gebhart/patrepeval huggingface dataset:
Selective G-Quadruplex DNA Recognition by a New Class of Designed Cyanines (2013)

A variety of cyanines provide versatile and sensitive agents acting as DNA stains and sensors and have been structurally modified to bind in the DNA minor groove in a sequence dependent manner. Similarly, we are developing a new set of cyanines that have been designed to achieve highly selective binding to DNA G-quadruplexes with much weaker binding to DNA duplexes. A systematic set of structurally analogous trimethine cyanines has been synthesized and evaluated for quadruplex targeting. The results reveal that elevated quadruplex binding and specificity are highly sensitive to the polymethine chain length, heterocyclic structure and intrinsic charge of the compound. Biophysical experiments show that the compounds display significant selectivity for quadruplex binding with a higher preference for parallel stranded quadruplexes, such as cMYC. NMR studies revealed the primary binding through an end-stacking mode and SPR studies showed the strongest compounds have primary KD values below 100 nM that are nearly 100-fold weaker for duplexes. The high selectivity of these newly designed trimethine cyanines for quadruplexes as well as their ability to discriminate between different quadruplexes are extremely promising features to develop them as novel probes for targeting quadruplexes in vivo.
Trichokirin, a ribosome‐inactivating protein from the seeds of <i>Trichosanthes kirilowii</i> Maximowicz (1988)

A protein, here named trichokirin, was extracted from the seeds of Trichosanthes kirilowii and purified by ion-exchange and gel-filtration chromatography. Trichokirin is a basic glycoprotein of apparent relative molecular mass of 27,000 with a strong ribosome-inactivating activity. Alignment of the trichokirin, trichosanthin and momordin N-terminal sequences shows a substantial degree of homology. Trichokirin was conjugated to a monoclonal antibody directed against the Thy 1.2 antigen with the cleavable dimethyl 3,3'-dithiobispropionimidate cross-linking reagent. This immunotoxin selectively killed leukemia cells expressing the Thy 1.2 antigen. The addition of ammonium chloride, which increases the cytotoxicity of ricin A-chain immunotoxins, blocks that of the trichokirin immunotoxin, suggesting that they enter cells by different mechanisms. In vivo studies showed that the pharmacokinetic properties of the trichokirin immunotoxin could be more advantageous than those of the ricin A-chain immunotoxins for in vivo applications.
Patient-specific models of wall stress in abdominal aortic aneurysm: a comparison between MR and CT (2006)

Finite element method based patient-specific wall stress in abdominal aortic aneurysm (AAA) may provide a more accurate rupture risk predictor than the currently used maximum transverse diameter. In this study, we have investigated the sensitivity of the wall stress in AAA with respect to geometrical variations. We have acquired MR and CT images for four patients with AAA. Three individual users have delineated the AAA vessel wall contours on the image slices. These contours were used to generate synthetic feature images for a deformable model based segmentation method. We investigated the reproducibility and the influence of the user variability on the wall stress. For sufficiently smooth models of the AAA wall, the peak wall stress is reproducible for three out of the four AAA geometries. The 0.99 percentiles of the wall stress show excellent reproducibility for all four AAAs. The variations induced by user variability are larger than the errors caused by the segmentation variability. The influence of the user variability appears to be similar for MR and CT. We conclude that the peak wall stress in AAA is sensitive to small geometrical variations. To increase reproducibility it appears to be best not to allow too much geometrical detail in the simulations. This could be achieved either by using a sufficiently smooth geometry representation or by using a more robust statistical parameter derived from the wall stress distribution.
Tunable fiber-optic parametric oscillator (1999)

We report operation of a tunable optical parametric oscillator that employs a nonlinear-fiber Sagnac interferometer as a parametric amplifier. The amplifier, which consists primarily of dispersion-shifted fiber that has zero dispersion at 1538 nm, is synchronously pumped with 7.7-ps pulses at 1539 nm. The wide bandwidth of the parametric gain permits tuning of the output signal pulses over a 40-nm range centered on the pump wavelength. The Sagnac interferometer decouples the pump wave from the oscillator cavity while a bandpass filter in the cavity transmits only the signal wave, thereby creating a singly resonant parametric oscillator that is phase insensitive. Whereas we demonstrate tuning over almost the entire bandwidth of Er-doped-fiber amplifiers, one could construct a similar device that operates near the 1310-nm zero-dispersion wavelength of standard telecommunication fiber.
Two glucosyltransferases are involved in detoxification of benzoxazinoids in maize (2001)

