gebhart/patrepeval huggingface dataset:
Reevaluation of Positivity Cutoff Values for the Pneumococcal Urinary Antigen Detection Assay (2017)

To improve the clinical diagnosis of pneumococcal infection in bacteremic and nonbacteremic community-acquired pneumonia (CAP), a Luminex technology-based multiplex urinary antigen detection (UAD) diagnostic assay was developed and validated. The UAD assay is a limit assay based on defined
In Situ Analysis of Gas Generation in Lithium-Ion Batteries with Different Carbonate-Based Electrolytes (2015)

Gas generation in lithium-ion batteries is one of the critical issues limiting their safety performance and lifetime. In this work, a set of 900 mAh pouch cells were applied to systematically compare the composition of gases generated from a serial of carbonate-based composite electrolytes, using a self-designed gas analyzing system. Among electrolytes used in this work, the composite γ-butyrolactone/ethyl methyl carbonate (GBL/EMC) exhibited remarkably less gassing because of the electrochemical stability of the GBL, which makes it a promising electrolyte for battery with advanced safety and lifetime.
Hybrid reduced order modeling applied to nonlinear models (2012)

SUMMARY Reduced order modeling plays an indispensible role for most real‐world complex models. The objective of this manuscript is to hybridize local and global sensitivity analysis methods to enable the application of reduced order modeling to complex nonlinear models, often encountered in real system design and analysis calculations, for example, nuclear reactors. This is achieved by first employing local variational methods to identify important nonlinear features of the original model that are required to reach a user‐defined accuracy for the reduced model. This information is obtained by sampling local first‐order derivatives of a pseudoresponse utilizing a modified representation of an infinite series expansion around some reference point. The resulting derivative information is aggregated in a subspace of dimension much less than the dimension of the input parameter space. The accuracy of the reduced model can be mathematically quantified using a bounding norm. Next, global sensitivity methods are employed to exhaustively search the reduced subspace for sensitivity information. The theory and implementation details of the proposed method are exposed in this manuscript. Numerical tests based on prototype nonlinear functions and radiation transport models with many input parameters and many responses are conducted as proof of principle. Copyright © 2012 John Wiley &amp; Sons, Ltd.
Effects of intravenous progesterone infusions on the epileptic discharge frequency in women with partial epilepsy (1984)

Earlier work showed that in a group of women suffering from partial epilepsy, there is a decrease in seizure frequency during the luteal phase of the menstrual cycle. Moreover, iv progesterone infusions decrease the discharge frequency from penicillin epileptic foci in cats, when given in doses that reach plasma concentrations as observed during pregnancy. In the present study, iv progesterone infusions, reaching plasma concentrations as during the luteal phase, were given to 7 women with partial epilepsy. The inclusion criterion was that they should have more than one epileptic discharge per 5 min on an ordinary EEG . A 6 h EEG-registration was made. Blank and progesterone solutions were infused for 2 h respectively and the progesterone infusion was followed by a 2 h EEG recording period. 4 of the 7 patients showed a significant decrease in spike frequency during the infusion. In the patients not showing this effect, the plasma progesterone binding capacity was high. The 2 patients with the most marked progesterone effect had low progesterone binding capacity and no antiepileptic treatment. Somnolence during the test might also have influenced the results in 2 of the patients.
The Position of the GFP Tag on Actin Affects the Filament Formation in Mammalian Cells (2017)

Actin, a major component of microfilaments, is involved in various eukaryotic cellular functions. Over the past two decades, actin fused with fluorescent protein has been used as a probe to detect the organization and dynamics of the actin cytoskeleton in living eukaryotic cells. It is generally assumed that the expression of fusion protein of fluorescent protein does not disturb the distribution of endogenous actin throughout the cell, and that the distribution of the fusion protein reflects that of endogenous actin. However, we noticed that EGFP-β-actin caused the excessive formation of microfilaments in several mammalian cell lines. To investigate whether the position of the EGFP tag on actin affected the formation of filaments, we constructed an expression vector harboring a β-actin-EGFP gene. In contrast to EGFP-β-actin, cells expressing β-actin-EGFP showed actin filaments in a high background from the monomer actin in cytosol. Additionally, the detergent insoluble assay revealed that the majority of the detergent-insoluble cytoskeleton from cells expressing EGFP-β-actin was recovered in the pellet. Furthermore, we found that the expression of EGFP-β-actin affects the migration of NBT-L2b cells and the mechanical stiffness of U2OS cells. These results indicate that EGFP fused to the N-terminus of actin tend to form excessive actin filaments. In addition, EGFP-actin affects both the cellular morphological and physiological phenotypes as compared to actin-EGFP.Key words: actin, GFP, cytoskeleton and probe.
Cerebral dopamine neurotrophic factor is essential for enteric neuronal development, maintenance, and regulation of gastrointestinal transit (2020)

