gebhart/patrepeval huggingface dataset:
Diffusion coefficients of propane and butane in peace river bitumen (1996)

Abstract Diffusion plays a vital role in the “Vapex” process. In the present work the results of experiments on “Vapex” using a Hele‐Shaw cell have been used to obtain empirical correlations for the diffusivities of propane and butane in Peace River bitumen. Additional data required for the estimation of diffusivities from these experiments are the solubilities of solvent in bitumen and a correlation for the viscosity of solvent bitumen mixture. Diffusivities are assumed to decline exponentially with viscosity. Computed values of diffusion coefficients fall within the range of the published data for similar systems. This simple experiment can be used to estimate the diffusivities of gaseous solvents in highly viscous fluids.
Evaluation of Tumor Cell–Tumor Microenvironment Component Interactions as Potential Predictors of Patient Response to Napabucasin (2019)

Napabucasin is an NAD(P)H:quinone oxidoreductase 1 (NQO1)-bioactivatable small molecule hypothesized to affect multiple oncogenic pathways. In a prespecified, retrospective analysis of the napabucasin phase III CO.23 study, overall survival was longer for napabucasin versus placebo in patients expressing phosphorylated STAT3 (pSTAT3) in tumor cells and cells of the tumor microenvironment (TME). We hypothesized that a connection may exist between NQO1 expression in cancer cells and pSTAT3 in tumor cells and the TME. In 3D spheroid cocultures of cancer cells and cancer-associated fibroblasts, the antitumor activity of napabucasin was NQO1 dependent. The levels of cytokines such as IL6, CXCL10, and GM-CSF were higher in NQO1-positive versus NQO1-deleted cocultures. These differentially secreted cytokines promoted STAT3 phosphorylation in tumor cells and the TME. NQO1-expressing, napabucasin-sensitive tumor cells can modify tumor cells and the TME to promote STAT3 phosphorylation, suggesting that pSTAT3 may be used to identify a subpopulation of patients who would likely respond to napabucasin. IMPLICATIONS: pSTAT3 is a potential biomarker for patient response to the anticancer drug napabucasin.<b>Visual Overview:</b> http://mcr.aacrjournals.org/content/molcanres/17/7/1429/F1.large.jpg.
Fabrication and Characterization of Large-Area, Semiconducting Nanoperforated Graphene Materials (2010)

We demonstrate the fabrication of nanoperforated graphene materials with sub-20-nm features using cylinder-forming diblock copolymer templates across >1 mm(2) areas. Hexagonal arrays of holes are etched into graphene membranes, and the remaining constrictions between holes interconnect forming a honeycomb structure. Quantum confinement, disorder, and localization effects modulate the electronic structure, opening an effective energy gap of 100 meV in the nanopatterned material. The field-effect conductivity can be modulated by 40x (200x) at room temperature (T = 105 K) as a result. A room temperature hole mobility of 1 cm(2) V(-1) s(-1) was measured in the fabricated nanoperforated graphene field effect transistors. This scalable strategy for modulating the electronic structure of graphene is expected to facilitate applications of graphene in electronics, optoelectronics, and sensing.
Efficient biochemical engineering of cellular sialic acids using an unphysiological sialic acid precursor in cells lacking UDP‐N‐acetylglucosamine 2‐epimerase (2001)

Sialic acids comprise a family of terminal sugars essential for a variety of biological recognition systems. N-Propanoylmannosamine, an unphysiological sialic acid precursor, is taken up and metabolized by mammalian cells resulting in oligosaccharide-bound N-propanoylneuraminic acid. N-Propanoylmannosamine, applied to endogenously hyposialylated subclones of the myeloid leukemia HL60 and of the B-cell lymphoma BJA-B, both deficient in UDP-N-acetylglucosamine 2-epimerase, is efficiently metabolized to CMP-N-propanoylneuraminic acid resulting in up to 85% of glycoconjugate-associated sialic acids being unphysiological N-propanoylneuraminic acid. Thus, UDP-N-acetylglucosamine 2-epimerase-deficient cell lines provide an important experimental progress in engineering cells to display an almost homogeneous population of defined, structurally altered sialic acids.
Monocyte Chemotactic Protein-3 (MCP3) Interacts with Multiple Leukocyte Receptors (1995)