Benzoxazinoids are major compounds involved in chemical defence in grasses. These toxins are stored in the vacuole as glucosides. Two glucosyltransferases, BX8 and BX9, that catalyse this last step of benzoxazinoid biosynthesis have been isolated via functional cloning. No close relative of these maize genes was found among the known glucosyltransferases. The enzymes display a very high degree of substrate specificity. DIMBOA, the major benzoxazinoid in young maize, is the preferred substrate. Both genes are highly expressed in young maize seedlings, the developmental stage with the highest activity of benzoxazinoid biosynthesis. Bx8 is included in the cluster of DIMBOA biosynthesis genes located on the short arm of chromosome 4. Hence, the gene cluster comprises three different enzymatic functions and a complete set of genes for the biosynthesis of DIBOA glucoside. Bx9 mapped to chromosome 1. Expression of Bx8 and Bx9 in Arabidopsis corroborated the potency of the enzymes in detoxification of their substrates. This capacity might have implications for allelopathic interactions.
Detection of Ambient NO by Laser-Induced Photoacoustic Spectrometry Using A<sup>2</sup>Σ<sup>+</sup> − X<sup>2</sup>Π (0,0) Transitions Near 226 nm (1996)

Trace concentrations of NO are detected under ambient conditions by laser-induced photoacoustic spectroscopy. NO is excited via its A 2 Σ + -X 2 π (0,0) band with radiation near 226 nm, and the subsequent heat released is monitored by a microphone. Rotationally resolved photoacoustic spectra are recorded and fit with the use of a multiparameter computer simulation based on a Boltzmann distribution. Transition probabilities and rotational energies are used as input parameters. The effect of buffer gas pressure, buffer gas, laser energy, and NO concentration on the PA signal is investigated both experimentally and by model calculations. Limits of detection (LODs) of 1.2, 2.8, and 4.9 ppm are obtained for NO in Ar, N 2 , and air, respectively. The ultimate sensitivity of this approach is greater with LODs projected in the low-ppb range by utilizing higher laser energies and an improved system design. The results are compared with those of previous studies using complementary laser-based spectroscopic techniques.
Regulation of Mammalian O<sub>2</sub>Homeostasis by Hypoxia-Inducible Factor 1 (1999)

Hypoxia-inducible factor 1 (HIF-1) is a heterodimeric basic-helix-loop-helix-PAS transcription factor consisting of HIF-1 alpha and HIF-1 beta subunits. HIF-1 alpha expression and HIF-1 transcriptional activity increase exponentially as cellular O2 concentration is decreased. Several dozen target genes that are transactivated by HIF-1 have been identified, including those encoding erythropoietin, glucose transporters, glycolytic enzymes, and vascular endothelial growth factor. The products of these genes either increase O2 delivery or allow metabolic adaptation to reduced O2 availability. HIF-1 is required for cardiac and vascular development and embryonic survival. In fetal and postnatal life, HIF-1 is required for a variety of physiological responses to chronic hypoxia. HIF-1 expression is increased in tumor cells by multiple mechanisms and may mediate adaptation to hypoxia that is critical for tumor progression. HIF-1 thus appears to function as a master regulator of O2 homeostasis that plays essential roles in cellular and systemic physiology, development, and pathophysiology.
New recombination lasers in Li, Al, Ca and Cu in a segmented plasma device employing foil electrodes (1982)

The use of foil electrodes in an expanding plasma recombination laser device has resulted in the generation of 30 laser transitions in Li I, Al I, Al II, Al III, Ca I, Ca II, Cu I, and Cu II. The generation of segmented arc plasmas in these metal vapors at the background gas pressures required for laser action had not previously been possible using bulk electrodes, and suggests that conditions necessary for recombination laser action may be obtained for any metal using this technique.
Green Polymer Chemistry: Enzymatic Functionalization of Liquid Polymers in Bulk (2010)

