gebhart/patrepeval huggingface dataset:
Antimicrobial Activity of Gallium Compounds on ESKAPE Pathogens (2018)

ESKAPE bacteria are a major cause of multidrug-resistant infections, and new drugs are urgently needed to combat these pathogens. Given the importance of iron in bacterial physiology and pathogenicity, iron uptake and metabolism have become attractive targets for the development of new antibacterial drugs. In this scenario, the FDA-approved iron mimetic metal Gallium [Ga(III)] has been successfully repurposed as an antimicrobial drug. Ga(III) disrupts ferric iron-dependent metabolic pathways, thereby inhibiting microbial growth. This work provides the first comparative assessment of the antibacterial activity of Ga(NO<sub>3</sub>)<sub>3</sub> (GaN), Ga(III)-maltolate (GaM), and Ga(III)-protoporphyrin IX (GaPPIX), belonging to the first-, second- and third-generation of Ga(III) formulations, respectively, on ESKAPE species, including reference strains and multidrug-resistant (MDR) clinical isolates. In addition to the standard culture medium Mueller Hinton broth (MHB), iron-depleted MHB (DMHB) and RPMI-1640 supplemented with 10% human serum (HS) (RPMI-HS) were also included in Ga(III)-susceptibility tests, because of their different nutrient and iron contents. All ESKAPE species were resistant to all Ga(III) compounds in MHB and DMHB (MIC > 32 μM), except <i>Staphylococcus aureus</i> and <i>Acinetobacter baumannii</i>, which were susceptible to GaPPIX. Conversely, the antibacterial activity of GaN and GaM was very evident in RPMI-HS, in which the low iron content and the presence of HS better mimic the <i>in vivo</i> environment. In RPMI-HS about 50% of the strains were sensitive (MIC < 32) to GaN and GaM, both compounds showing a similar spectrum of activity, although GaM was more effective than GaN. In contrast, GaPPIX lost its antibacterial activity in RPMI-HS likely due to the presence of albumin, which binds GaPPIX and counteracts its inhibitory effect. We also demonstrated that the presence of multiple heme-uptake systems strongly influences GaPPIX susceptibility in <i>A. baumannii</i>. Interestingly, GaN and GaM showed only a bacteriostatic effect, whereas GaPPIX exerted a bactericidal activity on susceptible strains. Altogether, our findings raise hope for the future development of Ga(III)-based compounds in the treatment of infections caused by multidrug-resistant ESKAPE pathogens.
Genetic Incorporation of a Reactive Isothiocyanate Group into Proteins (2016)

Methods for the site-specific modification of proteins are useful for introducing biological probes into proteins and engineering proteins with novel activities. Herein, we genetically encode a novel noncanonical amino acid (ncAA) that contains an aryl isothiocyanate group which can form stable thiourea crosslinks with amines under mild conditions. We show that this ncAA (pNCSF) allows the selective conjugation of proteins to amine-containing molecular probes through formation of a thiourea bridge. pNCSF was also used to replace a native salt bridge in myoglobin with an intramolecular crosslink to a proximal Lys residue, leading to increased thermal stability. Finally, we show that pNCSF can form stable intermolecular crosslinks between two interacting proteins.
BS-CPA: Built-In Determined Sub-Key Correlation Power Analysis (2010)

Correlation power analysis (CPA) is a well-known attack against cryptographic modules with which an attacker evaluates the correlation between the power consumption and the sensitive data candidates calculated from a guessed sub-key and known data such as plaintexts and ciphertexts. This paper enhances CPA to propose a new general power analysis, built-in determined sub-key CPA (BS-CPA), which finds a new sub-key by using the previously determined sub-keys recursively to compute the sensitive data candidates and to increase the signal-to-noise ratio in its analysis. BS-CPA also reuses the power traces in the repetitions of finding sub-keys to decrease the total number of the required traces for determining the all sub-keys. BS-CPA is powerful and effective when the multiple sensitive data blocks such as sbox outputs are processed simultaneously as in the hardware implementation. We apply BS-CPA to the power traces provided at the DPA contest and succeed in finding a DES key using fewer traces than the original CPA does.
Factoring as Optimization (2002)

