gebhart/patrepeval huggingface dataset:
YbdK is a carboxylate‐amine ligase with a γ‐glutamyl:Cysteine ligase activity: Crystal structure and enzymatic assays (2004)

The Escherichia coli open reading frame YbdK encodes a member of a large bacterial protein family of unknown biological function. The sequences within this family are remotely related to the sequence of gamma-glutamate-cysteine ligase (gamma-GCS), an enzyme in the glutathione biosynthetic pathway. A gene encoding gamma-GCS in E. coli is already known. The 2.15 A resolution crystal structure of YbdK reveals an overall fold similar to that of glutamine synthetase (GS), a nitrogen metabolism enzyme that ligates glutamate and ammonia to yield glutamine. GS and gamma-GCS perform related chemical reactions and require ATP and Mg2+ for their activity. The Mg2+-dependent binding of ATP to YbdK was confirmed by fluorescence spectroscopy employing 2'(or 3')-O-(trinitrophenyl)adenosine 5'-triphosphate, and yielding a dissociation constant of 3 +/- 0.5 microM. The structure of YbdK contains a crevice that corresponds to the binding sites of ATP, Mg2+ and glutamate in GS. Many of the GS residues that coordinate the metal ions and interact with glutamic acid and the phosphoryl and ribosyl groups of ATP are also present in YbdK. GS amino acids that have been associated with ammonia binding have no obvious counterparts in YbdK, consistent with a substrate specificity that is different from that of GS. Ligase activity between glutamic acid and each of the twenty amino acid residues was tested on high performance liquid chromatography (HPLC) by following the hydrolysis of ATP to ADP. Catalysis was observed only with cysteine. A pyruvate kinase/lactic acid dehydrogenase coupled assay was used to rule out GS activity and to determine that YbdK exhibits gamma-GCS activity. The catalytic rate was found to be approximately 500-fold slower than that reported for authentic gamma-GCS.
Respiratory Muscle Fatigue (1988)

Letters and Corrections1 November 1988Respiratory Muscle FatigueMarvin A. Sackner, MD, Bruce P. Krieger, MDMarvin A. Sackner, MDSearch for more papers by this author, Bruce P. Krieger, MDSearch for more papers by this authorAuthor, Article, and Disclosure Informationhttps://doi.org/10.7326/0003-4819-109-9-758_1 SectionsAboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinkedInRedditEmail ExcerptTo the Editor: Murciano and colleagues (1) showed that tracheal occlusion pressure (P0.1) provided a better predictive index for successful extubation than classic weaning criteria in patients with exacerbation of chronic obstructive pulmonary disease. The authors also correlated P0.1 with electromyographic evidence of diaphragmatic fatigue and concluded that P0.1 provided "a valid and simple index to assess the likelihood of respiratory muscle fatigue."The authors reported that respiratory frequency (f) significantly decreased (P< 0.005) in 11 patients successfully extubated (group 1) in contrast to the chronic elevations that occurred in five patients who later needed to have mechanical ventilatory...References1. MurcianoBoczkowskiLecocguicMilic EmiliParienteAubier DJYJRM. Tracheal occlusion pressure: a simple index to monitor respiratory muscle fatigue during acute respiratory failure in patients with chronic obstructive disease. Ann Intern Med. 1988;108:800-5. LinkGoogle Scholar2. KriegerFeinermanZaronBizousky BDAF. Continuous noninvasive monitoring of respiratory rate in critically ill patients. Chest. 1986;90:632-4. CrossrefMedlineGoogle Scholar3. EberhartWeigalt RJ. Respiratory monitoring: current techniques and some new developments. Bull Eur Physiopathol Respir. 1985;21:295-300. MedlineGoogle Scholar This content is PDF only. To continue reading please click on the PDF icon. Author, Article, and Disclosure InformationAffiliations: Mount Sinai Medical Center Miami Beach, FL 33140 PreviousarticleNextarticle Advertisement FiguresReferencesRelatedDetails Metrics 1 November 1988Volume 109, Issue 9Page: 758-758KeywordsChronic obstructive pulmonary diseaseElectromyographyExtubationFatigueMusclesWeaning Issue Published: 1 November 1988 PDF DownloadLoading ...
Mutational analysis of <i><scp>BRAF</scp></i> and <i><scp>KRAS</scp></i> in ovarian serous borderline (atypical proliferative) tumours and associated peritoneal implants (2013)

