gebhart/patrepeval huggingface dataset:
Synthesis and conformational analysis of N‐glycopeptides. II. CD, molecular dynamics, and nmr spectroscopic studies on linear N‐glycopeptides (1993)

The comprehensive structural analysis reported herein of eight N-glycopeptides, in three different solvents, is based on quantitative CD experiments, homonuclear nuclear Overhauser effect measurements, and molecular dynamics (MD) calculations. Although several orientations of the two amide planes attached to the carbohydrate pyranose ring are possible, according to NOE, CD data, and MD simulations, of all of the glycopeptide models, regardless of the type of the carrier peptide, only one dominant conformer population was found. This conformer is characterized by a nearly trans orientation of the CH and NH hydrogens of both acetamido groups. This finding is in perfect agreement with x-ray crystallographic data on the solid state conformation of the 1-N-acetyl- and 1-N-(beta-aspartyl)-2-acetamido-2-deoxy-beta-D-glucopyranosyla min e. The precise identification of this dominant conformer of N-glycopeptides in solution was the major question addressed herein by the structural analyses. A "CD additivity" experiment was carried out using an equimolar solution of Boc-Pro-Asp-NHCH3 and 1-N-acetyl-3,4,6- tri-O-acetyl-2-acetamido-2-deoxy-beta-D-glucopyranosylamine at ambient temperature in acetonitrile. The CD spectrum obtained from the equimolar solution of the above two molecules (the "spectroscopic sum") was identical with the CD curve obtained from the algebraic summation of the individually recorded CD spectra of the peptide and the carbohydrate moiety ("mathematical sum"). The global picture of the CD spectral analyses of the eight parent peptides with the eight N-glycopeptides revealed that in trifluoroethanol and acetonitrile, the side-chain modification of the Asn models (natural N-glycopeptide analogues) by N-glycosylation has a significant effect on the conformation of the carrier peptide, resulting in a decrease in the original type I beta-turn content. Simultaneously, the type II beta-turn conformational percentage increased to approximately 20%. Such a conformational ratio change seems to be larger than the expected errors arising from the CD analyses, and agrees with the results of MD calculations. N-glycosylation of Asn residues causes perturbations, not only through the covalent bond, but also through specific hydrogen bonds between the backbone and side chain atoms. CD spectroscopy, augmented by efficient CD curve deconvolution techniques, has proved to be a useful tool for studying multicomponent conformer mixtures of small linear peptides in solution and changes of conformational equilibria caused by N-glycosylation.
Secretion of Adrenomedullin by Renal Tubular Cell Lines (1997)

Adrenomedullin (AM) is a novel and potent vasodilator peptide originally isolated from human pheochromocytoma. The present study was designed to study whether AM is produced by and secreted from renal tubular cell lines and whether arginine vasopressin (AVP) affects AM secretion from these cell lines. Three renal tubular cell lines derived from different species (LLCPK1, MDCK, and MDBK) secrete AM-like immunoreactivity (AM-LI) into culture medium, the immunological and physicochemical properties of which are similar to that of synthetic human AM as evaluated by reverse-phase high-performance liquid chromatography. Among the three cell lines, AVP in combination with a phosphodiesterase inhibitor (isobutylmethylxanthine) stimulated AM-LI secretion most potently from MDCK cells in a time- and dose-dependent manner. In MDCK cells, a V2 receptor agonist (deamino-D-Arg8-vasopressin) dose-dependently stimulated AM-LI secretion in the same manner as AVP. Furthermore, the AVP-induced AM-LI secretion was blocked by a V2 receptor antagonist (OPC31260), but not by a V1 receptor antagonist (OPC21268). These data indicate that AM is secreted from renal tubular cell lines and that AVP stimulates AM secretion via V2 receptors, suggesting its autocrine/paracrine role in renal function.
The Chain Length Distribution of an Ideal Reversible Deactivation Radical Polymerization (2018)

