gebhart/patrepeval huggingface dataset:
A Novel Molecular Method for Simultaneous Identification of Vibrio parahaemolyticus 57 K-Serogroups Using Probe Melting Curve Analysis (2021)

The serotyping of <i>Vibrio parahaemolyticus</i>, which is crucial to the surveillance and detection of outbreaks of vibriosis infection, has been widely used in many countries. In this study, we developed a molecular assay, named multiplex ligation reaction based on probe melting curve analysis (MLMA), for simultaneous identification of <i>V. parahaemolyticus</i> 57 K-serogroups. Based on the previous genomes of 418 strains including 39 K-serogroups and the 18 K-serogroups sequences from public databases, we obtained 57 K-serogroups specific gene sequences for designing primers and probes. The developed MLMA assay for identifying the <i>V. parahaemolyticus</i> 57 K-serogroups showed high reproducibility, with the intra- and inter-assay standard deviations and coefficients of variation of no more than 1°C and 1%, respectively. The limit of detection for all gene targets ranged from 0.1 to 1.0 ng/µl. We validated the MLMA assay with a double-blind test identifying 595 <i>V. parahaemolyticus</i> isolates using conventional serotyping methods for comparison. The results showed the kappa value between the MLMA assay and the traditional serological method was 0.936 and that there was a 96.97% consistency rate with conventional serotyping methods for all detected isolates. Additionally, five rare K-serogroups were identified using the MLMA assay, as well as 18 strains that could not be identified using the traditional serotyping method. Thus, the MLMA assay provides a rapid, robust, and promising tool for the molecular serotyping of <i>V. parahaemolyticus</i> K-serogroups and has the potential application to the detection of outbreaks and surveillance of <i>V. parahaemolyticus</i> infection.
Sensibilité de la spectroscopie de réflectance diffuse aux variations d'épaisseur d'une couche mélanique: étude in vitro sur fantômes de peau (2007)

National audience
Finite element simulation of an active noise-canceling scheme (1989)

This paper details a finite-element computer simulation scheme of an axis-symmetric physical setup of an active noise canceling headset. The results of this simulation show the distribution of sound-pressure levels inside the ear canal. Two-dimensional simulations of an axis-symmetric configuration of the ear cup were carried out. A point source was used to cancel out the noise. From these simulations it can be concluded that the noise inside the ear canal can be reduced. The amount of reduction depends on the strength and phase of the canceling source. On the other hand, a point source is not a practical device. To overcome this problem, new structures for speakers have to be created and simulated to check if their radiation is in accordance with that of practical devices. An algorithm proposed earlier by these authors for the estimation of the SPL noise reduction that can be accomplished inside the ear canal has been added. [Work supported by the Florida High Technology and Industry Council.]
Cluster Error Correction for Real-Time Channels by Unbound Rotation of Two-Dimensional Parity-Check Codes (2015)

Circuit-level real-time channels like through-silicon vias generally admit only several levels of logic gates for decoding within a clock cycle. From our study two-dimensional parity check has the greatest potential for on-line monitoring and correcting. The bounded rotation scheme for cyclic decoding is first applied in real-time channels with four times of relative correctable cluster size. An unbound rotation scheme is further proposed for higher cluster error correcting capacitance. For an array with a long length H and a narrow width W, the correctable cluster error size can be improved from W to H. From circuit simulation both proposed schemes take only 1.45 ns and 0.76 ns of time penalties respectively. From block error rate analyses under a reasonable coupling model based on conditional probability posterior to additive white Gaussian noised binary symmetric channels, error rate reduction can be improved to 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</sup> times in a 9 dB SNR.
4-Methoxy-N-[2-(trifluoromethyl)biphenyl-4-ylcarbamoyl]nicotinamide: A Potent and Selective Agonist of S1P1 (2011)

The sphingosine-1-phosphate-1 receptor (S1P1) and its endogenous ligand sphingosine-1-phosphate (S1P) cooperatively regulate lymphocyte trafficking from the lymphatic system. Herein, we disclose 4-methoxy-N-[2-(trifluoromethyl)biphenyl-4-ylcarbamoyl]nicotinamide (8), an uncommon example of a synthetic S1P1 agonist lacking a polar headgroup, which is shown to effect dramatic reduction of circulating lymphocytes (POC = -78%) in rat 24 h after a single oral dose (1 mg/kg). The excellent potency that 8 exhibits toward S1P1 (EC50 = 0.035 μM, 96% efficacy) and the >100-fold selectivity that it displays against receptor subtypes S1P2-5 suggest that it may serve as a valuable tool to understand the clinical relevance of selective S1P1 agonism.
[Accurate placement of central venous catheter--ECG-guided method vs patient height method]. (2002)

