gebhart/patrepeval huggingface dataset:
Quantification of Peptide <i>m</i>/<i>z</i> Distributions from <sup>13</sup>C-Labeled Cultures with High-Resolution Mass Spectrometry (2014)

Isotopic labeling studies of primary metabolism frequently utilize GC/MS to quantify (13)C in protein-hydrolyzed amino acids. During processing some amino acids are degraded, which reduces the size of the measurement set. The advent of high-resolution mass spectrometers provides a tool to assess molecular masses of peptides with great precision and accuracy and computationally infer information about labeling in amino acids. Amino acids that are isotopically labeled during metabolism result in labeled peptides that contain spatial and temporal information that is associated with the biosynthetic origin of the protein. The quantification of isotopic labeling in peptides can therefore provide an assessment of amino acid metabolism that is specific to subcellular, cellular, or temporal conditions. A high-resolution orbital trap was used to quantify isotope labeling in peptides that were obtained from unlabeled and isotopically labeled soybean embryos and Escherichia coli cultures. Standard deviations were determined by estimating the multinomial variance associated with each element of the m/z distribution. Using the estimated variance, quantification of the m/z distribution across multiple scans was achieved by a nonlinear fitting approach. Observed m/z distributions of uniformly labeled E. coli peptides indicated no significant differences between observed and simulated m/z distributions. Alternatively, amino acid m/z distributions obtained from GC/MS were convolved to simulate peptide m/z distributions but resulted in distinct profiles due to the production of protein prior to isotopic labeling. The results indicate that peptide mass isotopologue measurements faithfully represent mass distributions, are suitable for quantification of isotope-labeling-based studies, and provide additional information over existing methods.
[High intensity focused ultrasound for localized prostate cancer]. (2000)

High-intensity focused ultrasound (HIFU) is a noninvasive treatment that induces complete coagulative necrosis of a tumor at depth through the intact skin. We evaluated a biochemical disease-free rate, safety and morbidity for localized prostate cancer treated with HIFU. A total of 132 consecutive patients with stage T1c-2N0M0 localized prostate cancer underwent HIFU using Sonablate-500 (Focus Surgery, Indianapolis, USA). The 5-year biochemical disease-free rate in all patients was 67%. The 5-year biochemical disease-free rates for patients with a pretreatment PSA less than 10 ng/ml, 10.01 to 20.0 ng/ml, 20.01-30.0 ng/ml and more than 30.01 ng/ml were 88%, 67%, 34% and 13% (log rank test, p < 0.0001), respectively. HIFU therapy appears to be a safe, efficacious and minimally invasive therapy for patients with localized prostate cancer.
Liquid Sampling–Atmospheric Pressure Glow Discharge as a Secondary Excitation Source for Laser Ablation-Generated Aerosols: Parametric Dependence and Robustness to Particle Loading (2015)

Liquid sampling-atmospheric pressure glow discharge (LS-APGD) microplasma is being developed as a secondary vaporization-excitation source for the optical emission analysis of laser ablation (LA)-generated particle populations. The practicalities of this coupling are evaluated by determining the influence of source parameters on the emission response and the plasma's robustness upon LA introduction of easily ionized elements (EIEs). The influence of discharge current (45-70 mA), LA carrier gas flow rate (0.1-0.8 L min(-1)), and electrode separation distance (0.5-3.5 mm) was studied by measuring Cu emission lines after ablation of a brass sample. Best emission responses were observed for high-discharge currents, low He carrier gas flow rates, and relatively small (<1.5 mm) electrode gaps. Plasma robustness and spectroscopic matrix effects were studied by monitoring Mg(II) : Mg(I) intensity ratios and N2-derived plasma rotational temperatures after the ablation of Sr- and Ca-containing pellets. Plasma robustness investigations showed that the plasma is not appreciably affected by the particle loadings, with the microplasma being slightly more ionizing in the case of Ca introduction. In neither case did the concentration of the concomitant element change the robustness values, implying a high level of robustness. Introduction of the LA particles results in slight increases in the rotational temperatures (∼10% relative), with Ca-containing particles having a greater effect than Sr-containing particles. The observed variation of 9% in the plasma rotational temperature is in the same order of magnitude as the short-term reproducibility determined by the proposed LA-LS-APGD system. The determined rotational temperatures ranged from 1047 to 1212 K upon introducing various amounts of Ca and Sr. The relative immunity to LA particle-induced matrix effects is attributed to the relatively long residence times and high power densities (>10 W mm(-3)) of the LS-APGD microplasma.
A Family of Locking Protocols for Database Systems that Are Modeled by Directed Graphs (1982)

