gebhart/patrepeval huggingface dataset:
Characterization of E. coli-Derived Recombinant Human Interferon-β as Compared with Fibroblast Human Interferon-β (1987)

Homogeneous E. coli-derived recombinant human interferon-beta (E. coli-rHuIFN-beta) was characterized in order to elucidate its physicochemical properties, as compared with those of fibroblast human interferon-beta (fibroblast HuIFN-beta). Purified E. coli-rHuIFN-beta and fibroblast HuIFN-beta exhibited a single band of Mr 19,000 and 23,000, respectively, on sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). The primary structure of E. coli-rHuIFN-beta was identical to the prediction from the cDNA sequence. Furthermore, both the circular dichroism (CD) spectra and the 1H nuclear magnetic resonance (NMR) spectra of E. coli-rHuIFN-beta and fibroblast HuIFN-beta at pH 6.8 were closely similar to each other. On the other hand, on reverse-phase high-performance liquid chromatography (HPLC) using a C18 column, the retention time of E. coli-rHuIFN-beta was longer than that of fibroblast HuIFN-beta. Moreover, although the isoelectric point of E. coli-rHuIFN-beta was pH 8.9, purified fibroblast HuIFN-beta exhibited multiple isoelectric points, probably due to heterogeneity of the carbohydrate moiety. These results indicate that the E. coli-rHuIFN-beta polypeptide folds similarly to fibroblast HuIFN-beta, and the carbohydrate moiety of natural HuIFN-beta has little influence on higher-order structure but does influence the hydrophobic and the electrostatic properties of the molecule.
Solution structure of a late embryogenesis abundant protein (LEA14) from <i>Arabidopsis thaliana</i>, a cellular stress‐related protein (2005)

We report the three-dimensional structure of a late embryogenesis abundant (LEA) protein from Arabidopsis thaliana gene At1g01470.1. This protein is a member of Pfam cluster PF03168, and has been classified as a LEA14 protein. LEA proteins are expressed under conditions of cellular stress, such as desiccation, cold, osmotic stress, and heat. The structure, which was determined by NMR spectroscopy, revealed that the At1g01470.1 protein has an alphabeta-fold consisting of one alpha-helix and seven beta-strands that form two antiparallel beta-sheets. The closest structural homologs were discovered to be fibronectin Type III domains, which have <7% sequence identity. Because fibronectins from animal cells have been shown to be involved in cell adhesion, cell motility, wound healing, and maintenance of cell shape, it is interesting to note that in plants wounding or stress results in the overexpression of a protein with fibronectin Type III structural features.
Spatial reasoning for human robot interaction (2007)

Robots' interaction with humans raises new issues for geometrical reasoning where the humans must be taken explicitly into account. We claim that a human-aware motion system must not only elaborate safe robot motions, but also synthesize good, socially acceptable and legible movement. This paper focuses on a manipulation planner and a placement mechanism that take explicitly into account its human partners by reasoning about their accessibility, their vision field and their preferences. This planner is part of a human-aware motion and manipulation planning and control system that we aim to develop in order to achieve motion and manipulation tasks in presence or in synergy with humans.
Low-power CMOS active resistor independent of the threshold voltage (2003)

This paper presents a new linearity improvement technique for a CMOS active resistor. The method is based on the cancellation of the main odd-order nonlinear terms and bulk effect, using a parallel connection of two active resistors opposite excited, with different polarisation voltages. The resistor is designed to work for an extended range of the input voltages, and achieves an improvement in linearity about a magnitude order. The utilization area of this active resistor includes, but is not limited to active filters, switched capacitor circuits or medical applications. Its theoretical estimated performance, linearity error 0.35% for an input range of /spl plusmn/500 mV, was confirmed by SPICE simulations. The circuit draws a very small amount of current from a /spl plusmn/3.3 V voltage source, being suitable for low-power applications. The resistor was implemented in 0.35 /spl mu/ CMOS AMS technology and the layout area is about 60 /spl mu/m/spl times/80 /spl mu/m.
Environmental and Sustainability Factors Associated With Next-Generation Biofuels in the U.S.: What Do We Really Know? (2009)

