gebhart/patrepeval huggingface dataset:
Optimal Construction of Redundant Multicast Trees in Directed Graphs (2009)

In this paper, we consider the problem of protection of multicast connections against single link or node failures using redundant multicast trees (RMTs). RMTs connect the source node of a multicast connection to all its destinations in such a way that in the event of a single link or node failure in the network, every destination node is still connected to the source node in at least one of the two trees. Construction of RMTs has been studied extensively for undirected graphs, but not for directed graphs. Computing RMTs in directed graphs can be important in networks, for instance, where link capacity is available in one direction but not the other. Also, none of the schemes proposed in previous work provide a solution for finding optimal (minimal-cost) RMTs even for weighted undirected graphs. We show that a whole class of earlier schemes that are based on the concept of ear-decomposition cannot find optimal redundant trees in certain network topologies. To our knowledge, we are the first to consider the problem of finding optimal RMTs in directed graphs. We present a novel efficient scheme for construction of optimal RMTs in networks modeled as weighted undirected as well as directed graphs.
Retinoic acid induction of human cellular retinoic acid-binding protein-II gene transcription is mediated by retinoic acid receptor-retinoid X receptor heterodimers bound to one far upstream retinoic acid-responsive element with 5-base pair spacing. (1994)

We previously cloned the human cellular retinoic acid-binding protein-II (CRABPII) gene and demonstrated a rapid and transient increase in retinoic acid (RA)-dependent transcription in cultured human skin fibroblasts. To determine whether retinoid receptors could regulate CRABPII gene transcription, cotransfection experiments were performed. When RAR alpha was cotransfected in Cos-1 cells with a reporter construct containing -8.0 kilobases of the upstream region, an 18-fold RA induction was obtained. By deletion analysis, a region essential for RA induction located approximately -5.6 kilobases upstream from the human CRABPII gene start site was identified. Sequencing and mutational analysis identified a direct repeat (GGGTCAttggaAGGACA) with 5-base pair spacing (DR-5) that is critical for RA-mediated induction of human CRABPII gene transcription. This is different from the mouse CRABPII gene in which two RAREs (DR-1 and DR-2) are required for full activation. To determine whether RAR and RXR can bind to the human CRABPII RARE, gel retardation assays were performed. In these assays, in vitro translated RAR alpha and RXR alpha were found to bind efficiently as heterodimers in gel retardation assays; weak binding of RAR alpha homodimers was observed. These data demonstrate that the human CRABPII gene is regulated by a far upstream RARE that most efficiently binds RAR-RXR heterodimers.
New DAG and cAMP Sensors Optimized for Live-Cell Assays in Automated Laboratories (2015)

Protein-based, fluorescent biosensors power basic research on cell signaling in health and disease, but their use in automated laboratories is limited. We have now created two live-cell assays, one for diacyl glycerol and another for cAMP, that are robust (Z' > 0.7) and easily deployed on standard fluorescence plate readers. We describe the development of these assays, focusing on the parameters that were critical for optimization, in the hopes that the lessons learned can be generalized to the development of new biosensor-based assays.
GIP-Based Therapeutics for Diabetes and Obesity (2008)

Glucose-dependent insulinotropic polypeptide (GIP or gastric inhibitory polypeptide) is a gut-derived incretin hormone which regulates glucose-induced insulin secretion. In addition to its actions on pancreatic beta-cells, GIP exerts a range of secondary extrapancreatic activities, which further augments its antihyperglycaemic properties. As such, GIP has attracted attention as a potential therapeutic agent for the treatment of diabetes, obesity and related metabolic disorders. However, a major drawback in utilising GIP as a therapeutic is its relatively short biological half-life due to degradation by the ubiquitous enzyme dipeptidylpeptidase-IV (DPP-IV) and rapid renal clearance. Consequently, efforts are presently focused on developing more stable and longer-acting forms of GIP which are resistant to DPP-IV-mediated degradation and have improved pharmacokinetic properties. In essence, structural modifications of GIP through N-terminal modification, amino acid substitution and/or fatty acid derivatisation have been shown to generate analogues which exhibit a range of activities from potent agonist action to specific antagonism of native GIP. The purpose of this review is to highlight recent advances in the development of GIP-based therapeutics and their potential in the treatment of type 2 diabetes and obesity. Keywords: DPP-IV, glucose-dependent insulinotropic polypeptide (GIP), GIP analogues, insulin secretion, obesity, type 2 diabetes
Cationic polymerization of isobutyl vinyl ether: livingness enhancement by dialkyl sulfides (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCationic polymerization of isobutyl vinyl ether: livingness enhancement by dialkyl sulfidesChang Gi Cho, Ben Ami Feit, and Owen W. WebsterCite this: Macromolecules 1990, 23, 7, 1918–1923Publication Date (Print):April 1, 1990Publication History Published online1 May 2002Published inissue 1 April 1990https://pubs.acs.org/doi/10.1021/ma00209a006https://doi.org/10.1021/ma00209a006research-articleACS PublicationsRequest reuse permissionsArticle Views898Altmetric-Citations162LEARN 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
A Proposed Carrier-Induced Electrooptical Switch In III-V Quantum-Well Waveguides (1988)