The use of enzymes as catalysts for organic synthesis has become an increasingly attractive alternative to conventional chemical catalysis. Enzymes offer several advantages including high selectivity, the ability to operate under mild conditions, catalyst recyclability and biocompatilibity. Although there are many examples involving enzymes for the synthesis of polymers, only a few are in the area of polymer functionalization and most of the examples are characterized by low conversion. In this paper, we present examples of quantitative enzyme-catalyzed methacrylation of liquid polymers. Specifically, vinyl methacrylate was transesterified with liquid α,ω-dihydroxy polyisobutylenes, α,ω-dihydroxy polydimethylsiloxane (PDMS), PDMS-mono and –dicarbinol, and low molecular weight poly(ethylene glycol) in the presence of Candida antarctica lipase B (CALB; Novozym® 435) under solventless conditions. 1H and 13C NMR spectroscopy verified the structure of the functionalized polymers.
Multifunctional Gas Sensor Array with Improved Selectivity Through Local Thermal Modification (2008)

This work involves the development of small, easily manufactured, potentiometric gas sensor arrays for continuous monitoring of pollutant (NOx, CO, HCs) concentrations. These low-power devices consist of coplanar sensing electrodes operating in the same gas environment without the need for an air-reference. The selectivity of a sensing electrode-pair is temperature dependent and may be enhanced with the use of integrated heating elements. Finite Element Modeling was used to predict thermal distributions and find the ideal locations of sensing electrodes and heating elements. General trends of baseline shift and sensitivity with changes in individual electrode temperatures are discussed. The results demonstrate that a gas sensor array with thermally modified sensing electrodes yields a device capable of selectively determining the concentrations of combustion byproducts.
Artificial Intelligence Assisted Infrastructure Assessment Using Mixed\n Reality Systems (2018)

Conventional methods for visual assessment of civil infrastructures have\ncertain limitations, such as subjectivity of the collected data, long\ninspection time, and high cost of labor. Although some new technologies i.e.\nrobotic techniques that are currently in practice can collect objective,\nquantified data, the inspectors own expertise is still critical in many\ninstances since these technologies are not designed to work interactively with\nhuman inspector. This study aims to create a smart, human centered method that\noffers significant contributions to infrastructure inspection, maintenance,\nmanagement practice, and safety for the bridge owners. By developing a smart\nMixed Reality framework, which can be integrated into a wearable holographic\nheadset device, a bridge inspector, for example, can automatically analyze a\ncertain defect such as a crack that he or she sees on an element, display its\ndimension information in real-time along with the condition state. Such systems\ncan potentially decrease the time and cost of infrastructure inspections by\naccelerating essential tasks of the inspector such as defect measurement,\ncondition assessment and data processing to management systems. The human\ncentered artificial intelligence will help the inspector collect more\nquantified and objective data while incorporating inspectors professional\njudgement. This study explains in detail the described system and related\nmethodologies of implementing attention guided semi supervised deep learning\ninto mixed reality technology, which interacts with the human inspector during\nassessment. Thereby, the inspector and the AI will collaborate or communicate\nfor improved visual inspection.\n
Zinc ionophores as neuroprotective agents (2003)

Zinc ionophores, molecules that carry zinc ions across the cell membrane, can decrease apoptosis in animals subjected to experimental heart attack, brain injury, neurodegeneration, and epilepsy. Here we show that zinc ionophores at low μg/kg BW doses have neuroprotective effects in three different stroke models in rodents: focal ischemia models (middle cerebral artery occlusion, MCAO) in mice and rats, and a model of global ischemia (four vessel occlusion, 4VO) in rats. Intravenous, postinjury, administration of zinc ionophores decreased neuronal cell death, the number of TUNEL‐positive cells in the lesioned brain areas, and brain infarct volumes. Zinc ionophores also significantly accelerated functional recovery after MCAO.
Favorable Pharmacodynamic Features and Superior Anti-Leukemic Activity of B43 (Anti-CD 19) Immunotoxins Containing Two Pokeweed Antiviral Protein Molecules Covalently Linked to each Monoclonal Antibody Molecule (1995)