In this paper, we assess what is known or anticipated about environmental and sustainability factors associated with next-generation biofuels relative to the primary conventional biofuels (i.e., corn grain-based ethanol and soybean-based diesel) in the United States during feedstock production and conversion processes. Factors considered include greenhouse (GHG) emissions, air pollutant emissions, soil health and quality, water use and water quality, wastewater and solid waste streams, and biodiversity and land-use changes. Based on our review of the available literature, we find that the production of next-generation feedstocks in the U.S. (e.g., municipal solid waste, forest residues, dedicated energy crops, microalgae) are expected to fare better than corn-grain or soybean production on most of these factors, although the magnitude of these differences may vary significantly among feedstocks. Ethanol produced using a biochemical or thermochemical conversion platform is expected to result in fewer GHG and air pollutant emissions, but to have similar or potentially greater water demands and solid waste streams than conventional ethanol biorefineries in the U.S. However, these conversion-related differences are likely to be small, particularly relative to those associated with feedstock production. Modeling performed for illustrative purposes and to allow for standardized quantitative comparisons across feedstocks and conversion technologies generally confirms the findings from the literature. Despite current expectations, significant uncertainty remains regarding how well next-generation biofuels will fare on different environmental and sustainability factors when produced on a commercial scale in the U.S. Additional research is needed in several broad areas including quantifying impacts, designing standardized metrics and approaches, and developing decision-support tools to identify and quantify environmental trade-offs and ensure sustainable biofuels production.
Torque and Drag Modeling; Soft-string versus Stiff-string Models (2016)

Abstract The wellbore friction, torque and drag, between drill string and the wellbore wall is one of the most critical issues which limits the drilling industry to go beyond a certain measured depth. For this reason many studies on torque & drag modeling have been performed. In this regard different approaches have been used; the difference in these approaches is often on how to include bending stiffness and shearing forces in the T&D calculations. These approaches are (1) the effect of shear forces calculations with the assumption of continuous contact of the wellbore wall and the drillstring as well as constant curvature trajectory, (2) the effect of bending stiffness and shearing forces calculations with assuming of clearance between drillstring and wellbore-wall and (3) the effect of bending moment and shearing forces, assuming continuous contact of the pipe and wellbore-wall and using a non-constant curvature trajectory in which the first and second derivatives of the curve exist (i.e. spline type trajectories). This paper consists of two main parts: first a review on literatures on the subject of stiff-string T&D will be considered. Secondly, an approach will be discussed in which despite of the assumption of constant curvature trajectory and full-contact of pipe and wellbore wall, the effect of bending stiffness on torque and drag calculations are considered. The simple and robust stiff-string model is implemented in two example wells in order to find out the importance of the stiff-string calculations.
Adjuvant Therapy of Stage IIIb Melanoma with Interferon Alfa-2b: Clinical and Immunological Relevance (1995)

Adjuvant IFN-alpha therapy in stage IIIb melanoma patients is well tolerated and seems to increase survival. However, multicenter randomized trials are needed to confirm these preliminary findings.
Ablation of Neurons Expressing Melanin-Concentrating Hormone (MCH) in Adult Mice Improves Glucose Tolerance Independent of MCH Signaling (2013)

