gebhart/patrepeval huggingface dataset:
Molecular basis for DNA strand displacement by NHEJ repair polymerases (2015)

The non-homologous end-joining (NHEJ) pathway repairs DNA double-strand breaks (DSBs) in all domains of life. Archaea and bacteria utilize a conserved set of multifunctional proteins in a pathway termed Archaeo-Prokaryotic (AP) NHEJ that facilitates DSB repair. Archaeal NHEJ polymerases (Pol) are capable of strand displacement synthesis, whilst filling DNA gaps or partially annealed DNA ends, which can give rise to unligatable intermediates. However, an associated NHEJ phosphoesterase (PE) resects these products to ensure that efficient ligation occurs. Here, we describe the crystal structures of these archaeal (Methanocella paludicola) NHEJ nuclease and polymerase enzymes, demonstrating their strict structural conservation with their bacterial NHEJ counterparts. Structural analysis, in conjunction with biochemical studies, has uncovered the molecular basis for DNA strand displacement synthesis in AP-NHEJ, revealing the mechanisms that enable Pol and PE to displace annealed bases to facilitate their respective roles in DSB repair.
Conservation and host specificity of Vpr-mediated cell cycle arrest suggest a fundamental role in primate lentivirus evolution and biology (1997)

The human immunodeficiency virus type 1 (HIV-1) Vpr protein prevents infected cells from passing through mitosis by arresting them in the G2 phase of the cell cycle. Vpr is conserved among all primate lentiviruses, suggesting an important role in the virus life cycle. Moreover, in this study we show that the ability to cause cell cycle arrest is also conserved in Vpr proteins from a wide variety of both tissue culture-passaged and uncultured human (HIV-1 and HIV-2), sooty mangabey (simian immunodeficiency virus SIV(SM)), African green monkey (SIV(AGM)), and Sykes' monkey (SIV(SYK)) isolates. However, this property is cell type specific and appears to depend on the particular primate species from which the cells are derived. SIV(AGM) and SIV(SYK) Vpr proteins are capable of arresting African green monkey cells but are completely inactive in human cells. By contrast, HIV-1, HIV-2, and SIV(SM) Vpr proteins function in both simian and human cell types, although SIV(SM) Vpr functions more efficiently in simian cells than it does in human cells. Neither differential protein stability nor subcellular localization explains the species-specific activities of these proteins. These results thus suggest that Vpr exerts its G2 arrest function by interacting with cellular factors that have evolved differently among the various primate species.
Highly stable, phase pure Cs<sub>2</sub>AgBiBr<sub>6</sub> double perovskite thin films for optoelectronic applications (2017)

Cs<sub>2</sub>AgBiBr<sub>6</sub> double perovskite thin films were prepared and incorporated into photovoltaic devices featuring power conversion efficiencies close to 2.5%.
No Vent Tank Fill and Transfer Line Chilldown Analysis by Generalized Fluid System Simulation Program (GFSSP) (2013)

The purpose of the paper is to present the analytical capability developed to model no vent chill and fill of cryogenic tank to support CPST (Cryogenic Propellant Storage and Transfer) program. Generalized Fluid System Simulation Program (GFSSP) was adapted to simulate chargeholdvent method of Tank Chilldown. GFSSP models were developed to simulate chilldown of LH2 tank in Ksite Test Facility and numerical predictions were compared with test data. The report also describes the modeling technique of simulating the chilldown of a cryogenic transfer line and GFSSP models were developed to simulate the chilldown of a long transfer line and compared with test data.
<title>Electroactive polyacrylonitrile nanofibers as artificial nanomuscles</title> (2002)

