gebhart/patrepeval huggingface dataset:
Runtime Semantic Interoperability for Gathering Ontology-based Network Context (2006)

The trends for pushing more operational intelligence towards network elements to achieve more context-aware and self-managing behavior often requires elements to gather network knowledge without necessarily binding explicitly to all of the potential sources of that knowledge. Though event-based publish-subscribe models allow efficient distribution of knowledge where the event types are known globally, dynamic service chains, ad hoc networks and pervasive computing application all introduce a more fluid and heterogeneous range of context knowledge. This requires some runtime translation of knowledge between sources and sinks of network context. This paper builds on existing mapping techniques that use ontological forms of existing management information models to examine the extent to which these can be employed for runtime semantic interoperability for network knowledge. It presents results in developing a management knowledge delivery framework based on existing models and platforms, but which offers a more decentralized knowledge exchange mechanism.
Crystal Structure and Enzyme Kinetics of the (<i>S</i>)-Specific 1-Phenylethanol Dehydrogenase of the Denitrifying Bacterium Strain EbN1<sup>,</sup> (2005)

(S)-1-Phenylethanol dehydrogenase (PED) from the denitrifying bacterium strain EbN1 catalyzes the NAD+-dependent, stereospecific oxidation of (S)-1-phenylethanol to acetophenone and the biotechnologically interesting reverse reaction. This novel enzyme belongs to the short-chain alcohol dehydrogenase/aldehyde reductase family. The coding gene (ped) was heterologously expressed in Escherichia coli and the purified protein was crystallized. The X-ray structures of the apo-form and the NAD+-bound form were solved at a resolution of 2.1 and 2.4 A, respectively, revealing that the enzyme is a tetramer with two types of hydrophobic dimerization interfaces, similar to beta-oxoacyl-[acyl carrier protein] reductase (FabG) from E. coli. NAD+-binding is associated with a conformational shift of the substrate binding loop of PED from a crystallographically unordered "open" to a more ordered "closed" form. Modeling the substrate acetophenone into the active site revealed the structural prerequisites for the strong enantioselectivity of the enzyme and for the catalytic mechanism. Studies on the steady-state kinetics of PED indicated a highly positive cooperativity of both catalytic directions with respect to the substrates. This is contrasted by the behavior of FabG. Moreover, PED exhibits extensive regulation on the enzyme level, being inhibited by elevated concentrations of substrates and products, as well as the wrong enantiomer of 1-phenylethanol. These regulatory properties of PED are consistent with the presence of a putative "transmission module" between the subunits. This module consists of the C-terminal loops of all four subunits, which form a special interconnected structural domain and mediate close contact of the subunits, and of a phenylalanine residue in each subunit that reaches out between substrate-binding loop and C-terminal domain of an adjacent subunit. These elements may transmit the substrate-induced conformational change of the substrate binding loop from one subunit to the others in the tetrameric complex and thus mediate the cooperative behavior of PED.
Solving linear arithmetic constraints for user interface applications (1997)

Linear equality and inequality constraints arise naturally in specifying many aspects of user interfaces, such as requiring that one window be to the left of another, requiring that a pane occupy the leftmost l/3 of a window, or preferring that an object be contained within a rectangle if possible. Current constraint solvers designed for UI applications cannot efficiently handle simultaneous linear equations and inequalities. This is a major limitation. We describe incremental algorithms based on the dual simplex and active set methods that can solve such systems of constraints efficiently.
The structure of some proteins as revealed by an x-ray scattering method (1955)