Standard immunotoxin production procedures using whole IgG as the MoAb moiety yield a heterogeneous mixture of 180 kDa, 210 kDa, and 240 kDa immunotoxin species with 1 to 1, 1 to 2, and 1 to 3 MoAb to toxin ratios. This heterogeneity makes it impossible to precisely deliver a predetermined immunotoxin dose to target cells and impairs the accuracy of pharmacologic studies. In this report, we describe the preparation and characterization of B43(anti-CD19)-pokeweed antiviral protein (PAP) immunotoxins containing either one or two 30 kDa PAP toxin molecules covalently linked to each 150 kDa B43 monoclonal antibody molecule. Compared to the 180 kDa immunotoxin, the 210 kDa immunotoxin displayed greater in vitro chemical stability, resulted in higher systemic exposure levels in vivo, and was a more effective anti-leukemic agent in a SCID mouse model of human B-lineage acute lymphoblastic leukemia. Taken together, the results of this study recommend the clinical evaluation of 210 kDa B43-PAP as a potentially more effective immunotoxin against relapsed B-lineage ALL.
Identification of Factor XIIIa-Reactive Glutamine Acceptor and Lysine Donor Sites within Fibronectin-Binding Protein (FnbA) from <i>Staphylococcus aureus</i> (2004)

Staphylococcal fibronectin-binding protein (FnbA) is a surface-associated receptor responsible for the reversible binding of bacteria to human fibronectin and fibrin(ogen). Recently we have shown that FnbA serves as a substrate for coagulation factor XIIIa and undergoes covalent cross-linking to its ligands, resulting in the formation of heteropolymers (Matsuka, Y. V., Anderson, E. T., Milner-Fish, T., Ooi, P., and Baker, S. (2003) Staphylococcus aureus fibronectin-binding protein serves as a substrate for coagulation factor XIIIa: Evidence for factor XIIIa-catalyzed covalent cross-linking to fibronectin and fibrin, Biochemistry 42, 14643-14652). Factor XIIIa also catalyzes the incorporation in FnbA of fluorescent probes dansylcadaverine and glutamine-containing synthetic peptide patterned on the NH(2)-terminal segment of fibronectin. In this study, the above probes were utilized for site-specific labeling and identification of reactive Gln and Lys residues targeted by factor XIIIa in rFnbA. Probe-decorated rFnbA samples were subjected to trypsin or Glu-C digestion, followed by separation of labeled peptides using reversed phase HPLC. Sequencing and mass spectral analyses of isolated probe-modified peptides have been employed for the identification of factor XIIIa-reactive Gln and Lys residues. Analysis of dansylcadaverine-labeled peptides resulted in the identification of one major, Gln103, and three minor, Gln105, Gln783, and Gln830, amine acceptor sites. The labeling procedure with dansyl-PGGQQIV probe revealed that Lys157, Lys503, Lys620, and Lys762 serve as amine donor sites. The identified reactive glutamine acceptor and lysine donor sites of FnbA may participate in transglutaminase-mediated cross-linking reactions resulting in the covalent attachment of pathogenic Staphylococcus aureus to human host proteins.
<i>Mycobacterium smegmatis</i> <scp>d</scp> -Alanine Racemase Mutants Are Not Dependent on <scp>d</scp> -Alanine for Growth (2002)

Mycobacterium smegmatis is a fast-growing nonpathogenic species particularly useful in studying basic cellular processes of relevance to pathogenic mycobacteria. This study focused on the D-alanine racemase gene (alrA), which is involved in the synthesis of D-alanine, a basic component of peptidoglycan that forms the backbone of the cell wall. M. smegmatis alrA null mutants were generated by homologous recombination using a kanamycin resistance marker for insertional inactivation. Mutants were selected on Middlebrook medium supplemented with 50 mM D-alanine and 20 microg of kanamycin per ml. These mutants were also able to grow in standard and minimal media without D-alanine, giving rise to colonies with a drier appearance and more-raised borders than the wild-type strain. The viability of the mutants and independence of D-alanine for growth indicate that inactivation of alrA does not impose an auxotrophic requirement for D-alanine, suggesting the existence of a new pathway of D-alanine biosynthesis in M. smegmatis. Biochemical analysis demonstrated the absence of any detectable D-alanine racemase activity in the mutant strains. In addition, the alrA mutants displayed hypersusceptibility to the antimycobacterial agent D-cycloserine. The MIC of D-cycloserine for the mutant strain was 2.56 microg/ml, 30-fold less than that for the wild-type strain. Furthermore, this hypersusceptibility was confirmed by the bactericidal action of D-cycloserine on broth cultures. The kinetic of killing for the mutant strain followed the same pattern as that for the wild-type strain, but at a 30-fold-lower drug concentration. This effect does not involve a change in the permeability of the cell wall by this drug and is consistent with the identification of D-alanine racemase as a target of D-cycloserine. This outcome is of importance for the design of novel antituberculosis drugs targeting peptidoglycan biosynthesis in mycobacteria.
Spin Readout and Initialization in a Semiconductor Quantum Dot (2004)