There is debate as to whether peritoneal implants associated with serous borderline tumours/atypical proliferative serous tumours (SBT/APSTs) of the ovary are derived from the primary ovarian tumour or arise independently in the peritoneum. We analysed 57 SBT/APSTs from 45 patients with advanced-stage disease identified from a nation-wide tumour registry in Denmark. Mutational analysis for hotspots in KRAS and BRAF was successful in 55 APSTs and demonstrated KRAS mutations in 34 (61.8%) and BRAF mutations in eight (14.5%). Mutational analysis was successful in 56 peritoneal implants and revealed KRAS mutations in 34 (60.7%) and BRAF mutations in seven (12.5%). Mutational analysis could not be performed in two primary tumours and in nine implants, either because DNA amplification failed or because there was insufficient tissue for mutational analysis. For these specimens we performed VE1 immunohistochemistry, which was shown to be a specific and sensitive surrogate marker for a V600E BRAF mutation. VE1 staining was positive in one of two APSTs and seven of nine implants. Thus, among 63 implants for which mutation status was known (either by direct mutational analysis or by VE1 immunohistochemistry), 34 (53.9%) had KRAS mutations and 14 (22%) had BRAF mutations, of which identical KRAS mutations were found in 34 (91%) of 37 SBT/APST-implant pairs and identical BRAF mutations in 14 (100%) of 14 SBT/APST-implant pairs. Wild-type KRAS and BRAF (at the loci investigated) were found in 11 (100%) of 11 SBT/APST-implant pairs. Overall concordance of KRAS and BRAF mutations was 95% in 59 of 62 SBT/APST-implant (non-invasive and invasive) pairs (p < 0.00001). This study provides cogent evidence that the vast majority of peritoneal implants, non-invasive and invasive, harbour the identical KRAS or BRAF mutations that are present in the associated SBT/APST, supporting the view that peritoneal implants are derived from the primary ovarian tumour.
Cytotoxicity of 1-deoxysphingolipid unraveled by genome-wide genetic screens and lipidomics in <i>Saccharomyces cerevisiae</i> (2019)

Hereditary sensory and autonomic neuropathy (HSAN) types IA and IC (IA/C) are caused by elevated levels of an atypical class of lipid named 1-deoxysphingolipid (DoxSL). How elevated levels of DoxSL perturb the physiology of the cell and how the perturbations lead to HSAN IA/C are largely unknown. In this study, we show that C<sub>26</sub>-1-deoxydihydroceramide (C<sub>26</sub>-DoxDHCer) is highly toxic to the cell, while C<sub>16</sub>- and C<sub>18</sub>-DoxDHCer are less toxic. Genome-wide genetic screens and lipidomics revealed the dynamics of DoxSL accumulation and DoxSL species responsible for the toxicity over the course of DoxSL accumulation. Moreover, we show that disruption of F-actin organization, alteration of mitochondrial shape, and accumulation of hydrophobic bodies by DoxSL are not sufficient to cause complete cellular failure. We found that cell death coincides with collapsed ER membrane, although we cannot rule out other possible causes of cell death. Thus, we have unraveled key principles of DoxSL cytotoxicity that may help to explain the clinical features of HSAN IA/C.
Antenna Radiation in Typical Office Environment: Theoretical Modeling and Measurements (2012)

The increasing deployment of wireless communication systems in indoor environment, with different standards, make necessary the research for a new approach allowing the efficient and accurate prediction of their electromagnetic coverage. It becomes essential to predict the behavior of antennas in the presence of various obstacles for planning the communicating devices in the most efficient way. This paper will present an accurate and efficient electromagnetic indoor propagation modeling, based on the FDTD method taking into account the environmental complexity and the dispersive nature of materials. Numerical results are compared with measurement results, other simulation results obtained by using the commercial software HFSS will be compared and discussed.
A laser tracking dynamic robot metrology instrument (1989)

Research work over several years has resulted in the development of a laser tracking instrument capable of dynamic 3-D measurements of robot end-effector trajectories. The instrument characteristics and experiments to measure the static and dynamic performance of a robot in an industrial manufacturing environment are described. The use of this technology for space applications is examined.
Journal of Plant Foods (1979)

