gebhart/patrepeval huggingface dataset:
ERA POST-GENÓMICA PARA EL DESARROLLO DE NUEVOS BIOCATALIZADORES (2012)

En la actualidad, la biologia molecular moderna experimenta un aumento hacia enfoques -omicas», y, en particular, la genomica y la (meta) genomica como herramientas emergentes para el estudio de genes que codifican las enzimas a nivel de microorganismos individuales y comunidades imposibles de cultivar y, microorganismos sin explorar hasta ahora. Durante los ultimos anos, hemos visto enormes avances en nuestra capacidad para aislar microbios y analizar los genomas individuales, y la informacion proporcionada por estas secuencias es bastante sorprendente en lo que respecta a descifrar nuevas enzimas con nuevas actividades. Los metodos moleculares, en particular, (meta) genomica, se aplican ampliamente para caracterizar nuevos biocatalizadores. La (meta) genomica es la aplicacion de modernas tecnicas de la genomica al estudio de las comunidades de organismos microbianos directamente en sus ambientes naturales, evitando la necesidad de aislamiento y cultivo en el laboratorio de las especies individuales. Desde entonces, la (meta) genomica ha revolucionado la biotecnologia desviando el interes lejos de cepas microbianas individuales hacia el 99% de las especies microbianas que actualmente se estima no se puede cultivar. Analizaremos las diferentes estrategias para aislar nuevas enzimas y como la aplicacion directa de la (meta) genomica sobre las comunidades microbianas y sus enzimas revierte en una amplia gama de aplicaciones biomedicas, industriales y ambientales.
ATOM TRANSFER AND EXCHANGE REACTIONS INVOLVING OXYGEN, SULFUR AND SELENIUM (1990)

Abstract A systematic comparison has been made of the reaction conditions required to bring about the thermal transfer or exchange of Group 16 terminal elements between Group 15 molecular centers. Where reaction conditions were suitable, kinetic analyses have been performed, with the observed second-order behavior supporting the presumed bimolecular character of these reactions.
Complementarity and Polarization Modulation in Photon Interference (2017)

We derive two general complementarity relations for the distinguishability and visibility of genuine vector-light quantum fields in double-pinhole photon interference involving polarization modulation. The established framework reveals an intrinsic aspect of wave-particle duality of the photon, not previously reported, thus providing deeper insights into foundational quantum interference physics.
Fluorescence resonance energy transfer analysis ofescherichia coli RNA polymerase and polymerase-DNA complexes (2002)

Fluorescence resonance energy transfer (FRET) is a technique allowing measurements of atomic-scale distances in diluted solutions of macromolecules under native conditions. This feature makes FRET a powerful tool to study complicated biological assemblies. In this report we review the applications of FRET to studies of transcription initiation by Escherichia coli RNA polymerase. The versatility of FRET for studies of a large macromolecular assembly such as RNA polymerase is illustrated by examples of using FRET to address several different aspects of transcription initiation by polymerase. FRET has been used to determine the architecture of polymerase, its complex with single-stranded DNA, and the conformation of promoter fragment bound to polymerase. FRET has been also used as a binding assay to determine the thermodynamics of promoter DNA fragment binding to the polymerase. Functional conformational changes in the specificity subunit of polymerase responsible for the modulation of the promoter binding activity of the enzyme and the mechanistic aspects of the transition from the initiation to the elongation complex were also investigated.
Effect of Jet Momentum Ratio and Equivalence Ratio on the Ignition Process of TMEDA and White Fuming Nitric Acid (WFNA) (2013)

