gebhart/patrepeval huggingface dataset:
Bias in the <i>Listeria monocytogenes</i> Enrichment Procedure: Lineage 2 Strains Outcompete Lineage 1 Strains in University of Vermont Selective Enrichments (2005)

Listeria monocytogenes can be isolated from a range of food products and may cause food-borne outbreaks or sporadic cases of listeriosis. L. monocytogenes is divided into three genetic lineages and 13 serotypes. Strains of three serotypes (1/2a, 1/2b, and 4b) are associated with most human cases of listeriosis. Of these, strains of serotypes 1/2b and 4b belong to lineage 1, whereas strains of serotype 1/2a and many other strains isolated from foods belong to lineage 2. L. monocytogenes is isolated from foods by selective enrichment procedures and from patients by nonselective methods. The aim of the present study was to investigate if the selective enrichment procedure results in a true representation of the subtypes of L. monocytogenes present in a sample. Eight L. monocytogenes strains (four lineage 1 strains and four lineage 2 strains) and one Listeria innocua strain grew with identical growth rates in the nonselective medium brain heart infusion (BHI), but differed in their growth rate in the selective medium University of Vermont medium I (UVM I). When coinoculated in UVM I, some strains completely outgrew other strains. This outcome was dependent on the lineage of L. monocytogenes rather than the individual growth rate of the strains. When inoculated at identical cell densities in UVM I, L. innocua outcompeted L. monocytogenes lineage 1 strains but not lineage 2 strains. In addition, lineage 2 L. monocytogenes strains outcompeted lineage 1 L. monocytogenes strains in all combinations tested, indicating a bias in strains selected by the enrichment procedures. Bias also occurred when coinoculating two lineage 2 or lineage 1 strains; however, it did not appear to correlate with origin (clinical versus food). Identical coinoculation experiments in BHI suggested that the selective compounds in UVM I and II influenced this bias. The results of the present study demonstrate that the selective procedures used for isolation of L. monocytogenes may not allow a true representation of the types present in foods. Our results could have a significant impact on epidemiological studies, as lineage 1 strains, which are often isolated from clinical cases of listeriosis, may be suppressed during enrichment by other L. monocytogenes lineages present in a food sample.
Résultats et réflexions sur une série de 156 hémorragies sous arachnoïdiennes (HSA) anévrismales de grades cliniques IV et V (WFNS) (1996)

info:eu-repo/semantics/nonPublished
Cation diffusion in calcite: Determining closure temperatures and the thermal history for the Allan Hills 84001 meteorite (1998)

The presence of zoned Fe, Mg, Ca, and Mn in the carbonate phases associated with the cracks and inclusions of the Allan Hills (ALH) 84001 meteorite provides evidence for constraining the thermal history of the meteorite. Using self- and tracer-diffusion coefficients obtained from laboratory experiments on natural calcite, cooling rates are calculated for various temperatures and diffusion distances to assist in the evaluation of the compositional zoning associated with the carbonate phases in ALH 84001. The closure temperature model provides the average temperature below which compositional zoning will be preserved for a given cooling rate, that is, the temperature at which diffusion will be ineffective in homogenizing the phase. The validity of various theories for the formation of the carbonate globules may be examined, therefore, in view of the diffusion-limited kinetic constraints. Experiments using a thin film-mineral diffusion couple and ion microprobe for depth profiling analysis were performed for the temperature range of 550-800 degrees C to determine self- and tracer-diffusion coefficients for Ca and Mg and in calcite. The resulting activation energies for Ca (Ea(Ca) = 271 +/- 80 kJ/mol) and for Mg (Ea(Mg) = 284 +/- 74 kJ/mol) were used then to calculate a series of cooling rate, grain size, and closure temperature curves. The data indicate, for example, that by the diffusion of Mg in calcite, a 10 micrometers compositional zone would be completely homogenized at a temperature of 300 degrees C for cooling rates <100 K/Ma. These data provide no constraint on formation models that propose a low-temperature fluid precipitation mechanism; however, they indicate that the carbonate globules were not exposed to a high-temperature environment for long time scales following formation.
Leonardo Reviews (2003)

