gebhart/patrepeval huggingface dataset:
Oligosaccharide sequences of endothelial cell surface heparan sulfate proteoglycan with affinity for lipoprotein lipase. (1994)

Lipoprotein lipase (LpL) catalyzes the hydrolysis of triglycerides in plasma lipoproteins at the luminal surface of the vascular endothelium. This enzyme is bound via electrostatic interactions to heparan sulfate (HS). The specific endothelial cell surface HS oligosaccharide sequences that are necessary for binding of LpL to HS have not been characterized. To identify this LpL-binding oligosaccharide sequence, oligosaccharides were isolated from bovine aortic endothelial cell-derived HS and assessed for LpL binding properties. Endothelial HS chains that were isolated from endothelial total cell-associated proteoglycans were deacetylated by complete hydrazinolysis, cleaved with nitrous acid (pH 4.5), and reduced with [3H]NaBH4. The resulting fragments composed of N-sulfated glucosamine-rich oligosaccharides terminating with [3H]2,5-anhydromannitol (AManR) were chromatographed on a LpL-Sepharose column. A high affinity decasaccharide was isolated and characterized. Disaccharide analysis of this decasaccharide indicated that it yielded only the disaccharide IdceA(2-SO4)-->AManR(6-SO4) on treatment with nitrous acid at low pH. Therefore, the sequence of the LpL-binding decasaccharide is [IdceA(2-SO4) alpha 1-4GlcNSO4(6-S0(4)) alpha 1-4]4-IdceA(2-SO4) alpha 1-4AManR(6-SO4) and is distinct from those that bind antithrombin and basic fibroblast growth factor. Partial depolymerization of endothelial HS chains with hydrazine/high pH nitrous acid treatment gave rise to lipase-binding oligosaccharides larger than decasaccharide. However, further complete depolymerization of these oligosaccharides resulted in only a high affinity decasaccharide composed of repeating disaccharide units of [IdceA(2-SO4) alpha 1-4GlcNSO4(6-S0(4))]. These results indicate that the decasaccharide is the active fragment that binds to LpL with high affinity. Molecular modeling studies of the decasaccharide indicate that it presents a linear array of negatively charged sulfate groups that may adopt a favorable disposition to bind to peptide region(s) comprised of basic amino acid residues of LpL with high affinity.
Hydrogen Bonding Networks Tune Proton-Coupled Redox Steps during the Enzymatic Six-Electron Conversion of Nitrite to Ammonia (2014)

Multielectron multiproton reactions play an important role in both biological systems and chemical reactions involved in energy storage and manipulation. A key strategy employed by nature in achieving such complex chemistry is the use of proton-coupled redox steps. Cytochrome c nitrite reductase (ccNiR) catalyzes the six-electron seven-proton reduction of nitrite to ammonia. While a catalytic mechanism for ccNiR has been proposed on the basis of studies combining computation and crystallography, there have been few studies directly addressing the nature of the proton-coupled events that are predicted to occur along the nitrite reduction pathway. Here we use protein film voltammetry to directly interrogate the proton-coupled steps that occur during nitrite reduction by ccNiR. We find that conversion of nitrite to ammonia by ccNiR adsorbed to graphite electrodes is defined by two distinct phases; one is proton-coupled, and the other is not. Mutation of key active site residues (H257, R103, and Y206) modulates these phases and specifically alters the properties of the detected proton-dependent step but does not inhibit the ability of ccNiR to conduct the full reduction of nitrite to ammonia. We conclude that the active site residues examined are responsible for tuning the protonation steps that occur during catalysis, likely through an extensive hydrogen bonding network, but are not necessarily required for the reaction to proceed. These results provide important insight into how enzymes can specifically tune proton- and electron transfer steps to achieve high turnover numbers in a physiological pH range.
Vergence and accommodation to multiple-image-plane stereoscopic displays: “real world” responses with practical image-plane separations? (2012)

