gebhart/patrepeval huggingface dataset:
Oxidative damage to DNA by diesel exhaust particle exposure in co-cultures of human lung epithelial cells and macrophages (2012)

Studies in mono-culture of cells have shown that diesel exhaust particles (DEPs) increase the production of reactive oxygen species (ROS) and oxidative stress-related damage to DNA. However, the level of particle-generated genotoxicity may depend on interplay between different cell types, e.g. lung epithelium and immune cells. Macrophages have important immune defence functions by engulfing insoluble foreign materials, including particles, although they might also promote or enhance inflammation. We investigated the effect of co-culturing type II lung epithelial A549 cells with macrophages upon treatment with standard reference DEPs, SRM2975 and SRM1650b. The exposure to DEPs did not affect the colony-forming ability of A549 cells in co-culture with THP-1a cells. The DEPs generated DNA strand breaks and oxidatively damaged DNA, measured using the alkaline comet assay as formamidopyrimidine-DNA glycosylase or oxoguanine DNA glycosylase (hOGG1) sensitive sites, in mono-cultures of A549 or THP-1a and co-cultures of A549 and THP-1a cells. The strongest genotoxic effects were observed in A549 mono-cultures and SRM2975 was more potent than SRM1650b. The ROS production only increased in cells exposed to SRM2975, with strongest concentration-dependent effect in the THP-1a mono-cultures. The basal respiration level in THP-1a cells increased on exposure to SRM1650b and SRM2975 without indication of mitochondrial dysfunction. This is consistent with activation of the cells and there was no direct relationship between levels of respiration and ROS production. In conclusion, exposure of mono-cultured cells to DEPs generated oxidative stress to DNA, whereas co-cultures with macrophages had lower levels of oxidatively damaged DNA than A549 epithelial cells.
Monolithically integrated widely tunable laser source operating at 2  μm (2016)

<p>We present a widely tunable extended cavity ring laser operating at 2 μm that is monolithically integrated on an indium phosphide substrate. The photonic integrated circuit is designed and fabricated within a multiproject wafer run using a generic integration technology platform. The laser features an intracavity tuning mechanism based on nested asymmetric Mach-Zehnder interferometers with voltage controlled electro-refractive modulators. The laser operates in a single-mode regime and is tunable over the recorded wavelength range of 31 nm, spanning from 2011 to 2042 nm. Its capability for high-resolution scanning is demonstrated in a single-line spectroscopy experiment using a carbon dioxide reference cell.</p>
The Mechanistic Architecture of Thermostable <i>Pyrococcus furiosus</i> Family B DNA Polymerase Motif A and Its Interaction with the dNTP Substrate (2009)

Thermostable DNA polymerases isolated from archaeal organisms have not been completely characterized kinetically and require further study if we are to understand both their dNTP binding mechanism and their role within the organism. Here, we demonstrate that the thermostable family B DNA polymerase from Pyrococcus furiosus (Pfu Pol) contains sensitive determinants of both dNTP binding and replicational fidelity within the highly conserved motif A. Site-directed mutagenesis of the motif A SYLP region revealed that small shifts in side chain volume result in significant changes in the dNTP binding affinity, steady state kinetics, and fidelity of the enzyme. Mutants of Y410 show high fidelity in both misincorporation assays and forward mutation assays, but display a substantially higher K(m) than the wild type. In contrast, mutations of upstream residue L409 result in a drastically reduced affinity for the correct dNTP, a much higher efficiency of both misincorporation and mismatch extension, and substantially lower fidelity as demonstrated by a PCR-based forward mutation assay. The A408S mutant, however, displayed a significant increase in both dNTP binding affinity and fidelity. In summary, these data show that modulation of motif A can greatly shift both the steady and pre-steady state kinetics of the enzyme as well as the fidelity of Pfu Pol.
Lipoamidase is a multiple hydrolase (1990)