Monocyte chemotactic protein-3 (MCP3) is recently identified and molecularly cloned C-C chemokine that is chemotactic for and activates a great variety of inflammatory cell types. MCP3 has been reported to interact with several C-C chemokine receptors, which can be simultaneously or selectively expressed on leukocyte subpopulations. In order to isolate receptor(s) for MCP3, a cDNA library was constructed using mRNA from a human NK-like cell line, YT. These cells showed high affinity binding sites for 125I-MCP3 and migrated in response to MCP3. A chemokine receptor cDNA clone, designated YT4, was sequenced and found to be identical to the known C-C CKR1 or macrophage inflammatory protein-1 alpha (MIP1 alpha)/Rantes receptor. YT4 cDNA was subcloned into a mammalian expression vector, and stable transfectants were prepared using the embryonic kidney cell line 293. The transfectants (YT4/293) showed high affinity binding for 125I-MCP3 in addition to specifically binding 125I-MIP1 alpha and 125I-Rantes. All three C-C chemokines were able to cross-compete for binding sites on YT4/293 cells and induced directional migration of YT4/293 cells in vitro, with MCP3 being the most potent chemoattractant. MCP3, MIP1 alpha, and Rantes were equally able to cross-attenuate the migratory response of YT4/293 cells to one another. In contrast, MCP1 and MIP1 beta had very limited capacity to compete for MCP3 binding on YT4/293 cells and had only a minor attenuating effect on MCP3-induced migration. Since MCP3 has been reported to use MCP1 receptor(s), our results with transfected 293 cells expressing only C-C CKR1 clearly establish that C-C CKR1 is also a functional receptor for MCP3.
Characterization of new membrane lipoproteins and their precursors of Escherichia coli. (1981)

By labeling cells heavily with [3H]glycerol or [3H]-palmitic acid several new species of lipoproteins, in addition to Braun's lipoprotein and a peptidoglycan-associated lipoprotein called PAL, were found in the envelope of Escherichia coli. The new lipoproteins were immunochemically different from both Braun's lipoprotein and PAL. A strain lacking the structural gene for Braun's lipoprotein contained new lipoproteins and PAL. In addition to Braun's lipoprotein and PAL, four new lipoproteins were found to be localized in the outer membrane, while other two species were found in the cytoplasmic membrane. The localization of one species is unknown. We previously reported that, on treatment of cells with globomycin, a precursor of Braun's lipoprotein accumulated in the cell envelope (Hussain, M., Ichihara, S., and Mizushima, S. (1980) J. Biol. Chem. 255, 3707-3712). Similarly, the putative precursors of new lipoproteins and that of PAL accumulated in globomycin-treated cells. These precursors contained glycerol and fatty acid(s) as that of Braun's lipoprotein did. It is suggested that the structures of the "signal" region and the mechanisms of processing of all the lipoproteins of E. coli are similar.
Pharmacokinetic Properties of Phosphorothioate Oligonucleotides (1997)

Abstract The pharmacokinetic parameters determined for different phosphorothioate oligonucleotides were compared. The data suggest that phosphorothioate pharmacokinetics are primarily determined by chemical class. The pharmacokinetics are consistent across species, show dose-dependency, and are independent of sequence.
City Pinhole (2005)

Essay| April 01 2005 City Pinhole Mccarthy Michael Mccarthy Michael Michael McCarthy was born in Ithaca, NY. He was educated at the University of Vermont (BA in History), and the Tyler School of Art (MFA in Photography). He currently teaches photography and digital imaging at the Santa Reparta International School of Art in Florence, Italy. Search for other works by this author on: This Site PubMed Google Scholar Afterimage (2005) 32 (5): 10–11. https://doi.org/10.1525/aft.2005.32.5.10 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Twitter LinkedIn Tools Icon Tools Get Permissions Cite Icon Cite Search Site Citation Mccarthy Michael; City Pinhole. Afterimage 1 April 2005; 32 (5): 10–11. doi: https://doi.org/10.1525/aft.2005.32.5.10 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 ContentAfterimage Search This content is only available via PDF. © 2005 by The Regents of the University of California2005 Article PDF first page preview Close Modal You do not currently have access to this content.
Ras Activation by Insulin and Epidermal Growth Factor through Enhanced Exchange of Guanine Nucleotides on p21ras (1993)