Correct positioning of central venous catheters (CVC) is important. We compared the positioning of CVCs by ECG-monitoring via the guidewire and that by method using patient height. "Certofix" triple-lumen CVCs were inserted in 60 cardiac surgical patients via right internal jugular puncture. Of these, 30 were placed with ECG guidance via the guidewire (Group ECG), and 30 with reference to patient height (modified Pere's method) (Group H). The distance from CVC tip to the superior vena cava/right atrial junction (C-J distance) was measured by postoperative chest X-ray. There was no difference in height between the two groups. The depth of insertion of CVC and C-J distance (cm) were 15.1 +/- 0.3 and 3.6 +/- 2.0 in group H and 14.3 +/- 1.5 and 4.9 +/- 1.2 in group ECG, respectively, with no statistically significant differences between the two groups. In one case of group H, the catheter tip was placed in the right atrium. In group ECG, there was a significant correlation between height and the depth of insertion of CVC. In conclusion, ECG guidance via the guidewire is useful for avoiding CVC displacement.
Influence of β<sub>3</sub> Integrin Gene Leu<sup>33</sup>/Pro<sup>33</sup> Polymorphism on Primary Glomerulonephritis (2004)

Our results indicate that beta3 integrin Leu33/Pro33 polymorphism is not a risk factor or a marker of progression in primary glomerulonephritis.
The Stability of Concentrated Thiosulphate Solutions at High Temperature. Part II. The Loss of the Sulphite (1965)

The decomposition of concentrated thiosulphate fixers at elevated temperatures occurs because the sulphite is converted into sulphate and thiosulphate in a reaction catalyzed by the thiosulphate. When the sulphate is gone the thiosulphate decomposes giving sulphur and sulphurous acid which latter is also lost by the above mechanism.
Higher α‐olefins carbonylation in aqueous media by Pd(II) catalysts modified with substituted diphosphine ligands: Aqueous polyketone latices with high solid contents and molecular weights (2009)

Abstract Water‐soluble palladium complexes ci s‐[Pd(L)(OAc) 2 ] ( 1–8 ) (L represents a diphosphine ligands of the general formula CH 2 (CH 2 PR 2 ) 2 , where for a : R  (CH 2 ) 6 OH; b–g : R  (CH 2 ) n P(O)(OEt) 2 , n = 2–6 and n = 8; h : R  (CH 2 ) 3 NH 2 ) have been employed, after activation with a large excess of HBF 4 , for emulsion polymerization of alkenes (propene, butene, and their equimolar mixtures) with carbon monoxide. Aliphatic polyketone lattices with a high solid content (21%), high molecular weight (6.3 × 10 4 g mol −1 ), and narrow polydispersities ( M w / M n ≈ 2) were isolated. The catalytic activity of the dicationic palladium (II) based catalysts, C1–C8 is highly dependent on the length of the alkyl chain of the ligand. Catalyst 3 proved to be highly active for propene/CO copolymers, whereas 6 is active for butene/CO and propene/CO‐butene/CO systems. The presence of methyl β‐cyclodextrin, as a phase‐transfer agent, and undecenoic acid, as an emulsifier, increase the molar mass and the stability of the polyketones and finally the activity of the catalyst. © 2009 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 47: 6715–6725, 2009
Chemical and sonochemical approaches to the formation of VO{sub 2} films and VO{sub 2}-impregnated materials (1997)

A new chemical and chemical/ultrasonic approach to the preparation of VO{sub 2} films and VO{sub 2}-impregnated bulk materials has been developed. In this approach, a V{sub 2}O{sub 5} sol prepared by quenching is used to coat SiO{sub 2} substrates. The resulting gel-film is heat treated in a reducing atmosphere to form a film identified as VO{sub 2} from the results of X-ray diffraction and both optical and resistivity measurements, which reveal the phase transition characteristic of vanadium dioxide. The advantage of this approach to the formation of VO{sub 2} is that the V{sub 2}O{sub 5} sol can be used to impregnate porous materials, which are then heated treated to form an optically active composite material. The switching properties of the VO{sub 2} films are investigated using optical and resistivity measurements, and the results are compared to those obtained for VO{sub 2}-films prepared by more-conventional methods.
An Adaption of the Lucy-Richardson Deconvolution Algorithm to Noncentral Chi-Square Distributed Data (2011)