August 01 2003 From Energy to Information: Representation in Science and Technology, Art, and Literature From Energy to Information: Representation in Science and Technology, Art, and Literature edited by BruceClarke and Linda DalrympleHenderson. Stanford Univ. Press, Stanford, CA, U.S.A., 2002. 364 pp., illus. ISBN 0-8047-4176-1. Robert Pepperell Robert Pepperell Polar (Posthuman Laboratory for Arts Research). E-mail:pepperell@ntlworld.com. Search for other works by this author on: This Site Google Scholar Author and Article Information Robert Pepperell Polar (Posthuman Laboratory for Arts Research). E-mail:pepperell@ntlworld.com. Online ISSN: 1530-9282 Print ISSN: 0024-094X © 2003 ISAST2003 Leonardo (2003) 36 (4): 326–328. https://doi.org/10.1162/leon.2003.36.4.326 Cite Icon Cite Permissions Share Icon Share Facebook Twitter LinkedIn MailTo Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Search Site Citation Robert Pepperell; From Energy to Information: Representation in Science and Technology, Art, and Literature. Leonardo 2003; 36 (4): 326–328. doi: https://doi.org/10.1162/leon.2003.36.4.326 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsLeonardo Search Advanced Search This content is only available as a PDF. © 2003 ISAST2003 Article PDF first page preview Close Modal You do not currently have access to this content.
TargetableSignalingPathwayMutationsAreAssociatedwith Malignant Phenotype in IDH-Mutant Gliomas (2014)

Purpose:Isocitratedehydrogenase(IDH)genemutationsoccurinlow-gradeandhigh-gradegliomas.We sought to identify the genetic basis of malignant phenotype heterogeneity in IDH-mutant gliomas. Methods: We prospectively implanted tumor specimens from 20 consecutive IDH1-mutant glioma resections into mouse brains and genotyped all resection specimens using a CLIA-certified molecular panel. Gliomas with cancer driver mutations were tested for sensitivity to targeted inhibitors in vitro. Associations between genomic alterations and outcomes were analyzed in patients. Results: By 10 months, 8 of 20 IDH1-mutant gliomas developed intracerebral xenografts. All xenografts maintained mutant IDH1 and high levels of 2-hydroxyglutarate on serial transplantation. All xenograft- producing gliomas harbored lineage-defining mutations in CIC (oligodendroglioma) or TP53 (astrocy- toma), and6of 8additionally hadactivatingmutationsinPIK3CAoramplification ofPDGFRA,MET,orN- MYC. Only IDH1 andCIC/TP53 mutations were detected in non-xenograft-forming gliomas (P ¼0.0007). Targeted inhibition of the additional alterations decreased proliferation in vitro. Moreover, we detected alterationsinknowncancerdrivergenesin13.4%ofIDH-mutantgliomapatients,includingPIK3CA,KRAS, AKT ,o rPTEN mutation or PDGFRA, MET ,o rN-MYC amplification. IDH/CIC mutant tumors were associated with PIK3CA/KRAS mutations whereas IDH/TP53 tumors correlated with PDGFRA/MET ampli- fication. Presence of driver alterations at progression was associated with shorter subsequent progression- free survival (median 9.0 vs. 36.1 months; P ¼ 0.0011). Conclusion: A subset of IDH-mutant gliomas with mutations in driver oncogenes has a more malignant phenotype in patients. Identification of these alterations may provide an opportunity for use of targeted therapies in these patients. Clin Cancer Res; 20(11); 2898-909. � 2014 AACR.
Characterization of Ruthenium Oxide Nanocluster as a Cocatalyst with (Ga<sub>1-<i>x</i></sub>Zn<i><sub>x</sub></i>)(N<sub>1-<i>x</i></sub>O<i><sub>x</sub></i>) for Photocatalytic Overall Water Splitting (2005)

