gebhart/patrepeval huggingface dataset:
Involvement of Lipids in Different Steps of the Flavivirus Fusion Mechanism (2003)

Flavivirus membrane fusion is triggered by acidic pH and mediated by the major envelope protein E. A structurally very similar fusion protein is found in alphaviruses, and these molecules are designated class II viral fusion proteins. In contrast to that of flaviviruses, however, alphavirus fusion has been shown to be absolutely dependent on the presence of cholesterol and sphingomyelin in the target membrane, suggesting significant differences in the fusion protein-membrane interactions that lead to fusion. With the flavivirus tick-borne encephalitis virus (TBEV), we have therefore conducted a study on the lipid requirements of viral fusion with liposomes and on the processes preceding fusion, specifically, the membrane-binding step and the fusion-associated oligomeric switch from E protein dimers to trimers. As with alphaviruses, cholesterol had a strong promoting effect on membrane binding and trimerization of the fusion protein, and-as shown by the use of cholesterol analogs-the underlying interactions involve the 3beta-hydroxyl group at C-3 in both viral systems. In contrast to alphaviruses, however, these effects are much less pronounced with respect to the overall fusion of TBEV and can only be demonstrated when fusion is slowed down by lowering the temperature. The data presented thus suggest the existence of structurally related interactions of the flavivirus and alphavirus fusion proteins with cholesterol in the molecular processes required for fusion but, at the same time, point to significant differences between the class II fusion machineries of these viruses.
An object-centered multi-dimensional data model with hierarchically structured dimensions (2002)

We propose a formal framework based on description logics as a basis for both modeling multidimensional databases and understanding related reasoning problems and services. We extend a description logic with new constructors for defining operators on cubes together with a representational framework for hierarchically structured dimensions. The constructors we propose correspond in part to the operators on data cubes given by R. Agrawal et al. (1997). Finally, our representation of cubes naturally allows a symmetric treatment of dimensions and measures.
Application of phasor measurement units to estimate power system inertial frequency response (2013)

The inherent reduction in inertial frequency response resulting from a shift in generation mix towards renewables, is presenting a range of operational planning challenges for transmission system operators (TSOs) globally. Dictating the ability to maintain frequency following significant mismatches in supply and demand, it is of great consequence to the real-time operation of the power system. In this paper we discuss the estimation of system inertia constant using synchronised data, provided by installed phasor measurement units (PMUs). Results are presented from analysing the impact of over 50 transmission system events that were observed on the electricity transmission network of Great Britain.
Predicting the Tolerated Sequences for Proteins and Protein Interfaces Using RosettaBackrub Flexible Backbone Design (2011)

Predicting the set of sequences that are tolerated by a protein or protein interface, while maintaining a desired function, is useful for characterizing protein interaction specificity and for computationally designing sequence libraries to engineer proteins with new functions. Here we provide a general method, a detailed set of protocols, and several benchmarks and analyses for estimating tolerated sequences using flexible backbone protein design implemented in the Rosetta molecular modeling software suite. The input to the method is at least one experimentally determined three-dimensional protein structure or high-quality model. The starting structure(s) are expanded or refined into a conformational ensemble using Monte Carlo simulations consisting of backrub backbone and side chain moves in Rosetta. The method then uses a combination of simulated annealing and genetic algorithm optimization methods to enrich for low-energy sequences for the individual members of the ensemble. To emphasize certain functional requirements (e.g. forming a binding interface), interactions between and within parts of the structure (e.g. domains) can be reweighted in the scoring function. Results from each backbone structure are merged together to create a single estimate for the tolerated sequence space. We provide an extensive description of the protocol and its parameters, all source code, example analysis scripts and three tests applying this method to finding sequences predicted to stabilize proteins or protein interfaces. The generality of this method makes many other applications possible, for example stabilizing interactions with small molecules, DNA, or RNA. Through the use of within-domain reweighting and/or multistate design, it may also be possible to use this method to find sequences that stabilize particular protein conformations or binding interactions over others.
Reverse genetic analysis of <i>Caenorhabditis elegans</i> presenilins reveals redundant but unequal roles for <i>sel-</i> <i>12</i> and <i>hop-</i> <i>1</i> in Notch-pathway signaling (1999)