Cerebral dopamine neurotrophic factor (CDNF) is expressed in the brain and is neuroprotective. We have previously shown that CDNF is also expressed in the bowel and that its absence leads to degeneration and autophagy in the enteric nervous system (ENS), particularly in the submucosal plexus. We now demonstrate that enteric CDNF immunoreactivity is restricted to neurons (submucosal > myenteric) and is not seen in glia, interstitial cells of Cajal, or smooth muscle. Expression of CDNF, moreover, is essential for the normal development and survival of enteric dopaminergic neurons; thus, expression of the dopaminergic neuronal markers, dopamine, tyrosine hydroxylase, and dopamine transporter are deficient in the ileum of Cdnf <sup>-/-</sup> mice. The normal age-related decline in proportions of submucosal dopaminergic neurons is exacerbated in Cdnf <sup>-/-</sup> animals. The defect in Cdnf <sup>-/-</sup> animals is not dopamine-restricted; proportions of other submucosal neurons (NOS-, GABA-, and CGRP-expressing), are also deficient. The deficits in submucosal neurons are reflected functionally in delayed gastric emptying, slowed colonic motility, and prolonged total gastrointestinal transit. CDNF is expressed selectively in isolated enteric neural crest-derived cells (ENCDC), which also express the dopamine-related transcription factor Foxa2. Addition of CDNF to ENCDC promotes development of dopaminergic neurons; moreover, survival of these neurons becomes CDNF-dependent after exposure to bone morphogenetic protein 4. The effects of neither glial cell-derived neurotrophic factor (GDNF) nor serotonin are additive with CDNF. We suggest that CDNF plays a critical role in development and long-term maintenance of dopaminergic and other sets of submucosal neurons.
High Resolution Tem Observation and Eels Analysis of Carbon Nanotubes at Elevated Temperatures (2002)

Journal Article High Resolution Tem Observation and Eels Analysis of Carbon Nanotubes at Elevated Temperatures Get access T Yaguchi, T Yaguchi Hitachi Science Systems, Ltd., 882 Ichige, Hitachinaka, Ibaraki, 312-8504 Japan Search for other works by this author on: Oxford Academic Google Scholar T Sato, T Sato Hitachi Science Systems, Ltd., 882 Ichige, Hitachinaka, Ibaraki, 312-8504 Japan Search for other works by this author on: Oxford Academic Google Scholar T Kamino, T Kamino Hitachi Science Systems, Ltd., 882 Ichige, Hitachinaka, Ibaraki, 312-8504 Japan Search for other works by this author on: Oxford Academic Google Scholar T Hashimoto, T Hashimoto Hitachi High-technologies cooperation, 882 Ichige, Hitachinaka, Ibaraki, 312-8504 Japan Search for other works by this author on: Oxford Academic Google Scholar K Motomiya, K Motomiya Dept. of Geoscience and Technology, Tohoku Univ., Sendai, 980-8579, Japan Search for other works by this author on: Oxford Academic Google Scholar K Tohji, K Tohji Dept. of Geoscience and Technology, Tohoku Univ., Sendai, 980-8579, Japan Search for other works by this author on: Oxford Academic Google Scholar A Kasuya A Kasuya Center for Interdisciplinary Research, Tohoku Univ., Sendai, 980-8578, Japan Search for other works by this author on: Oxford Academic Google Scholar Microscopy and Microanalysis, Volume 8, Issue S02, 1 August 2002, Pages 1152–1153, https://doi.org/10.1017/S1431927602103837 Published: 01 August 2002
Robust Direction Estimation from Hydroacoustic Array Data (1993)