This paper is concerned with the problem of ensuring the integrity of database systems that are accessed concurrently by a number of independent asychronously running transactions. It is assumed that the database system is partitioned into small units that are referred to as the database entities. The relation between the entities is represented by a directed acyclic graph in which the vertices correspond to the database entities and the arcs correspond to certain access rights. We develop a family of non-two-phase locking protocols for such systems that will be shown to ensure serializability and deadlock-freedom. This family is sufficientdy general to encompass all the previously developed non-two-phase lose locking protocols as well as a number of new protocols. One of these new protocols that seems to be particularly useful is also presented in this paper.
Adenoma Detection Rate and Risk of Colorectal Cancer and Death (2014)

The adenoma detection rate was inversely associated with the risks of interval colorectal cancer, advanced-stage interval cancer, and fatal interval cancer. (Funded by the Kaiser Permanente Community Benefit program and the National Cancer Institute.).
Multiparticulate Chitosan-Dispersed System for Drug Delivery (2003)

A multiparticulate chitosan-dispersed system (CDS), which is composed of the drug reservoir and the drug release-regulating layer, was developed for drug delivery. The drug release-regulating layer is a mixture of water-insoluble polymer and chitosan powder. The drug is released from CDS pellets in all regions of the gastrointestinal tract (from the stomach to the colon). CDS pellets containing chitosan powder were designed to dissolve chitosan powder partly in the release-regulating layer in the stomach and release part of drug. After passing through the stomach, the drug is released from CDS pellets at a constant speed in the small intestine. In the large intestine, CDS pellets were designed to disintegrate the remaining chitosan powder at an accelerated speed and the remaining drug in CDS pellets is released. The drug release rate can be controlled with the thickness of the chitosan-dispersed water-insoluble layer. Furthermore, for colon-specific drug delivery, an additional outer enteric coating is necessary to prevent drug release from CDS pellets in the stomach, because the chitosan-dispersed water-insoluble layer dissolves gradually under acidic conditions. The resulting enteric-coated CDS (E-CDS) pellets were found to permit colon-specific drug delivery. In this study, the multiparticulate CDS was adopted not only for colon-specific drug delivery but also for sustained drug release.
A new class of dual-mode directional couplers for compact dual-polarization beam-forming networks (1997)

A new class of directional couplers for the realization of compact dual-polarization beam-forming networks is presented. This component functions as two independent directional couplers for the TE/sub 01/ mode and the TE/sub 10/ mode of a rectangular waveguide. The two modes are not coupled. Different values of the coupling for the two modes can be obtained. This coupler can be used twice for two orthogonal polarizations. Therefore a considerable reduction of size and complexity of the overall network can be obtained. Experimental data for a 3-dB dual mode coupler are also presented here.
Partitioning strategy based on safety in integrated modular avionics (2016)

Integrated Modular Avionics, which has replaced traditional federal architecture, is now widely used in the aircraft. Robust partitioning is adopted by new architecture to cope with the failure propagation due to resource sharing. However, if the activity of allocating applications to partitions doesn't consider the common cause failure and coupling relations among avionic functions, it can intensify the failure propagation. At present, a lot of researches take into account the application software's functionality and criticality in the software configuration activities, but not include other factors which are also indispensable. In this paper, we proposed a partitioning method from the safety perspective. Firstly, we identified the process of allocating applications to partitions from the partitioning configuration activities referred to Do-297 and built the partitioned system model. Three safety factors which should be satisfied by the process were introduced. Then, we presented the safety constraints based on the safety factors. Finally, we proposed the partitioning strategy on the basic of safety constraints and partitioned system model. This partitioning strategy will be the theoretical basis for the scientific partitioning method in future and ensure the implementation of robust partitioning in Integrated Modular Avionics.
Combined Omics Analysis Identifies Transmembrane 4 L6 Family Member 1 as a Surface Protein Marker Specific to Human Mesenchymal Stem Cells (2010)