Mutations in the human presenilin genes PS1 and PS2 cause early-onset Alzheimer's disease. Studies in Caenorhabditis elegans and in mice indicate that one function of presenilin genes is to facilitate Notch-pathway signaling. Notably, mutations in the C. elegans presenilin gene sel-12 reduce signaling through an activated version of the Notch receptor LIN-12. To investigate the function of a second C. elegans presenilin gene hop-1 and to examine possible genetic interactions between hop-1 and sel-12, we used a reverse genetic strategy to isolate deletion alleles of both loci. Animals bearing both hop-1 and sel-12 deletions displayed new phenotypes not observed in animals bearing either single deletion. These new phenotypes-germ-line proliferation defects, maternal-effect embryonic lethality, and somatic gonad defects-resemble those resulting from a reduction in signaling through the C. elegans Notch receptors GLP-1 and LIN-12. Thus SEL-12 and HOP-1 appear to function redundantly in promoting Notch-pathway signaling. Phenotypic analyses of hop-1 and sel-12 single and double mutant animals suggest that sel-12 provides more presenilin function than does hop-1.
Preparation of Semiconducting Cubic Boron Nitride (1962)

Semiconducting crystals of cubic BN may be prepared at high pressures and temperatures by adding small amounts of selected impurities to the synthesis mixture (hexagonal boron nitride plus lithium or magnesium nitride). P-type crystals, blue in color, can be prepared by adding Be; they may have resistivities of about 103 ohm-cm and activation energies for conduction of about 0.2 ev. N-type crystals can be prepared by adding S, Si, KCN, and other impurities; they were found to have resistivities of 103 ohm-cm or higher and activation energies for conduction of 0.05 to 0.20 v. The diffusion of impurities into cubic BN crystals was not found to proceed as rapidly as with diamond. Point-contact rectification effects have been observed among semiconducting cubic BN and diamond crystals.
Development of idursulfase therapy for mucopolysaccharidosis type II (Hunter syndrome): the past, the present and the future (2017)

Mucopolysaccharidosis type II (MPS II; Hunter syndrome; OMIM 309900) is a rare, multisystemic, progressive lysosomal storage disease caused by deficient activity of the iduronate-2-sulfatase (I2S) enzyme. Accumulation of the glycosaminoglycans dermatan sulfate and heparan sulfate results in a broad range of disease manifestations that are highly variable in presentation and severity; notably, approximately two-thirds of individuals are affected by progressive central nervous system involvement. Historically, management of this disease was palliative; however, during the 1990s, I2S was purified to homogeneity for the first time, leading to cloning of the corresponding gene and offering a means of addressing the underlying cause of MPS II using enzyme replacement therapy (ERT). Recombinant I2S (idursulfase) was produced for ERT using a human cell line and was shown to be indistinguishable from endogenous I2S. Preclinical studies utilizing the intravenous route of administration provided valuable insights that informed the design of the subsequent clinical studies. The pivotal Phase II/III clinical trial of intravenous idursulfase (Elaprase<sup>®</sup>; Shire, Lexington, MA, USA) demonstrated improvements in a range of clinical parameters; based on these findings, intravenous idursulfase was approved for use in patients with MPS II in the USA in 2006 and in Europe and Japan in 2007. Evidence gained from post-approval programs has helped to improve our knowledge and understanding of management of patients with the disease; as a result, idursulfase is now available to young pediatric patients, and in some countries patients have the option to receive their infusions at home. Although ERT with idursulfase has been shown to improve somatic signs and symptoms of MPS II, the drug does not cross the blood-brain barrier and so treatment of neurological aspects of the disease remains challenging. A number of novel approaches are being investigated, and these may help to improve the care of patients with MPS II in the future.
Highly robust biometric smart card design (2000)

An architecture of a highly reliable smart card is proposed. Dual on-chip biometric fingerprint sensors, implemented with different technologies, are integrated with the smart card architecture for increase security and reliability.
A device for probability density function measurements (1974)

The working principle of an analogue instrument for probability density function measurements is presented together with the results obtained by a simple and inexpensive prototype.
Iridium-Catalyzed Intermolecular Hydroamination of Unactivated Aliphatic Alkenes with Amides and Sulfonamides (2012)

The intermolecular addition of N-H bonds to unactivated alkenes remains a challenging, but desirable, strategy for the synthesis of N-alkylamines. We report the intermolecular amination of unactivated α-olefins and bicycloalkenes with arylamides and sulfonamides to generate synthetically useful protected amine products in high yield. Mechanistic studies on this rare catalytic reaction revealed a resting state that is the product of N-H bond oxidative addition and coordination of the amide. Rapid, reversible dissociation of the amide precedes reaction with the alkene, but an intramolecular, kinetically significant rearrangement of the species occurs before this reaction with alkene.
Arterial stiffening and vascular calcifications in end‐stage renal disease (2000)

The results of this study showed that the presence of vascular calcifications in ESRD patients was associated with increased stiffness of large capacity, elastic-type arteries, like the aorta and CCA. The extent of arterial calcifications increased with the use of calcium-based phosphate-binders.
Surface-Enhanced and Normal Stokes and Anti-Stokes Raman Spectroscopy of Single-Walled Carbon Nanotubes (2000)