Conventional stereoscopic displays present images on a single focal plane. The resulting mismatch between the stimuli to the eyes' focusing response (accommodation) and to convergence causes fatigue and poor stereo performance. One solution is to distribute image intensity across a number of widely spaced image planes-a technique referred to as depth filtering. Previously, we found this elicits accurate, continuous monocular accommodation responses with image-plane separations as large as 1.1 Diopters (D, the reciprocal of distance in meters), suggesting that a small number of image planes could eliminate vergence-accommodation conflicts over a large range of simulated distances. Evidence exists, however, of systematic differences between accommodation responses to binocular and monocular stimuli when the stimulus to accommodation is degraded, or at an incorrect distance. We examined the minimum image-plane spacing required for accurate accommodation to binocular depth-filtered images. We compared accommodation and vergence responses to changes in depth specified by depth filtering, using image-plane separations of 0.6 to 1.2 D, and equivalent real stimuli. Accommodation responses to real and depth-filtered stimuli were equivalent for image-plane separations of ∼ 0.6 to 0.9 D, but differed thereafter. We conclude that depth filtering can be used to precisely match accommodation and vergence demand in a practical stereoscopic display.
Regulation of transforming growth factor β- and activin-induced transcription by mammalian Mad proteins (1996)

Members of the transforming growth factor beta (TGF-beta) superfamily are involved in diverse physiological activities including development, tissue repair, hormone regulation, bone formation, cell growth, and differentiation. At the cellular level, these functions are initiated by the interaction of ligands with specific transmembrane receptors with intrinsic serine/threonine kinase activity. The signaling pathway that links receptor activation to the transcriptional regulation of the target genes is largely unknown. Recent work in Drosophila and Xenopus signaling suggested that Mad (Mothers against dpp) functions downstream of the receptors of the TGF-beta family. Mammalian Mad1 has been reported to respond to bone morphogenetic protein (BMP), but not to TGF-beta or activin. We report here the cloning and functional studies of a novel mammalian Mad molecule, Mad3, as well as a rat Mad1 homologue. Overexpression of Mad3 in a variety of cells stimulated basal transcriptional activity of the TGF-beta/activin-responsive reporter construct, p3TP-Lux. Furthermore, expression of Mad3 could potentiate the TGF-beta- and activin-induced transcriptional stimulation of p3TP-Lux. By contrast, overexpression of Mad1 inhibited the basal as well as the TGF-beta/activin induced p3TP-Lux activity. These findings, therefore, support the hypothesis that Mad3 may serve as a mediator linking TGF-beta/activin receptors to transcriptional regulation.
The Impact of NFC on Multimodal Social Media Application (2010)

In this paper we describe the NFC-based multimodal social media application Hot in the City. This application allows users to make friends by touching other users’ NFC devices through the peer-to-peer mode. Users can also inform friends of their current location by touching hotspot tags. This study describes the three NFC modes in detail and delineates what kind of impact NFC has had in the creation of the Hot in the City social media application. In addition, we analyse how the use of different NFC modes – reader/writer and peer-to-peer – has unique consequences on user interface and system design. Even though NFC offers intuitive, natural interactions, the changing between modes seemed to confuse less experienced users.
[A digital micromirror device-based Hadamard transform near infrared spectrometer]. (2011)

A Hadamard transform near infrared spectrometer based on a digital micromirror device was constructed. The optical signal was collected by optical fiber, a grating was used for light diffraction, a digital micromirror device (DMD) was applied instead of traditional mechanical Hadamard masks for optical modulation, and an InGaAs near infrared detector was used as the optic sensor. The original spectrum was recovered by fast Hadamard transform algrithms. The advantages of the spectrometer, such as high resolution, signal-noise-ratio, stability, sensitivity and response speed were proved by experiments, which indicated that it is very suitable for oil and food-safety applications.
Tailoring the Selectivity for Electrocatalytic Oxygen Evolution on Ruthenium Oxides by Zinc Substitution (2010)

Controlling gas emissions: Versatile control of the selectivity of an oxide electrocatalyst in the oxygen- and chlorine-evolution reactions was demonstrated by Zn substitution in RuO2 (see picture: O red, Cl green, Zn blue, Ru white). The incorporation of Zn into the rutile structure alters the cation sequence along the [001] direction and modifies the structure of the active sites for both gas-evolution processes.
The Biosynthesis and Processing of Proteins in the Mouse 7S Nerve Growth Factor Complex (1983)