The substrate specificity of lipoamidase, purified from the pig brain membrane with lipoyl 4-aminobenzoate (LPAB) as a substrate, was extensively studied. This single polypeptide was found to hydrolyse the bonding between amide, ester and peptide compounds. However, stringent structural requirements were found in the substrates, e.g. LPAB was hydrolysed, whereas biotinyl 4-aminobenzoate was not, as stated in our previous paper [Oizmui & Hayakawa (1990) Biochem. J. 266, 427-434]. The enzyme specifically recognized the whole molecular structure of the substrate, whereas it loosely recognized the bond structure of the substrate; e.g. the dipeptide Asp-Phe was not hydrolysed, whereas the methyl ester of Asp-Phe (aspartame) was. The exopeptidase activity was demonstrated by lipoamidase; however, longer peptides than the hexamer seemed not to be substrates. Lipoyl esters, which were electrically neutral, exhibited higher specificity with longer acyl groups. Molecular mass and molecular hydrophobicity (hydropathy) seemed to determine the substrate specificity. Lipoyl-lysine, acetylcholine and oligopeptides were hydrolysed at similar Km values; however, acetylcholine was hydrolysed at a velocity 100 times higher. Although many similar specificities were found between electric eel acetylcholinesterase and lipoamidase, distinctly different specificity was demonstrated with lipoyl compounds. The role of lipoamidase, which resides on the brain membrane and possesses higher specificity for hydrophobic molecules, remains to be elucidated.
Optical properties of dilute hydrogen tungsten bronze thin films (1991)

Transmission and reflection spectra in the range of 0.5–4.1 eV have been obtained for HxWO3 polycrystalline thin films of 5-nm mean grain size. The composition range x=0–0.16 has been investigated. The measurements were refined to give the absorption coefficient and other optical parameters versus photon energy. The data have been interpreted in terms of the interband transition model due to Green and Travlos [Philos. Mag. B 51, 501 (1985)]. It is noted that main gap changes because of changes in crystal structure, and there is a sensitivity of the main gap value to grain size which may have its origins in quantum confinement effects.
All <i>trans</i> retinoic acid nanodisks enhance retinoic acid receptor mediated apoptosis and cell cycle arrest in mantle cell lymphoma (2010)

Mantle cell lymphoma (MCL) is characterized by translocation t(11;14)(q13;q32), aggressive clinical behaviour, and poor patient outcomes following conventional chemotherapy. New treatment approaches are needed that target novel biological pathways. All trans retinoic acid (ATRA) is a key retinoid that acts through nuclear receptors that function as ligand-inducible transcription factors. The present study evaluated cell killing effects of ATRA-enriched nanoscale delivery particles, termed nanodisks (ND), on MCL cell lines. Results show that ATRA-ND induced cell death more effectively than naked ATRA (dimethyl sulphoxide) or empty ND. ATRA-ND induced reactive oxygen species (ROS) generation to a greater extent than naked ATRA. The antioxidant, N-acetylcysteine, inhibited ATRA-ND induced apoptosis. Compared to naked ATRA, ATRA-ND enhanced G1 growth arrest, up-regulated p21and p27, and down regulated cyclin D1. At ATRA concentrations that induced apoptosis, expression levels of retinoic acid receptor-alpha (RARalpha) and retinoid X receptor-gamma (RXRgamma) were increased. Compared to naked ATRA, ATRA-ND significantly stimulated transcriptional activity of RARA in a model carcinoma cell line. Furthermore, the RAR antagonist, Ro 41-5253, inhibited ATRA-ND induced ROS generation and prevented ATRA-ND induced cell growth arrest and apoptosis. In summary, incorporation of ATRA into ND enhanced the biological activity of this retinoid in cell culture models of MCL.
Application of Classification Models to Pharyngeal High-Resolution Manometry (2012)

Classification models show high accuracy in segregating HRM data sets and represent 1 method of facilitating application of HRM to the clinical setting by eliminating the time required for some aspects of data extraction and interpretation.
Approximate graph coloring by semidefinite programming (1998)