In this multi-institutional effort, polyacrylonitrile- nanofibers (PAN-N) have been fabricated by the electro- spinning method. Realizing that the response time of PAN is governed by the diffusional processes of ions/solvents interaction, the use of sucn PAN-N are promising for fabricating fast response PAN artificial muscles. PAN-N fibers were suitably annealed, cross-linked and hydrolyzed to become active. It should be noted that activated PAN fibers have their capability of changing effective longitudinal strain more than 100%, and their comparable strength to human muscle. Therefore, such high strength of the PAN fibers is a dfinite advantage over other types of ionic gels that are usually very weak. A key molecular structure of PAN, hydrogen bonding between hydrogen and the neighboring nitrogen of the nitrile group, exhibiting insolubility, thermal stability, and resistance to swelling in most organic solvents, is thought to be due to its cross-linked polymer structure. In this paper, the authors present the analytic results of such PAN fibers, including micrographs and solid-states NMR. These results provide a great potential in developing fast activating PAN-N muscles and linear actuators, as well as integrated pairs of antagonistic muscles and muscle sarcomere and myosin/actin- like assembly.
Morphinane Alkaloids with Cell Protective Effects from <i>Sinomenium </i><i>a</i><i>cutum</i> (2005)

One new morphinane alkaloid, sinomenine N-oxide (1), and one new natural occurring morphinane alkaloid, N-demethylsinomenine (2), together with six known alkaloids, 7,8-didehydro-4-hydroxy-3,7-dimethoxymorphinan-6-ol (3), sinomenine (4), sinoacutine (5), N-norsinoacutine, acutumine, and acutumidine, were isolated from the stems of Sinomenium acutum. Their structures were elucidated on the basis of spectroscopic analysis and chemical methods. Compounds 2, 3, and 5 have protective effects against hydrogen peroxide-induced cell injury.
Organizational emergence in networked collaboration (2002)

Abstract Research on complex adaptive systems has generated several conceptual parables to explain systems with emergent behaviour. One prominent use for terms such as self‐organization, evolutionary trajectories, co‐evolution and punctuated equilibrium has been in understanding human organizations. In such systems, emergent behaviour is demonstrated in novel structures, processes and spin‐offs that cannot be explained just by studying single components of the organization and the intelligence embedded in them. Instead of solely exploiting the qualitative explanatory power of the evolutionary concepts, this paper focuses also on quantitative methods to track emergent behaviour in a globally distributed, constantly fluctuating and highly networked project organization. The underlying case is that of CERN (CERN, the European Laboratory for Particle Physics, has its headquarters in Geneva. At present, its Member States are Austria, Belgium, the Czech Republic, Denmark, Finland, France, Germany, Greece, Hungary, Italy, Netherlands, Norway, Poland, Portugal, the Slovak Republic, Spain, Sweden, Switzerland and the United Kingdom. Israel, the Russian Federation, Turkey, Yugoslavia (status suspended after the UN embargo, June 1992), the European Commission and UNESCO have observer status.) and its decade long accelerator project, which strongly relies on electronic communication and networking to achieve its major objectives due to be accomplished by the year 2006. By using time series and self‐organizing maps to analyse the global interaction among project groups and individuals the paper provides new insight to the understanding of emergent behaviour in human organizations. The key result of the study concerns the rigid deep structure of each case organization that seems to remain intact for the duration of the whole project. Copyright © 2002 John Wiley & Sons, Ltd.
Do mediators walk their talk in civil cases? (2010)

Abstract In this article we examine initial joint sessions in civil case mediations and note that, although understudied, they are a key element in the mediation process. Here mediators can set the tone of the mediation by delineating the goals, proffering advice to the disputants, and relating their experiences. They can indicate which strategy or style they will subsequently use. To investigate these aspects, we observed one hundred civil case mediations and found that mediators in the opening joint sessions typically did provide goals, advice, and descriptions. In about one‐half of the mediations, the mediators stated which style—neutral, evaluative, or pressing—they would use. Observations of the subsequent mediations revealed that mediators who said they would employ a neutral style seldom did so, whereas the mediators who said they would evaluate or press were more apt to follow their espoused strategy. An examination of the agreements in the mediations revealed that the evaluative strategy was most often associated with agreement, the pressing style was a close second, and the neutral style was a distant third. Moreover, it was noted that the evaluative and pressing mediators who walked their talk—who employed the strategy they said they would use—were effective in getting agreements. In contrast, the lowest number of agreements came when mediators initially stated they would use an evaluative strategy but subsequently pressed the disputants.
High <i>T</i> <i>c</i> superconductor-normal-superconductor Josephson junctions using CaRuO3 as the metallic barrier (1993)