Melanin-concentrating hormone (MCH)-expressing neurons have been ascribed many roles based on studies of MCH-deficient mice. However, MCH neurons express other neurotransmitters, including GABA, nesfatin, and cocaine-amphetamine-regulated transcript. The importance of these other signaling molecules made by MCH neurons remains incompletely characterized. To determine the roles of MCH neurons in vivo, we targeted expression of the human diphtheria toxin receptor (DTR) to the gene for MCH (Pmch). Within 2 weeks of diphtheria toxin injection, heterozygous Pmch(DTR/+) mice lost 98% of their MCH neurons. These mice became lean but ate normally and were hyperactive, especially during a fast. They also responded abnormally to psychostimulants. For these phenotypes, ablation of MCH neurons recapitulated knock-out of MCH, so MCH appears to be the critical neuromodulator released by these neurons. In contrast, MCH-neuron-ablated mice showed improved glucose tolerance when compared with MCH-deficient mutant mice and wild-type mice. We conclude that MCH neurons regulate glucose tolerance through signaling molecules other than MCH.
Analysis of the <b><i>Shewanella oneidensis</i></b> proteome by two‐dimensional gel electrophoresis under nondenaturing conditions (2003)

Proteomes are dynamic, i.e., the protein components of living cells change in response to various stimuli. Protein changes can involve shifts in the abundance of protein components, in the interactions of protein components, and in the activity of protein components. Two-dimensional gel electrophoresis (2-DE) coupled with peptide mass spectrometry is useful for the analysis of relative protein abundance, but the denaturing conditions of classical 2-DE do not allow analysis of protein interactions or protein function. We have developed a nondenaturing 2-DE method that allows analysis of protein interactions and protein functions, as demonstrated in our analysis of the cytosol and crude membrane fractions of the facultative anaerobe Shewanella oneidensis MR-1. Our experiments demonstrate that enzymatic activity is retained under the sample and protein separation methods described, as shown by positive malate dehydrogenase activity results. We have also found protein interactions within both the soluble and membrane fractions. The method described will be useful for the characterization of the functional proteomes of microbial systems.
Introduction to Frontiers in Corpus Annotation (2004)

Oral midazolam syrup is easier for parents to administer and has better medication acceptance in children when compared to intranasal midazolam spray.
Complexity based rate control for MPEG encoder (2002)

Bit rate control is an important step in the video encoding process in that it transforms a variable rate bit stream into a constant rate one for communication channels or storage of fixed bandwidth. The authors propose a hierarchical approach to this problem based on a novel method to characterize the activity or complexity of the image sequence. They introduce a local discrepancy measure, AME (average of maximum 10% of mean square error) of the macroblock. The method performs better than the others in AME with similar mean square error per pixel.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Quinolones: Recent Structural and Clinical Developments (2005)

Quinolones are a very important family of antibacterial agents that are widely prescribed for the treatment of infections in humans. Since their discovery in the early 1960s, the quinolone group of antibacterials has generated considerable clinical and scientific interest. Two major groups of compounds have been developed from the basic molecule: quinolones and naphthyridones. The 4-pyridone-3-carboxylic acid associated with a 5, 6-fused aromatic ring is the common chemical feature of bactericidal quinolones. In the resulting bicyclic ring, the 1-, 5-, 6-, 7-, and 8-positions are the major targets of chemical variation. Manipulations of the basic molecule, including replacing hydrogen with fluorine at position 6, substituting a cyclic amine residue at position 7 and adding new residues at position 1 of the quinolone ring, have led to improved breadth and potency of antibacterial activity and pharmacokinetics. One of the most significant developments has been the improved anti-Gram-positive activity of the newer compounds, such as moxifloxacin and garenoxacin. However, some of these structural changes have been found to correlate with specific adverse effects: the addition of fluorine or chlorine at position 8 being associated with photoreactivity, e.g. sparfloxacin; and the substitution of an amine or a methyl group at position 5 having a potential role in QTc prolongation, e.g. sparfloxacin and grepafloxacin. The clinical utility of this expanding class of antimicrobial agents, and the lower propensity for the development of resistance with the newer quinolones will need to be continually monitored in the changing therapeutic environment. Antibiotic drug choice will remain difficult in the presence of increasing resistance, but introduction of the new quinolones has created a new and exciting era in antimicrobial chemotherapy.
Nuclear Accumulation of IE62, the Varicella-Zoster Virus (VZV) Major Transcriptional Regulatory Protein, Is Inhibited by Phosphorylation Mediated by the VZV Open Reading Frame 66 Protein Kinase (2000)