The formation and structural characteristics of Ru species applied as a cocatalyst on (Ga(1)(-)(x)()Zn(x)())(N(1)(-)(x)()O(x)()) are examined by scanning electron microscopy, X-ray photoelectron spectroscopy, and X-ray absorption spectroscopy. RuO(2) is an effective cocatalyst that enhances the activity of (Ga(1)(-)(x)()Zn(x)())(N(1)(-)(x)()O(x)()) for overall water splitting under visible-light irradiation. The highest photocatalytic activity is obtained for a sample loaded with 5.0 wt % RuO(2) from an Ru(3)(CO)(12) precursor followed by calcination at 623 K. Calcination is shown to cause the decomposition of initial Ru(3)(CO)(12) on the (Ga(1)(-)(x)()Zn(x)())(N(1)(-)(x)()O(x)()) surface (373 K) to form Ru(IV) species (423 K). Amorphous RuO(2) nanoclusters are then formed by an agglomeration of finer particles (523 K), and the nanoclusters finally crystallize (623 K) to provide the highest catalytic activity. The enhancement of catalytic activity by Ru loading from Ru(3)(CO)(12) is thus shown to be dependent on the formation of crystalline RuO(2) nanoparticles with optimal size and coverage.
Extraction of Breathing Signal and Suppression of Its Effects in Oscillometric Blood Pressure Measurement (2011)

Breathing causes fluctuations in blood pressure and contributes to variations in blood pressure estimates. In order to reduce the variability in the blood pressure estimates induced by breathing, either the breathing signal should be removed from the oscillometric blood pressure signal, or its effects should be suppressed. This paper presents a hybrid method that combines homomorphic and adaptive signal processing techniques to extract the breathing signal from the oscillometric signal with or without a simultaneously recorded electrocardiogram (ECG). The quality of the extracted breathing signal and the depth of breathing are assessed using the reference breathing signals. The breathing signals extracted using the accompanying ECG signal were found to be superior in quality compared to the ones extracted from the oscillometric waveform. The blood pressure estimates were evaluated before and after the breathing suppression techniques were implemented. As a result of the breathing suppression, the fluctuation of the systolic and diastolic blood pressure estimates obtained from a database of 85 healthy subjects is reduced.
Constrained Empirical Risk Minimization Framework for Distance Metric Learning (2012)

Distance metric learning (DML) has received increasing attention in recent years. In this paper, we propose a constrained empirical risk minimization framework for DML. This framework enriches the state-of-the-art studies on both theoretic and algorithmic aspects. Theoretically, we comprehensively analyze the generalization by bounding the sample and the approximation errors with respect to the best model. Algorithmically, we carefully derive an optimal gradient descent by using Nesterov's method, and provide two example algorithms that utilize the logarithmic loss and the smoothed hinge loss, respectively. We evaluate the new framework on data classification and image retrieval experiments. Results show that the new framework has competitive performance compared with the representative DML algorithms, including Xing's method, large margin nearest neighbor classifier, neighborhood component analysis, and regularized metric learning.
A low-cost, multiplexed electrophysiology system for chronic &#x03BC;ECoG recordings in rodents (2014)

Micro-Electrocorticography (μECoG) offers a minimally invasive, high resolution interface with large areas of cortex. However, large arrays of electrodes with many contacts that are individually wired to external recording systems are cumbersome and make chronic recording in freely behaving small animals challenging. Multiplexed headstages overcome this limitation by combining the signals from many electrodes to a smaller number of connections directly on the animal's head. Commercially available multiplexed headstages provide high performance integrated amplification, multiplexing and analog to digital conversion. However, the cost of these systems can be prohibitive for small labs or for experiments that require a large number of animals to be continuously recorded at the same time. Here we have developed a multiplexed 60-channel headstage amplifier optimized to chronically record electrophysiological signals from high-density μECoG electrode arrays. A single, ultraflexible (2 mm thickness) microHDMI cable provided the data interface. Using low cost components, we have reduced the cost of the multiplexed headstage to ~$125. Paired with a custom interface printed circuit board (PCB) and a general purpose data acquisition system (M-series DAQ, National Instruments), an inexpensive and customizable electrophysiology system is assembled. Open source LabVIEW software that we have previously released controlled the system. It can also be used with other open source neural data acquisition packages. Combined, we have presented a scalable, low-cost platform for high-channel count electrophysiology.
[Synthesis and physico-chemical parameters of clanobutin (author's transl)]. (1979)

Synthesis and physico-chemical parameters (pKa, partition coefficient, permeability coefficient, critical micelle concentration, surface pressure, etc.) of 4-[4-chloro-N-(4-methoxy-phenyl)-benzamido]-butyric acid (clanobutin) are described.
Quantitative Targeted Proteomics of Pancreatic Cancer: Deoxycytidine Kinase Protein Level Correlates to Progression-Free Survival of Patients Receiving Gemcitabine Treatment (2015)