The factoring of biprimes is proposed as a framework for exploring unconstrained optimization algorithms. A mapping from a given factoring problem to a positive degree four polynomial F is described. F has the properties that the global minima, which specify the factors, are at F = 0, and that all coefficients can be chosen to be of order unity. The factoring of biprimes is an attractive test bed because a large number of different F functions can be generated easily, in such a way that the complexity of the resulting minimization problem can be easily controlled. Representing the problem in this form also gives interesting perspectives on why factoring is hard. This framework suggests new approaches for optimization algorithms aimed at solving combinatorically hard problems. In this paper a new unconstrained optimization algorithm, ‘curvature inversion descent ’ (CID), is described. It has the property that local minima can often be deterministically escaped. CID is illustrated with an 8-dimensional minimization problem generated by factoring a small biprime. For that problem, gradient descent with restarts finds the solution 31 % of the time; with CID, this increases to 88 % of the time.
Inhibition of Herpes Simplex Virus Type 1 Infection by Silver Nanoparticles Capped with Mercaptoethane Sulfonate (2009)

Interactions between biomolecules and nanoparticles suggest the use of nanoparticles for various medical interventions. The attachment and entry of herpes simplex virus type 1 (HSV-1) into cells involve interaction between viral envelope glycoproteins and cell surface heparan sulfate (HS). Based on this mechanism, we designed silver nanoparticles that are capped with mercaptoethane sulfonate (Ag-MES). These nanoparticles are predicted to target the virus and to compete for its binding to cellular HS through their sulfonate end groups, leading to the blockage of viral entry into the cell and to the prevention of subsequent infection. Structurally defined Ag-MES nanoparticles that are readily redispersible in water were sonochemically synthesized. No toxic effects of these nanoparticles on host cells were observed. Effective inhibition of HSV-1 infection in cell culture by the capped nanoparticles was demonstrated. However, application of the soluble surfactant MES failed to inhibit viral infection, implying that the antiviral effect of Ag-MES nanoparticles is imparted by their multivalent nature and spatially directed MES on the surface. Our results suggest that capped nanoparticles may serve as useful topical agents for the prevention of infections with pathogens dependent on HS for entry.
Ocean surface wind vector measurements from high-altitude aircraft using GPS delay-doppler maps (2013)

Reflectometry of opportunity signals such as Global Positioning Satellites System, known as GNSS-R, has been developed in the last years as a technique with a great potential for ocean scatterometry, among other applications. Different approaches have been proposed to use GNSS-R for remote sensing of the ocean surface roughness. One of them is based on deriving some descriptor/metric from the measured delay-Doppler map (DDM) and directly relating it to a geophysical property of the scattering surface. For instance, different descriptors have been proposed in the literature to measure the DDM spreading caused by increase in ocean surface mean square slopes due to surface winds.
ChemInform Abstract: Tumor Promoters. Part 7. The Synthesis of a Potentially General Precursor of the Tiglianes, Daphnanes, and Ingenanes. (1990)

Abstract The polycycle (XIX), obtained in 23 steps and 10% overall yield from furfurylalcohol (I), represents a general precursor of the phorbol, daphnane and ingenane family.
Transesophageal endoscopic ultrasound-guided access to the heart (2007)

These animal studies and clinical cases suggest that transesophageal intracardiac procedures could become feasible and that further exploration by gastroenterologists and cardiologists may be justified.
Chaperonin-mediated assembly of wild-type and mutant subunits of human propionyl-CoA carboxylase expressed in Escherichia coli (1996)

We developed a bacterial expression system for the human alpha and beta cDNAs of propionyl-CoA carboxylase (PCC). These cDNAs (less the putative mitochondrial matrix targeting presequences) were co-expressed in Escherichia coli on one plasmid vector with each cDNA having its own IPTG-inducible promoter. Only negligible amounts of active PCC were measured despite the presence of both alpha and beta subunits as indicated by Western blot analysis and the almost complete biotinylation of the alpha subunit. Co-expression of this plasmid with a second plasmid vector over-expressing the E. coli chaperonin proteins, groES and groEL, resulted in a several hundred-fold increase in PCC specific activity, to a level comparable with that found in crude human liver extracts. PCC was partially purified on monomeric avidin affinity resin and the presence of both alpha and beta subunits was demonstrated, thereby confirming the assembly of both subunits into an active enzyme. Deficiency of either alpha PCC or beta PCC results in propionic acidemia, an autosomal recessive disorder. We used this expression system to characterize one missense mutation previously described in five Japanese alleles, namely C1283T (Thr428lle) in beta PCC. This mutation, when expressed in E.coli under the same conditions as that of wild-type PCC, had null activity, despite the presence of assembled alpha PCC and beta PCC subunits. This bacterial expression system can be useful for analysis of either alpha PCC or beta PCC mutations. Our findings indicated that the groES and groEL chaperonin proteins were essential for folding and assembly of the human PCC heteromeric subunits.
Effect of IGF/IGF2 on rat metatarsal bone growth in vitro (1994)