Surface enhancement factors of at least 10(12) for the Raman scattering of single-walled carbon nanotubes in contact with fractal silver colloidal clusters result in measuring very narrow Raman bands corresponding to the homogeneous linewidth of the tangential C-C stretching mode in semiconducting nanotubes. Normal and surface-enhanced Stokes and anti-Stokes Raman spectra are discussed in the framework of selective resonant Raman contributions of semiconducting or metallic nanotubes to the Stokes or anti-Stokes spectra, respectively, of the population of vibrational levels due to the extremely strong surface-enhanced Raman process, and of phonon-phonon interactions.
Intersection management for autonomous vehicles using iCACC (2012)

Recently several artificial intelligence labs have suggested the use of fully equipped vehicles with the capability of sensing the surrounding environment to enhance roadway safety. As a result, it is anticipated in the future that many vehicles will be autonomous and thus there is a need to optimize the movement of these vehicles. This paper presents a new tool for optimizing the movements of autonomous vehicles through intersections: iCACC. The main concept of the proposed tool is to control vehicle trajectories using Cooperative Adaptive Cruise Control (CACC) systems to avoid collisions and minimize intersection delay. Simulations were executed to compare conventional signal control with iCACC considering two measures of effectiveness - delay and fuel consumption. Savings in delay and fuel consumption in the range of 91 and 82 percent relative to conventional signal control were demonstrated, respectively.
Transverse-mode-selectable microlens vertical-cavity surface-emitting laser (2010)

A new vertical-cavity surface-emitting laser structure employing a thin microlens is suggested and numerically investigated. The laser can be made to emit in either a high-power Gaussian-shaped single-fundamental mode or a high-power doughnut-shaped higher-order mode. The physical origin of the mode selection properties of the new structure is rigorously analyzed and compared to other structures reported in the literature. The possibility of engineering the emission shape while retaining strong single mode operation is highly desirable for low-cost mid-range optical interconnects applications as well as the compact optical trapping of high-refractive-index dielectric particles and low-refractive-index, absorbing, or metallic particles.
Caching and the Java Virtual Machine (2001)

Most of the research done to improve the performance of Java Virtual Machines (JVM’s) has focused on software implementations of the JVM specification. Very little consideration has been given to how Java programs interact with hardware resources and how hardware components can be used to improve Java performance. We generated and analyzed opcode and memory access traces for eight different Java benchmarks, finding that each Java opcode typically causes multiple memory accesses. We next investigated the effectiveness of unified and split caches at caching Java programs, using the performance of traditional compiled programs for a basis of comparison. Motivated by the subdivision of memory by the JVM specification into heap memory, constant pool data, and operand stacks, we examined the possible benefits of adding small specialized caches to hold constant pool data and stack data. We found that constant pool accesses have very low locality of reference and that the addition of a constant cache is detrimental to cache performance for large main caches. The 24 % of memory accesses made to operand stacks were found to be efficiently cached in a 64 byte cache. We simulated
Cross-Coupled Series-Capacitor Quadruple Step-Down Buck Converter (2020)

This paper introduces a novel two-phase dc-dc multi-level Hying capacitor converter topology. This topology is well-suited for emerging high step-down applications. It features both natural balancing of the inductor phase currents as well as inherent Hying capacitor voltage stabilisation. The switching node voltage swing reduction of V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">g</sub> /4 is achieved with the same number of switches required by the 5-level multi-level Hying capacitor buck, which does not have inherent balancing features, and the 4-phase series capacitor buck which requires components with higher voltage ratings. The functionality of the topology is demonstrated with a prototype with peak operating efficiencies of 94.5% for 48V-to-1V operation and 95.9% for 24V-to-1V operation.
Quantitative evaluation of protein recoveries in two-dimensional electrophoresis with immobilized pH gradients (2000)

In this study, metabolically radiolabeled Escherichia coli cell extracts were used to systematically evaluate protein recoveries at each step of two-dimensional (2-D) electrophoresis and using different sample application methods. Sample application using sample cups resulted in better protein recovery compared with sample loading by rehydration when the Multiphor system was used. At least 50% or more of an E. coli extract was lost when high protein amounts (500 microg) were loaded by rehydration using this system, which employs separate holders for rehydration and isoelectric focusing (IEF). In contrast, when the IPGphor system was used, rehydration sample loading consistently yielded the highest overall protein recoveries. These improved protein recoveries were due to integration of rehydration and electrophoretic separation in a single unit. Even at high protein loads (500 microg), less than 15-20% of the proteins were lost when proteins were loaded by rehydration using sample buffer containing 2% carrier ampholytes in the ceramic immobilized pH gradient (IPG) strip holders used for both rehydration and IEF. Regardless of the loading conditions used, carrier ampholytes in the sample buffer increased protein recoveries. Use of thiourea did not significantly affect protein recoveries but did improve protein resolution in 2-D gels as expected. In summary, these results show the best protein recoveries are obtained for all protein loads when samples are applied to IPG strips during rehydration using a single device for both rehydration and IEF. In contrast, the poorest recoveries are obtained when rehydration and IEF are performed in separate devices, and losses increase dramatically with increasing protein loads using this approach.
Submicrometer-Thick Low-Loss As$_2$S$_3$ Planar Waveguides for Nonlinear Optical Devices (2010)

