gebhart/patrepeval huggingface dataset:
Selectively primed adaptive driver RDA (SPAD‐RDA): An improved method for subtractive hybridization (2003)

A modification of the Representational Difference Analysis (RDA) method for subtractive hybridization, termed Selectively Primed Adaptive Driver (SPAD) RDA, is described. It differs from conventional RDA primarily in the manner by which initial driver (D) and tester (T) amplicon complexities are determined, and by optimizing the composition of D with respect to T for each round of subtraction. Total nucleic acid is extracted from serum or plasma and converted to double-stranded DNA/cDNA. A polymerase chain reaction (PCR) primer containing a selective nucleotide(s) at its 3'-end is used to generate amplicons of reduced complexity. Parallel subtractions are carried out, D vs. T (DT) for enrichment of tester-unique sequences and D vs. D (Driver Control or DC) to generate an optimized driver for use in the subsequent round. Following each round, agarose gel electrophoresis is used to visually identify any DT-unique bands through a side-by-side comparison of DT and DC subtraction products. In comparison to conventional RDA, SPAD-RDA achieved greater enrichment of viral sequences from an HCV infected chimpanzee, resulting in isolation of 13.7% of the viral genome, and an overall enrichment for HCV sequences of 239-fold. Virus fragments were also obtained from an HCV-infected human sample subtracted against non-paired human driver sequences. J. Med. Virol. 71:150-159, 2003.
<title>Massively parallel image restoration</title> (1991)

An image restoration method that performs piecewise smooth restorations on images corrupted with very high noise levels is presented. The restoration is based on a Markov random field (MRF) model using a neural network sigmoid nonlinearity between pixels to produce a restoration with sharp boundaries while providing noise reduction. The model is currently implemented using an efficient deterministic search algorithm that typically requires less than 200 iterations in a digital computer simulation. The algorithm is able to restore images with up to 71% of the pixels corrupted with sensor noise (non-gaussian). Results from simulation indicate that the MRF restoration is capable of operating at signal-to-noise ratios 5 to 6 dB lower than the median filtering. The same model can be applied to a large number of sensor measurements (Doppler, intensity, passive infrared, range, and video sensors) by simply adjusting a single parameter. This is especially relevant for hardware implementation, since a single chip can be used for processing a wide variety of imagery. The model has a massively parallel architecture with local neighbor interactions (four nearest neighbors), and can be implemented on a large parallel computer or a custom analog VLSI chip. Implementation of the model in analog VLSI would allow video rate restoration of 512 X 512 pixel images.
Aggregated modeling of thermostatic loads in demand response: A systems and control perspective (2011)

Demand response is playing an increasingly important role in smart grid research and technologies being examined in recently undertaken demonstration projects. The behavior of load as it is affected by various load control strategies is important to understanding the degree to which different classes of end-use load can contribute to demand response programs at various times. This paper focuses on developing aggregated control models for a homogeneous population of thermostatically controlled loads. The different types of loads considered in this paper include, but are not limited to, water heaters and HVAC units. The effects of demand response and user over-ride on the load population dynamics are investigated. The controllability of the developed lumped models is validated which forms the basis for designing different control strategies.
One-Step, Nonenzymatic Synthesis of <i>O</i>-Acetyl-ADP-ribose and Analogues from NAD and Carboxylates (2011)

O-Acetyl-ADP-ribose (OAADPR) is a metabolite produced from nicotinamide adenine dinucleotide (NAD) as a product of sirtuin-mediated protein deacetylation. We present here a simple, one-step, nonenzymatic synthesis of OAADPR from NAD and sodium acetate in acetic acid. We extended the reaction to other carboxylic acids, demonstrating that the reaction between NAD and nonaqueous carboxylate buffers produces mixtures of the corresponding 2'- and 3'-carboxylic esters.
Smoothed Sarsa: Reinforcement learning for robot delivery tasks (2009)