Lossless guided-wave switches with more than 30 dB of crosstalk-isolation are proposed and analyzed. The switches are comprised of branched channel waveguides with laser-like cross-sections. Optical gain, sufficient to overcome power-splitting losses, is provided by carrier-injection currents. Due to its low-noise properties, the single-quantum-well structure is found to be optimum for cascading switches into a multi-stage network. A lossless 1 x N network with 1024 switched outputs should be feasible.
Genome Sequence of Propionibacterium acidipropionici ATCC 55737 (2016)

Propionibacterium acidipropionici produces propionic acid as its main fermentation product. Traditionally derived from fossil fuels, environmental and sustainable issues have revived the interest in producing propionic acid using biological resources. Here, we present the closed sequence of Propionibacterium acidipropionici ATCC 55737, an efficient propionic acid producer.
Defense Against Primary User Emulation Attacks in Cognitive Radio Networks Using Advanced Encryption Standard (2014)

This paper considers primary user emulation attacks in cognitive radio networks operating in the white spaces of the digital TV (DTV) band. We propose a reliable AES-assisted DTV scheme, in which an AES-encrypted reference signal is generated at the TV transmitter and used as the sync bits of the DTV data frames. By allowing a shared secret between the transmitter and the receiver, the reference signal can be regenerated at the receiver and used to achieve accurate identification of the authorized primary users. In addition, when combined with the analysis on the autocorrelation of the received signal, the presence of the malicious user can be detected accurately whether or not the primary user is present. We analyze the effectiveness of the proposed approach through both theoretical analysis and simulation examples. It is shown that with the AES-assisted DTV scheme, the primary user, as well as malicious user, can be detected with high accuracy under primary user emulation attacks. It should be emphasized that the proposed scheme requires no changes in hardware or system structure except for a plug-in AES chip. Potentially, it can be applied directly to today's DTV system under primary user emulation attacks for more efficient spectrum sharing.
2-Methylene-19-nor-(20S)-1,25-dihydroxyvitamin D3 Potently Stimulates Gene-specific DNA Binding of the Vitamin D Receptor in Osteoblasts (2003)

2-Methylene-19-nor-(20S)-1,25-dihydroxyvitamin D3 (2MD) is a highly potent analog of 1,25-dihydroxyvitamin D3 (1,25(OH)2D3) whose actions are mediated through the vitamin D receptor (VDR). In this report, we have replicated this increased potency of 2MD in vitro using osteoblastic cells and explored its underlying molecular mechanism. 2MD stimulates the expression of several vitamin D-sensitive genes including 25-hydroxyvitamin D3-24 hydroxylase (Cyp24), osteopontin and receptor activator of NF kappa B ligand and suppresses osteoprotegerin at concentrations two logs lower than that for 1,25(OH)2D3. 2MD is also more potent in stimulating transfected chimeric reporter genes under either Cyp24 or the osteocalcin promoter control. Enhanced potency is retained regardless of medium serum content. Interestingly, the uptake of both 1,25(OH)2D3 and 2MD into cells is similar, as is their rapid association with the VDR. This indicates that comparable levels of occupied VDR do not elicit equivalent levels of transactivation. Using chromatin immunoprecipitation (ChIP), however, we observed a strong correlation between DNA-bound receptor and the level of induced transcription suggesting a 2MD-induced increase in affinity of the VDR for DNA. Additional studies using a mammalian two-hybrid system and ChIP indicate that 2MD is also more potent in promoting interaction with RXR and the coactivators SRC-1 and DRIP205. Finally, protease digestion studies revealed a unique VDR conformation in the presence of 2MD. These studies suggest that the molecular mechanism of 2MD potency is due to its ability to promote enhanced levels of specific DNA binding by the VDR and could suggest possible explanations for the tissue- and gene-selective actions of 2MD.
Lithography process optimization using linear superposition of commonly available illumination modes (2006)