International audience
State Space Decoupling Control Design Methodology for Switcing Converters (2012)

This paper derives an approach for analyzing dc-dc converters for feedback control design. The control-to-output voltage transfer function of the converters, usually predicted by averaging models, and the classical feedback control techniques is replaced by the state space average block diagram analysis. These state block diagrams are obtained from state space averaging matrixes of the converters combined with their continuous conduction mode differential equations. This decoupling technique yields first order control transfer functions allowing easier synthesis of controllers. The disturbance rejection properties of the controller are analyzed and improved by disturbance input decoupling. The technique is applied to the design of buck converters controllers, and the simulation and experimental results demonstrate good transient response when compared to classical voltage controllers. The structure is easy to implement with relevant applications in integrated circuit manufacturing and general industrial environments.
Ternary ZIF-8-derived dual-metal CoCu nanoparticles in porous carbon polyhedra as efficient catalysts for methanol oxidation (2020)

Novel ternary-metallic ZIFs are synthesized in one step and then converted into efficient dual-metal/nanoporous carbon electrocatalysts for the methanol oxidation reaction.
Long‐term follow‐up of de novo allergy in pediatric liver transplantation – 10 yr experience of a single center (2013)

We conducted a study to clarify the incidence, clinical course, and risk factors of de novo allergies after liver transplantation. Ninety-three patients who had been followed longer than one yr and who had no previous allergy history were included. Forty-two patients (45.2%) developed de novo allergy. Of them, food allergy developed in 35 (37.6%). Respiratory allergy was observed in three (3.2%), and a patient (1.1%) had drug allergy. Fifty-two (55.9%) of the 93 patients developed eosinophilia. The median age of patients with de novo allergy was 15 months (IR 11.3-20 months). De novo allergy developed five months after liver transplantation (IR 2.3-9.5 months) and lasted for 16 months (IR 8-34.5 months). Younger age at liver transplantation displayed statistically significant differences in development of allergy between allergy and non-allergy groups. Twenty-nine (69.0%) patients improved from allergy during the follow-up period. No patient with de novo gastrointestinal allergy progressed to any respiratory allergy such as asthma. Older age at transplantation, EBV non-risk, and CMV non-risk had statistical significance in allergy improvement. Younger age at transplant predisposes to the development of allergy, while improvement of allergy is achieved more in older age.
On the Performance of Very High Temperature Reactor Plants With Direct and Indirect Closed Brayton Cycles (2009)

The performance of very high temperature reactor plants with direct and indirect closed Brayton cycles (CBCs) is compared and the effects of the molecular weight of the CBC working fluid on the number of stages and sizes of the axial flow, single shaft compressor and turbine are investigated. The working fluids considered are helium (4 g/mole), He–Xe, and He–N2 binary mixtures (15 g/mole). Also investigated are the effects of using low and high pressure compressors with intercooling, instead of a single compressor, and changing the reactor exit temperature from 700°C to 950°C on the plant thermal efficiency, the CBC pressure ratio, and the number of stages in and size of the turbomachines. For plants with direct CBCs, the effect of cooling the reactor pressure vessel with He bled off at the exit of the compressor is also investigated. The present analyses are performed for a reactor thermal power of 600 MW, shaft rotation speed of 3000 rpm, and intermediate heat exchanger temperature pinch of 50°C.
Organic Superconductivity Enhanced by Asymmetric-Anion Random Potential in (MDT-TS)I0.85Br0.41 [MDT-TS = 5H-2-(1,3-diselenole-2-ylidene)-1,3,4,6-tetrathiapentalene] (2009)