Our goal in this work is to make high level decisions for mobile robots. In particular, given a queue of prioritized object delivery tasks, we wish to find a sequence of actions in real time to accomplish these tasks efficiently. We introduce a novel reinforcement learning algorithm called Smoothed Sarsa that learns a good policy for these delivery tasks by delaying the backup reinforcement step until the uncertainty in the state estimate improves. The state space is modeled by a Dynamic Bayesian Network and updated using a Region-based Particle Filter. We take advantage of the fact that only discrete (topological) representations of entity locations are needed for decision-making, to make the tracking and decision making more efficient. Our experiments show that policy search leads to faster task completion times as well as higher total reward compared to a manually crafted policy. Smoothed Sarsa learns a policy orders of magnitude faster than previous policy search algorithms. We demonstrate our results on the Player/Stage simulator and on the Pioneer robot.
Highly birefringent microstructured fibers with enhanced sensitivity to hydrostatic pressure (2010)

We designed, manufactured and characterized two birefringent microstructured fibers that feature a 5-fold increase in polarimetric sensitivity to hydrostatic pressure compared to the earlier reported values for microstructured fibers. We demonstrate a good agreement between the finite element simulations and the experimental values for the polarimetric sensitivity to pressure and to temperature. The sensitivity to hydrostatic pressure has a negative sign and exceeds -43 rad/MPa x m at 1.55 microm for both fibers. In combination with the very low sensitivity to temperature, this makes our fibers the candidates of choice for the development of microstructured fiber based hydrostatic pressure measurement systems.
Human dendritic cell activation by Neisseria meningitidis: phagocytosis depends on expression of lipooligosaccharide (LOS) by the bacteria and is required for optimal cytokine production (2004)

Group B Neisseria meningitidis is a human pathogen, for which a universally effective vaccine is still not available. Immune responses to bacteria are initiated by dendritic cells (DC), which internalize and process bacterial antigens for presentation to T cells. We show here that optimal IL-12 and TNF-alpha production by human monocyte derived DC in response to killed serogroup B N. meningitidis depends on physical contact and internalization of the bacteria by DC. The majority of DC producing cytokines had internalized N. meningitidis while inhibition of bacterial internalization markedly impaired IL-12 and TNF-alpha, but not IL-6 production. Internalization of N. meningitidis was shown to depend on lipooligosaccharide (LOS) expressed by the bacteria with poor internalization of LOS deficient bacteria compared to wild-type bacteria. Restoration of LOS biosynthesis in a LOS regulatory strain also restored both internalization and cytokine production and was enhanced in the presence of LPS binding protein (LBP). These results suggest that DC phagocytosis depends on expression of LOS within the bacteria and that optimal cytokine production, particularly IL-12, requires internalization of the bacteria. These findings have important implications for designing vaccines that will induce protective immune responses to group B N. meningitidis.
Evidence for Involvement of at Least Six Proteins in Adaptation of <i>Lactobacillus sakei</i> to Cold Temperatures and Addition of NaCl (2004)

Lactobacillus sakei is a lactic acid bacterium widely represented in the natural flora of fresh meat. The aim of this study was to analyze the differences in protein expression during environmental changes encountered during technological processes in which L. sakei is involved in order to gain insight into the ability of this species to grow and survive in such environments. Using two-dimensional electrophoresis, we observed significant variation of a set of 21 proteins in cells grown at 4 degrees C or in the presence of 4% NaCl. Six proteins could be identified by determination of their N-terminal sequences, and the corresponding gene clusters were studied. Two proteins belong to carbon metabolic pathways, and four can be clustered as general stress proteins. A phenotype was observed at low temperature for five of the six mutants constructed for these genes. The survival of four mutants during stationary phase at 4 degrees C was affected, and surprisingly, one mutant showed enhanced survival during stationary phase at low temperatures.
Exhaust Emission Control Through a Hydrogen Peroxide Fuel Augmentation System. (1996)

Abstract : A system for improving efficiency and reducing harmful emissions in an internal combustion engine and for allowing the engine to run in oxygen poor environments. An oxidant, such as hydrogen peroxide, is introduced into the induction air stream of the engine. A controller senses the temperature and oxygen level in the exhaust stream of the engine and operates a valve to vary the amount of oxidant introduced to maintain maximum efficiency and minimum emissions. The oxidant provides for near stoichiometric combustion to reduce combustion products and reduce the engine's air requirements. The reduced air requirements allow for operation of the engine in oxygen poor environments, such as operation at high altitudes. Water is added to the oxidant to cool the stoichiometric combustion temperature to prevent excessive engine wear and to further block the formation of oxides of nitrogen.
AC characterisation of thermal flow sensor with fluid characterisation feature (2011)