A number of growth factors, including insulin and epidermal growth factor (EGF), induce accumulation of the GTP-bound form of p21ras. This accumulation could be caused either by an increase in guanine nucleotide exchange on p21ras or by a decrease in the GTPase activity of p21ras. To investigate whether insulin and EGF affect nucleotide exchange on p21ras, we measured binding of [alpha-32P]GTP to p21ras in cells permeabilized with streptolysin O. For this purpose, we used a cell line which expressed elevated levels of p21 H-ras and which was highly responsive to insulin and EGF. Stimulation with insulin or EGF resulted in an increase in the rate of nucleotide binding to p21ras. To determine whether this increased binding rate is due to the activation of a guanine nucleotide exchange factor, we made use of the inhibitory properties of a dominant negative mutant of p21ras, p21ras (Asn-17). Activation of p21ras by insulin and EGF in intact cells was abolished in cells infected with a recombinant vaccinia virus expressing p21ras (Asn-17). In addition, the enhanced nucleotide binding to p21ras in response to insulin and EGF in permeabilized cells was blocked upon expression of p21ras (Asn-17). From these data, we conclude that the activation of a guanine nucleotide exchange factor is involved in insulin- and EGF-induced activation of p21ras.
Functional analysis of an eye specific enhancer of the eyeless gene in Drosophila (1999)

The development of the Drosophila compound eye requires the function of a set of evolutionarily conserved genes. Among these, the Drosophila Pax-6 gene eyeless (ey) plays a major role. ey has been considered a master control gene of eye development in the animal kingdom because targeted expression of ey and vertebrate as well as invertebrate homologs lead to the formation of ectopic eyes in Drosophila. We demonstrate that an intron of the ey gene contains an enhancer that regulates the eye specific expression of the gene in the eye disc primordia of embryos and in the eye imaginal discs of third instar larvae. Moreover, a 212-bp enhancer element is necessary and sufficient for the enhancer function. It is partially conserved in Drosophila hydei and contains putative Pax-6 Paired domain binding sites. We show that several binding sites are required for the eye specific expression, and, therefore, we propose a Pax-6-like molecule to be a positive transactivator for the eye specific ey expression. This transactivator recently has been identified as twin of eyeless, the second Pax-6 gene in Drosophila.
Imiquimod 5% cream for actinic keratosis. (2004)

Imiquimod 5% cream has been available since 1997 for the treatment of genital warts. Health Canada has expanded the indication to include actinic keratosis (AK). There are no trials comparing imiquimod 5% cream to standard AK therapy; placebo-controlled trials have shown an increased lesion clearance rate of 30% to 55% eight weeks post-treatment. Side effects include local skin reactions that can be severe and require discontinuation of treatment in 2% to 4% of patients. Imiquimod has shown a great potential for use in unapproved indications.
STING-Dependent Recognition of Cyclic di-AMP Mediates Type I Interferon Responses during Chlamydia trachomatis Infection (2013)

This study shows that the Gram-negative obligate pathogen Chlamydia trachomatis, a major cause of pelvic inflammatory disease and infertility, synthesizes cyclic di-AMP (c-di-AMP), a nucleic acid metabolite that thus far has been described only in Gram-positive bacteria. We further provide evidence that the host cell employs an endoplasmic reticulum (ER)-localized cytoplasmic sensor, STING (stimulator of interferon [IFN] genes), to detect c-di-AMP synthesized by Chlamydia and induce a protective IFN response. This detection occurs even though Chlamydia is confined to a membrane-bound vacuole. This raises the possibility that the ER, an organelle that innervates the entire cytoplasm, is equipped with pattern recognition receptors that can directly survey membrane-bound pathogen-containing vacuoles for leaking microbe-specific metabolites to mount type I IFN responses required to control microbial infections.
Influence of Hot Electron Scattering and Electron–Phonon Interactions on Thermal Boundary Conductance at Metal/Nonmetal Interfaces (2014)

It has recently been demonstrated that under certain conditions of electron nonequilibrium, electron to substrate energy coupling could represent a unique mechanism to enhance heat flow across interfaces. In this work, we present a coupled thermodynamic and quantum mechanical derivation of electron–phonon scattering at free electron metal/nonmetal substrate interfaces. A simplified approach to the Fermi's Golden Rule with electron energy transitions between only three energy levels is adopted to derive an electron–phonon diffuse mismatch model, that account for the electron–phonon thermal boundary conductance at metal/insulator interfaces increases with electron temperature. Our approach demonstrates that the metal-electron/nonmetal phonon conductance at interfaces can be an order of magnitude larger than purely phonon driven processes when the electrons are driven out of equilibrium with the phonons, consistent with recent experimental observations.
Fibre optic confocal imaging (FOCI) of keratinocytes, blood vessels and nerves in hairless mouse skin in vivo (1998)