In hydro-acoustic array signal processing we are often concerned with accurate determination of signal parameters from array measurements. To obtain accurate direction estimates, knowledge of the array response is required. Most estimation techniques are sensitive to errors in the array response model. Thus, reliable array calibration schemes are of great importance. In practice, calibration is done by measuring the array response when only one emitter is present and the signal parameters of which are allowed to vary in a known way. Herein, methods for generating an array model from noise corrupted calibration vectors is developed. The performance of the technique is examined on data collected from a full-scale hydro-acoustic array. 1 Introduction Parameter estimation from sensor array data is an important problem in several signal processing applications. Herein we focus on the direction finding problem, assuming that only the azimuthal angle, termed the direction-of-arrival (DOA) i...
Small-molecule inhibitors directly target CARD9 and mimic its protective variant in inflammatory bowel disease (2017)

Advances in human genetics have dramatically expanded our understanding of complex heritable diseases. Genome-wide association studies have identified an allelic series of <i>CARD9</i> variants associated with increased risk of or protection from inflammatory bowel disease (IBD). The predisposing variant of CARD9 is associated with increased NF-κB-mediated cytokine production. Conversely, the protective variant lacks a functional C-terminal domain and is unable to recruit the E3 ubiquitin ligase TRIM62. Here, we used biochemical insights into CARD9 variant proteins to create a blueprint for IBD therapeutics and recapitulated the mechanism of the CARD9 protective variant using small molecules. We developed a multiplexed bead-based technology to screen compounds for disruption of the CARD9-TRIM62 interaction. We identified compounds that directly and selectively bind CARD9, disrupt TRIM62 recruitment, inhibit TRIM62-mediated ubiquitinylation of CARD9, and demonstrate cellular activity and selectivity in CARD9-dependent pathways. Taken together, small molecules targeting CARD9 illustrate a path toward improved IBD therapeutics.
Successful placement of a pyeloamniotic shunt catheter for ureteropelvic junctional obstruction in utero (1987)

A fetus with severe left ureteropelvic junctional obstruction was managed by the insertion of a left pyeloamniotic shunt catheter at 28 weeks' gestation. An otherwise healthy baby boy was delivered seven weeks later. The place of fetal surgical techniques for obstructive uropathies is discussed.
Gold Nanoparticle-Based Label-Free Detection of BRCA1 Mutations Utilizing DNA Ligation on DNA Microarray (2009)

Here we describe a label-free detection strategy for point mutation in breast cancer susceptibility gene BRCA1 utilizing ligation chain reaction (LCR) and zip-code array. We amplified the genomic regions containing mutation sites by polymerase chain reaction (PCR) to prepare the template for LCR. Then we ligated a primary probe extended by zip-code complementary at the 5' end with a 3'-thiol modified secondary probe. The resulting ligated product was labeled with gold nanoparticles and allowed to hybridize with corresponding zip-code sequences on the microarray. Finally, we applied silver enhancement to amplify the signals. Using this strategy, we successfully genotyped BRCA1 mutation, which was detected by naked eye.
ChemInform Abstract: Synthesis, Crystal Structure, and Optical Properties of Ba2Cu2ThS5, and Electronic Structures of Ba2Cu2ThS5 and Ba2Cu2US5. (2013)

Abstract Ba 2 Cu 2 ThS 5 is synthesized by solid state reaction of a stoichiometric mixture of BaS, S, Cu, and Th (evacuated fused silica tube, 1173 K, 4 d, controlled cooling).
Optical Imaging and Pupil Reflex by Trans-corneal Electrical Stimulation to Evaluate Inner-Retinal Function (2007)

To investigate if Trans-corneal Electrical Stimulation (TcES) is effective to evaluate the inner-retinal function.Pupil reflex evoked by TcES was assessed in eyes of normal subject and of optic neuropathy. Optical imaging of the retina in response to TcES was also investigated in a cat. The relative amplitude of pupil reflex increased linearly with the current and the threshold was higher and the amplitude was lower in eyes with optic neuropathy. Optical imaging by TcES showed reflectance changes in the retina, optic disc and artery with similar time-course. The reflectance change in the artery was related to the current intensity. Pupil reflex by TcES is effective to assess the inner-retinal function. Optical imaging by TcES has a potential to demonstrate the inner-retinal function 2-dimensionally.
Human immunodeficiency virus does not induce interleukin-1, interleukin-6, or tumor necrosis factor in mononuclear cells (1990)