The Lucy-Richardson Algorithm is a well-known iterative method for the deconvolution of images convolved with a known point spread function. It is derived from a statistical point of view as it converges to the maximum-likelihood solution under the condition that the data follow a Poisson distribution. This assumption holds true for images detected by a digital camera. However, there are images not following a Poisson but rather a noncentral chi-square distribution. Here we show an adaption of the Lucy-Richardson algorithm to be used for data following this probability distribution. Its application to simulated and real data from an imaging radar sensor shows its advantage over the original algorithm. with the radar wavelength λ and the azimuth angle φ. The convolution of objects with the wide antenna beam makes the width and the lateral position of other vehicles hard to determine (see Figure 1). 1
Lamin A/C Mechanotransduction in Laminopathies (2020)

Mechanotransduction translates forces into biological responses and regulates cell functionalities. It is implicated in several diseases, including laminopathies which are pathologies associated with mutations in lamins and lamin-associated proteins. These pathologies affect muscle, adipose, bone, nerve, and skin cells and range from muscular dystrophies to accelerated aging. Although the exact mechanisms governing laminopathies and gene expression are still not clear, a strong correlation has been found between cell functionality and nuclear behavior. New theories base on the direct effect of external force on the genome, which is indeed sensitive to the force transduced by the nuclear lamina. Nuclear lamina performs two essential functions in mechanotransduction pathway modulating the nuclear stiffness and governing the chromatin remodeling. Indeed, A-type lamin mutation and deregulation has been found to affect the nuclear response, altering several downstream cellular processes such as mitosis, chromatin organization, DNA replication-transcription, and nuclear structural integrity. In this review, we summarize the recent findings on the molecular composition and architecture of the nuclear lamina, its role in healthy cells and disease regulation. We focus on A-type lamins since this protein family is the most involved in mechanotransduction and laminopathies.
In Vitro Inhibition of Root-Knot Nematode Meloidogyne Incognita By Sesame Root Exudate and Its Amino Acids (1989)

Root exudates and extracts from in vitro grown seedlings of sesame showed an inhibitory effect on egg hatch and juvenile penetration by root-knot nematode, Meloidogyne incognita. Analysis of root exudates of sesame showed seven free amino acids, i.e. aspartic acid, glutamic acid, valine, proline, serine, glycine and leucine, whereas the exudates of okra had ten free amino acids, viz., glycine, serine, leucine, isoleucine, alanine, arginine, glutamic acid, glutamine, lysine and cystine. Three sugars viz. fructose, glucose and sucrose were found in sesame root exudates and extracts. Commercial amino acids both singly, and in combination inhibited egg hatching. The significance of this work in the development of nematicides is discussed.
Cellulose nanoparticles are a biodegradable photoacoustic contrast agent for use in living mice (2014)

Molecular imaging with photoacoustic ultrasound is an emerging field that combines the spatial and temporal resolution of ultrasound with the contrast of optical imaging. However, there are few imaging agents that offer both high signal intensity and biodegradation into small molecules. Here we describe a cellulose-based nanoparticle with peak photoacoustic signal at 700 nm and an <i>in vitro</i> limit of detection of 6 pM (0.02 mg/mL). Doses down to 0.35 nM (1.2 mg/mL) were used to image mouse models of ovarian cancer. Most importantly, the nanoparticles were shown to biodegrade in the presence of cellulase both through a glucose assay and electron microscopy.
Inhibition of 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone carcinogenesis in mice by D-limonene and citrus fruit oils (1991)

The effects of D-limonene and citrus fruit oils, i.e. orange oil and lemon oil, on 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK)-induced neoplasia of the lungs and forestomach of female A/J mice were investigated. D-Limonene and the citrus fruit oils given p.o. 1 h prior to NNK, also administered p.o., inhibited pulmonary adenoma formation and the occurrence of forestomach tumors. In an additional experiment, D-limonene given p.o. 1 h prior to NNK administered i.p. again showed pronounced inhibition of pulmonary adenoma formation. This study provides additional data demonstrating that non-nutrient constituents of the diet can inhibit carcinogen-induced neoplasia when administered at a short time interval prior to carcinogen challenge.
Geometry of serrated magnetic film strips for the cross-tie memory (1977)