Although a great deal is known about the structure of the nerve growth factor (NGF) and its role in the development and maintenance of sensory and sympathetic neurons, a number of significant questions remain to be answered concerning both the physiological sources of the factor and the mechanisms of its actions. Two main approaches to the first question, the identity of the tissues or cells that produce NGF, have involved the development of specific and highly sensitive radioimmunoassays for NGF (Thoenen et al., this volume) and the isolation of the cDNA for the NGF mRNA (Scott et al. 1983; Ullrich et al. 1983). It is reasonable to assume that the application of these two methodologies will lead quite rapidly to a better understanding of the sites of biosynthesis of NGF. A considerable amount of indirect evidence suggests that the target tissues of both sensory and sympathetic neurons are principal sites...
Universal Vaccines: Shifting to One for Many (2010)

Human vaccines, with their exquisite antigenic specificity, have greatly helped to eliminate or dramatically abate the incidence of a number of historical and current plagues, from smallpox to bacterial meningitis. Nonetheless, as new infectious agents emerge and the number of vaccine-preventable diseases increases, the practice and benefits of single-pathogen- or disease-targeted vaccination may be put at risk by constraints of timely production, formulation complexity, and regulatory hurdles. During the last influenza pandemic, extraordinary efforts by vaccine producers and health authorities have had little or no influence on disease prevention or mitigation. Recent research demonstrating the possibility of protecting against all influenza A virus types or even phylogenetically distant pathogens with vaccines based on highly conserved peptide or saccharide sequences is changing our paradigm. "Universal vaccine" strategies could be particularly advantageous to address protection from antibiotic-resistant bacteria and fungi for which no vaccine is currently available.
Theoretical Study of the Hydrogen Exchange Coupling in the Metallocene Trihydride Complexes [(C<sub>5</sub>H<sub>5</sub>)<sub>2</sub>MH<sub>3</sub>]<i><sup>n</sup></i><sup>+</sup> (M = Mo, W, <i>n</i> = 1; M = Nb, Ta, <i>n</i> = 0) (1996)

The effect on the hydrogen exchange coupling in metallocene [(C5H5)2MH3]n+ complexes under the substitution of the transition metal M is theoretically analyzed using a simple methodology that requires a modest number of ab initio electronic energy calculations that are used in a one-dimensional tunneling model within a basis set method. Concretely, the cases M = Mo, W (n = 1) and M = Nb, Ta (n = 0) whose hydrogen exchange couplings have been experimentally measured through the corresponding 1H NMR spectra are considered. Our results of the exchange couplings at different temperatures for the considered cases are in satisfactory agreement (within the correct order of magnitude) with experimental results. This agreement seems to confirm that the mechanism we previously established for some formally d4 iridium complexes that involved a dihydrogen-like transition state is also operative in the case of d0 transition metal trihydride complexes. As a matter of fact, it is the stability of the η2-H2 structure relative to the minimum energy trihydride that is the main parameter governing the magnitude of the exchange coupling.
A Low-Cost GPS Spoofing Detector Design for Internet of Things (IoT) Applications (2017)

The civilian Global Positioning System (GPS) is widely used for precise positioning, timekeeping, and synchronization in embedded systems. As a result, emerging digital infrastructure such as the Internet of Things (IoT) are dependent on GPS to locate and synchronize \textit{Things} in the network. From a security perspective, civilian GPS signals are vulnerable to malintent because they are not encrypted and can easily be spoofed. Several countermeasures have been proposed to detect GPS spoofing attacks, but most of them require extensive signal processing capabilities and additional electronic components to capture and analyze RF signals. These add-ons may not be available to IoT devices, and if present, they will affect the device\textquoteright s power budget significantly. Therefore, new techniques for spoofing detection and survival are required before integrating GPS receivers with IoT devices and other critical infrastructures where energy and computation power are limited. In this work, we propose a novel GPS spoofing detection scheme based on hardware oscillators. Our design depends on measuring the frequency drift and offset of a free-running crystal oscillator with respect to the GPS signals. In our secure GPS spoofing detector design the trust is intrinsic, \textit{i.e.}, the receiver only trusts the on-board free running local oscillator. Intrinsic properties of these oscillators exhibit a strong correlation with the authentic GPS signals and any anomaly in this measurement will indicate potential attacks on the received GPS signals. This proposed design is cost-effective, secure, backward compatible with existing receivers, and does not require additional RF circuitry or network connection with other clocks for detecting attacks.
The novel sodium channel modulator <scp>GS</scp>‐458967 (<scp>GS</scp>967) is an effective treatment in a mouse model of <i><scp>SCN</scp>8A</i> encephalopathy (2018)