The production of interleukin-1 beta (IL-1 beta), IL-6, and tumor necrosis factor alpha (TNF-alpha) by fresh peripheral blood mononuclear cells was evaluated after exposure to human immunodeficiency virus (HIV) or purified recombinant HIV-1 envelope glycoprotein (rgp120). To exclude the role of contaminating endotoxin in this study, all media were subjected to ultrafiltration and reagents contained less than 25 pg of endotoxin per ml by Limulus assay. Under endotoxin-free conditions, no increases in IL-1 beta, IL-6, or TNF-alpha mRNA or protein were detectable in cell cultures exposed to HIV-1, HIV-2, or rgp120 (0.1 to 10 micrograms/ml), as compared with cytokine levels in mock-exposed cultures. However, concentrations of endotoxin (lipopolysaccharide) as low as 0.5 ng/ml induced significant production of mRNA and protein for these three cytokines. Preincubation of mononuclear cells with "shake" HIV-1 preparations and also mock-infected shake preparations prior to lipopolysaccharide stimulation resulted in a two- to threefold increase in IL-1 beta and TNF-alpha production. This priming effect was not observed with rgp120 (0.1 to 10 micrograms/ml) or standard HIV-1 or mock-infected supernatants, suggesting the presence of biologically active material independent of virus in the shake preparations. Our studies indicate that, in the absence of endotoxin, HIV-1, HIV-2, and HIV gp120 do not induce production of IL-1 beta, IL-6, or TNF-alpha by peripheral blood mononuclear cells.
Ultra low power wireless ECG sensor tag with wearable antenna (2013)

A novel wireless ECG sensor tag using 2.4 GHz band for an ultra low power consumption and a long reading range is proposed. Consumption power of the proposed ECG sensor tag is 340 μW by using a 2 V battery and 300 sps continuous data transmitting operation. Experimental study of the wireless ECG monitoring system using -20 dBm (10μW) RF output power of tag reader is described, where 4.5 m reading range is achieved. Proposed ECG sensor tag can yield about 100 m reading range under the FCC 15.247 standard specification of tag reader and the consumption power is less than 1/10 compared with the conventional active type wireless ECG sensors using Bluetooth Class 3 or XBee.
Predictive Bandits. (2020)

We introduce and study a new class of stochastic bandit problems, referred to as predictive bandits. In each round, the decision maker first decides whether to gather information about the rewards of particular arms (so that their rewards in this round can be predicted). These measurements are costly, and may be corrupted by noise. The decision maker then selects an arm to be actually played in the round. Predictive bandits find applications in many areas; e.g. they can be applied to channel selection problems in radio communication systems. In this paper, we provide the first theoretical results about predictive bandits, and focus on scenarios where the decision maker is allowed to measure at most one arm per round. We derive asymptotic instance-specific regret lower bounds for these problems, and develop algorithms whose regret match these fundamental limits. We illustrate the performance of our algorithms through numerical experiments. In particular, we highlight the gains that can be achieved by using reward predictions, and investigate the impact of the noise in the corresponding measurements.
The Universal Triangulation System For Gastro-Enterology (2012)

info:eu-repo/semantics/nonPublished
Intermittent high-dose treatment with erlotinib enhances therapeutic efficacy in EGFR-mutant lung cancer (2015)

// Jakob Sch&ouml;ttle 1,2,3 , Sampurna Chatterjee 1,2,10 , Caroline Volz 1,2 , Maike Siobal 2 , Alexandra Florin 4 , Dennis Rokitta 5 , Yvonne Hinze 6 , Felix Dietlein 3 , Dennis Plenker 3 , Katharina K&ouml;nig 4 , Kerstin Albus 4 , Johannes M. Heuckmann 7 , Daniel Rauh 8 , Thomas Franz 6 , Bernd Neumaier 2,9 , Uwe Fuhr 5 , Lukas C. Heukamp 4,7 and Roland T. Ullrich 1,2 1 Department I of Internal Medicine, Center of Integrated Oncology K&ouml;ln-Bonn, University of Cologne, Germany and Center of Molecular Medicine Cologne (ZMMK), University of Cologne, Cologne, Germany 2 Max-Planck-Institute for Metabolism, with Klaus-Joachim-Z&uuml;lch Laboratories of the Max Planck Society and the Medical Faculty of the University of Cologne, Cologne, Germany 3 Department of Translational Genomics, University of Cologne, Medical Faculty, Weyertal, Cologne, Germany 4 Department of Pathology, University Hospital Medical Center, University of Cologne, Cologne, Germany 5 Department of Pharmacology, University Hospital Medical Center, University of Cologne, Cologne, Germany 6 Max-Planck-Institute for Ageing, Cologne, Germany 7 NEO New Oncology AG, Cologne, Germany 8 Technical University Dortmund, Dortmund, Germany 9 Institut f&uuml;r Radiochemie und Experimentelle Molekulare Bildgebung (IREMB), University Hospital Medical Center, University of Cologne, Cologne, Germany 10 Department of Radiation Oncology, Cox-7, Harvard Medical School, Massachusetts General Hospital, Boston, MA, USA Correspondence to: Roland T. Ullrich, email: // Keywords : lung cancer, NSCLC, EGFR, erlotinib, high-dose scheduling, PET Received : July 09, 2015 Accepted : October 01, 2015 Published : November 02, 2015 Abstract Treatment with EGFR kinase inhibitors improves progression-free survival of patients with EGFR-mutant lung cancer. However, all patients with initial response will eventually acquire resistance and die from tumor recurrence. We found that intermittent high-dose treatment with erlotinib induced apoptosis more potently and improved tumor shrinkage significantly than the established low doses. In mice carrying EGFR-mutant xenografts intermittent high-dose treatment (200 mg/kg every other day) was tolerable and prolonged progression-free survival and reduced the frequency of acquired resistance. Intermittent EGFR-targeted high-dose schedules induce more profound as well as sustained target inhibition and may afford enhanced therapeutic efficacy.
Supplementary Figures 1-2 from Deletion of Chromosome 11q Predicts Response to Anthracycline-Based Chemotherapy in Early Breast Cancer (2023)