A method of utilizing edge demagnetizing effects for placing data tracks (i,e. cross-tie walls) for a serially accessed crosstie memory is described. Lorentz micrographs show results using a proposed, rounded and slightly asymmetrical, edge geometry.
FlavorGraph: a large-scale food-chemical graph for generating food representations and recommending food pairings (2021)

Food pairing has not yet been fully pioneered, despite our everyday experience with food and the large amount of food data available on the web. The complementary food pairings discovered thus far created by the intuition of talented chefs, not by scientific knowledge or statistical learning. We introduce FlavorGraph which is a large-scale food graph by relations extracted from million food recipes and information of 1,561 flavor molecules from food databases. We analyze the chemical and statistical relations of FlavorGraph and apply our graph embedding method to better represent foods in dense vectors. Our graph embedding method is a modification of metapath2vec with an additional chemical property learning layer and quantitatively outperforms other baseline methods in food clustering. Food pairing suggestions made based on the food representations of FlavorGraph help achieve better results than previous works, and the suggestions can also be used to predict relations between compounds and foods. Our research offers a new perspective on not only food pairing techniques but also food science in general.
Allgemeine Charakteristika und Fragen zur Galenik von Fettemulsionen (1983)

Das Bemühen, den Bedarf an Energie und/oder essentiellen Fettsäuren durch die subkutane bzw. intravenöse Gabe von Fettemulsionen zu decken, reicht weit in die Vergangenheit zurück. Die Entwicklung von klinisch einsetzbaren Fettemulsionen weist einen schubartigen Verlauf auf und führte zu drei abgrenzbaren Generationen von Fettemulsionen. Bei der Beurteilung der Verträglichkeit einer Fettemulsion ist es wichtig, daβ Befunde nicht von einer auf die andere Generation übertragen werden. Die Nichtbeachtung dieser Forderung hat die Einführung der Fettemulsionen der dritten Generation in die Therapie stark verzögert. Bei Berücksichtigung von Kontraindikationen, Dosierungsrichtlinien und basalen galenischen Grundsätzen sind die Fettemulsionen der dritten Generation als nahezu nebenwirkungsfrei zu bezeichnen. Während die Kontraindikationen und Dosierungsgrenzen von Fettemulsionen allgemein geläufig sind, werden bei der Anwendung von Fettemulsionen häufig schwerwiegende galenische Fehler gemacht. Bei gleichzeitiger Infusion von Fettemulsionen mit Kohlenhydraten, Aminosäuren, Elektrolyten, Vitaminen und Spuren-elementen muβ die Frage der Kompatibilität genau geprüft werden. Elektronenmikroskopische Untersuchungen haben gezeigt, daβ Soja-bohnenöl-Emulsionen unter Einhaltung bestimmter Bedingungen mit alien für die intravenöse Ernährung erforderlichen Nahrungsstoffen gemischt werden können und bei 4°C mindestens 1 Monat, bei 22° C mindestens 48 Stunden ohne Stabilitätsverlust gelagert werden können. Solche Gesamtnährlösungen erleichtern die Durchführung der parenteralen Ernährung.
Integrin-dependent translocation of LASP-1 to the cytoskeleton of activated platelets correlates with LASP-1 phosphorylation at tyrosine 171 by Src-kinase (2009)

During platelet adhesion, the complex cytoskeletal structure is rearranged resulting in the formation of F-actin-based filopodia and lamellipodia. Stimulatory platelet signalling pathways include binding of integrin alpha(IIb)beta(3) to fibrinogen followed by activation of protein tyrosine kinases (PTK) and phosphorylation of downstream signalling proteins. In this study, we demonstrate that the scaffolding and F-actin binding protein LASP-1 undergoes tyrosine phosphorylation in thrombin-stimulated human platelets. By means of specific inhibitors we identified Src-kinase as the primary enzyme phosphorylating LASP-1 in intact cells. These data were confirmed in platelet model cells (A5-CHO cells), constitutively expressing integrin alpha(IIb)beta(3). Fibrinogen-mediated cell stimulation resulted in a similar tyrosine phosphorylation of transiently transfected LASP-1. Site directed mutagenesis identified tyrosine 171 as the Src-kinase phosphorylation site. Immunofluorescence microscopic analysis of these cells revealed a relocation of LASP-1 to focal contacts and the leading edge of the membrane upon fibrinogen activation and tyrosine 171 phosphorylation. This translocation was also seen in adherent platelets. Concomitant with adhesion, LASP-1 translocated from the cytosol along the arms of the pseudopodia into the leading lamellae of the spreading platelets, indicating a crucial role of the protein in platelet cytoskeleton rearrangement.
Purinergic Signaling and Vascular Cell Proliferation and Death (2002)