Journal of Plant Foods is a venue for the publication of interdisciplinary original unpublished papers dealing with the production, preservation and presentation of potential foods from plants. Emphasis is on nutrition and on sensory qualities. Papers on agricultural, technological, toxicological and socio-economic aspects will be considered. Occasional invited reviews on important topics will be published.
Fuel Economy and Performance Comparison of Alternative Mechanical Hybrid Powertrain Configurations (2008)

<div class="htmlview paragraph">Hybrid vehicles provide the most viable medium term solution to meet the demands of the automotive marketplace. Currently electric hybrids dominate the marketplace but mechanical hybrid systems, including flywheel, pneumatic and hydraulic systems all have the potential to compete with electrical systems.</div> <div class="htmlview paragraph">This paper provides an overview of a mechanical hybrid project created by the University of Warwick. The aim of the project is to assess alternative hybrid powertrains, in particular pneumatic, hydraulic and flywheel systems.</div> <div class="htmlview paragraph">This paper provides a description of a simulation tool to investigate and evaluate the mechanical alternatives to electric hybrid vehicles and the results from two fuel economy case studies using the simulation tool: 2.6 ton SUV and 17 ton bus applications. The paper also outlines a feasibility study of the mechanical hybrid options, including a cost benefit analysis of the different systems. Finally the paper provides an overview of the Warwick FIVT (flywheel and infinitely variable transmission) transmission, an innovative hybrid transmission concept, and details the future work for the project.</div>
MET (2002)

Despite the use of state of the art methods to protect against malicious programs, they continue to threaten and damage computer systems around the world. In this paper we present MET, the Malicious Email Tracking system, designed to automatically report statistics on the flow behavior of malicious software delivered via email attachments both at a local and global level. MET can help reduce the spread of malicious software worldwide, especially self-replicating viruses, as well as provide further insight toward minimizing damage caused by malicious programs in the future. In addition, the system can help system administrators detect all of the points of entry of a malicious email into a network. The core of MET's operation is a database of statistics about the trajectory of email attachments in and out of a network system, and the culling together of these statistics across networks to present a global view of the spread of the malicious software. From a statistical perspective sampling only a small amount of traffic (for example, .1 %) of a very large email stream is sufficient to detect suspicious or otherwise new email viruses that may be undetected by standard signature-based scanners. Therefore, relatively few MET installations would be necessary to gather sufficient data in order to provide broad protection services. Small scale simulations are presented to demonstrate MET in operation and suggests how detection of new virus propagations via flow statistics can be automated.
Nonradiative lifetime measurements in time-domain photoacoustic spectroscopy of condensed phases (1980)

A theoretical model is presented for the time-domain photoacoustic response of a condensed sample with a two-level optical-absorption band. The nonradiative lifetime of the excited state and the transfer function of the pressure transducer are included in the formalism. The limitations of the technique for nonradiative lifetime measurements are discussed and the experimental conditions necessary for optimum relaxation time determinations are evaluated. It is found that the limitations imposed by the modified gas thermal transport equations used in the model restrict it to relaxation times greater than ∼10−5 sec. This is of the same order as the limit imposed on experimental measurements by the transfer function of commercial microphones.
Graphene-Passivated Nickel as an Oxidation-Resistant Electrode for (2012)

We report on graphene-passivated ferromagnetic electrodes (GPFE) for spin devices. GPFE are shown to act as spin-polarized oxidation-resistant electrodes. The direct coating of nickel with few layer graphene through a readilyscalablechemicalvapordeposition(CVD)processallowsthepreservationofanunoxidizednickelsurfaceuponair exposure. Fabrication and measurement of complete reference tunneling spin valve structures demonstrate that the GPFEismaintainedasaspinpolarizerandalsothatthepresenceofthegraphenecoatingleadstoaspecificsignreversal ofthemagneto-resistance.Hence,thisworkhighlightsanoveloxidation-resistantspinsourcewhichfurtherunlockslow cost wet chemistry processes for spintronics devices.
A novel phase-locked loop (PLL) architecture without an analog loop filter for better integration in ultra-deep submicron SoCs (2008)