Abstract The intensity of scattering of monochromatic X-rays by isotropic specimens of thirty proteins (or protein fractions) and two synthetic polypeptides has been measured by means of a proportionalcounter diffractometer. The curves fall into only three essentially different types, calleda, /? and y. The a-proteins are the most numerous and some twenty have been examined; all the intensity curves are very similar and suggest that a single polypeptide-chain configuration is common to all as the predominant constituent. This predominant configuration is considered to be best represented by one of the variants of the a-helix of Pauling & Corey (1951 a) and Pauling, Corey & Branson (1951) to which the term aj-helix is given. The method of interpretation used was to calculate the intensity of scattering that would be produced by independent polypeptide chains in random orientation, various regular configurations being assigned to them in accordance with existing hypotheses. In this way, the scattering characteristics of the following helical chain configurations were derived: a, y, 7r, 413, 310, 38 and 27; in the first five mentioned, the two alternative positions of the ^-carbon atom were considered. Comparison with the observed curves for a -proteins showed that the curve for theaj-helix was in best agreement with experiment, and with the synthetic polypeptides the correlation was particularly convincing. It was further shown that the several helices, or parts of helices, that constitute a whole protein molecule are usually packed together compactly in a nearly parallel fashion; in certain cases, a more pronounced skewness is indicated.
Multiple copies of IS10 in the Enterobacter cloacae MD36 chromosome (1991)

Repetitive sequences were isolated and characterized as double-stranded DNA fragments by treatment with S1 nuclease after denaturation and renaturation of the total DNA of Enterobacter cloacae MD36. One repetitive sequence was identical to the nucleotide sequence of IS10-right (IS10R), which is the active element in the plasmid-associated transposon Tn10. Unexpectedly, 15 copies of IS10R were found in the chromosomal DNA of E. cloacae MD36. One copy of the central region of Tn10 was found in the total DNA of E. cloacae MD36. IS10Rs in restriction fragments isolated from the E. cloacae MD36 total DNA showed 9-bp duplications adjacent to the terminal sequences that are characteristic of Tn10 transposition. This result suggests that many copies of IS10R in E. cloacae MD36 are due to transposition of IS10R alone, not due to transposition of Tn10 or to DNA rearrangement. I also found nine copies of IS10 in Shigella sonnei HH109, two and four copies in two different natural isolates of Escherichia coli, and two copies in E. coli K-12 strain JM109 from the 60 bacterial strains that were examined. All dam sites in the IS10s in E. cloacae MD36 and S. sonnei HH109 were methylated. Tn10 and IS10 transpose by a mechanism in which the element is excised from the donor site and inserted into the new target site without significant replication of the transposing segment; thus, the copy numbers of the elements in the cell are thought to be unchanged in most circumstances. Accumulation of IS10 copies in E. cloacae MD36 has interesting evolutionary implications.
An Extended Role-Based Access Control Model for CSCW Systems (2010)

Due to the increasing threat of network attacks, network and information security is an upmost concern for CSCW. Traditional Role-Based Access made focus on the typical roles divided according to organizational roles in CSCW. It is insufficient to have role permissions based on object types for collaborative environments. An extended role-based access control model is proposed in this article to expand role to construct the hierarchy of security domain for CSCW. The total CSCW system was called security domain. Subdomain roles inherit security domain roles. Atomic domain roles inherit subdomain roles under role constrains. All extended role and role constraint are partial ordering and are used to restrict the range of access control for all CSCW participants.
A simulation environment for developing Intelligent Headlight Systems (2010)

This paper presents a simulation environment for developing Intelligent Headlight Systems (IHS). These are systems that actively adapt the headlights based on events in the traffic environment such as curves, oncoming vehicles and pedestrians. The results of applying the simulation environment to two IHS research projects of an OEM are presented. One of the findings is that the behaviour and performance of the IHS concepts could be evaluated without using road tests. The paper concludes with discussing how the simulation environment can also be applied for developing intelligent vehicle systems such as ACC, FCW, CMB, LDW and LKA.
Virtual Network Embedding with Coordinated Node and Link Mapping (2009)