Electron spin qubits in semiconductors are attractive from the viewpoint of long coherence times. However, single spin measurement is challenging. Several promising schemes incorporate ancillary tunnel couplings that may provide unwanted channels for decoherence. Here, we propose a novel spin-charge transduction scheme, converting spin information to orbital information within a single quantum dot by microwave excitation. The same quantum dot can be used for rapid initialization, gating, and readout. We present detailed modeling of such a device in silicon to confirm its feasibility.
Cooperative cumulants-based Modulation Classification under flat Rayleigh fading channels (2015)

Automatic Modulation Classification is a key technology in Cognitive Radio Networks. Blind identification of the modulation scheme of an unknown detected signal has various commercial and military applications. Performance of Automatic Modulation Classifiers degrades severely under low Signal-to-Noise ratios and fading channel scenarios. Cooperative classification is presented as a means to enhance the classification performance as well as to relax the computational constraints on individual nodes. In this work, the performance of cooperative cumulants-based modulation classification is studied under flat Rayleigh fading channels. The degradation in performance of a single node under flat Rayleigh fading is first presented in comparison to Additive White Gaussian Noise channels. Next, performance improvement obtained through cooperative combining of classification data from several nodes is presented. Analytical results as well as simulations show that cooperation will improve the overall performance of modulation classifiers, overcoming the performance loss due to fading and reaching classification results comparable to the AWGN scenario.
Neural Episodic Control (2017)

Deep reinforcement learning methods attain super-human performance in a wide range of environments. Such methods are grossly inefficient, often taking orders of magnitudes more data than humans to achieve reasonable performance. We propose Neural Episodic Control: a deep reinforcement learning agent that is able to rapidly assimilate new experiences and act upon them. Our agent uses a semi-tabular representation of the value function: a buffer of past experience containing slowly changing state representations and rapidly updated estimates of the value function. We show across a wide range of environments that our agent learns significantly faster than other state-of-the-art, general purpose deep reinforcement learning agents.
Machine Learning for the New York City Power Grid (2011)

Power companies can benefit from the use of knowledge discovery methods and statistical machine learning for preventive maintenance. We introduce a general process for transforming historical electrical grid data into models that aim to predict the risk of failures for components and systems. These models can be used directly by power companies to assist with prioritization of maintenance and repair work. Specialized versions of this process are used to produce 1) feeder failure rankings, 2) cable, joint, terminator, and transformer rankings, 3) feeder Mean Time Between Failure (MTBF) estimates, and 4) manhole events vulnerability rankings. The process in its most general form can handle diverse, noisy, sources that are historical (static), semi-real-time, or realtime, incorporates state-of-the-art machine learning algorithms for prioritization (supervised ranking or MTBF), and includes an evaluation of results via cross-validation and blind test. Above and beyond the ranked lists and MTBF estimates are business management interfaces that allow the prediction capability to be integrated directly into corporate planning and decision support; such interfaces rely on several important properties of our general modeling approach: that machine learning features are meaningful to domain experts, that the processing of data is transparent, and that prediction results are accurate enough to support sound decision making. We discuss the challenges in working with historical electrical grid data that were not designed for predictive purposes. The “rawness” of these data contrasts with the accuracy of the statistical models that can be obtained from the process; these models are sufficiently accurate to assist in maintaining New York City’s electrical grid.
Multiple drug resistance gene atrC of Aspergillus nidulans (X-11765) (1997)

The invention provides isolated nucleic acid compounds encoding a multiple drug resistance protein of Aspergillus nidulans. Vectors and transformed host cells comprising the multiple drug resistance-encoding DNA of Aspergillus nidulans atrC are also provided. The invention further provides assays which utilize these transformed host cells