The chain length distribution (CLD) of a reversible deactivation radical polymerization at full conversion is shown to be a negative binomial distribution with parameters that are simple functions of the number-average degree of polymerization and either the chain transfer constant (in the case of polymerizations that incorporate a reversible chain transfer step) or the concentrations of dormant polymer chains and deactivating agent and the rate constants of propagation and deactivation (other types of RDRP). Expressions for the CLD at intermediate conversions are also derived, and shown to be consistent with known expressions for the number-average degree of polymerization and dispersity. It is further demonstrated that these CLDs are well-approximated by negative binomial distributions with appropriate choice of parameters. The negative binomial distribution is thus a useful model for CLDs of reversible deactivation radical polymerizations.
Mars rover sample return: An exobiology science scenario (1988)

A mission designed to collect and return samples from Mars will provide information regarding its composition, history, and evolution. At the same time, a sample return mission generates a technical challenge. Sophisticated, semi-autonomous, robotic spacecraft systems must be developed in order to carry out complex operations at the surface of a very distant planet. An interdisciplinary effort was conducted to consider how much a Mars mission can be realistically structured to maximize the planetary science return. The focus was to concentrate on a particular set of scientific objectives (exobiology), to determine the instrumentation and analyses required to search for biological signatures, and to evaluate what analyses and decision making can be effectively performed by the rover in order to minimize the overhead of constant communication between Mars and the Earth. Investigations were also begun in the area of machine vision to determine whether layered sedimentary structures can be recognized autonomously, and preliminary results are encouraging.
Overlooked Difference between Hydrogen Bonds of Equal Strength Formed between Catechol and an Oxygen or Nitrogen Base. Experiments and DFT Calculations (2003)

The IR spectrum of catechol in CCl(4) shows two fairly sharp O-H stretching bands of roughly equal absorbance at 3615.0 and 3569.6 cm(-1) due, respectively, to the "free" OH and the intramolecularly H-bonded OH groups. Intermolecular H-bond formation between the "free" OH and a hydrogen bond acceptor (HBA) decreases its stretching frequency by several hundred wavenumbers and simultaneously decreases the frequency of the intramolecularly H-bonded OH by a few tens of wavenumbers. The magnitude of these frequency shifts, Deltaupsilon(inter) and Deltaupsilon(intra), respectively, are very well reproduced by DFT calculations. As would be expected, the magnitudes of Deltaupsilon(inter) and Deltaupsilon(intra) increase as the HB accepting ability of the HBA increases as quantified, on a relative scale, by the HBA's values (Abraham et al. J. Chem. Soc. Perkin Trans. 2 1990, 521). However, plots of experimental, or calculated, frequency shifts versus reveal that Deltaupsilon(inter) and Deltaupsilon(intra) are ca. 40% larger for a nitrogen atom HBA than for an oxygen atom HBA having equal HBA activity. We hypothesize that for HBAs of equal strength, i.e., of equal, the H-bond in (O-H- - -O)(inter) is shorter and, hence, intrinsically stronger than the H-bond in the (O-H- - -N)(inter). However, we further hypothesize that there is more charge separation in the H-bond to N because N is a better proton acceptor than O. Hence, it is the greater Coulombic attraction in (O-H- - -N)(inter) which strengthens this H-bond and compensates for its greater length. Theoretical calculations lend support to these hypotheses.
Design of missile-aircraft component white noise isolators (1974)

Relationships are given from which the optimum design of missile-aircraft component isolators can be specified from white noise vibration. These relationships are derived from theories of linear viscoelasticity, vibration, heat conduction, and statistics of extremes. A Voigt model is used to demonstrate the thesis. A design format is given which relates mission time, environmental temperature, white noise intensity level, reliability, weight of the isolated component to rattlespace, isolator thickness, and the effective stressed area of an isolator all as a function of storage modulus, loss tangent (damping), melt temperature, and thermal conductivity of a polymeric isolator. An example calculation demonstrates the procedure that can be used for specifying an optimum vibration isolator to suit a given mission.
Selective long‐range <sup>1</sup>H<sup>13</sup>C polarization transfer in nucleosides (1992)