Recently network virtualization has been proposed as a promising way to overcome the current ossification of the Internet by allowing multiple heterogeneous virtual networks (VNs) to coexist on a shared infrastructure. A major challenge in this respect is the VN embedding problem that deals with efficient mapping of virtual nodes and virtual links onto the substrate network resources. Since this problem is known to be NP-hard, previous research focused on designing heuristic-based algorithms which had clear separation between the node mapping and the link mapping phases. This paper proposes VN embedding algorithms with better coordination between the two phases. We formulate the VN embedding problem as a mixed integer program through substrate network augmentation. We then relax the integer constraints to obtain a linear program, and devise two VN embedding algorithms D-ViNE and R-ViNE using deterministic and randomized rounding techniques, respectively. Simulation experiments show that the proposed algorithms increase the acceptance ratio and the revenue while decreasing the cost incurred by the substrate network in the long run.
Involvement of p72syk kinase, p53/561yn kinase and phosphatidyl inositol‐3 kinase in signal transduction via the human B lymphocyte antigen CD22 (1996)

CD22 is a B lymphocyte-specific membrane protein that functions as an adhesion molecule via its interactions with a subset of alpha 2-6-linked sialic acid-containing glycoproteins. Engagement of CD22 with a monoclonal antibody (HB22.23) that blocks the binding of CD22 to its ligands results in rapid CD22 tyrosine phosphorylation and in increased association of CD22 with p53/56lyn kinase, p85 phosphatidyl inositol-3 kinase, and p72syk kinase. Synthetic peptides that span various regions of the intracellular portion of CD22 were used to map potential kinase binding sites. All three kinases associated with a tyrosine-phosphorylated peptide that spans tyrosine amino acid residues 822 and 842, implicating this as an important region in mediating CD22 signal transduction. In addition, purified p56lyn directly bound to the same peptide. Engagement of CD22 with HB22.23 was sufficient to stimulate normal B cell proliferation. This study further substantiates the importance of CD22 as a B lymphocyte signaling molecule and begins to unravel the mechanisms by which CD22 cross-linking can alter B cell function.
A Web-Based Search Engine for Triplex-forming Oligonucleotide Target Sequences (2006)

Triplex technology offers a useful approach for site-specific modification of gene structure and function both in vitro and in vivo. Triplex-forming oligonucleotides (TFOs) bind to their target sites in duplex DNA, thereby forming triple-helical DNA structures via Hoogsteen hydrogen bonding. TFO binding has been demonstrated to site-specifically inhibit gene expression, enhance homologous recombination, induce mutation, inhibit protein binding, and direct DNA damage, thus providing a tool for gene-specific manipulation of DNA. We have developed a flexible web-based search engine to find and annotate TFO target sequences within the human and mouse genomes. Descriptive information about each site, including sequence context and gene region (intron, exon, or promoter), is provided. The engine assists the user in finding highly specific TFO target sequences by eliminating or flagging known repeat sequences and flagging overlapping genes. A convenient way to check for the uniqueness of a potential TFO binding site is provided via NCBI BLAST. The search engine may be accessed at spi.mdanderson.org/tfo.
System architecture directions for a software-defined lighting infrastructure (2014)

After years of development, cost-effective, energy-efficient, and long-lasting solid-state lighting technology is finally a viable alternative to incandescent and fluorescent lights. Unfortunately, the remarkable march of semiconductor technology into the lighting industry is almost entirely in the form of a substitute good - one kind of lighting technology that replaces another - but this, we argue, squanders a unique opportunity for lighting to enable a bevy of new applications. In this paper, we discuss applications in health, energy efficiency, entertainment, communications, indoor positioning, device configuration, and time synchronization. We then prototype several of the indoor applications to explore a software-defined lighting (SDL) architecture that could support them.
Immobilized functional ionic liquids: efficient, green, and reusable catalysts (2012)