The focus of this research work was to characterize ignition and combustion of TMEDA / DMAZ fuels and white fuming nitric acid oxidizer, using a single-element injector to provide characteristics on hypergolic propellant reactants in terms of ignition delays under atmospheric pressure and ambient temperature conditions. This study assists in determining whether TMEDA and DMAZ are viable replacements for highly toxic fuels such as hydrazine. A series of experiments was conducted to determine the ignition delay as a function of: volumetric flow rate, momentum ratio, L/D ratio, and equivalence ratio. Highspeed images of the ignition transient were ascertained. As the total reactant volumetric flow rate increases, the ignition delay was reduced for  = 1 and MTMEDA/MWFNA = 1. The ignition time delay decreased from nearly 17 ms down to approximately 5 ms when the total propellant flow rate was increased by a factor of six. The jet velocity of the fuel stream, VTMEDA, ranged from 8 to 66 m/s (ReD from ~ 0.3x10 4 to 3x10 4 ), while the jet velocity in the oxidizer stream, VWFNA, ranged from 2 to 60 m/s (ReD from ~ 0.4x10 4 to 4x10 4 ) in order to change the momentum ratio. The effect of equivalence ratio on ignition delay shows that at very fuel rich conditions ( = 5.8) the ignition delay was approximately 3 times longer. However, for cases at  = 3.2 and below, it was evident that the ignition delay is not significantly affected by stoichiometry. This can be interpreted, that for ignition, stoichiometry is not as nearly as important as for combustion. Blends of TMEDA and DMAZ fuels were examined. It was found for 70%TMEDA/30%DMAZ (by wt%), the ignition delay decreased nearly 38%. To simulate the reactants being introduced into a rocket engine, a curved glass surface was applied tangent to the injector exit to study the effect of wall impingement. Data show that when the curved glass surface is present, up to an 8 ms increase in ignition delay is observed.
ChemInform Abstract: ACYLATION OF 1,3,3‐TRIMETHYLCYCLOPROPENE WITH ACYL BOROFLUORIDES (1981)

Abstract Die bei Additionen von Acetyl‐ bzw. Cyclopropancarbonyl‐tetrafluoroborat an das Titelole‐ fin (I) entstehenden Allyl‐Kationen (III) gehen bei Zusatz von methanolischer Triethylamin‐Lösung zum Reaktionsgemisch in die ungesättigten fluorierten Ketone (IV) über; unter gleichen Bedingungen erhält man aus (I) und Pivaloyl‐tetrafluoroborat infolge Cyclisierung des Kations vom Typ (III) das Dihydrofuran (V), aus (I) und Isobutyryl‐tetrafluoroborat ein Gemisch des Dihydrofurans (VI) mit dem Keton (VII).
It's the psychology stupid (2014)

Despite the security community's emphasis on the importance of building secure software, the number of new vulnerabilities found in our systems is increasing. In addition, vulnerabilities that have been studied for years are still commonly reported in vulnerability databases. This paper investigates a new hypothesis that software vulnerabilities are blind spots in developer's heuristic-based decision-making processes. Heuristics are simple computational models to solve problems without considering all the information available. They are an adaptive response to our short working memory because they require less cognitive effort. Our hypothesis is that as software vulnerabilities represent corner cases that exercise unusual information flows, they tend to be left out from the repertoire of heuristics used by developers during their programming tasks.
Calculation of Thermodynamic Properties and Phase Diagrams for the CaO-CaF<SUB>2</SUB>, BaO-CaO and BaO-CaF<SUB>2</SUB> Systems by Molecular Dynamics Simulation (2005)

The thermodynamic properties for the CaO-CaF2, BaO-CaO and BaO-CaF2 systems were calculated by molecular dynamics (MD) simulation using the simple Born-Mayer-Huggins type potential model. The interatomic potential parameters were determined by fitting the thermodynamic properties of pure CaO, BaO and CaF2. The calculated thermodynamic properties for CaO, BaO and CaF2 were in good agreement with measured results, and the superionic conductivity on the solid-solid phase transition of CaF2 has also been successfully assessed by MD simulation. The ΔHM, ΔSM and ΔGM for each binary system were calculated based on the thermodynamic parameters obtained by MD simulation and thermodynamic solution model. The calculated enthalpy interaction parameters for the BaO-CaF2 system represented the possibility of formation of the compounds such as BaO·CaF2 in the BaO-CaF2 system. The calculated phase diagrams for the CaO-CaF2 and BaO-CaO systems were in good agreement with experimentally measured and CALPHAD method results. The calculated eutectic points for the CaO-CaF2 and BaO-CaO systems were about 20 mol% CaO at 1650 K and about 20 mol% CaO at 2050 K, respectively. The BaO-CaF2 system has also been estimated the liquidus lines in the CaF2-rich and BaO-rich region by MD simulation.
Characterization of a novel anti-human TNF-α murine monoclonal antibody with high binding affinity and neutralizing activity (2008)