We consider the problem of coloring k -colorable graphs with the fewest possible colors. We present a randomized polynomial time algorithm that colors a 3-colorable graph on n vertices with min{ O (Δ 1/3 log 1/2 Δ log n ), O ( n 1/4 log 1/2 n )} colors where Δ is the maximum degree of any vertex. Besides giving the best known approximation ratio in terms of n , this marks the first nontrivial approximation result as a function of the maximum degree Δ. This result can be generalized to k -colorable graphs to obtain a coloring using min{ O (Δ 1-2/ k log 1/2 Δ log n ), O ( n 1−3/( k +1) log 1/2 n )} colors. Our results are inspired by the recent work of Goemans and Williamson who used an algorithm for semidefinite optimization problems , which generalize linear programs, to obtain improved approximations for the MAX CUT and MAX 2-SAT problems. An intriguing outcome of our work is a duality relationship established between the value of the optimum solution to our semidefinite program and the Lovász θ-function. We show lower bounds on the gap between the optimum solution of our semidefinite program and the actual chromatic number; by duality this also demonstrates interesting new facts about the θ-function.
Endothelium-dependent vasodilation in the brachial artery is impaired in smokers: effect of vitamin C (1997)

Cigarette smoking has been shown to cause endothelial dysfunction. To examine the effects of vitamin C and cigarette smoking on endothelium-dependent vasodilation, we measured the lumen diameter and flow velocity of the brachial arteries at rest, during reactive hyperemia following transient arterial occlusion, and after sublingual nitroglycerin (0.3 mg) in smokers (n = 20) and nonsmokers (n = 20) with high-resolution ultrasound after infusion of saline or saline plus vitamin C (10 mg/min for 20 min). We also performed the same study in smokers (n = 15) before and 10 min after cigarette smoking. In addition, we measured the serum levels of vitamin C and the plasma levels of thiobarbituric acid-reactive substances (TBARS) as an index of lipid peroxidation. The smokers had lower vitamin C levels, higher TBARS levels, and showed impairment of flow-dependent vasodilation (5.3 +/- 1.9 vs. 9.2 +/- 1.5%, P < 0.0001) compared with nonsmokers. Vitamin C administration improved the impairment of flow-dependent vasodilation (5.3 +/- 1.9 to 9.0 +/- 3.2%, P < 0.001) and decreased TBARS in smokers but not in nonsmokers. Furthermore, cigarette smoking acutely worsened the impairment of flow-dependent vasodilation (5.4 +/- 1.8 to 1.5 +/- 1.3%, P < 0.01) and increased TBARS. We conclude that 1) endothelium-dependent vasodilation in the brachial arteries is impaired in smokers and this impairment is improved by vitamin C administration in association with a decrease in TBARS and 2) cigarette smoking produces acute impairment of endothelium-dependent vasodilation in smokers in association with an increase in TBARS.
Quality Aware Network for Set to Set Recognition (2017)

This paper targets on the problem of set to set recognition, which learns the metric between two image sets. Images in each set belong to the same identity. Since images in a set can be complementary, they hopefully lead to higher accuracy in practical applications. However, the quality of each sample cannot be guaranteed, and samples with poor quality will hurt the metric. In this paper, the quality aware network (QAN) is proposed to confront this problem, where the quality of each sample can be automatically learned although such information is not explicitly provided in the training stage. The network has two branches, where the first branch extracts appearance feature embedding for each sample and the other branch predicts quality score for each sample. Features and quality scores of all samples in a set are then aggregated to generate the final feature embedding. We show that the two branches can be trained in an end-to-end manner given only the set-level identity annotation. Analysis on gradient spread of this mechanism indicates that the quality learned by the network is beneficial to set-to-set recognition and simplifies the distribution that the network needs to fit. Experiments on both face verification and person re-identification show advantages of the proposed QAN. The source code and network structure can be downloaded at https://github.com/sciencefans/Quality-Aware-Network.
SRST2: Rapid genomic surveillance for public health and hospital microbiology labs (2014)

Abstract Rapid molecular typing of bacterial pathogens is critical for public health epidemiology, surveillance and infection control, yet routine use of whole genome sequencing (WGS) for these purposes poses significant challenges. Here we present SRST2, a read mapping-based tool for fast and accurate detection of genes, alleles and multi-locus sequence types (MLST) from WGS data. Using >900 genomes from common pathogens, we show SRST2 is highly accurate and outperforms assembly-based methods in terms of both gene detection and allele assignment. Here we have demonstrated the use of SRST2 for microbial genome surveillance in a variety of public health and hospital settings. In the face of rising threats of antimicrobial resistance and emerging virulence amongst bacterial pathogens, SRST2 represents a powerful tool for rapidly extracting clinically useful information from raw WGS data. Source code is available from http://katholt.github.io/srst2/ .
The Ecological and Physiological Significance of the Growth of Heterotrophic Microorganisms with Mixtures of Substrates (1995)