Abstract Selective INEPT (INAPT) experiments were used to correlate the nitrogen‐ and carbon‐bound hydrogens of nucleosides with 13 C resonances via 2 J (C, H) and 3 J (C, H). Such experiments are useful as part of a strategy to distinguish the imino hydrogens of uridine and thymidine, which cannot be accomplished on the basis of chemical shift. The strategy involves correlation of the imino hydrogen with C‐5 using INAPT and testing whether or not the C‐5 resonance is quaternary. Polarization transfer is ineffecient for most positions in nucleosides owing to the small long‐range couplings, except the H‐6C‐5 transfer in adenosine, which results in enhancement of the 13 C resonance over its equilibrium value. The efficiency of polarization transfer from H‐3 to C‐5 of thymidine depends on the base‐paired status of the nucleoside indicating a change in the 3 J (C, H) on base‐pair formation. This sensitivity to electronic reorganization on base‐pair formation makes the INAPT experiment a useful probe for the base‐paired status of nucleosides and of the electronic properties of uridine and thymidine analogues.
Global Emissions of Trace Gases, Particulate Matter, and Hazardous Air Pollutants from Open Burning of Domestic Waste (2014)

The open burning of waste, whether at individual residences, businesses, or dump sites, is a large source of air pollutants. These emissions, however, are not included in many current emission inventories used for chemistry and climate modeling applications. This paper presents the first comprehensive and consistent estimates of the global emissions of greenhouse gases, particulate matter, reactive trace gases, and toxic compounds from open waste burning. Global emissions of CO2 from open waste burning are relatively small compared to total anthropogenic CO2; however, regional CO2 emissions, particularly in many developing countries in Asia and Africa, are substantial. Further, emissions of reactive trace gases and particulate matter from open waste burning are more significant on regional scales. For example, the emissions of PM10 from open domestic waste burning in China is equivalent to 22% of China's total reported anthropogenic PM10 emissions. The results of the emissions model presented here suggest that emissions of many air pollutants are significantly underestimated in current inventories because open waste burning is not included, consistent with studies that compare model results with available observations.
Differentiation of Medicinal Codonopsis Species from Adulterants by Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (1999)

DNA sequence analysis of rDNA internal transcribed spacer (ITS) and polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) were exploited for their applications in differentiating medicinal species Codonopsis pilosula, C. tangshen, C. modesta, and C. nervosa var. macrantha, from two related adulterants Campanumoea javania and Platycodon grandiflorus. The data demonstrated that the rDNA ITSI and ITSII sequences of the four Codonopsis are highly homologous but not identical, and are significantly different from those of the two adulterants. The sequence difference allows effective and reliable differentiation of Codonopsis from the adulterants by PCR-RFLP.
Inducible and constitutive nucleoside-binding sites in Escherichia coli: differential inhibition by nucleoside analogues (1974)

Constitutive and inducible nucleoside-binding sites on the surface of the cells of E. coli B have different patterns of inhibition by nucleoside analogues. 1(beta-D-Ribofuranosyl)-4-aminopyrimidine-6-one and isoguanosine preferentially inhibit the inducible binding sites while showdomycin and N(4)-dimethylcytidine interfere more strongly with the constitutive function.
Transients of perforin pore formation observed by fluorescence microscopic single channel recording (1990)

A new type of single channel recording is described.Large pores were generated in the membranes of reseal- ed human erythrocyte ghosts by incubation with perforin (cytolysin).The flux of the polar fluorescent probe Lucifer Yellow was measured in single ghosts by the fluorescence microphotolysis (photobleaching) technique.The distribution of flux rates for ghosts treated with a limiting perforin concentration showed equidistantly spaced peaks suggesting that subpopulations of ghosts with 0, 1 and 2 pores were resolved.Furthermore, distributions obtained for very different perforin concentrations could be well sinulated by using one com- mon value for the flux rate of the single pore (k = 4.65 x i0-S) and assuming a Poisson distribution of pores among ghosts.The flux rate of the single pore corresponds to a pore radius of -50 A, a value which is much smaller than that obtained previously by electron microscopic studies but which agrees well with recent electrical single channel recordings.Mature perforin pores were observed to be very stable.No closing events were detected at a time resolution of 0.2 s for a wide range of temperatures and Ca2' concentrations.However, the formation of new pores was an unexpectedly slow process.Fluorescence microscopic single channel record- ing as introduced by this study is applicable to a variety of cellular systems and fluorescent probes and thus may complement the information obtainable by electrical single channel recording of anorganic ion fluxes.Key words: cytolysin/erythrocyte
Application of the Shear Band Propagation Method to Slope Stability Analysis of a Palaeo-Landslide in the Caspian Sea (2015)

