thermopower measurements, we previously found an activated mobility, which is indicative of the small polaron mechanism. However, (ii) employing the recent developments in correcting density functional methodologies for hole localization, we predict that the self‐trapped hole is unstable and that Rh 2 ZnO 4 is instead a band conductor with a large effective mass. The hole mobility measured by high‐field room temperature Hall effect also suggests band rather than polaron conduction. The apparent contradiction between the conclusion of the traditional procedure (i) and first‐principles theory (ii) is resolved by taking into account in the previous transport analysis the temperature dependence of the effective density of states, which leads to the result that the mobility is actually temperature‐independent in Rh 2 ZnO 4 . Our case study on Rh 2 ZnO 4 illustrates the range of experimental and theoretical approaches at hand to determine whether the transport mechanism of a semiconductor is band or small polaron conduction.
Cost‐effective diagnostic test sequencing (1989)

Proper diagnostic test selection and logical sequencing can minimize cost without compromising care. This study analyzes the logic for sequencing tests either in series (one after another) or in parallel (simultaneously). A model is created using 2 diagnostic tests for 2 diseases. Tests are assumed to have perfect performance characteristics. Factors involved in cost-effective test sequencing include cost of each test, test performance characteristics, per diem hospital charge, and the clinician's prior probability of the suspected diagnosis based on history, physical examination, and previous laboratory data. At a given point of clinical suspicion, cost-effective sequencing strategy should shift. In general, a cheap test can effectively be used in parallel even at low diagnostic probabilities; an expensive test should, in general, be used in series only when there is a high prior probability of diagnosis. High per diem hospitalization costs--such as for a patient in the intensive care unit--favor in parallel testing. Clinical acumen and suspicion of diagnosis (prior probability) primarily direct cost-effective diagnostic test sequencing. Decision analysis of diagnostic test sequencing represents a technique for making cost-effective decisions for sequencing and, thereby, minimizing costs while achieving optimal patient care.
Nanotechnologies for Biosensor and Biochip (2015)

status: Published
Buckling Testing and Analysis of Honeycomb Sandwich Panel Arc Segments of a Full-Scale Fairing Barrel Part 1: 8-Ply In-Autoclave Facesheets (2013)

Four honeycomb sandwich panels, representing 1/16th arc segments of a 10-m diameter barrel section of the heavy lift launch vehicle, were manufactured under the NASA Composites for Exploration program and the NASA Space Launch Systems program. Two configurations were chosen for the panels: 6-ply facesheets with 1.125 in. honeycomb core and 8-ply facesheets with 1.000 in. honeycomb core. Additionally, two separate carbon fiber/epoxy material systems were chosen for the facesheets: inautoclave IM7/977-3 and out-of-autoclave T40-800b/5320-1. Smaller 3.00- by 5.00-ft panels were cut from the 1/16th barrel sections. These panels were tested under compressive loading at the NASA Langley Research Center. Furthermore, linear eigenvalue and geometrically nonlinear finite element analysis was performed to predict the compressive response of the 3.00- by 5.00-ft panels. This manuscript summarizes the experimental and analytical modeling efforts pertaining to the panel composed of 8-ply, IM7/977-3 facesheets (referred to Panel A). To improve the robustness of the geometrically nonlinear finite element model, measured surface imperfections were included in the geometry of the model. Both the linear and nonlinear models yield good qualitative and quantitative predictions. Additionally, it was predicted correctly that the panel would fail in buckling prior to failing in strength. Furthermore, several imperfection studies were performed to investigate the influence of geometric imperfections, fiber misalignments, and three-dimensional (3 D) effects on the compressive response of the panel.
Cryptographie quantique à plusieurs participants par multiplexage en longueur d'onde (2003)

extraits substantiels de ce document, ne doivent tre imprims ou autrement reproduits sans l'autorisation de l'auteur.
Two-dimensional MHD generator model. [GEN code] (1980)

A steady state, two-dimensional MHD generator code, GEN, is presented. The code solves the equations of conservation of mass, momentum, and energy, using a Von Mises transformation and a local linearization of the equations. By splitting the source terms into a part proportional to the axial pressure gradient and a part independent of the gradient, the pressure distribution along the channel is easily obtained to satisfy various criteria. Thus, the code can run effectively in both design modes, where the channel geometry is determined, and analysis modes, where the geometry is previously known. The code also employs a mixing length concept for turbulent flows, Cebeci and Chang's wall roughness model, and an extension of that model to the effective thermal diffusities. Results on code validation, as well as comparisons of skin friction and Stanton number calculations with experimental results, are presented.
Dynamic Viscosity of Mixture of Heavy Fuel Oil “C Grade” and Liquefied Butane (1980)

Under present circumstances on the urgent relation of demand and supply of petroleum, it is significant that other form of the use offuel for the combustion installations such as furnaces and boilersis disscused for the purpose of energy saving, countermeasures of air pollution and so onWe have noticed the mixing firingsystem with heavy fuel oil “C grade” and liquefied butane whic is expected to improve atmization characteristics and to decrease th power for transportation of fuel.The viscosity of mixed fuel ha been investigated to take the basic data with respect to the mixing firing burner.The followings have been obtained.(1) Suitable heating for heavy fuel oil “C grade” and intense agitation are effective for the mixing process.(2) At the mixing ratio of 3, (the ratio of the weight of heavy fuel oil “C grade” to the weight of liquefied butane) dynamic viscosity of about 20 [cst] which is required for good atmization have been obtained under room temperature.(3) By the measurement using capillary tube, following experimental equation of f he relation between dynamic viscosity and temperature has been obtained within the accuracy of ±30%.ν/θα=4RM4.1α=0.09RM2-0.83RM+0.41RM : mixing ratio, θ : temperature of mixture