It has been estimated that globally some 500 × 1012 kg of carbon dioxide are assimilated into biomass by autotrophic organisms annually. More than 99% of this assimilated carbon is remineralized, keeping the global biogeochemical carbon cycle roughly in balance (Hedges, 1992). In both terrestrial and aquatic ecosystems the majority of this primary biomass is not consumed directly by herbivorous animals, but decays to detritus and serves as a nutritional basis for the growth of consumers (for an extensive discussion, see Fenchel and Jørgensen, 1977). There is now substantial evidence suggesting that a large part of the energy and nutrients contained in this primary biomass is processed via the microbial detritus food chain, and this mineralizing ability makes heterotrophic microorganisms an important link in the global carbon cycle (Fenchel and Jørgensen, 1977; Paul and Voroney, 1980; Wetzel, 1984; Cole et al., 1988; Mann, 1988). In addition, their ability to mineralize man-made xenobiotic organic chemicals has become increasingly important. This is illustrated by the fact that in industrialized countries the flux of synthetically produced organic material, much of which is ending up in the environment, has increased within the past two centuries to some 40 g C m−2 year−1. This figure is equivalent to approximately 15% of the net primary biomass production in these regions (Egli, 1992).
A simple experimental method for separating loss parameters of a microstrip antenna (1981)

A simple method is presented for the computation of both the dielectric loss tangent and the conductivity of the metal cladding of printed circuit boards at microwave frequencies. Since the treatment of the cladding in the lamination process affects its conductivity, losses in the dielectric and the metal cannot be measured separately. Thus an analytical means for separating these losses must be employed. The method described accomplishes this by utilizing the different dependence of the two losses on dielectric thickness in thin cavities.
Intelligent use of stable isotopes in proteomics (2002)

Intelligent use of stable isotopes could greatly improve throughput, quantification accuracy, and peptide sequencing in proteome research. Proteins from experimental and control samples were digested into peptides, which were isotopically derivatized and mixed together. The peptide mixture was separated by multidimensional chromatography and detected in mass spectrometers, where they were quantified by measuring the abundance ratios between the isotopically coded peptides in mass spectra and sequenced if the abundance ratio exceeded the preset threshold and presented significant changes between the experimental and control samples. Isotopically coded peptides were found to be fractionated during reversed-phase chromatography (RPC). This could compromise the accuracy of the abundance ratio measurement. Using carbon 13 coding agents instead of deuterium coding eliminated this problem and enabled real-time intelligent data acquisition (IDA). Real-time IDA means selecting peptides for MS/MS experiments based on their abundance ratios and therefore focusing on significantly changed peptides. Among deuterated coding agents, resolution could be controlled by placing the deuterium atoms around hydrophilic groups. A double isotope coding scheme, i.e. code the peptide C-terminus with two oxygen-18 atoms during trypsin digestion in oxygen-18 enriched water and the N-terminus with three deuterium atoms by subsequent derivatization, was demonstrated to greatly improve peptide sequencing because of the recognition of b and y ions in MS/MS spectra based on the unique mass differences between the isotopically coded fragmented ions. A novel algorithm was developed to deconvolute overlap between isotopically coded peptides to facilitate pattern recognition and quantification, when there were not enough mass differences between the isotopically coded peptides. It is superior to the existing algorithms, which required either extra experiments or knowledge of the peptide sequences.
Characterization of the Clostridium Difficile Biofilm (2012)

Clostridium difficile is a Gram-positive, spore forming bacterium and an opportunistic gastrointestinal pathogen. Clostridium difficile infection (CDI) is a common nosocomial infection. Upon antibiotic treatment, patients can be colonized with C. difficile from ingestion of spores. After colonization, cells produce toxins creating symptoms from diarrhea to pseudomembranous colitis, and many patients develop recurrent infections. Interactions between host epithelium and the bacteria is a critical step in infection, yet the interaction is not well understood. It is not known how C. difficile evades host immune responses. These are important mechanisms to answer in advancing CDI treatment. A biofilm could contribute to CDI by facilitating attachment to host epithelium; by resisting host defenses and antimicrobials; by accumulating toxin; and by harboring spores for recurrence. This thesis aims to characterize the C. difficile biofilm by determining biofilm structure, identifying matrix components, determining the role of extracellular DNA in biofilm structure, and quantifying toxin in the matrix.
Nucleotide sequence of the xylanase A gene of alkalophilic Bacillus sp. strain C-125. (1987)