Persistent sodium current modulators like GS967 may be an effective precision targeting strategy for SCN8A encephalopathy and other functionally similar channelopathies when elevated persistent sodium current is the primary dysfunction.
Monoclonal Antibody-based Genetic Immunotherapy (2004)

The clinical application potential of monoclonal antibodies concerns a wide range of diseases including, among others, viral infections, cancer and autoimmune diseases. Intravenous injection is a simple and obvious mode of administration of purified therapeutic antibodies to patients but may not always be appropriate for long-term treatments for a variety of reasons. One limitation concerns the elevated costs of recombinant proteins certified for human use. Moreover, hour-long infusions require a hospital environment and are often associated with mild to very severe side effects. This makes large-scale clinical applications of a number of monoclonal antibodies with demonstrated therapeutic activity impossible or, at least, severely compromised. In vivo production of therapeutic antibodies in patients, through either genetic modification of their tissues or implantation of antibody-producing cells, might represent an attractive alternative to overcome these drawbacks. Moreover, this method should also provide other benefits. Continuous and sustained delivery of antibodies at a low, but therapeutic level should prevent, or at least delay, induction of neutralizing anti-idiotypic immune responses, which sometimes develop when massive doses of purified immunoglobulins are repeatedly injected into patients. Additionally, it should also limit variations in the bioavailability of therapeutic antibodies that are often detrimental to the efficacy of treatments. The present review reports on the recent developments of gene/cell therapies aiming at the in vivo production and systemic delivery of monoclonal antibodies with the final goal of treating severe chronic diseases.
Structural Organization of Virulence-Associated Plasmids of <i>Yersinia pestis</i> (1998)

The complete nucleotide sequence and gene organization of the three virulence plasmids from Yersinia pestis KIM5 were determined. Plasmid pPCP1 (9,610 bp) has a GC content of 45.3% and encodes two previously known virulence factors, an associated protein, and a single copy of IS100. Plasmid pCD1 (70,504 bp) has a GC content of 44.8%. It is known to encode a number of essential virulence determinants, regulatory functions, and a multiprotein secretory system comprising the low-calcium response stimulation that is shared with the other two Yersinia species pathogenic for humans (Y. pseudotuberculosis and Y. enterocolitica). A new pseudogene, which occurs as an intact gene in the Y. enterocolitica and Y. pseudotuberculosis-derived analogues, was found in pCD1. It corresponds to that encoding the lipoprotein YlpA. Several intact and partial insertion sequences and/or transposons were also found in pCD1, as well as six putative structural genes with high homology to proteins of unknown function in other yersiniae. The sequences of the genes involved in the replication of pCD1 are highly homologous to those of the cognate plasmids in Y. pseudotuberculosis and Y. enterocolitica, but their localization within the plasmid differs markedly from those of the latter. Plasmid pMT1 (100,984 bp) has a GC content of 50.2%. It possesses two copies of IS100, which are located 25 kb apart and in opposite orientations. Adjacent to one of these IS100 inserts is a partial copy of IS285. A single copy of an IS200-like element (recently named IS1541) was also located in pMT1. In addition to 5 previously described genes, such as murine toxin, capsule antigen, capsule anchoring protein, etc., 30 homologues to genes of several bacterial species were found in this plasmid, and another 44 open reading frames without homology to any known or hypothetical protein in the databases were predicted.
<i>Handbook of Mathematical Functions with Formulas, Graphs, and Mathematical Tables</i> (1988)

Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Twitter Facebook Reddit LinkedIn Tools Icon Tools Reprints and Permissions Cite Icon Cite Search Site Citation Milton Abramowitz, Irene A. Stegun, Robert H. Romer; Handbook of Mathematical Functions with Formulas, Graphs, and Mathematical Tables. Am. J. Phys. 1 October 1988; 56 (10): 958. https://doi.org/10.1119/1.15378 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAmerican Association of Physics TeachersAmerican Journal of Physics Search Advanced Search |Citation Search
Medium access control with a dynamic duty cycle for sensor networks (2004)

Energy conservation is a primary concern in sensor networks. Several MAC protocols have been proposed to address this concern. However, the tradeoff between power consumption and latency has not been thoroughly studied. In this paper, we propose a sensor medium access control protocol with dynamic duty cycle, DSMAC, which achieves a good tradeoff between the two performance metrics without incurring much overhead. Moreover, DSMAC is able to adjust its duty cycle with varying traffic conditions without assuming any prior knowledge of application requirements. Both analytical and simulation results have been presented in this paper.
Light-to-input nonlinearities in an R-LED series network (1992)

The light-to-current (L-I) and light-to-voltage (L-V) differential nonlinearities in the simple network of a customary LED and an external resistor R in series are analyzed and calculated theoretically and compared with experimental data. Particular emphasis is placed on the influence of the log-arithmetic slope nu of the L-I characteristic and the bias current I upon the ratio of the corresponding nonlinearity parameters. It is thus deduced that, for a given optical power P, over superlinear portions of the L-I curve ( nu >1) the L-I linearity is typically better than its corresponding L-V linearity. On the contrary, when the L-I dependence is sublinear ( nu <1) the voltage driving scheme may ensure for the R-LED network, or the LED alone, a local L-V response much more linear than the L-I response, provided that appropriate (optimum) I and/or R values are chosen.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Attribute-Distributed Learning: Models, Limits, and Algorithms (2010)

This paper introduces a framework for distributed learning (regression) on attribute-distributed data. First, the convergence properties of attribute-distributed regression with an additive model and a fusion center are discussed, and the convergence rate and uniqueness of the limit are shown for some special cases. Then, taking residual refitting (or <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">$L_{2}$</tex> </formula> boosting) as a prototype algorithm, three different schemes, Simple Iterative Projection, a greedy algorithm, and a parallel algorithm (with its derivatives), are proposed and compared. Among these algorithms, the first two are sequential and have low communication overhead, but are susceptible to overtraining. The parallel algorithm has the best performance, but has significant communication requirements. Instead of directly refitting the ensemble residual sequentially, the parallel algorithm redistributes the residual to each agent in proportion to the coefficients of the optimal linear combination of the current individual estimators. Designing residual redistribution schemes also improves the ability to eliminate irrelevant attributes. The performance of the algorithms is compared via extensive simulations. Communication issues are also considered: the amount of data to be exchanged among the three algorithms is compared, and the three methods are generalized to scenarios without a fusion center.
Activation of HSF and selective increase in heat-shock proteins by acute dexamethasone treatment (2000)

Heat-shock proteins (HSPs) are an important family of endogenous protective proteins, which increase in response to myocardial ischemia and other stresses. Overexpression of HSP72 is cardioprotective. We were interested in the regulation of heat-shock factor (HSF), the transcription factor for HSP genes. Previously we have observed that the inflammatory cytokine tumor necrosis factor-alpha increases HSP72 levels and postulated that dexamethasone might effect the heat shock response. In the adult rat cardiac myocyte we found that treatment with either low (10 microM)- or high (100 microM)-dose dexamethasone activated HSF by 2-6 h as determined by gel shift assay without evidence of cytotoxicity. Although HSF activation is a key step in expression of HSP72, this may not result in an increase in HSP72. We found that 10 microM dexamethasone increased HSP72 38%, and 100 microM dexamethasone increased HSP72 62% (P < 0.05). HSP27 and HSP60 were unchanged. The selective increase in HSP72 was associated with protection of the cardiac myocytes from hypoxia and reoxygenation. We conclude that dexamethasone is a novel inducer of the heat shock response.