Josephson junctions of the SNS type have been fabricated in the edge and trilayer junction geometries using YBa2Cu3O7−δ/CaRuO3/YBa2Cu3O7−δ. The conducting oxide CaRuO3 was chosen because it grows epitaxially on YBa2Cu3O7−δ and its resistivity shows metallic behavior. Current-voltage characteristics display behavior with significant deviations from the resistivity shunted junction model. The dependence of critical currents and junction resistances on the CaRuO3 thickness suggest that the interface resistance between YBa2Cu3O7−δ and CaRuO3 plays an important role in determining the critical parameters of the junctions. A dc SQUID functioning at 77 K has been demonstrated with this type of junction.
Aneuploidy in twin gestations: When is maternal age advanced? (1997)

Invasive prenatal diagnosis for detection of fetal aneuploidy should be offered to all women with twin gestations at age 31, regardless of race.
Erratum: Structures and Potential Superconductivity in<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:msub><mml:mi>SiH</mml:mi><mml:mn>4</mml:mn></mml:msub></mml:math>at High Pressure: En Route to “Metallic Hydrogen” [Phys. Rev. Lett.<b>96</b>, 017006 (2006)] (2006)

Received 21 August 2006DOI:https://doi.org/10.1103/PhysRevLett.97.119901©2006 American Physical Society
Molecular Pathology of Lewy Body Diseases (2009)

Lewy body diseases are characterized by the presence of Lewy bodies, alpha-synuclein(AS)-positive inclusions in the brain. Since their main component is conformationally modified AS, aggregation of the latter is thought to be a key pathogenic event in these diseases. The analysis of inclusion body constituents gives additional information about pathways also involved in the pathology of synucleinopathies. Widespread mitochondrial dysfunction is very closely related to disease development. The impairment of protein degradation pathways, including both the ubiquitin-proteasome system and the autophagy-lysosome pathway also play an important role during the development of Lewy body diseases. Finally, differential expression changes of isoforms corresponding to genes primarily involved in Lewy body formation point to alternative splicing as another important mechanism in the development of Parkinson's disease, as well as dementia with Lewy bodies. The present paper attempts to give an overview of recent molecular findings related to the pathogenesis of Lewy body diseases.
Analysis of a diffusion-model-based approach for efficient quantification of superficial tissue properties (2010)

Previously, we reported using a diffusing probe in conjunction with a two-layer diffusion model for accurately recovering the optical properties of superficial volumes. However, the two-layer diffusion equation is computationally less efficient than a standard diffusion equation (SDE) by 3 orders of magnitude. In this Letter, we present a new approach extended from the diffusing probe geometry that enables the use of a diffusion model that has efficiency comparable to an SDE. Our Monte Carlo simulation results indicate that this new approach is not only very accurate but also sensitive to the presence of 0.5 mm(3) inhomogeneities and could be used for monitoring the early progression of skin melanoma.
Printed touch sensor for interactive packaging and display (2007)

In this work we present a study on the performance of printed touch sensor fabricated using conductive ink on paper substrates. The sensor system is intended to add values in surveillance of packages or in interactive point-of-purchase displays. The printed sensor changes its capacitance when it is touched or manipulated. The capacitance variations are readout using either a wireless or wired communication link. The most advanced system will utilize RFID or ZigBee readout technology while the simplest systems utilize a simple analog wire solution. The sensor technology has been developed to be easily integrated into high quality prints targeting applications such as large area touch sensitive commercial stands, flat keyboards at point-of-purchase and touch and manipulation surveillance in logistic chains.
Ru-TsDPEN with Formic Acid/Hünig’s Base for Asymmetric Transfer Hydrogenation, a Practical Synthesis of Optically Enriched <i>N</i>-Propyl Pantolactam (2008)