IE62, the major transcriptional activator protein encoded by varicella-zoster virus (VZV), locates to the nucleus when expressed in transfected cells. We show here that cytoplasmic forms of IE62 accumulate in transfected and VZV-infected cells as the result of the protein kinase activity associated with VZV open reading frame 66 (ORF66). Expression of the ORF66 protein kinase but not the VZV ORF47 protein kinase impaired the ability of coexpressed IE62 to transactivate promoter-reporter constructs. IE62 that was coexpressed with the ORF66 protein accumulated predominantly in the cytoplasm, whereas the normal nuclear localization of other proteins was not affected by the ORF66 protein. In cells infected with VZV, IE62 accumulated in the cytoplasm at late times of infection, whereas in cells infected with a VZV recombinant unable to express ORF66 protein (ROka66S), IE62 was completely nuclear. Point mutations introduced into the predicted serine/threonine catalytic domain and ATP binding domain of ORF66 abrogated its ability to influence IE62 nuclear localization, indicating that the protein kinase activity was required. The region of IE62 that was targeted by ORF66 was mapped to amino acids 602 to 733. IE62 peptides containing this region were specifically phosphorylated in cells coexpressing the ORF66 protein kinase and in cells infected with wild-type VZV but were not phosphorylated in cells infected with ROka66S. We conclude that the ORF66 protein kinase phosphorylates IE62 to induce its cytoplasmic accumulation, most likely by inhibiting IE62 nuclear import.
Lunar exploration rover program developments (1994)

The Robotic All Terrain Lunar Exploration Rover (RATLER) design concept began at Sandia National Laboratories in late 1991 with a series of small, proof-of-principle, working scale models. The models proved the viability of the concept for high mobility through mechanical simplicity, and eventually received internal funding at Sandia National Laboratories for full scale, proof-of-concept prototype development. Whereas the proof-of-principle models demonstrated the mechanical design's capabilities for mobility, the full scale proof-of-concept design currently under development is intended to support field operations for experiments in telerobotics, autonomous robotic operations, telerobotic field geology, and advanced man-machine interface concepts. The development program's current status is described, including an outline of the program's work over the past year, recent accomplishments, and plans for follow-on development work.
<i>Ab initio</i>calculation of structural and lattice-dynamical properties of silicon carbide (1994)

The plane-wave pseudopotential approach to density-functional theory (DFT) in the local-density approximation has been applied to investigate a variety of ground-state properties of the 3C, 2H, and 4H polytypes of silicon carbide. The linear-response theory within DFT has been used to obtain lattice-dynamical properties of cubic SiC such as the phonon-dispersion curves, phonon eigenvectors, elastic and Gr\"uneisen constants, as well as the thermal expansion coefficient and specific heat within the quasiharmonic approximation. Finally, we present some results for phonon-dispersion curves in the hexagonal 2H (wurtzite) and 4H structure. These results are analyzed and discussed in view of further applications to temperature-dependent properties.
Aircraft free-space MIMO communications (2009)

We investigate the use of MIMO to increase the data rate of air to air wireless links without scattered propagation. The conditions for significant improvement over SISO are outlined.
De novo Biosynthesis of “Non‐Natural” Thaxtomin Phytotoxins (2018)

Thaxtomins are diketopiperazine phytotoxins produced by Streptomyces scabies and other actinobacterial plant pathogens that inhibit cellulose biosynthesis in plants. Due to their potent bioactivity and novel mode of action there has been considerable interest in developing thaxtomins as herbicides for crop protection. To address the need for more stable derivatives, we have developed a new approach for structural diversification of thaxtomins. Genes encoding the thaxtomin NRPS from S. scabies, along with genes encoding a promiscuous tryptophan synthase (TrpS) from Salmonella typhimurium, were assembled in a heterologous host Streptomyces albus. Upon feeding indole derivatives to the engineered S. albus strain, tryptophan intermediates with alternative substituents are biosynthesized and incorporated by the NRPS to deliver a series of thaxtomins with different functionalities in place of the nitro group. The approach described herein, demonstrates how genes from different pathways and different bacterial origins can be combined in a heterologous host to create a de novo biosynthetic pathway to "non-natural" product target compounds.
Momentum transfer of a Boltzmann-lattice fluid with boundaries (2001)