In this paper, we propose a novel architecture of a hybrid phase-locked loop (PLL) that does not require conventional analog filters. The architecture replaces the loop filter by an Incrementer/Decrementer (INC/DEC), a digital-to-analog converter (DAC) and a charge pump. The proposed solution helps alleviate many of the problems encountered with analog loop filters, which become more prominent as technology scales down. In order to prove the validity of the architecture, the design was implemented at the schematic level in 180nm TSMC CMOS technology. The design was simulated using SPECTRE in the Cadence’s Virtuoso analog environment, and results show that the proposed architecture performs as expected. When compared to an analog PLL with similar settling time, the proposed 180nm design even provides 1.8X better deterministic jitter.
Sound wave channelling in near-critical sulfur hexafluoride (SF6) (2004)

Strong density and speed of sound gradients exist in fluids near their liquid-vapor critical point under gravity. The speed of sound has an increasingly sharp minimum and acoustic waves are channelled within a layer of fluid. Geometrical acoustic calculations are presented for different isothermal fluid columns of sulfur hexafluoride (SF6) under gravity using a semiempirical crossover equation of state. More than 40% of the emitted acoustic energy is channelled within a 20 mm high duct at 1 mK above the critical temperature. It is shown how, by changes in temperature, frequency, and gravitational strength, the governing length scales (wavelength, radius of ray curvature, and correlation length of the critical density fluctuations) can be varied. Near-critical fluids allow table-top sound channel experiments.
Different requirements for productive interaction between the active site of HIV-1 proteinase and substrates containing -hydrophobic-hydrophobic- or -aromatic-Pro- cleavage sites (1992)

The sequence requirements for HIV-1 proteinase catalyzed cleavage of oligopeptides containing two distinct types of junctions (-hydrophobic*hydrophobic- or -aromatic*Pro-) has been investigated. For the first type of junction (-hydrophobic*hydrophobic-) the optimal residues in the P2 and P2' positions were found to be Val and Glu, respectively, in accord with recent statistical analysis of natural cleavage sites [Poorman, R. A., Tomasselli, A. G., Heinrikson, R. L., & Kézdy, F. J. (1991) J. Biol. Chem. 266, 14554-14561]. For the -aromatic*Pro- type of junction, in the specific sequence context studied here, the value of Glu in the P2' position was again observed. An explanation for the inefficient cleavage observed for peptides with the sequence -Val-Tyr*Pro- has been provided from molecular modeling of the putative enzyme-substrate complex. A significant effect upon cleavage rates due to the amino acid in the P5 position has also been documented. While lysine in the P5 position in one sequence of the -hydrophobic*hydrophobic- type produces a peptide cleaved very efficiently (kcat greater than 15 s-1 for Lys-Ala-Arg-Val-Nle*p-nitrophenylalanine-P2'-Ala-Nle-NH2, for P2' = Glu, Gln, Ile, Val, or Ala), for substrates of the -aromatic*Pro- type, the P5 residue can exert either a positive or negative effect on cleavage rates. These results have again been interpreted in light of molecular modeling. We suggest that interaction of the substrate sequence on the periphery of the active site cleft may influence the match of the enzyme-substrate pair and, hence, control the efficiency of catalysis.(ABSTRACT TRUNCATED AT 250 WORDS)
Glucocorticoid-Induced Differential Expression of the Sialylated and Nonsialylated Lewis<sup>a</sup> Epitopes and Respective Binding Sites in Human Nasal Polyps Maintained under ex vivo Tissue Culture Conditions (2002)

We characterized the anti-inflammatory effects of budesonide on the expression of adhesion molecules involving Lewis(a) (Le(a)) epitope, its sialylated derivative (sLe(a)), and their respective binding sites in human nasal polyposis. By computer-assisted microscopy, we quantitatively characterized the level of histochemical expression of L- and P-selectins, sialylated and nonsialylated Le(a) epitopes, and their respective binding sites in both surface epithelium and glandular epithelium of human nasal polyps obtained from surgical resection, maintained under ex vivo tissue culture conditions for 24 hours, and treated or not with budesonide. Intercellular adhesion molecule 1 (ICAM-1) and vascular cell adhesion molecule 1 (VCAM-1) were chosen as methodological controls, because data already published in the literature clearly indicated budesonide-mediated effects on ICAM-1 and VCAM-1 levels of expression. The present data show that budesonide significantly modified the levels of expression of ICAM-1 and VCAM-1, and to a lesser extent that of P-selectin, in the surface and glandular epithelia. Budesonide markedly decreased the levels of expression of the binding sites for both Le(a) and sLe(a), while those of Le(a) and sLe(a) remained globally unchanged. In conclusion, the present study documents that glucocorticoid-induced effects can encompass receptors for Le(a) epitopes different from E- and P-selectins on epithelial cells of human nasal polyps.
New Etching System with a Large Diameter Using Electron Beam Excited Plasma (1992)