We describe a fabrication process for and the characterization of submicrometer-thick As <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> S <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> waveguides. Poly(methylmethacrylate) and bottom antireflective coating were employed as thin protective layers prior to photoresist patterning in order to prevent the attack of the As <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> S <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> film by an alkaline developer. Propagation losses of ~0.2 and 0.6 dB/cm were measured for 4- and 2-¿m-wide waveguides fabricated from 0.85-¿m-thick films. Slightly higher loss in the transverse-magnetic mode may be the result of surface scattering of the rougher etched sidewalls.
The Cloud Adoption Toolkit: supporting cloud adoption decisions in the enterprise (2011)

SUMMARY Cloud computing promises a radical shift in the provisioning of computing resources within the enterprise. This paper describes the challenges that decision makers face when assessing the feasibility of the adoption of cloud computing in their organizations, and describes our Cloud Adoption Toolkit, which has been developed to support this process. The toolkit provides a framework to support decision makers in identifying their concerns, and matching these concerns to appropriate tools/techniques that can be used to address them. Cost Modeling is the most mature tool in the toolkit, and this paper shows its effectiveness by demonstrating how practitioners can use it to examine the costs of deploying their IT systems on the cloud. The Cost Modeling tool is evaluated using a case study of an organization that is considering the migration of some of its IT systems to the cloud. The case study shows that running systems on the cloud using a traditional ‘always on’ approach can be less cost effective, and the elastic nature of the cloud has to be used to reduce costs. Therefore, decision makers have to model the variations in resource usage and their systems' deployment options to obtain accurate cost estimates. Copyright © 2011 John Wiley & Sons, Ltd.
Semi‐Automated Registration Of Close‐Range Hyperspectral Scans Using Oriented Digital Camera Imagery And A 3d Model (2014)

Abstract Diverse applications can benefit from the integration of data acquired by a new generation of close‐range imaging sensors with high‐resolution three‐dimensional (3D) geometric data. However, such integration requires increased automation and efficiency of image‐data registration to guarantee adoption by users beyond the geomatics community. This paper presents a semi‐automated method for registering terrestrial panoramic hyperspectral imagery with lidar models and conventional digital photography. The method relies on finding corresponding points between images acquired in significantly different parts of the electromagnetic spectrum, from different viewpoints, and with different spatial resolution and geometric projections. Optimisation of the scale invariant feature transform ( SIFT ) operator was required to ensure a sufficient number of homologous points, as well as a routine for eliminating false matches. A band selection routine maximises the number of points found while minimising the input data for SIFT . Three‐dimensional object coordinates were derived in the lidar model and used as control points in a bundle block adjustment to determine the hyperspectral exterior orientation and intrinsic camera parameters. The method developed was applied to two datasets with different characteristics, and the results indicate that the proposed method is a time‐saving alternative to manual approaches.
A combined successive and Σ-Δ A/D conversion scheme (2002)

A mismatch-insensitive approach to the multi-bit /spl Sigma/-/spl Delta/ modulator design is presented. The multi-bit conversion is realized by a successive approximation. A simple controlled averaging technique is introduced to cancel the first-order mismatch error. The cost in circuit complexity increase is very modest.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Comparative Biological Chemistry of Cobalt Hemoglobin (1973)

Abstract Cobaltohemoglobin A binds oxygen cooperatively with a Hill coefficient of up to 2.3 and its p1/2 is found to be 91 mm. Its oxygen affinity is controlled by diphosphoglycerate which the protein binds very strongly. Cobaltohemoglobin A possesses only 40% of the alkaline Bohr effect of the native enzyme; carbon dioxide has no effect upon oxygen binding. The oxidation-reduction potential of cobaltohemoglobin A is +0.100 volt which is about 50 mv less positive than that of native hemoglobin. The electron paramagnetic resonance of the nitroxide spin label attached to the sulfhydryl groups of cys(92)β and the rates of reaction of these groups with paramercuribenzoate indicate that the heme crevice is more open near that residue. A detailed comparison of these properties with those of the native protein suggests subtle and intricate alterations of the quaternary structures of the oxy and deoxy species which result from substitution of the metal atom.