We have investigated the determination of flow speed and simultaneously gas concentration in a binary gas mixture. The fabrication process and characterization of a sensor element, based on the thermal principle, is presented in this paper. The sensor is equipped with an unsymmetrical 1D-array of temperature sensors and a heater. Time modulated heating is used to extract flow speed from thermal gas properties. Phase shift determines the thermal conductivity of the gas mixture. The accurate flow velocity can be calculated from amplitude measurement afterwards. Thermal conductivity can be already determined with an accuracy of 90%.
Waveguide modulators with extended linear dynamic range-a theoretical prediction (1990)

A novel modification of the directional coupler modulator is described that reduces the nonlinear distortion and improves the linear dynamic range. The calculated results indicate that the ratio of optical signal power to the spurious signal power of this device is 30-40 dB larger than that of a Mach-Zehnder interferometric modulator.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
High performance fused-type mode selective coupler for two-mode fiber devices (2002)

We demonstrate a high performance fused-type mode selective coupler that couples the LP11 mode of a two-mode fiber and the LP01 mode of a matching single-mode fiber, the phase-matching condition was satisfied by etching and pre-pulling of a two-mode fiber, the excess loss and the maximum coupling ratio of 0.15 dB and 92%, respectively, are achieved.
P2–060: Anti‐aggregation effect of AA‐peptide on beta‐amyloid peptides in Alzheimer's disease (2013)

Since the development of research in Alzheimer's diseases in 1990s, the disease was discovered close related to endogenous ß-Amyloid peptides, especially aggregated oligomers and fibrils of which neurotoxicity has been confirmed. Therefore, Inhibition of Aß, instead of blocking their production (e.g. secretase inhibitors), is rather promising in pharmaceutical research in AD. However, the identification of short sequences that effectively inhibit or prevent aggregation is still challenging. Taking advantage of the combinatory chemistry, we designed and screened 400,000 of N-Acetylated-N-Aminoethyl peptides (AApeptide, unnatural peptidomimetics developed by our group) targeting the anti-aggregation effect of ß-amyloid peptide. In this study, both the effect of anti-aggregation of AApeptide and also their potential on anti-Alzheimer's diseases was evaluated. Herein, one bead one compound AApeptide library was designed for the selection of ligand that targets on Abeta. Selected AApeptides was evaluated for their effect on Aß1–40 monomer peptides in their progress of aggregation. Methods are listed as follows: 1. Thioflavin T assay, ß-sheet formation assay for anti-aggregation screening. 2. TEM assay was used to image the morphological change of Aß fibrils with/without presence of AApeptide. 3. Western Blot, in vitro aggregation of HFIP treated Aß1–40 was produced to aggregate under room temperature, theformation of oligomers were detected using 6E10 anti-Aß antibodies. Following LI-COR western was used and quantification was performed for evaluation. Tissue culture, MTT assay on Neuroblastoma cell to test their toxicity. Kit using commercial available methods from Roche. One of screened AApeptides shows great potential of anti-aggregation at concentration of 2.5μM at 1:1 ratio with Abeta. TEM assay also confirmed clearance of Aß fibrils in the presence of AApeptide. Toxicity of neuroblastma cells of AApeptide is not obvious at effective concentration.
Rheologically Stable, Nontoxic, High-Temperature, Water-Based Drilling Fluid (1997)

Summary An exceptionally stable, high-temperature, water-based drilling fluid has been developed based on a fundamental redesign of drilling fluid components and functions, while still using commercially available materials. Rheological stability was characterized by extensive Fann 50C low-shear-rate viscosity vs. temperature studies and supporting viscoelastic rheological data. The fluid has been used in both offshore and land applications, at temperatures as high as 420°F and densities as high as 15.5 lbm/gal.
Synthetic Glycosylated Ether Glycerolipids as Anticancer Agents (2015)