In order to develop an anti-human TNF-alpha mAb, mice were immunized with recombinant human TNF-alpha. A murine mAb, TSK114, which showed the highest binding activity for human TNF-alpha was selected and characterized. TSK114 specifically bound to human TNF-alpha without cross-reactivity with the homologous murine TNF-alpha and human TNF-beta. TSK114 was found to be of IgG1 isotype with kappa light chain. The nucleotide sequences of the variable regions of TSK114 heavy and light chains were determined and analyzed for the usage of gene families for the variable (V), diversity (D), and joining (J) segments. Kinetic analysis of TSK114 binding to human TNF-alpha by surface plasmon resonance technique revealed a binding affinity (K(D)) of approximately 5.3 pM, which is about 1,000- and 100-fold higher than those of clinically relevant infliximab (Remicade) and adalimumab (Humira) mAbs, respectively. TSK114 neutralized human TNF-alpha-mediated cytotoxicity in proportion to the concentration, exhibiting about 4-fold greater efficiency than those of infliximab and adalimumab in WEHI 164 cells used as an in vitro model system. These results suggest that TSK114 has the potential to be developed into a therapeutic TNF-alpha-neutralizing antibody with picomolar affinity.
Self-Phase Modulation Compensation in a Regenerative Amplifier Using Cascaded Second-Order Nonlinearities (2014)

Cascaded nonlinearities are theoretically and experimentally investigated for intracavity nonlinearity compensation in a Nd:YLF regenerative amplifier. Spectral broadening is significantly reduced, in agreement with simulations, allowing for efficient amplification in a Nd:YLF power amplifier.
Results of Nondestructive Inspection of Layered Composites Using IR Thermography and Ultrasonics (2009)

Polymeric layered composites exhibit a variety of damages following in service loading conditions, like delamination, matrix cracking or even fibre breaking. Detection of such damages and assessing their extension and severity is vital during maintenance cycle, in view of keeping the normal operational reliability. For local inspections, IR thermography and ultrasonic scanning are among the best valued NDT methods. The paper describes the inspections performed by IR active thermography, in different variants, and pulse-echo ultrasonic scanning on GFRP. A variety of layered composites and defects/damages were inspected and the results are evaluated independently, in some cases being compared each other, with valuable conclusions for the users of the mentioned NDI techniques.
Testosterone Production in Chromatin-Positive Klinefelter's Syndrome (1965)

Testosterone production rate calculated from the specific activity of urinary testosterone glucuronoside was measured in 5 men with Klinefelter's syndrome and the plasma testosterone level in 3. The production rates and plasma levels were either below or just at the lower level of the normal range. In only 1 of 4 subjects did the administration of 5000 IU of HCG for 5 days increase the production rate.
A software testbed for digital handwriting analysis and training (2012)

In many skilled labor jobs, workers develop extremely valuable specialized knowledge about the jobs they perform. Large manufacturing companies, such as Rolls-Royce Corporation, see great value in developing software systems that can monitor skilled workers and quantify the characteristics associated with productive performance. The quantification of the characteristics associated with the most highly skilled workers could later be built into training or automation systems for skilled tasks. The goal of this project was to create a software system that is able to capture the expert knowledge of a skilled user on a particular task. The design effort explored the use of individual handwriting styles. The project team created a system that recognized and captured the subtle nuances of a person's handwriting. The algorithm created used an individual's writing sample to identify characteristics that made that individual's writing style unique and recognized one person's handwriting over another person's handwriting. The information captured could later be used in experiments in which an individual can try to mimic the handwriting style of an "expert" and gain feedbacks for improvement. The handwriting recognition system showed a proof-of-concept for knowledge management software in the absence of a highly technical process.
<title>Focal Plane Signal Processing Requirements For Scanned Charge-Injection Device (CID) Arrays</title> (1980)

The major requirements in focal plane signal processing for scanned CID's are the low noise detection of signal charge, the enhancement of signal to noise ratio, the rejection of background signal and the low noise multiplexing of data onto a few signal lines. For implementation on the focal plane, these functions must be designed to operate at cryogenic temperatures, where bipolar and JFET technologies are inappropriate for reasons of low gain or high noise. It is proposed that a combination of linear MOS and Charge Coupled Device technology is the most appropriate for implementing scanned CID systems and in this paper the design and evaluation of these circuit functions are discussed. The implementation of an optimum design for a low noise MOS preamplifier is first considered followed by a discussion of the design aspects of a time delay and integrate device. The novel implementation of a high pass filter in conjunction with a low noise multiplexer completes the focal plane design. Experimental results obtained from a number of fabricated devices will be presented to illustrate the relative maturity of the design approach.
An overview on different drive topologies and strategies for power ultrasonic piezoelectric transducers (2016)