The objective of this work is to demonstrate a simple Linear Superposition approach to creating an optimized illumination scheme from commonly available apertures (e.g. conventional, annular, quadrupole, dipole, etc.) that meet a variety of lithographic process metrics. Previous authors have demonstrated a variety of approaches to optimize the illumination for a given lithographic process. One common example is to use an optimized illumination for a specific pitch range and breaking the exposure into multiple reticles designed to print only nested or isolated features. A second example that has been widely demonstrated is to develop a single custom illuminator, which requires long lead times for delivery and a large capital investment. The true on-wafer performance of this custom illuminator can only be determined post-installation, providing limited ability to verify the simulation work a priori. The linear superposition method described here produces an optimal illumination scheme for a given photolithographic process. The success of this approach is due to the acceptably small nature of the electric field interaction terms between individual illumination modes allowing a multiple-exposure system to model a composite source. Images from optimized sub-components can be added to generate a composite image that is superior overall to any one process alone. After each exposure in a multiple exposure system there is a latent image that is only developable after a specific energy or dose level has been surpassed. It is the additive process of these latent images that creates the composite image. The composite image has the additive properties of the sub-components according to their dose fractions. Once the optimal process and dose split have been determined, it is straightforward to create a composite aperture to produce the same process by a single exposure. The composite aperture is the addition of the multiple sub-components with the relative transmission of each related to the illuminated surface area for systems designed to deliver uniform brightness. This approach produces superior pattern fidelity and an optimized common lithography process without the pitfalls of any one of the sub-component illumination modes.
Compact Feedback for MIMO-OFDM Systems over Frequency Selective Channels (2005)

Transmit beamforming can improve the performance of multiple-input multiple-output (MIMO) antenna systems. However, the feedback overhead of beamforming matrixes may significantly reduce the FDD system throughput. Efficient feedback techniques were reported recently. However, their complexities can be prohibitively high for systems with large numbers of transmit antennas (M/sub t/) and spatial streams (M/sub s/) since numerous large matrix codebooks of Grassman manifold packing G(M/sub f/,M/sub s/) are required. In Roh et al. (2004), it is shown that the beamforming matrix can be parameterized by independent unit vectors. This implies that quantizing the matrix jointly is equivalent to quantizing the vectors separately. Firsts we show that the distributions of the unit vectors are isotropic on unit spheres. Secondly, a low-complexity, scalable quantization scheme is derived. The key innovation lies in the quantization of the large dimension unit vectors. Each large dimension unit vector is partitioned into smaller dimension vectors and quantized by small size codebooks designed for low dimension unit vectors, and the partition itself is quantized by a 3-bit codebook. Finally, an interpolation scheme is proposed for beamforming matrixes downsampled in frequency domain, which significantly reduces overhead for MIMO-OFDM systems. The missing beamforming vectors are interpolated along the geodesic connecting two fed back vectors on a unit sphere. Simulations demonstrate that the overhead in IEEE 802.16d/e draft can be reduced by a factor of three using the proposed scheme.
Development and testing of paraffin-based hybrid rocket fuels (2001)

The classical hybrid combustion theory is generalized to solid fuels that form a liquid layer on their burning surface. For several classes of liquefying fuels, the layer is hydrodynamically unstable leading to substantial droplet entrainment from the melt layer into the gas stream. The susceptibility of a given fuel to this shear driven instability increases with decreasing viscosity and surface tension of the melt layer. The entrainment mass transfer, which acts in addition to the conventional gasification mechanism, is not affected by the blocking phenomenon induced by blowing from the surface. For practical oxidizer flux levels encountered in hybrid rocket applications, droplet entrainment can dominate direct gasification. Such liquefying fuels can exhibit greatly increased surface regression rates compared to classical materials such as HTPB. One application of the theory is to solid cryogenic hybrids, which utilize frozen materials for the solid propellant. The theory successfully predicts why high regression rates are observed in tests of cryogenic solid pentane, solid pentane and solid oxygen. In addition, the theory explains the dependence of the burning rates of other tested cryogenic materials on the physical properties of the liquid layer. The theory also leads to the conclusion that certain non-cryogenic materials such as paraffin and PE waxes will also exhibit high regression rates. This important result is confirmed by lab scale tests performed at Stanford University on a paraffin-based fuel.
Localized synthesis of silicon nanowires (2004)

Localized resistive heating of microstructures has been used to activate vapor-deposition synthesis of silicon nanowires in a room-temperature chamber. The process is localized, selective, scalable and compatible with on-chip microelectronics and, in addition, removes necessity of post-synthesis assembly of nanowires to accomplish integrated nano-electromechanical systems. Synthesized nanowires with dimensions of 30-80 nm in diameter and up to 10 /spl mu/m in length have been successfully demonstrated and growth rates of up to 1/spl mu/m/min have been observed. This new class of manufacturing method enables direct integration of nanotechnology with larger-scale systems for potential sensing and actuation applications.
Subsurface flaw detection in reflective materials by thermal-transfer imaging (1991)