Evidence for the role of purinergic signaling (via P1 and P2Y receptors) in the proliferation of vascular smooth muscle and endothelial cells is reviewed. The involvement of the mitogen-activated protein kinase second-messenger cascade in this action is clearly implicated, although details of the precise intracellular pathways involved still remain to be determined. Synergistic actions of purines and pyrimidines with growth factors occur in promoting cell proliferation. Interaction between purinergic signaling for vascular cell proliferation and cell death mediated by P2X7 receptors is discussed. There is evidence of the release of ATP from endothelial cells, platelets, and sympathetic nerves as well as from damaged cells in atherosclerosis, hypertension, restenosis, and ischemia; furthermore, there is evidence that vascular smooth muscle and endothelial cells proliferate in these pathological conditions. Thus, the involvement of ATP and its breakdown product, adenosine, is implicated; it is hoped that with the development of selective P1 (A2) and P2Y receptor agonists and antagonists, new therapeutic strategies will be explored.
The use of desiccation to treat Staphylococcus aureus biofilm‐infected wounds (2015)

Chronic wounds colonized with biofilm present a major burden to our healthcare system. While the current paradigm for wound healing is to maintain a moist environment, we sought to evaluate the effects of desiccation, and the ability of honey to desiccate wounds, on wound healing characteristics in Staphylococcus aureus biofilm wounds. In vivo biofilm wound healing after exposure to open-air desiccation, honey, molasses, and saline was analyzed using a rabbit ear model of S. aureus biofilm wounds previously developed by our group. Wound morphology was examined using scanning electron microscopy and granulation tissue deposition was measured using light microscopy with hematoxylin and eosin staining. Viable bacterial counts in rabbit ear biofilm wounds and scabs were measured using a drop dilution method. In vitro S. aureus growth curves were established using tryptic soy broth containing honey and glycerol. Gene expression analysis of rabbit ear wounds was performed using reverse transcription quantitative PCR. Rabbit ear S. aureus biofilm wounds exposed to open-air desiccation, honey, and molasses developed a dry scab, which displaced the majority of biofilm bacteria off of the wound bed. Wounds treated with open-air desiccation, honey, and molasses expressed lower levels of the inflammatory markers tumor necrosis factor-α and interleukin-1β at postoperative day 12 compared with wounds treated with saline, and had increased levels of granulation tissue formation. In vitro growth of S. aureus in tryptic soy broth was inhibited by the presence of honey to a greater extent than by the presence of osmolality-matched glycerol. Desiccation of chronic wounds colonized with biofilm via exposure to open air or honey leads to improved wound healing by decreasing bacterial burden and inflammation, and increasing granulation tissue formation. The ability of honey to help heal chronic wounds is at least in part due to its ability to desiccate bacterial biofilm, but other factors clearly contribute.
Design considerations for ultrasound detectors in photoacoustic breast imaging (2013)

The ultrasound detector is the heart of a photoacoustic imaging system. In photoacoustic imaging of the breast there is a requirement to detect tumors located a few centimeters deep in tissue, where the light is heavily attenuated. Thus a sensitive ultrasound transducer is of crucial importance. As the frequency content of photoacoustic waves are inversely proportional to the dimensions of the absorbing structures, and in tissue can range from hundreds of kHz to tens of MHz, a broadband ultrasound transducer is required centered on an optimum frequency. A single element piezoelectric transducer structurally consists of the active piezoelectric material, front- and back-matching layers and a backing layer. To have both high sensitivity and broad bandwidth, the materials, their acoustic characteristics and their dimensions should be carefully chosen. In this paper, we present design considerations of an ultrasound transducer for imaging the breast such as the detector sensitivity and frequency response, which guides the selection of active material, matching layers and their geometries. We iterate between simulation of detector performance and experimental characterization of functional models to arrive at an optimized implementation. For computer simulation, we use 1D KLM and 3D finite-element based models. The optimized detector has a large-aperture possessing a center frequency of 1 MHz with fractional bandwidth of more than 80%. The measured minimum detectable pressure is 0.5 Pa, which is two orders of magnitude lower than the detector used in the Twente photoacoustic mammoscope.