International audience
Transcription of the Epstein-Barr virus gene EBNA-1 from different promoters in nasopharyngeal carcinoma and B-lymphoblastoid cells (1992)

Transcriptional expression of the Epstein-Barr virus (EBV) genome has been shown to differ markedly between nasopharyngeal carcinoma (NPC) cells and latent B-cell lines, with a more limited pattern of gene expression seen in NPC. EBNA-1 is the only nuclear antigen so far detected in both NPC and Burkitt's lymphoma cells. We found previously that in a human NPC tumor passaged in nude mice, designated C15, the EBNA-1 mRNA contained a novel splice site in the BamHI Q region of EBV which had not previously been described for B-cell lines. This lies within a region of the EBV genome to which EBNA-1 binds. Here, we further characterize the 5' region of EBNA-1 transcripts and identify two splicing patterns in C15 cells; we show that they are derived from a common promoter region in the BamHI F region of the viral genome. We also demonstrate that this region can function to initiate transcription of the chloramphenicol acetyltransferase gene in epithelial cells and that the promoter region is only partially methylated at CpG sites in the tumor. In contrast, a B-lymphoblastoid cell line derived from C15 uses a conventional promoter in BamHI-C/W for expression of EBNA-1.
Pharmacogenetics of Nevirapine-Associated Hepatotoxicity: An Adult AIDS Clinical Trials Group Collaboration (2006)

Associations have been reported between an MDR1 variant and responses to nonnucleoside reverse-transcriptase inhibitors. We explored associations between MDR1, CYP2B6, and CYP3A polymorphisms and nevirapine hepatotoxicity. Among participants in a randomized study in South Africa (FTC-302), MDR1 3435C-->T was significantly associated with decreased risk of hepatotoxicity (risk ratio, 0.30; P=.016).
Dengue Virus neither Directly Mediates Hyperpermeability nor Enhances Tumor Necrosis Factor-^|^alpha;-Induced Permeability In Vitro (2014)

The mechanisms of endothelial barrier dysfunction in dengue disease remain poorly understood. Endothelial cell (EC) death due to virus infection or in combination with an infection-induced cytokine storm is deemed as one of the major causes of plasma leakage. Using an in vitro model of human endothelia and several dengue virus (DENV) strains (including a clinical isolate), the direct consequence of infection on endothelial permeability was investigated throughout the course of the infection. All employed DENV-2 strains were able to infect and replicate in ECs. Rather than increase endothelial permeability, DENV infection alone enhanced cell barrier integrity up to 7 days postinfection. Improved cell barrier function was mediated by type I interferon activation at the early phase of infection and by the survival advantage of the infected cells at the late phase of infection. Consistent with this phenomenon, DENV infection did not augment tumor necrosis factor-α-induced permeability. Our results prove that DENV infection does not directly account for vascular permeability; DENV neither induces hyperpermeability nor exacerbates the permeabilizing effect of cytokines. The contributory role of other factors on plasma leakage during dengue disease warrants further investigation.
Localization and molecular characterization of putative O antigen gene clusters of Providencia species (2012)

Enterobacteria of the genus Providencia are opportunistic human pathogens associated with urinary tract and wound infections, as well as enteric diseases. The lipopolysaccharide (LPS) O antigen confers major antigenic variability upon the cell surface and is used for serotyping of Gram-negative bacteria. Recently, Providencia O antigen structures have been extensively studied, but no data on the location and organization of the O antigen gene cluster have been reported. In this study, the four Providencia genome sequences available were analysed, and the putative O antigen gene cluster was identified in the polymorphic locus between the cpxA and yibK genes. This finding provided the necessary information for designing primers, and cloning and sequencing the O antigen gene clusters from five more Providencia alcalifaciens strains. The gene functions predicted in silico were in agreement with the known O antigen structures; furthermore, annotation of the genes involved in the three-step synthesis of GDP-colitose (gmd, colD and colC) was supported by cloning and biochemical characterization of the corresponding enzymes. In one strain (P. alcalifaciens O39), no polysaccharide product of the gene cluster in the cpxA-yibK locus was found, and hence genes for synthesis of the existing O antigen are located elsewhere in the genome. In addition to the putative O antigen synthesis genes, homologues of wza, wzb, wzc and (in three strains) wzi, required for the surface expression of capsular polysaccharides, were found upstream of yibK in all species except Providencia rustigianii, suggesting that the LPS of these species may be attributed to the so-called K LPS (K(LPS)). The data obtained open a way for development of a PCR-based typing method for identification of Providencia isolates.
Predictors of Adverse Outcome and Transient Neurological Dysfuntion Following Surgical Treatment of Acute Type A Dissections (2003)