We study the velocity boundary condition for curved boundaries in the lattice Boltzmann equation (LBE). We propose a LBE boundary condition for moving boundaries by combination of the “bounce-back” scheme and spatial interpolations of first or second order. The proposed boundary condition is a simple, robust, efficient, and accurate scheme. Second-order accuracy of the boundary condition is demonstrated for two cases: (1) time-dependent two-dimensional circular Couette flow and (2) two-dimensional steady flow past a periodic array of circular cylinders (flow through the porous media of cylinders). For the former case, the lattice Boltzmann solution is compared with the analytic solution of the Navier–Stokes equation. For the latter case, the lattice Boltzmann solution is compared with a finite-element solution of the Navier–Stokes equation. The lattice Boltzmann solutions for both flows agree very well with the solutions of the Navier–Stokes equations. We also analyze the torque due to the momentum transfer between the fluid and the boundary for two initial conditions: (a) impulsively started cylinder and the fluid at rest, and (b) uniformly rotating fluid and the cylinder at rest.
A Semi-Automatic Segmentation Method for the Structural Analysis of Carotid Atherosclerotic Plaques by Computed Tomography Angiography (2014)

This new semi-automatic segmentation method for CTA provides a fast and reliable tool to quantify the severity of carotid artery stenosis.
Two dimensional spreading codes for the downlink in a multiuser system with multiple antennas (2003)

We present a novel space-time spreading scheme for the down-link in a multiuser system. The primary goals of this work are to increase bandwidth efficiency, and to provide joint multiuser detection and space-time decoding, in each mobile station. Each receiver just needs to know its own spreading code and no information about the channel is required in the transmitter. In the proposed architecture, to achieve high bandwidth efficiency, the number of user-channels, is maximized by taking advantage of the large potential capacity of a multiple antenna system.
Long-range movement of large mechanically interlocked DNA nanostructures (2016)

Interlocked molecules such as catenanes and rotaxanes, connected only via mechanical bonds have the ability to perform large-scale sliding and rotational movements, making them attractive components for the construction of artificial molecular machines and motors. We here demonstrate the realization of large, rigid rotaxane structures composed of DNA origami subunits. The structures can be easily modified to carry a molecular cargo or nanoparticles. By using multiple axle modules, rotaxane constructs are realized with axle lengths of up to 355 nm and a fuel/anti-fuel mechanism is employed to switch the rotaxanes between a mobile and a fixed state. We also create extended pseudo-rotaxanes, in which origami rings can slide along supramolecular DNA filaments over several hundreds of nanometres. The rings can be actively moved and tracked using atomic force microscopy.
Efficient L-shape fitting of laser scanner data for vehicle pose estimation (2015)

In this paper, we propose an efficient algorithm to fit a cluster of laser scan points with an L-shape. The algorithm partitions a cluster into two disjoint sets optimally in the sense of the least square error, and then fits them with two perpendicular lines. By exploiting the characteristics of both the laser scanner sensor and the fitting problem, the algorithm can test all the possible corner points while keeping the complexity as low as 9 times that of fitting a single pair of orthogonal lines, where the 9 times scaling factor is independent of the number of points in the cluster. Specifically, we exploit the property that the scanner data points are ordered either clockwise or counterclockwise, and incrementally construct the L-shape fitting problem rather than from scratch when the corner point is different. We extend our algorithm to provide multiple hypotheses on pose estimation, which are derived from L-shape fitting, to account for the ambiguity on the corner points. The extended algorithm only requires slightly more computation, which is tested and verified with real laser scanner data. The experimental results justify the correctness and efficacy of our algorithm.