A new etching system using electron-beam-excited plasma (EBEP) has been developed. This EBEP system is able to steadily produce a high-density plasma with a large diameter by introducing a high-current low electron beam into the etching chamber. The nonuniformity of plasma density and floating potential in an 8-inch wafer are improved up to ±2.5% and ±2 V, respectively. Anisotropic etching of n + -poly-Si in a pure Cl 2 plasma is achieved with a high etch rate of 360 nm/min. The etching selectivity is 40 for poly-Si/photoresist and 150 for poly-Si/SiO 2 . These experimental results show that the EBEP etching system is suitable for manufacturing advanced ULSI.
Tests minimax adaptatifs pour les modèles fonctionnels linéaires (2013)

National audience
Comparing Functional Outcomes After Injury-Specific Fixation of Posterior Malleolar Fractures and Equivalent Ligamentous Injuries in Rotational Ankle Fractures (2018)

Therapeutic Level III. See Instructions for Authors for a complete description of levels of evidence.
Healing Voids In Interconnections In Integrated Circuits (1989)

Unusual heat treatment heals voids in aluminum interconnections on integrated circuits (IC's). Treatment consists of heating IC to temperature between 200 degrees C and 400 degrees C, holding it at that temperature, and then plunging IC immediately into liquid nitrogen. Typical holding time at evaluated temperature is 30 minutes.
Interferometer Signal Processing (2013)

In this chapter, the fundamental signal processing required to implement an interferometer is introduced. The processing required for an interferometer is similar to the processing required for radars in general with the exception that angle estimation is implemented using phase comparison. Because phase is defined only over an interval [0 2p], the phase can wrap over many 2p intervals, creating an ambiguity in the phase measurement. For the interferometer, that relative phase ambiguity between two antennas must be resolved in order to estimate angle-of-arrival. In this chapter, we discuss methods to resolve interferometer phase ambiguities. In particular, all receive interferometer antennas or arrays must be calibrated to ensure that relative phase is consistent across the radar field of regard. The orthogonal interferometer has unique processing requirements due to its implementation of pseudoorthogonal waveforms. Calibration of an orthogonal interferometer requires that all antennas be calibrated for transmit as well as receive. The derivation of angle-ofarrival from relative phase measurements is presented for various far-field conditions. The first-order derivation assumes that the constant phase contours that emanate from a target are essentially linear across the interferometer distributed antennas. This linear far-field condition is satisfied when the target is sufficiently far in range from the interferometer but depends on the interferometer baseline and radar operating frequency. Second-order derivations are also presented for quadratic phase behavior across the interferometer antenna.
Autofocusing on Phase Image for Pure Phase Object in Digital Holography (2012)

The digital holography has been widely employed in the microscopic imaging, which enables quantitative phase analysis. The phase image is obtained in the numerical reconstruction procedure. The in-focus reconstruction distance could be determined according to the extremum of the autofocusing criterion function, which is commonly applied to the amplitude image of the object. With regard to a pure phase sample, such as the living cell, its in-focus amplitude image should be a uniform bright field, so the minimum value needs be found. Then the in-focus reconstruction distance for the phase image is considered to be equal to the one for the amplitude image. However, in the experiment, the in-focus amplitude image is often not an ideal uniform bright field, so this method will result in some deviation. In this contribution, two derivatives-based criterion functions are applied to the phase image directly to accomplish the in-focus phase contrast imaging, which is proved to be more intuitive and precise. In our experiments, two optical configurations of the digital holography are established firstly. Then the standard phase grating and the living cervical carcinoma cells are detected. The phase aberration is corrected by two-step algorithm. The final autofocusing results verify the principle proposed in this paper.
The effect of salicylates on insulin sensitivity (2001)

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