X-ray investigation and conducting and magnetic properties of a novel organic superconductor composed of an organic donor MDT-TS and an asymmetric I2Br− anion are reported, where MDT-TS is 5H-2-(1,3-diselenol-2-ylidene)-1,3,4,6-tetrathiapentalene. The X-ray oscillation photograph and the energy dispersion spectroscopy (EDS) measurements determine the composition to be (MDT-TS)I0.85Br0.41, where the anion composition is approximately I2Br. The donor and the anion construct an incommensurate lattice similar to (MDT-TS)(AuI2)0.441. The magnetic susceptibility of the complex behaves anisotropically below 50 K, indicating an antiferromagnetic order, while a metal−insulator (M−I) transition is observed at a lower temperature, TMI = 30 K. Application of hydrostatic pressure suppresses the M-I transition, and a superconducting phase appears above 9.8 kbar. The midpoint Tc rises to 6.1 K under 13.8 kbar, which is the highest Tc among the MDT-TSF series salts. The asymmetric I−I−Br− anion reduces TMI by considerably influencing the incommensurate antiferromagnetic insulating state but does not destroy the superconductivity because the incommensurate lattice originally has a kind of random potential on the donors. Consequently, this is the first organic superconductor with an asymmetric linear anion.
Applicalbility of Hi-Vision video camera to ferromagnetic nano-particles visualization using darkfield microscopy (2006)

We are aiming at the development of an inexpensive system that can shoot, record, and analyze the minute world of nano-scale. As the first step, a new visualization system was built using a household high-definition video camera (HDR-HC3) and an optical microscope with the darkfield illumination. And, we evaluate its usage in ferromagnetic nano-particles visualization of magnetic fluid, and make sure its effectiveness in it.
In vivo imaging of the pathophysiological changes and neutrophil dynamics in influenza virus-infected mouse lungs (2018)

The pathophysiological changes that occur in lungs infected with influenza viruses are poorly understood. Here we established an in vivo imaging system that combines two-photon excitation microscopy and fluorescent influenza viruses of different pathogenicity. This approach allowed us to monitor and correlate several parameters and physiological changes including the spread of infection, pulmonary permeability, pulmonary perfusion speed, number of recruited neutrophils in infected lungs, and neutrophil motion in the lungs of live mice. Several physiological changes were larger and occurred earlier in mice infected with a highly pathogenic H5N1 influenza virus compared with those infected with a mouse-adapted human strain. These findings demonstrate the potential of our in vivo imaging system to provide novel information about the pathophysiological consequences of virus infections.
The addition of acetic acid to pyridynes and quinolynes (1971)

The oxidation of the aminotriazolopyridines (1) and (3) and the aminotriazoloquinolines (2) and (4) with lead tetra-acetate in the absence of tetracyclone is described. The products from 2,3-pyridyne and 2,3-quinolyne are 2-acetoxypyridine (5) and 2-acetoxyquinoline respectively. From 3,4-pyridyne, the identifiable organic products are acetic anhydride and a mixture of N-4′-pyridyl-4-pyridone (8) and N-3′-pyridyl-4-pyridone (9) with no detectable amount of 3- or 4-acetoxypyridine. 2,3-Pyridynes undergo ionic addition by acetic acid in preference to cycloaddition to tetracyclone; but 3,4-pyridynes undergo cycloaddition to tetracyclone in preference to ionic addition of acetic acid. There is no sign of bipyridylenes: pyridynes undergo both cycloaddition and ionic addition in preference to dimerisation.
Hydrogénation du CO2 en hydrocarbures sur des catalyseurs bifonctionnels CFA-HZSM-5 (2015)

L’augmentation de la concentration des gaz à effet de serre dans l’atmosphère, notamment le CO 2 , produit essentiellement par la combustion d’énergies fossiles, est l’une des causes du réchauffement climatique. La transformation du CO 2 en produits valorisables tels que les carburants et/ou les produits de base pour la pétrochimie (méthanol, hydrocarbures) est l’une des voies envisageables. La synthèse des hydrocarbures par hydrogénation du CO 2 peut se faire en une seule étape sur des catalyseurs de type oxydes/zéolithes. L’objectif de notre travail est d’évaluer l’effet de l’ajout de la zéolithe et de la proximité entre les deux sites oxyde–zéolithe, où la phase oxyde est à base de fer et où la zéolithe est représentée par la HZSM-5. Pour cela, une série de catalyseurs hybrides CuO–Fe 2 O 3 –Al 2 O 3 /HZSM-5 a été préparée par mélange mécanique. La transformation catalytique du CO 2 a été réalisée dans un réacteur à lit fixe dans les conditions opératoires suivantes : T = 350 °C, P = 30 bars, H 2 /CO 2 = 3. Les résultats obtenus montrent que l’ajout de la zéolithe par mélange intime n’améliore pas les propriétés catalytiques et que le meilleur rendement en hydrocarbures est obtenu avec le catalyseur oxyde CuO–Fe 2 O 3 –Al 2 O 3 selon le procédé Fisher–Tropsch (FT). Toutefois, l’augmentation de la proximité oxyde–zéolithe inhibe la formation des hydrocarbures et favorise la formation du monoxyde de carbone.
From data Processing to Knowledge Processing: Working with Operational Schemas by Autopoietic Machines (2021)