Mesenchymal stem cells (MSCs) are promising for cell therapy and regenerative medicine; but their lack of specific markers renders the cell culture at potential contamination risk with other cell types, in particular, fibroblasts. In this study, we mapped 2 differential transcriptome data of MSCs compared, one to mononuclear cells and the other to fibroblasts, onto the membrane proteome data, the analysis of which led to an identification of transmembrane 4 L6 family member 1 (TM4SF1) as a surface protein marker candidate that could discriminate MSCs simultaneously from blood cells and fibroblasts. Our analyses confirmed that TM4SF1 was abundantly expressed on MSCs but neither on other blood/tissue cells nor on fibroblasts. TM4SF1 immunoselection from bone marrow and adipose tissues yielded homogeneous cell populations that were highly similar to MSCs, in terms of morphology, immunophenotype, and differentiation potential. These findings indicate that TM4SF1 can serve as a surface protein marker which singly identifies MSCs from diverse cell sources, in particular, fibroblast-rich connective tissues.
<title>Optical active gallium arsenide probes for scanning probe microscopy</title> (1998)

In order to produce microelectromechanical systems on base of gallium arsenide it is necessary to develop novel etching techniques. The conventional dip etching is not suitable to fabricate such systems reliably and with sufficiently small thickness variations. To overcome this problem we used a modified spray etching technique. A comparison between both methods is given.
Motor unit potential abnormalities in multiple sclerosis: further evidence for a peripheral nervous system defect. (1980)

We have recently reported abnormalities of single fibre EMG in patients with multiple sclerosis. The present study applies quantitative electrophysiological techniques to the same group of patients. The number of motor units in the extensor digitorum brevis muscle was measured and their characteristics recorded. Also the shortest distal motor latency and fastest motor conduction velocities were estimated. Abnormalities suggesting a patchy denervating/reinnervating process due to pathology in the intramuscular nerve network or at the endplate were found in a number of patients. There was a good correlation between patients with abnormal motor unit potentials and those with abnormal single fibre EMG "jitter".
Comparative Results of Autogenous Ignition Temperature Measurements by ASTM G 72 and Pressurized Scanning Calorimetry in Gaseous Oxygen (1986)

The autogenous ignition temperature of four materials was determined by ASTM (G 72) and pressurized differential scanning calorimetry at 0.68-, 3.4-, and 6.8-MPa oxygen pressure. All four materials were found to ignite at lower temperatures in the ASTM method. The four materials evaluated in this program were Neoprene®, Vespel SP-21®, Fluorel E-2160®, and nylon 6/6.
Autonomic Management of Dynamically Partially Reconﬁgurable FPGA Architectures Using Discrete Control (2013)

International audience
Local logic substitution algorithm for post-layout re-synthesis (2003)

As the interconnect delay has become the most dominant factor of circuit performances, logic synthesis results without considering interconnect delay tend to lead to unsatisfactory circuit performance. In this paper, a post-layout re-synthesis scheme is proposed to tackle such a problem. In this algorithm, a local logic substitution scheme based on Alternative Logic Equivalent Block (ALEB) is used. Using the interconnect delay information provided by placement, this algorithm improves the circuit delay by substitutions of local logic blocks located on critical paths, followed by an incremental placement, is applied upon those altered blocks. The experimental results show that the algorithm reduces nearly 30% of the critical path delay without causing much area overhead.
Effect of fluorine implantation dose on boron thermal diffusion in silicon (2004)