The Noyori-Ikariya catalysts, Ru-TsDPEN 1 or 2, in combination with HCOOH/Hunig's base (5:2) have been successfully utilized for catalytic asymmetric transfer hydrogenation of alpha-ketopantolactam, and optically enriched N-substituted pantolactam was prepared (S/C = 500, up to 95% ee and 99% conversion in HCOOH/Hunig's base condition). More than 2 kg of this key intermediate 9 has been synthesized efficiently with excellent chemical yield and chiral purity.
Effects of the cytokines on the proliferation of and collagen synthesis by human cataract lens epithelial cells. (1996)

These cytokines may play an important role in an autocrine or paracrine pathway in the proliferation of residual LECs after cataract surgery. Elucidation of the role of these cytokines may lead to the development of new therapies for the prevention of secondary cataract.
Investigation of Atmospheric Pressure CVD‐Produced Aluminum Coatings for the Protection of Steel from Corrosion (2010)

Abstract This study investigates the use of atmospheric pressure (AP)CVD‐produced aluminum (Al) coatings for the protection of steel from corrosion. Coatings produced through thermal decomposition of a triisobutylaluminum (TIBAL)‐based precursor at 548 and 573 K are shown to exhibit growth rates of 0.5 and 1.1 µm min −1 , respectively. Glow discharge optical emission spectroscopy (GDOES) reveals that, in the main, the coatings consist of pure Al with oxygen present as a minor constituent. Results of the structural, morphological, electrical, and mechanical characterization reveal that the APCVD Al coatings exhibit a face center cubic (fcc) structure with no preferred orientation, a non‐columnar grain structure with grain size ranging from 3 to 10 µm, and a surface roughness close to 2 µm. Such coatings are also shown to offer an electrical resistivity of 3.5 µΩ·cm, a density of 2.60 g cm −3 , and an adhesive strength of 703 kg cm −2 . Cross‐sectional examination of coated samples indicate that the APCVD process can yield excellent step coverage and throwing power. Hydrogen embrittlement (HE) tests reveal that Al‐coated bars with no post baking experience premature failure due to the presence of incorporated reaction product, hydrogen, in the steel substrate. Samples post‐baked at 463 K for 23 h to remove the hydrogen from the substrate are shown to withstand the load for as long as 202 h. Corrosion studies conducted using potentiodynamic polarization measurements, electrochemical impedance spectroscopy, and salt fog tests show that the corrosion resistance of the APCVD Al coatings is comparable to that of pure Al foils, and that such coatings provide acceptable sacrificial protection for steel substrates.
Electrochemical Investigation of Oligonucleotide-DNA Hybridization on Poly(4-Methoxyphenethylamine) (2008)

This work describes the immobilization of purine and pyrimidine bases and immobilization/hybridization of synthetic oligonucleotides on graphite electrodes modified with poly(4-methoxyphenethylamine) produced in acid medium. The immobilization of adenine, guanine, cytosine and thymine on these modified electrodes was efficient, producing characteristic peaks. Another relevant observation is that, according to the literature, pyrimidine bases, cytosine and thymine are more difficult to detect. However, when immobilized onto the poly(4-methoxyphenethylamine), a significant increase in the magnitude of the current was obtained. The observation of the hybridization between the poly(GA) probe and its complementary, poly(CT) target, was possible by monitoring the guanosine and adenosine peaks or through methylene blue indicator, using differential pulse voltammetry. Hybridization results in a decrease of the peak current of guanosine and adenosine or the signal of methylene blue accumulated on the modified electrode surface. The hybridization with the complementary target was also investigated by electrochemical impedance spectroscopy. The results showed a significant modification in the Nyquist plot, after addition of the complementary target, with increase of the charge transference resistance.
Immune complex erythrocyte complement receptor interactions in vivo during induction of glomerulonephritis in nonhuman primates. (1990)