Many alkalophilic microorganisms which grow well at high pH (10.0~1 1.0) have been isolated in our laboratory. These organisms produce manykinds of enzymes which have optimum pHs in the alkaline region.1} The genes for certain enzymesisolated from alkalophilic Bacillus strains have been cloned in Escherichia coli.2~5) Alkalophilic
Cutting Edge: The Nucleotide Receptor P2X7 Contains Multiple Protein- and Lipid-Interaction Motifs Including a Potential Binding Site for Bacterial Lipopolysaccharide (2001)

The nucleotide receptor P2X7 has been shown to modulate LPS-induced macrophage production of numerous inflammatory mediators. Although the C-terminal portion of P2X7 is thought to be essential for multiple receptor functions, little is known regarding the structural motifs that lie within this region. We show here that the P2X7 C-terminal domain contains several apparent protein-protein and protein-lipid interaction motifs with potential importance to macrophage signaling and LPS action. Surprisingly, P2X7 also contains a conserved LPS-binding domain. In this report, we demonstrate that peptides derived from this P2X7 sequence bind LPS in vitro. Moreover, these peptides neutralize the ability of LPS to activate the extracellular signal-regulated kinases (ERK1, ERK2) and to promote the degradation of the inhibitor of kappaB-alpha isoform (IkappaB-alpha) in RAW 264.7 macrophages. Collectively, these data suggest that the C-terminal domain of P2X7 may directly coordinate several signal transduction events related to macrophage function and LPS action.
Increased specificity of PCR-amplified products by size-fractionation of restriction enzyme-digested template genomic DNA (1988)

Journal Article Increased specificity of PCR-amplified products by size-fractionation of restriction enzyme-digested template genomic DNA Get access Barbara N. Beck, Barbara N. Beck Department of Immunology, Mayo ClinicRochester, MN 55902, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Steffan N. Ho Steffan N. Ho Department of Immunology, Mayo ClinicRochester, MN 55902, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 16, Issue 18, 26 September 1988, Page 9051, https://doi.org/10.1093/nar/16.18.9051 Published: 26 September 1988 Article history Received: 22 July 1988 Published: 26 September 1988
Magnetothermal oscillations in<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msub><mml:mrow><mml:mi mathvariant="normal">RuO</mml:mi></mml:mrow><mml:mrow><mml:mn>2</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math>,<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msub><mml:mrow><mml:mi mathvariant="normal">OsO</mml:mi></mml:mrow><mml:mrow><mml:mn>2</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math>, and<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msub><mml:mrow><mml:mi mathvariant="normal">IrO</mml:mi></mml:mrow><mml:mrow><mml:mn>2</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math> (1976)

Magnetothermal oscillations in ${\mathrm{RuO}}_{2}$, ${\mathrm{OsO}}_{2}$, and ${\mathrm{IrO}}_{2}$ at 1.3 K and fields up to 10.5 T allow a detailed mapping of the Fermi surfaces of these isomorphous transition-metal oxides. Relatively simple Fermi surfaces are deduced for ${\mathrm{RuO}}_{2}$ and ${\mathrm{OsO}}_{2}$, though magnetic breakdown of orbits in the former give rise to uncertainties in the interpretation of the data. A very complicated Fermi surface is found to fit the data of ${\mathrm{IrO}}_{2}$. The topology of the Fermi surfaces in all three cases was suggested by perliminary band-structure calculations of Mattheiss. The same band structure was used for all three materials, with slight modifications between isoelectronic ${\mathrm{RuO}}_{2}$ and ${\mathrm{OsO}}_{2}$ to account for greater spin-orbit coupling in ${\mathrm{OsO}}_{2}$. The fact that the same band structure can be made to fit the (extra-electron) ${\mathrm{IrO}}_{2}$ at a higher Fermi energy confirms the basic correctness of the band structure over an energy range of \ensuremath{\sim}0.5 eV.