Abstract Geophysical observations of palaeolandslides in offshore settings include long and relatively thin failures that occur on very mild slopes. Back analysis of such failures using the limiting equilibrium approach and measured geotechnical soil properties is typically used to inform the likely causes of past failures. An assessment can then be made of the present day significance of causal factors (e.g. the presence of excess pore water pressure), with the limiting equilibrium approach used to assess factors of safety for present-day slopes and predict the potential size of any future failures. However, for long, thin slides, use of the limiting equilibrium approach can lead to the conclusion that either a significantly large seismic trigger or other, abnormal geological condition was required to initiate failure. A result has been the focusing of academic research into other failure causes and conditioning factors. Further, the stability of the present day seabed for offshore developments can be overestimated, given the rarity of large seismic events in many areas and geotechnical measurements that not always show abnormal soil conditions. The shear band propagation approach offers an alternative view, where an initial small failure can grow into a larger failure at the point of initiation. A result is that an explanation of the conditions leading to failure can be attributed to many submarine landslides. Further, accounting for the potential propagation of a shear band in the future prediction of submarine landslides can result in greater predicted failure sizes and lower factors of safety than using limiting equilibrium only. The application of the shear band propagation approach to back analyse a palaeolandslide in the ACG Field, Caspian Sea, is used to demonstrate the methodology and compare with results using the limiting equilibrium approach. Results show that the shear band propagation approach successfully predicts observed failure geometries and suggests triggering conditions from a lower magnitude seismic event compared to that predicted using limiting equilibrium. The future application of shear band propagation theory to submarine landslide analysis is also discussed.
An efficient, bus-layout based method for early diagnosis of bussed driver shorts in printed circuit boards (1996)

This paper presents a new, layout-based approach to board-level shorts diagnosis for bussed drivers, with the goal of early repair of interconnect shorts so as to minimize (a) fault masking during opens testing and (b) driver abuse. This approach leads to an early diagnosis of more than 96% of shorts and simplifies the subsequent rest for opens considerably. Besides, this approach improves the production yield and field survivability of boards.
Analysis of a Customer Demand Driven Semiconductor Supply Chain in a Distributed Simulation Test Bed (2005)

Effective supply chain management (SCM) enables organizations to be more competitive in the current world of global manufacturing by reducing costs and improving the quality of customer service. Simulation can assist in moving towards these goals by evaluating the feasibility of alternative policies for managing a supply chain. However, simulation of multiple factories within the supply chain, with a high level of granularity in particular, can be very complex and computationally intensive. In this paper, we describe how a distributed simulation test bed enabling very detailed supply chain simulation can be used to study a customer-demand driven semiconductor supply chain.
Quantification of Intracellular Proteins and Monitoring Therapy Using Flow Cytometry (2010)

Here we review phospho-specific, quantitative flow cytometry approach as a rapid and reliable tool for measuring intracellular signaling proteins with potential applications in monitoring efficacy of targeted therapy. The single cell, multiparameter nature of flow cytometry allows simultaneous investigation of specific cell type and the corresponding intracellular markers. Peripheral blood can be directly stained with surface markers to delineate cell populations of interest, followed by fixation, permeabilization, and immunostaining with specific antibodies to the cellular targets. By using calibrated standardized phycoerythrin (PE)-conjugated beads for signal quantification, an informative Index value can be generated for each sample by multiplication of percentages of positive cells with fluorescence intensity per cell. This technique can yield both qualitative and quantitative information on effects of cellular markers upon targeted therapy, thereby providing another layer of advantages over the conventional flow cytometry analysis. Advances in this technology: high-throughput capability and automation, making it a valuable platform in modern drug discovery.
Identification of common cystic fibrosis mutations in African-Americans with cystic fibrosis increases the detection rate to 75%. (1997)