The purpose of the present study is to identify the determinant(s) of gemcitabine (dFdC)-sensitivity in pancreatic cancer tissues of patients treated with dFdC alone and in pancreatic cancer cell lines exposed to dFdC in vitro. Protein expression levels of 12 enzymes and 13 transporters potentially involved in transport and metabolism of dFdC in pancreatic cancer cell lines and tissues were quantified by means of our LC-MS/MS-based quantitative targeted proteomics technology. Protein expression levels of deoxycytidine kinase (dCK), uridine monophosphate-cytidine monophosphate (UMP-CMP) kinase, cytosolic nucleotidase III (cN-III), and equilibrative nucleoside transporter 1 (ENT1) were significantly correlated with IC50 or 1/IC50 in five cell lines with different sensitivities to dFdC (p < 0.05). Expression levels of the selected proteins in pancreatic cancer tissues of 10 patients with different progression-free survival (PFS) (49-955 days) were quantified, and their relationship with PFS was examined. Only the protein expression level of dCK was significantly correlated with PFS (p < 0.05). Multiple regression analysis was also performed, and combinations of ENT1, UMP-CMP kinase, CTPS1, and dCK were highly correlated with PFS. Our results indicate that the protein expression level of dCK in pancreatic cancer tissue is a good predictor of PFS, and thus dCK may be the best biomarker of dFdC sensitivity in pancreatic cancer patients treated with dFdC, although other proteins would also contribute to dFdC-sensitivity at the cellular level in vivo and in vitro.
Spectrotype analysis and clonal characteristics of human anti‐Gal alpha1–3Gal antibodies (2002)

Galalpha1-3Gal (anti-Gal), a polyclonal so-called natural antibody (Ab), is present in large amounts in human serum not only as IgG-, but also as IgM- and IgA-isotypes. It has gained a particular interest in the context of xenotransplantation, because the endothelial pig cells express the terminal Galalpha1-3Gal determinant on several adhesion molecules. Little is known of it's function and direct examination of the structure of the Ig genes responsible for coding anti-Gal is lacking. We used the technique of isoelectric focussing (IEF)/affinity immunoblotting for direct analysis of the clonal distribution and spectrotype analysis of IgM- and IgG anti-Gal. By single cell analysis of magnetic bead and fluorescent-activated cell sorter (FACS) isolated mature anti-Gal bearing human B cells from whole blood we analyzed the VH gene families involved in anti-Gal production. Oligoclonal and individually distinct IgG banding patterns were found with isoelectric points between 4 and 9. IgM spectrotypes revealed to be more uniform with a polyclonal banding pattern of more than 12 bands at a pH between 4.7 and 7. IgG- and IgM-banding patterns over a period of 6 months remained unchanged. Single cell polymerase chain reaction (PCR), with all family specific primers, revealed the use of the VH2f gene family for the IgG2 isoptype. The differences found in the spectrotype banding patterns of IgG and IgM could be explained by the suggestion that anti-Gal IgM were produced by the use of unmutated germline genes and the possibility of the absence of somatic mutations. The greater clonal heterogeneity in the IgG population could be explained by somatic hypermutations during the switch from IgM to IgG. The use of this VH2f gene family, which is also involved in the generation of Abs against bacterial pathogens, could mean that this is a predominant region used for the generation of such natural occurring antibodies.
Protein adsorption and platelet adhesion onto polyurethane grafted with methoxy‐poly(ethylene glycol) methacrylate by plasma technique (1993)

Graft polymerization of methoxy-poly(ethylene glycol) methacrylate, an ester of methacrylic acid and monomethoxy-poly(ethylene glycol) (PEO), was performed onto a polyetherurethane (PU) film and tube under different polymerization conditions by a plasma treatment technique. The surface of grafted PU film was characterized by staining with dye, x-ray photoelectron spectroscopy, contact angle, and zeta potential. All these measurements indicated that water-soluble chains were immobilized on the PU surface, their location being restricted to the film surface region. The PU surface showed reduced protein adsorption in vitro and reduced platelet adhesion in vitro and ex vivo. The optimum graft density suppressing the protein adsorption was as low as 5 micrograms cm(-2). When a small amount of dimethacrylate was added to the monomer solution for graft polymerization to introduce crosslinking in the grafted layer, protein adsorption was further slightly reduced. The extent of reduction in serum albumin adsorption was always less than that of gamma-globulin. Although platelet adhesion was largely reduced by the surface graft polymerization, a definite amount of protein was always adsorbed to the grafted surface.
Influence of Morphological Transition on Crystallization Process in Si (2010)