This paper investigates how the thermal diffusion of boron in silicon is influenced by a high energy fluorine implant with a dose in the range 5×1014–2.3×1015cm−2. Secondary Ion Mass Spectroscopy (SIMS) profiles of boron marker layers are presented for different fluorine doses and compared with fluorine profiles to establish the conditions under which thermal boron diffusion is suppressed. The (SIMS) profiles show significantly reduced boron thermal diffusion above a critical F+ dose of 0.9–1.4×1015cm−2. Fitting of the measured boron profiles gives suppressions of the boron thermal diffusion coefficient by factors of 1.9 and 3.7 for F+ implantation doses of 1.4×1015 and 2.3×1015cm−2, respectively. The suppression of boron thermal diffusion above the critical fluorine dose correlates with the appearance of a shallow fluorine peak on the (SIMS) profile in the vicinity of the boron marker layer. This shallow fluorine peak is present in samples with and without boron marker layers, and hence it is not due to a chemical interaction between the boron and the fluorine. Analysis of the (SIMS) profiles and cross-section Transmission Electron Microscope micrographs suggests that it is due to the trapping of fluorine at vacancy-fluorine clusters, and that the suppression of the boron thermal diffusion is due to the effect of the clusters in suppressing the interstitial concentration in the vicinity of the boron profile.
Fused chemical reactions to remediate paraffin plugging in sub-sea pipelines. (2004)

In this work, a timed release scheme of the citric acid-catalyst was used to fuse the highly exothermic reaction between ammonium chloride and sodium nitrite in a fused chemical reaction (FCR) system. The timed release was obtained by encapsulating the acid-catalyst in gelatin capsules then coating the capsules with a water-soluble polymer. The highly exothermic FCR system is demonstrated to be a feasible solution for the billion-dollar problem of paraffin deposition during crude oil production and transportation operations in sub-sea pipelines. Studies of the exothermic reaction in an isothermal reactor showed that hydrogen ions catalyze the reaction by changing the concentration of the reacting species, not by changing the reaction pathways. The rate-limiting step involves the S<sub>N</sub>2 reaction between aqueous molecular ammonia and nitrogen trioxide to form nitrosamine. The activation energy of the reaction was found to be about 65.7 kJ/mol experimentally which compares very favorably (within 11%) with the value found from molecular modeling. The facilitated diffusion of hydrogen ions away from the polymer interface is the principal process that determines the rate limiting step as well as the overall rate of the polymer dissolution. The facilitated diffusion effect increases significantly with an initial increase in the carrier concentration, then approaches a limit at high carrier concentration. However, there are optimum values of the carrier's <italic>pK<sub>a</sub></italic> and of the solution pH which give a maximum facilitation effect. A homogenous chemico-diffusion model can predict concentration profiles of all species across the diffusion boundary layer and polymer dissolution rates which agree well with experimental results. Good agreement between simulation and experimental results for the FCR system in both batch and flow conditions was achieved. Batch experiments showed that the heat release is controlled by the thickness of the polymeric coating and can be delayed as long as 20 hours. Flow experiments demonstrated that the FCR system could be controlled to provide a substantial amount of effective heat in-situ. This large amount of effective heat is sufficient to soften and melt the wax deposit. The model for the FCR system in flow conditions was also extended to apply in a typical sub-sea pipeline.
Glyceraldehyde 3-phosphate dehydrogenase is bound to the fibrous sheath of mammalian spermatozoa (1997)