Cystic fibrosis (CF)--an autosomal recessive disorder caused by mutations in CF transmembrane conductance regulator (CFTR) and characterized by abnormal chloride conduction across epithelial membranes, leading to chronic lung and exocrine pancreatic disease--is less common in African-Americans than in Caucasians. No large-scale studies of mutation identification and screening in African-American CF patients have been reported, to date. In this study, the entire coding and flanking intronic sequence of the CFTR gene was analyzed by denaturing gradient-gel electrophoresis and sequencing in an index group of 82 African-American CF chromosomes to identify mutations. One novel mutation, 3120+1G-->A, occurred with a frequency of 12.3% and was also detected in a native African patient. To establish frequencies, an additional group of 66 African-American CF chromosomes were screened for mutations identified in two or more African-American patients. Screening for 16 "common Caucasian" mutations identified 52% of CF alleles in African-Americans, while screening for 8 "common African" mutations accounted for an additional 23%. The combined detection rate of 75% was comparable to the sensitivity of mutation analysis in Caucasian CF patients. These results indicate that African-Americans have their own set of "common" CF mutations that originate from the native African population. Inclusion of these "common" mutations substantially improves CF mutation detection rates in African-Americans.
Microstructure and Phase Relationship of Aluminum Boride/Carbide Composites (2017)

This chapter discusses how the demand for low density, high hardness materials in wear and armor applications continues to drive the development of new composite systems. Borides and carbides have been used in such applications and now that the availability of high quality, low cost synthetic diamond particles is emerging, these too are finding a place in these applications. In an experiment, an alloy containing approximately 50% Si and 50% Al was used to infiltrate the boron, boron-boron carbide, and the boron-diamond performs. The presence of a large amount of silicon carbide, from the silicon in the infiltration alloy, can be seen as well as high carbon containing regions. These areas correspond to the diamond particles and can be seen as isolated regions surrounded by silicon rich areas (SiC). The light gray region, highlighted by a B in the microstructure image, was found to be SiC via EDS analysis.
Analysis Method of the Dynamic Force and Torque Distribution in the Magnet Array of a Commutated Magnetically Levitated Planar Actuator (2011)

This paper concerns the analysis of the dynamic forces and torques acting on the magnets in a Halbach permanent magnet array of a magnetically levitated moving-magnet planar actuator. A new analysis tool is presented which predicts the dynamic force and torque distribution on the magnet array. This design tool uses lookup table data, which are generated by numerically solving the Lorentz force and torque integral, to describe the force and torque between each magnet and coil in the topology. It offers a fast and accurate solution for the analysis of magnetically levitated planar actuators. The results for two different commutation methods are presented.
Detailed Electrochemistry and Gas Transport in a SOFC Anode Using the Lattice Boltzmann Method (2006)

A coupled electrochemical reaction and diffusion model has been developed and verified for investigation of mass transport processes in Solid Oxide Fuel Cell (SOFC) anode triple-phase boundary (TPB) regions. The coupled model utilizes a two-dimensional (2D), multi-species Lattice Boltzmann Method (LBM) to model the diffusion process. The electrochemical model is coupled through localized flux boundary conditions and is a function of applied activation overpotential and the localized hydrogen and water mole fractions. This model is designed so that the effects of the anode microstructure within TPB regions can be examined in detail. Results are provided for the independent validation of the electrochemical and diffusion sub-models, as well as for the coupled model. An analysis on a single closed pore is completed and validated with a Fick's law solution. A competition between the electrochemical reaction rate and the rate of mass transfer is observed to be dependent on inlet hydrogen mole fraction. The developed model is presented such that future studies on SOFC anode microstructures can be completed.