Ionic liquids (ILs) which are made up of cationic and anionic components can be designed to possess a definite set of properties. In this context, the term “designer solvents” has been used to demonstrate the potential of these environment-friendly ionic liquids in chemical reactions. Since these liquids are able to dissolve several transition metal complexes, they have often been employed in recent times in several catalytic reactions to enhance reaction rates and selectivities. The concept of “immobilized” liquids has been derived from supported liquid phase catalysts; the immobilization process transferring the desired catalytic properties of the liquids to solid catalysts could combine the advantages of ILs with those of heterogeneous support materials and various catalytically functional groups or active species. The immobilized functional ionic liquids (IFILs) capable to restrict many of the negative effects of the conventional ILs have successfully been used in various potent catalytic areas affording high catalytic activity. In this review, structural characteristics, properties and preparation of immobilized functional ionic liquids have been described and the results are compared with those of traditional ILs. Special emphasis has been paid to comprehend the mechanism of various catalytic processes using immobilized ionic liquids functionalized by different groups.
Synaptic Core Complex of Synaptobrevin, Syntaxin, and SNAP25 Forms High Affinity -SNAP Binding Site (1995)

SNAPs (soluble NSF attachment proteins) are cytoplasmic proteins that bind to specific membrane receptors and mediate the membrane binding of NSF (N-ethylmaleimide-sensitive factor), a protein that is required for membrane fusion reactions. Three synaptic proteins in brain (SNAP25 (synaptosomal-associated protein of 25 kDa; no relation to the SNAPs for NSF), synaptobrevin/VAMP, and syntaxin) were identified as SNAP receptors by affinity chromatography on immobilized alpha-SNAP complexed to NSF (Söllner, T., Whiteheart, S. W., Brunner, M., Erdjument-Bromage, H., Geromanos, S., Tempst, P. and Rothman, J. E. (1993) Nature 362, 318-324). However, the nature of the alpha-SNAP binding site is unclear. We now show that alpha-SNAP binds tightly to the complex of syntaxin with synaptobrevin. SNAP25 is not required for tight binding of alpha-SNAP to this complex but stabilizes the syntaxin-synaptobrevin complex by forming a trimeric core complex with it. alpha-SNAP does not bind to synaptobrevin individually and binds only weakly to syntaxin and SNAP25 in the absence of synaptobrevin. These data suggest that the complex of the vesicular protein synaptobrevin with the plasma membrane protein syntaxin is required for physiological alpha-SNAP binding. Thus, alpha-SNAP probably functions in a late step of the membrane fusion reaction after the formation of the synaptobrevin-syntaxin-SNAP25 core complex.
Efficiency improvement of optical fiber wavelength converter without spectral spread using synchronous phase/frequency modulations (2003)

We investigate a novel technique to improve the conversion efficiency of optical fiber wavelength converter without spectral spread. It is based on synchronous modulations of the signal phase and the pump phase or frequency, and can suppress not only the stimulated Brillouin scattering (SBS) but also the spread of the converted spectrum.
Visual servoing with modified Smith predictor for micromanipulation tasks (2006)

A control scheme with a modified Smith predicator (MSP) for the position-based dynamic look-and-move visual servoing for the control of micromanipulation is proposed. Due to the time consuming image acquisition, transfer, and processing, the visual servoing has an inherent time delay, which seriously damage the system performance. Previously, the most common method is to decrease the primary gains to increase damping, thus making the system more robust in the presence of delays. However, the resultant response of the system is lowered, leading to a sluggish overall performance. In this paper, a control scheme with a similar structure to the Smith predictor, called modified Smith predictor is employed to eliminate the vision delay. A detailed analysis and experiments available are presented to demonstrate the vision control system with the proposed control scheme has better dynamics performance than the single vision control system.
Chemoselective Building Blocks for Dendrimers from Relative Reactivity Data (2003)

Competition reactions for the substitution of monochlorotriazines with different amines provide relative reactivity data that can be used to identify new groups for the chemoselective syntheses of dendrimers based on melamine. Target 1 is prepared using a one-pot per generation strategy without protecting group manipulations or functional group interconversions.
<i>In Situ</i> Detection of Altered Particle Size Distributions during Simulated Powdered Sorbent Injection for Mercury Emissions Control (2010)