Using CO2 laser equipped electro-magnetic levitator, we carried out the crystallization of Si at undercoolings from 0 K to 200 K. From the point of the interface morphologies, the relationship between growth velocities and undercoolings was classified into two regions, Iand II, respectively. In regionIwhere the undercooling is approximately less than 100 K, thin plate crystals whose interface consists of faceted plane were observed. In region II, the morphology of growing crystals changed to massive dendrites. Although the interface morphologies in region II look quite different from that in regionI, the growth velocities are expressed by two dimensional (2D) nucleation-controlled growth model, and at undercoolings larger than 150 K, the growth velocities asymptotically close to the analysis of the mono-parametric linear kinetics growth model. In this stage, the kinetic coefficient of 0.1 m/sK is equivalent with that derived by the diffusion-controlled growth model. This result means that with increase of undercooling, the rate-determining factor changes from 2D nucleation on the faceted interface to random incorporation of atoms on the rough interface.
Determination of formaldehyde in air by flow injection using pararosaniline and spectrophotometric detection (1989)

Two flow injection (Fl) methods, conventional and stopped-flow, are described for the determination of formaldehyde based on its reaction with pararosaniline in the presence of sulphite ion followed by spectrophotometric detection at 570 nm. The calibration graphs are linear over the ranges 2.0–50 and 0.2–10 µg ml–1 of formaldehyde for conventional and stopped-flow Fl, respectively. The coefficient of variation was 6.3% at the 0.6 µg ml–1 level in the stopped-flow mode, the detection limit being 0.1 µg ml–1 of formaldehyde. Sampling rates of 41 and 18 samples h–1 were achieved in the conventional and stopped-flow modes, respectively, this being a major advantage of these methods. The effect of several organic and inorganic species was studied and only low relative molecular mass aldehydes were found to interfere. The stopped-flow method was applied to the determination of formaldehyde in air in work environments and its accuracy was confirmed by comparing the results with those obtained using the standard chromotropic acid method.
Effect of Antibiotics on Growth and Nutrient Absorption of Chicks (1963)

IN A recent study from this laboratory, on the mode of action of antibiotics as growth stimulants for young animals, a transitory period of growth depression was observed around the 8th day of life in chicks fed an antibiotic-free, casein-sucrose diet (Eyssen and De Somer, 1963). The inhibition of weight gain was found to be associated with decreased efficiency of feed utilization and malabsorption of fats and carbohydrates, and the syndrome was most pronounced when sucrose was fed as the sole source of dietary carbohydrate. Addition to the feed of 20 p.p.m. of virginiamycin, an antibiotic active only against Gram-positive microorganisms, resulted in improved intestinal absorption and stimulated growth. As a result of these studies, the hypothesis was proposed that the growth-stimulating effect of antibiotics is most likely due to suppression of intestinal Gram-positive microorganisms which interfere with the absorption of nutrients. The present investigations were performed to obtain…
Continuous and Simultaneous On-Line Measurements of &OV0312;o2 and &OV0312;co2 during Endotracheal Anesthesia (1982)

A single method was developed for the continuous measurement of oxygen consumption (VO2) and carbon dioxide production (VCO2) during endotracheal anesthesia. The total vented flow from a Bain circuit was measured during anesthesia in 28 adult patients and was found to attain at least 97% of a 6-L/min fresh gas inflow (FGI). Therefore, the circuit overflow was assumed to approximate the FGI. Total volume of vented oxygen was calculated by multiplying FGI by oxygen concentration in the vented (mixed expired) gas. VO2 was assessed as the difference between the oxygen volumes entering and leaving the circuit. VCO2 was derived from the product of FGI and mixed expired CO2 concentration. VO2 measured on the Bain circuit correlated with measurements made on a non-breathing circuit (n = 60 pairs, r = 0.99). A good correlation was also found between VCO2 obtained on both circuits (n = 60 pairs, r = 0.99).