Predictors of adverse outcome after replacement of the ascending aorta with resection of the intimal tear and open distal anastomosis were analyzed in 167 patients (109 male, median age 56). Median hypothermic circulatory arrest (HCA) time was 30 minutes (range 12 to 113). Eighty-six patients (pts) had surgery within 24 hours and 81 within 72 hours of symptom onset. Thirty-seven pts had only ascending aortic replacement, 128 had hemiarch repair, and in 2 the entire arch was replaced. The aortic valve was replaced in 37 pts, resuspended in 116, and untouched in 14. Either death or permanent neurological dysfunction was considered an adverse outcome (AO). AO occurred in 30.5% (51/167) of patients overall. Multivariate analysis revealed that the only significant (P<0.05) independent preoperative predictor of AO was hemodynamic instability (OR 6.0). Transient neurological dysfunction (TND) occurred in 19 of 116 patients (16.4%). Significant predictors of TND were increasing age >60 (OR 3.4 and 7.0 in the second and third tertile as compared with the lowest tertile) and coronary heart disease (OR 3.4). Cumulative survival of patients (median follow-up 34 months) was 55% at 1, 49% at 5, and 44% at 8 years, indicating an excessive in-hospital mortality, but excellent long term outcome. Surgical treatment of acute type A dissections is still associated with a high incidence of adverse outcome, but results in excellent long-term survival. Earlier diagnosis, before the development of cardiac tamponade and hemodynamic compromise, is critical to improve the operative salvage rate.
A Novel Candidate for the True Fructose-1,6-bisphosphatase in Archaea (2002)

Fructose-1,6-bisphosphatase (FBPase) is one of the key enzymes of the gluconeogenic pathway. Although enzyme activity had been detected in Archaea, the corresponding gene had not been identified until a presumable inositol monophosphatase gene from Methanococcus jannaschii was found to encode a protein with both inositol monophosphatase and FBPase activities. Here we display that a gene from the hyperthermophilic archaeon, Thermococcus kodakaraensis KOD1, which does not correspond to the inositol monophosphatase gene from M. jannaschii, displays high FBPase activity. The FBPase from strain KOD1 was partially purified, its N-terminal amino acid sequence was determined, and the gene (Tk-fbp) was cloned. Tk-fbp encoded a protein of 375 amino acid residues with a molecular mass of 41,658 Da. The recombinant Tk-Fbp was purified and characterized. Tk-Fbp catalyzed the conversion of fructose 1,6-bisphosphate to fructose 6-phosphate following Michaelis-Menten kinetics with a K(m) value of 100 microm toward fructose 1,6-bisphosphate, and a k(cat) value of 17 s(-1) subunit(-1) at 95 degrees C. Unlike the inositol monophosphatase from M. jannaschii, Tk-Fbp displayed strict substrate specificity for fructose 1,6-bisphosphate. Activity was enhanced by Mg(2+) and dithioerythritol, and was slightly inhibited by fructose 2,6-bisphosphate. AMP did not inhibit the enzyme activity. We examined whether expression of Tk-fbp was regulated at the transcription level. High levels of Tk-fbp transcripts were detected in cells grown on pyruvate or amino acids, whereas no transcription was detected when starch was present in the medium. Orthologue genes corresponding to Tk-fbp with high similarity are present in all the complete genome sequences of thermophilic Archaea, including M. jannaschii, Pyrococcus furiosus, Sulfolobus solfataricus, and Archaeoglobus fulgidus, but are yet to be assigned any function. Taking into account the high FBPase activity of the protein, the strict substrate specificity, and its sugar-repressed gene expression, we propose that Tk-Fbp may represent the bona fide FBPase in Archaea.