Evidence is provided that the glycolytic enzyme glyceraldehyde 3-phosphate dehydrogenase is covalently linked to the fibrous sheath. The fibrous sheath is a typical structure of mammalian spermatozoa surrounding the axoneme in the principal piece of the flagellum. More than 90% of boar sperm glyceraldehyde 3-phosphate dehydrogenase activity is sedimented after cell disintegration by centrifugation. Detergents, different salt concentrations or short term incubation with chymotrypsin do not solubilize the enzyme, whereas digestion with trypsin or elastase does. Short term incubation with trypsin (15 minutes) even resulted in an activation of glyceraldehyde 3-phosphate dehydrogenase. Purification on phenyl-Sepharose yielded a homogeneous glyceraldehyde 3-phosphate dehydrogenase as judged from gel electrophoresis SDS-PAGE and native gradient PAGE. The molecular masses are 41.5 and 238 kDa, respectively, suggesting native glyceraldehyde 3-phosphate dehydrogenase to be a hexamer. Rabbit polyclonal antibodies raised to purified glyceraldehyde 3-phosphate dehydrogenase show a high specificity for mammalian spermatozoal glyceraldehyde 3-phosphate dehydrogenase, while other proteins of boar spermatozoa or the muscle glyceraldehyde 3-phosphate dehydrogenase are not labelled. Immunogold staining performed in a post-embedding procedure reveals the localization of glyceraldehyde 3-phosphate dehydrogenase along the fibrous sheath in spermatozoa of boar, bull, rat, stallion and man. Other structures such as the cell membrane, dense fibres, the axoneme or the mitochondria are free of label. During the process of sperm maturation, most of the cytoplasm of the sperm midpiece is removed as droplets during the passage through the epididymis. The labelling of this cytoplasm, in immature boar spermatozoa and in the droplets, indicates that glyceraldehyde 3-phosphate dehydrogenase is completely removed from the midpiece during sperm maturation in the epididymis. The inverse compartmentation of the glycolytic enzyme and mitochondria in the mammalian sperm flagella suggests that ATP-production in the principal piece mainly occurs by glycolysis and in the midpiece by respiration.
Clinical Implications of Hedgehog Pathway Signaling in Prostate Cancer (2015)

Activity in the Hedgehog pathway, which regulates GLI-mediated transcription, is important in organogenesis and stem cell regulation in self-renewing organs, but is pathologically elevated in many human malignancies. Mutations leading to constitutive activation of the pathway have been implicated in medulloblastoma and basal cell carcinoma, and inhibition of the pathway has demonstrated clinical responses leading to the approval of the Smoothened inhibitor, vismodegib, for the treatment of advanced basal cell carcinoma. Aberrant Hedgehog pathway signaling has also been noted in prostate cancer with evidence suggesting that it may render prostate epithelial cells tumorigenic, drive the epithelial-to-mesenchymal transition, and contribute towards the development of castration-resistance through autocrine and paracrine signaling within the tumor microenvironment and cross-talk with the androgen pathway. In addition, there are emerging clinical data suggesting that inhibition of the Hedgehog pathway may be effective in the treatment of recurrent and metastatic prostate cancer. Here we will review these data and highlight areas of active clinical research as they relate to Hedgehog pathway inhibition in prostate cancer.
The relation between dicarbocyanine dye fluorescence and the membrane potential of human red blood cells set at varying Donnan equilibria. (1979)

The fluorescence, F, of two dicarbocyanine dyes, diS-C3(5) and diI-C3(5), depends both on the membrane potential, E, and on the intracellular pH, pHc, or human red blood cells. Compositions of isotonic media have been devised in which the equilibrium Donnan potential, E, varies at constant pHc and in which pHc varies at constant E. Dye fluorescence measurements in these suspensions yield calibrations of +1.7 % delta F/mV for diS-C3(5) and +0.6 % delta F/mV for diI-C3 (5). While pHo does not affect F of either dye, changes in pHc of 0.1 unit at constant E cause changes of F equivalent to those induced by 2--3mV. Based on these results, a method is given for estimating changes in E from dye fluorescence in experiments in which E and pHc co-vary. The relation of F to E also depends in a complex way on the type and concentration of cells and dye, and the wavelengths employed. The equilibrium calibration of dye fluorescence, when applied to diffusion potentials induced by 1 microM valinomycin, yields a value for the permeability ratio, PK.VAL/PCl, of 20 +/- 5, in agreement with previous estimates by other methods. The calibration of F is identical both for diffusion potentials and for equilibrium potentials, implying that diC-C3(5) responds to changes in voltage independently of ionic fluxes across the red cell membrane. Changes in the absorption spectra of dye in the presence of red cells in response to changes in E show that formation of nonfluorescent dimers contributes to fluorescence quenching of diS-C3(5). In contrast, only a hydrophobic interaction of dye monomers need be considered for diI-C3(5), indicating the occurrence of a simpler mechanism of fluorescence quenching.