Knowledge processing is an important feature of intelligence in general and artificial intelligence in particular. To develop computing systems working with knowledge, it is necessary to elaborate the means of working with knowledge representations (as opposed to data), because knowledge is an abstract structure. There are different forms of knowledge representations derived from data. One of the basic forms is called a schema, which can belong to one of three classes: operational, descriptive, and representation schemas. The goal of this paper is the development of theoretical and practical tools for processing operational schemas. To achieve this goal, we use schema representations elaborated in the mathematical theory of schemas and use structural machines as a powerful theoretical tool for modeling parallel and concurrent computational processes. We describe the schema of autopoietic machines as physical realizations of structural machines. An autopoietic machine is a technical system capable of regenerating, reproducing, and maintaining itself by production, transformation, and destruction of its components and the networks of processes downstream contained in them. We present the theory and practice of designing and implementing autopoietic machines as information processing structures integrating both symbolic computing and neural networks. Autopoietic machines use knowledge structures containing the behavioral evolution of the system and its interactions with the environment to maintain stability by counteracting fluctuations.
Urolithiasis, Endourology and Laparoscopy (2007)

No AccessJournal of UrologyUrological survey1 Mar 2007Urolithiasis, Endourology and Laparoscopy Ralph ClaymanM.D. Ralph ClaymanRalph Clayman More articles by this author View All Author Informationhttps://doi.org/10.1016/j.juro.2006.11.011AboutFull TextPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail Antegrade Versus Retrograde Endopyelotomy for Pelvi-Ureteric Junction (PUJ) Obstruction 1 : Cost-effective treatment for ureteropelvic junction obstruction: a decision tree analysis. J Urol2003; 169: 228. Link, Google Scholar Laparoscopic Decortication of Symptomatic Simple Renal Cysts: 10-Year Experience From one Institution 1 : Laparoscopic management of peripelvic renal cysts: University of California, San Francisco, experience and review of literature. Urology2005; 65: 882. Google Scholar 2 : Laparoscopic ablation of peripelvic renal cysts. J Urol1997; 158: 1345. Link, Google Scholar © 2007 by American Urological AssociationFiguresReferencesRelatedDetails Volume 177Issue 3March 2007Page: 988-991 Advertisement Copyright & Permissions© 2007 by American Urological AssociationMetricsAuthor Information Ralph Clayman More articles by this author Expand All Advertisement PDF downloadLoading ...
De novo CpG Island Methylation in Human Cancer Cells (2006)

A major obstacle toward understanding how patterns of abnormal mammalian cytosine DNA methylation are established is the difficulty in quantitating the de novo methylation activities of DNA methyltransferases (DNMT) thought to catalyze these reactions. Here, we describe a novel method, using native human CpG island substrates from genes that frequently become hypermethylated in cancer, which generates robust activity for measuring de novo CpG methylation. We then survey colon cancer cells with genetically engineered deficiencies in different DNMTs and find that the major activity against these substrates in extracts of these cells is DNMT1, with minor contribution from DNMT 3b and none from DNMT3a, the only known bona fide de novo methyltransferases. The activity of DNMT1 against unmethylated CpG rich DNA was further tested by introducing CpG island substrates and DNMT1 into Drosophila melanogaster cells. The exogenous DNMT1 methylates the integrated mammalian CpG islands but not the Drosophila DNA. Additionally, in human cancer cells lacking DNMT1 and DNMT3b and having nearly absent genomic methylation, gene-specific de novo methylation can be initiated by reintroduction of DNMT1. Our studies provide a new assay for de novo activity of DNMTs and data suggesting a potential role for DNMT1 in the initiation of promoter CpG island hypermethylation in human cancer cells.