A thermal imaging apparatus is described for the nondestructive detection of subsurface defects in materials that would not usually lend themselves to thermal imaging because of their low emissivity and high susceptibility to background reflection noise. This is accomplished by transferring the thermal image produced by surface temperature perturbation of the workpiece material to a high emissivity material with which it is continuously brought in contact. The transferred thermal image may be observed by a suitable infrared device, resulting in a high radiance image with minimum reflectivity or variable emissivity noise. Numerical simulations, as well as experimental results, are presented.
C <sub>6</sub> Test as an Indicator of Therapy Outcome for Patients with Localized or Disseminated Lyme Borreliosis (2003)

Management of Lyme disease would benefit from a test to assess therapy outcome. Such a test could be employed to ascertain if treatment of early Lyme disease was successful and would be helpful to clinicians assessing patients with lingering posttreatment symptoms. We reported recently that levels of the antibody to C(6), a Borrelia burgdorferi-derived peptide that is used as an antigen in the C(6)-Lyme diagnostic test, declined after successful antibiotic treatment of Lyme borreliosis patients. We assessed retrospectively the change in anti-C(6) antibody titers in 131 patients with either early localized disease (erythema migrans) or disseminated disease. All of these patients were treated with antibiotics and were free of the clinical signs shown at presentation within 12 weeks after the initiation of treatment. Decreases in reciprocal geometric mean titers (rGMT) of the anti-C(6) antibody were quantified for the subpopulation of 45 patients whose baseline rGMT were >/=80 and whose second serum specimens were obtained at least 6 months after the baseline specimen. Eighty percent of this patient group (36 of 45) experienced a >/=4-fold decrease in their rGMT (P < 0.0003). These results suggest that a change in the anti-C(6) antibody titer may serve as an indicator of therapy outcome for patients with localized or disseminated Lyme borreliosis.
Genome-wide analysis of influenza viral RNA and nucleoprotein association (2017)

Influenza A virus (IAV) genomes are composed of eight single-stranded RNA segments that are coated by viral nucleoprotein (NP) molecules. Classically, the interaction between NP and viral RNA (vRNA) is depicted as a uniform pattern of 'beads on a string'. Using high-throughput sequencing of RNA isolated by crosslinking immunoprecipitation (HITS-CLIP), we identified the vRNA binding profiles of NP for two H1N1 IAV strains in virions. Contrary to the prevailing model for vRNA packaging, NP does not bind vRNA uniformly in the A/WSN/1933 and A/California/07/2009 strains, but instead each vRNA segment exhibits a unique binding profile, containing sites that are enriched or poor in NP association. Intriguingly, both H1N1 strains have similar yet distinct NP binding profiles despite extensive sequence conservation. Peaks identified by HITS-CLIP were verified as true NP binding sites based on insensitivity to DNA antisense oligonucleotide-mediated RNase H digestion. Moreover, nucleotide content analysis of NP peaks revealed that these sites are relatively G-rich and U-poor compared to the genome-wide nucleotide content, indicating an as-yet unidentified sequence bias for NP association in vivo. Taken together, our genome-wide study of NP-vRNA interaction has implications for the understanding of influenza vRNA architecture and genome packaging.
A new Variable step-Size strategy for adaptive networks (2011)

Several algorithms have been developed over the last few years that utilize the distributed nature of an ad hoc wireless sensor network to estimate a certain parameter of interest. One such algorithm is called the diffusion least mean squares (DLMS) algorithm. This algorithm estimates the parameter of interest using the cooperation between neighboring sensors within the network. Among the various algorithms that improved the performance of the DLMS algorithm is the Variable Step-Size DLMS (VSSDLMS) algorithm. The VSSDLMS algorithm used the instantaneous error energy to update the step-size. The algorithm showed remarkable improvement. In this work, a new strategy for updating the step-size by utilizing the distributed nature of the network is presented. The proposed algorithm was compared to other similar algorithms and found to exhibit better performance.
RF photonic receiver with Zooming capability (2015)

We have demonstrated an RF photonic receiver with agile tunable reception center frequency as well as bandwidth. The RF Q-factor of the receiver was modified from unity to 30,000, and the frequency was changed from 30 MHz to 3 GHz. The device is realized for VHF/UHF tactical radio applications; however, the technology allows modifying the center frequency of the receiver within much broader frequency range. The receiver front-end paves a way for development of a new generation of agile multi-octave tunable RF photonic devices. This research was supported by the Office of Naval Research (Contract #N00014-12-C-0166).