During full-scale sorbent injection tests for mercury removal at coal-fired power plants (CFPPs), a common trend has been observed in which the overall mercury removal efficiency reaches a performance plateau as the sorbent injection rate increases. Two common explanations for this trend are (1) the increased sorbent injection rate induces increased rates of particle agglomeration within sorbent feeding lines, which eventually shifts the particle size distribution to larger sizes and reduces the available particle surface area for heterogeneous oxidation and adsorption, and (2) the increased sorbent injection rate limits the available acid gas concentration for heterogeneous oxidation of Hg0 to Hg2+. In this experimental study, an in situ measurement technique based on the principles of light extinction is used to assess the degree of particle agglomeration. The present in situ measurement technique applies a simple inline HeNe laser, and a sorbent feeder fluidizes powdered activated carbon (PAC) and drives the suspension through a length of rubber tubing to simulate the sorbent feeding process. Each experimental trial yields a time-dependent function of the light extinction ratio, I(t)/I0, for the time-dependent evolution of the PAC suspensions. Observed differences in I(t)/I0 for suspensions ejected directly from the feeder as compared to those directed through the tubing indicate changes in the overall particle size distribution. A numerical model of the experiment provides excellent agreement and facilitates interpretation of the experimental results.
Antibodies to the unfolded form of a helix-rich region in staphylococcal nuclease (1974)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAntibodies to the unfolded form of a helix-rich region in staphylococcal nucleaseBruce Furie, Alan N. Schechter, David H. Sachs, and Christian B. AnfinsenCite this: Biochemistry 1974, 13, 8, 1561–1566Publication Date (Print):April 1, 1974Publication History Published online1 May 2002Published inissue 1 April 1974https://pubs.acs.org/doi/10.1021/bi00705a001https://doi.org/10.1021/bi00705a001research-articleACS PublicationsRequest reuse permissionsArticle Views29Altmetric-Citations23LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
AMP kinase is required for mitochondrial biogenesis in skeletal muscle in response to chronic energy deprivation (2002)

Mitochondrial biogenesis is a critical adaptation to chronic energy deprivation, yet the signaling mechanisms responsible for this response are poorly understood. To examine the role of AMP-activated protein kinase (AMPK), an evolutionarily conserved fuel sensor, in mitochondrial biogenesis we studied transgenic mice expressing a dominant-negative mutant of AMPK in muscle (DN-AMPK). Both DN-AMPK and WT mice were treated with beta-guanidinopropionic acid (GPA), a creatine analog, which led to similar reductions in the intramuscular ATPAMP ratio and phosphocreatine concentrations. In WT mice, GPA treatment resulted in activation of muscle AMPK and mitochondrial biogenesis. However, the same GPA treatment in DN-AMPK mice had no effect on AMPK activity or mitochondrial content. Furthermore, AMPK inactivation abrogated GPA-induced increases in the expression of peroxisome proliferator-activated receptor gamma coactivator 1alpha and calciumcalmodulin-dependent protein kinase IV (both master regulators of mitochondrial biogenesis). These data demonstrate that by sensing the energy status of the muscle cell, AMPK is a critical regulator involved in initiating mitochondrial biogenesis.
Neuroendocrine Neoplasms (2011)

Neuroendocrine neoplasms (NEN) appear homogeneous in terms of morphology, but constitute a very heterogeneous group of lesions in terms of biological and clinical features. Neuroendocrine neoplasms may occur in any organ, but are most commonly observed in the lung and the gastroenteropancreatic system (GEP). The aim of this Special Issue of Hormone and Metabolic Research is to give an overview on recent advances in the molecular understanding of NEN and also on clinical aspects of these tumors including new therapy strategies.