Supplementary Figures 1-2 from Deletion of Chromosome 11q Predicts Response to Anthracycline-Based Chemotherapy in Early Breast Cancer
DNA purification by triplex-affinity capture and affinity capture electrophoresis (2023)

The invention provides a method for purifying or isolating double stranded DNA intact using triple helix formation. The method includes the steps of complexing an oligonucleotide and double stranded DNA to generate a triple helix and immobilization of the triple helix on a solid phase by means of a molecular recognition system such as avidin/biotin. The purified DNA is then recovered intact by treating the solid phase with a reagent that breaks the bonds between the oligonucleotide and the intact double stranded DNA while not affecting the Watson-Crick base pairs of the double helix. The present invention also provides a method for purifying or isolating double stranded DNA intact by complexing the double stranded DNA with a specific binding partner and recovering the complex during electrophoresis by immobilizing it on a solid phase trap imbedded in an electrophoretic gel.
Elevation of FAM129A in neutrophils exposed to serum of patients with severe sepsis: in silico investigations during a hands on training workshop and follow on validation of protein expression in neutrophils (2019)

ABSTRACT Steps involved in reductionist investigation approaches can be imitated using public transcriptome datasets as source of training material. In the present report trainees explored an apparent gap in biological knowledge for FAM129A (family with sequence similarity 129 member A). Elevated abundance of FAM129A transcripts were observed in a transcriptome dataset where neutrophils were exposed in vitro to plasma of patients with sepsis. However, no literature linking FAM129A and either neutrophils, sepsis or inflammation could be identified. Additional datasets were selected to independently validate this initial observation and further explore differential expression of FAM129A in the context of sepsis studies. Follow on investigations carried out at the bench confirmed restriction of the expression of FAM129A protein at the surface of circulating blood neutrophils and monocytes. A potential role for FAM129A in neutrophil survival was inferred from profiling of literature associated with FAM129A, which remains to be investigated in further follow on investigations.
Synthetic DNA encoded antibody prophylaxis confers rapid protective immunity in vivo against Chikungunya virus infection (2016)

Background: Chikungunya (CHIKV) disease is a serious emerging mosquito-transmitted viral infection responsible for epidemic outbreaks. Currently, no licensed vaccines or therapies are available against this virus, resulting in significant global spread with concurrent population morbidity. Methods & Materials: This study describes a novel immune-based intervention that utilizes in vivo deliver of synthetic DNA plasmids encoding a monoclonal antibody (mAb) targeting the CHIKV envelope protein. Results: Importantly, a single intramuscular injection with a DNA plasmid expressing an anti-CHIKV mAb produced antibodies in mice more rapidly than vaccination with CHIKV-Env-encoding DNA plasmids. DNA-mediated delivery of anti-CHIKV antibodies neutralized diverse clinical isolates in vitro and protected mice from lethal CHIKV challenge. Conclusion: This study illustrates the ability of antibody-encoding plasmids to induce rapid protection against CHIKV highlighting the potential of this novel immunoprophylaxis and therapeutic applications platform for other emerging infectious pathogens.