Glycosylated antitumor ether lipids (GAELs) are a class of synthetic antitumor ether lipids (AELs) with a sugar moiety in place of the phosphocholine found in the prototypical AEL, edelfosine. This chapter reviews the development of GAELs as antitumor agents. Studies on structure–activity relationships, mechanism of induction of cell death, metabolism, selectivity against cancer cells, toxicity, hemolysis and thrombogenic effects are discussed. The requirements for significant cytotoxic activity include a glycerol moiety, a cationic sugar other than mannose and an O- or C-glycosidic bond with either α- or β-configuration. Compounds with S- and N-glycosidic linkages are not very active. The most active GAEL to date, 1-O-hexadecyl-2-O-methyl-3-O-(2′-amino-2′-deoxy-α-d-galactopyranosyl)-sn-glycerol, displays greater in vitro activity than edelfosine, the AEL “gold standard”. The unique properties of GAELs as antitumor agents include their apoptotic-independent mechanism of inducing cell death and the ability to kill cancer stem cells. These characteristics of GAELs offer the potential for their development into chemotherapeutic agents to prevent the recurrence of tumors as well as for treatment against drug-resistant cancers.
Characterization of a Novel Fructosyltransferase from <i>Lactobacillus reuteri</i> That Synthesizes High-Molecular-Weight Inulin and Inulin Oligosaccharides (2002)

Fructosyltransferase (FTF) enzymes produce fructose polymers (fructans) from sucrose. Here, we report the isolation and characterization of an FTF-encoding gene from Lactobacillus reuteri strain 121. A C-terminally truncated version of the ftf gene was successfully expressed in Escherichia coli. When incubated with sucrose, the purified recombinant FTF enzyme produced large amounts of fructo-oligosaccharides (FOS) with beta-(2-->1)-linked fructosyl units, plus a high-molecular-weight fructan polymer (>10(7)) with beta-(2-->1) linkages (an inulin). FOS, but not inulin, was found in supernatants of L. reuteri strain 121 cultures grown on medium containing sucrose. Bacterial inulin production has been reported for only Streptococcus mutans strains. FOS production has been reported for a few bacterial strains. This paper reports the first-time isolation and molecular characterization of (i) a Lactobacillus ftf gene, (ii) an inulosucrase associated with a generally regarded as safe bacterium, (iii) an FTF enzyme synthesizing both a high molecular weight inulin and FOS, and (iv) an FTF protein containing a cell wall-anchoring LPXTG motif. The biological relevance and potential health benefits of an inulosucrase associated with an L. reuteri strain remain to be established.
Compressive Spectral Imaging via Polar Coded Aperture (2016)

A compressive spectral imager based on a polar coded aperture and a continuous variable circular bandpass filter is proposed for spinning munitions. As the imager rotates with the munition, compressive projections are sequentially captured with embedded spatial and spectral modulation. The polar coded aperture design is introduced, aiming at optimizing the sensing process. Both discrete and continuous rotation models of the proposed imager are derived and used to characterize the compressive imager. Computer simulations validate the computational models and the reconstruction algorithm.
A redox-controlled electrolyte for plasmonic enhanced dye-sensitized solar cells (2017)

Plasmonic enhanced dye-sensitized solar cells (DSSCs) with metallic nanostructures suffer from corrosion problems, especially with the presence of the iodine/triiodide redox couple in the electrolyte. Herein, we introduce an alternative approach by compensating the corrosion with a modified liquid electrolyte. In contrast to the existing method of surface preservation for plasmonic nanostructures, the redox-controlled electrolyte (RCE) contains iodoaurate intermediates, i.e. gold(i) diiodide (AuI<sub>2</sub><sup>-</sup>) and gold(iii) tetraiodide (AuI<sub>4</sub><sup>-</sup>) with optimal concentrations, such that these intermediates are readily reduced to gold nanoparticles during the operation of DSSCs. As corrosion and redeposition of gold occur simultaneously, it effectively provides corrosion compensation to the plasmonic gold nanostructures embedded in the photoanode. Cycling tests of the specific amount of gold contents in the RCE of DSSCs support the fact that the dissolution and deposition of gold are reversible and repeatable. This gold deposition on the TiO<sub>2</sub> photoanode results in forming a Schottky barrier (SB) at the metal-semiconductor interface and effectively inhibits the recombination of electron-hole pairs. Therefore, the RCE increases the short-circuit current, amplifies the open-circuit voltage, and reduces the impedance of the TiO<sub>2</sub>/dye interface. The power conversion efficiency of DSSCs was improved by 57% after incorporating the RCE.
Abstract 1201: Anti-B7-H3 antibody-drug conjugates as potential therapeutics for solid cancer (2016)