Multiple lines of evidence indicate that the erythrocyte complement receptor (E-CR) system, which is unique to the primate, may play an important role in the clearing of immune complexes (ICs) from the circulation. However, all previous investigations of IC/E-CR interactions in vivo have involved the study of small amounts of preformed or passively formed ICs interacting with E-CR that were numerically in vast excess. The present study was undertaken to assess IC/E-CR interactions under conditions in which large amounts of ICs were formed in the circulation, amounts that when sustained for several weeks by daily intravenous administration of antigen resulted in the development of active glomerulonephritis. Twelve cynomolgus monkeys with E-CR levels ranging from 25 to 5000 mean CRs per erythrocyte (CR/E) were actively immunized to BGG, and 6 to 12 weeks later they were studied first at low levels of IC formation in vivo (L-Protocol experiments, mean 125I-labeled BGG dose of 0.04 mg/kg given over 1 minute, a marked antibody excess state) and then at high levels of IC formation in vivo (H-Protocol experiments, mean 125I-labeled BGG dose 4.9 mg/kg given over 10 minutes, a state approximating antigen-antibody equivalence). Cynomolgus monkeys with fewer than 100 CR/E showed no evidence of binding of ICs to erythrocytes with either low-dose or high-dose 125I-labeled BGG. However, cynomolgus monkeys with greater than 450 CR/E showed significant binding of ICs to erythrocytes: mean peak binding of 125I-labeled BGG to erythrocytes was 22.1% +/- 1.1% in the L-Protocol experiments and 33.4% +/- 8.0% in the H-Protocol experiments. During H-Protocol experiments, mean CR/E, measured by using a monoclonal anti-human CR1 antibody, decreased acutely (mean decrease 36.2% +/- 14.1%, p less than 0.05), with recovery of E-CR levels within the next 24 to 72 hours. The acute decrease in E-CR levels could not be accounted for by occupancy of E-CR by ICs or by change in hematocrit. In summary, the present study demonstrates that during the development of glomerulonephritis, IC/E-CR interactions occur and the E-CR system is altered by these interactions. The present observations are consistent with the hypothesis that the E-CR system may play a role in the pathogenesis of IC-mediated disease in the primate.
A Service-Oriented Virtual Machine for Grid Applications (2006)

Grid computing is a new paradigm for distributed computing, and service has become building block of grid applications. However, current approaches can not free developers from low-level laborious work when building grid applications. We propose a service-oriented virtual machine called Abacus Virtual Machine to simplify the task of grid application development. As a language level virtual machine, it provides a service-oriented instruction set to abstract the operations on the services of a grid application. It also virtualizes services and creates a virtual global system image for grid applications, thus services can be transparently distributed and shared. In this way, Abacus Virtual Machine hides the cumbersome underlying details from programmers and reduces the complexity greatly in grid application development
Phase-Shifting for Nonseparable 2-D Haar Wavelets (2008)

In this paper, we present a novel and efficient solution to phase-shifting 2-D nonseparable Haar wavelet coefficients. While other methods either modify existing wavelets or introduce new ones to handle the lack of shift-invariance, we derive the explicit relationships between the coefficients of the shifted signal and those of the unshifted one. We then establish their computational complexity, and compare and demonstrate the superior performance of the proposed approach against classical interpolation tools in terms of accumulation of errors under successive shifting.
Continuous optical automatic speech recognition by lipreading (2002)

We describe a continuous optical automatic speech recognizer (OASR) that uses optical information from the oral-cavity shadow of a speaker. The system achieves a 25.3 percent recognition on sentences having a perplexity of 150 without using any syntactic, semantic, acoustic, or contextual guides. We introduce 13, mostly dynamic, oral-cavity features used for optical recognition, present phones that appear optically similar (visemes) for our speaker, and present the recognition results for our hidden Markov models (HMMs) using visemes, trisemes, and generalized trisemes. We conclude that future research is warranted for optical recognition, especially when combined with other input modalities.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Inactivation of poliomyelitis virus for the preparation of vaccines. I. Formalin and ultraviolet irradiation. (1957)

An extensive series of experiments designed to establish the practicality of combining formaldehyde inactivation with ultraviolet irradiation as a method for the inactivation of poliomyelitis virus for the production of vaccines has been reviewed. The actual use of the combination method is illustrated by safety, stability and potency test data obtained in a series of experimental vaccines. These vaccines were also subjected to trial in humans. The objective has been to introduce and illustrate the feasibility of producing virus vaccines according to standards (11), particularly poliomyelitis, by the use of a combination of chemical (formaldehyde) and physical (ultraviolet) methods of inactivation.