Abstract Introduction: Monoclonal antibodies (mAbs) were generated via a target-unbiased approach based on intact cell immunization with cell lines, fetal progenitor cells, and cancer stem cells. An immunohistochemical screen for cancer-specific candidates identified a panel of anti-B7-H3 (CD276) mAbs with highly differential tumor-versus-normal tissue binding. B7-H3 expression was observed in tumor epithelium as well as tumor-associated vasculature and stroma. Consistent with our findings, B7-H3 has been reported to be overexpressed in a growing number of solid cancers, including breast, lung, pancreatic, prostate, kidney, and colon cancer, as well as melanoma and glioblastoma. Furthermore, overexpression of B7-H3 has been correlated with disease severity and poor outcome in a number of these cancer types. A humanized version of an anti-B7-H3 mAb engineered with an enhanced Fc domain (enoblituzumab or MGA271) and a humanized Dual-Affinity Re-Targeting (DART®) protein that recognizes both B7-H3 and CD3 and redirects T cells to kill B7-H3-expressing cells (MGD009) are being investigated in Phase 1 clinical studies. In this nonclinical study, we evaluated the therapeutic potential of anti-B7-H3 antibody-drug conjugates (ADCs) toward B7-H3-expressing solid cancers. Methods: A panel of anti-B7-H3 mAbs was screened for internalization and a subset of mAbs that were efficiently internalized by tumor cells was identified. These mAbs were converted to ADCs via chemical conjugation; in vitro and in vivo activity studies were then conducted with a range of tumor cell lines representing human cancer types that overexpress B7-H3. Results: The anti-B7-H3 ADCs exhibited specific, dose-dependent cytotoxicity toward B7-H3-positive tumor cell lines in vitro, including breast, lung, ovarian, pancreatic, and prostate cancer lines, with IC50 values generally in the sub-nM range. Cytotoxicity was not observed with cell lines lacking B7-H3 expression. The anti-B7-H3 ADCs exhibited potent antitumor activity in vivo, resulting in tumor stasis and tumor regression in mice bearing B7-H3-positive human breast, lung, and ovarian tumor xenografts. Conclusion: Anti-B7-H3 ADCs exhibited dose-dependent cytotoxicity in vitro and potent antitumor activity in vivo toward a range of B7-H3-expressing tumor cell lines representing cancer types that overexpress B7-H3. Our findings demonstrate that ADCs targeting B7-H3 may serve as potential therapeutics for B7-H3-expressing solid cancers. Citation Format: Deryk Loo, Juniper A. Scribner, Thomas Son, Jeff Hooley, Timothy Hotaling, Michael Chiechi, Pam Li, Anushka De Costa, Yan Chen, Ann Easton, Francine Z. Chen, Bhaswati Barat, Valentina Ciccarone, James Tamura, Mark Kubik, Scott Koenig, Syd Johnson, Paul A. Moore, Ezio Bonvini. Anti-B7-H3 antibody-drug conjugates as potential therapeutics for solid cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1201.
Overshadow (2008)

Commodity operating systems entrusted with securing sensitive data are remarkably large and complex, and consequently, frequently prone to compromise. To address this limitation, we introduce a virtual-machine-based system called Overshadow that protects the privacy and integrity of application data, even in the event of a total OScompromise. Overshadow presents an application with a normal view of its resources, but the OS with an encrypted view. This allows the operating system to carry out the complex task of managing an application's resources, without allowing it to read or modify them. Thus, Overshadow offers a last line of defense for application data.Overshadow builds on multi-shadowing, a novel mechanism that presents different views of physical memory, depending on the context performing the access. This primitive offers an additional dimension of protection beyond the hierarchical protection domains implemented by traditional operating systems and processor architectures.We present the design and implementation of Overshadow and show how its new protection semantics can be integrated with existing systems. Our design has been fully implemented and used to protect a wide range of unmodified legacy applications running on an unmodified Linux operating system. We evaluate the performance of our implementation, demonstrating that this approach is practical.