Fibre optic confocal imaging (FOCI) enabled subsurface fluorescence microscopy of the skin of hairless mice in vivo. Application of acridine orange enabled imaging of the layers of the epidermis. The corneocytes of the stratum corneum, the keratinocytes in the basal layers and redundant hair follicles were visualised at depths greater than 100 microm. Cellular and nuclear membranes of keratinocytes of the skin were visualised by the use of acridine orange and DIOC5(3). Imaging of the skin after injection of FITC-dextran revealed an extensive network of blood vessels with a size range up to 20 microm. Blood cells could be seen moving through dermal vessels and the blood circulation through the dermal vascular bed was video-taped. The fluorescent dye 4-di-2-ASP showed the presence of nerves fibres around the hair follicles and subsurface blood vessels. Comparison was made between images obtained in vivo using FOCI and in vitro scanning electron microscopy and conventional histology. FOCI offers the potential to study dynamic events in vivo, such as blood flow, skin growth, nerve regeneration and many pathological processes, in ways which have not previously been possible.
Petrographie Image Analysis: An Effective Technology for Delineating Reservoir Quality (1993)

Abstract Petrographie Image Analysis (PIA) is an emerging technology used to estimate the properties of pore systems that occur worldwide in sandstone, carbonate and conglomerate reservoir rock samples. It provides quantitative evaluations from standard core plugs as well as from material unsuitable for conventional core analysis such as core rubble and drill cuttings. PIA technology also supplements routine core analysis by estimating other parameters like the specific pore size interval that regulates fluid flow. The method described here is based on a simulated capillary pressure curve. It has been used routinely to estimate pore and pore-throat size distributions, porosity, permeability, air-mercuiy capillary pressure, irreducible water saturation, effective porosity, microporosity, seal capacity, and the minimum saturation of the non-wetting phase at which it becomes mobile throughout the pore system. These and other new relationships being developed and tested can be mapped to help delineate trends in reservoir quality. PIA procedures and relationships are discussed and illustrated with an example application from a large gas reservoir in the Western Canadian Sedimentary Basin.
100 GHz on-wafer S-parameter measurements by electrooptic sampling (2003)

The authors describe an electrooptic sampling system with a measurement bandwidth in excess of 200 GHz for on-wafer millimeter-wave measurements. An active probe frequency-multiplier has been developed to supply the millimeter-wave stimulus signal to the device under test. On-wafer measurements of S-parameters of linear circuits, time-waveforms of nonlinear circuits, and propagation characteristics of uniplanar waveguides on GaAs to 100 GHz by direct electrooptic sampling have been demonstrated.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A pharmacokinetic model for alpha interferon administered subcutaneously (1999)

The present pharmacokinetic model will allow one to obtain individual parameters such as, the area under the curve of concentration vs time from a limited-sampling strategy, and to perform pharmacokinetic-pharmacodynamic analysis of combined alphaIFN plasma concentrations and viraemic data.
PCGEM1, a prostate-specific gene, is overexpressed in prostate cancer (2000)

A prostate-specific gene, PCGEM1, was identified by differential display analysis of paired normal and prostate cancer tissues. Multiple tissue Northern blot analysis revealed that PCGEM1 was expressed exclusively in human prostate tissue. Analysis of PCGEM1 expression in matched normal and primary tumor specimens revealed tumor-associated overexpression in 84% of patients with prostate cancer by in situ hybridization assay and in 56% of patients by reverse transcription-PCR assay. Among various prostate cancer cell lines analyzed, PCGEM1 expression was detected only in the androgen receptor-positive cell line LNCaP. Extensive DNA sequence analysis of the PCGEM1 cDNA and genomic DNA revealed that PCGEM1 lacks protein-coding capacity and suggests that it may belong to an emerging class of noncoding RNAs, also called "riboregulators." The PCGEM1 locus was mapped to chromosome 2q32. Taken together, the remarkable prostate-tissue specificity and androgen-dependent expression of PCGEM1 as well as its elevated expression in a significant percentage of tumor tissues suggest specific functions of PCGEM1 in the biology and tumorigenesis of the prostate gland.
Hydroxyalkylated phosphoramidate, phosphoramidothioate and phosphorodiamidothioate derivatives as thiophosphate protecting groups in the development of thermolytic DNA prodrugs (2010)

The hydroxyalkylated phosphoramidate 4a, phosphoramidothioates 4b, 4e–j, and phosphorodiamidothioates 4c and 4d have been identified as a new class of heat-sensitive thiophosphate protecting groups in the development of thermolytic immunomodulatory DNA prodrugs. These alcohols are converted to their deoxyribonucleoside phosphoramidite derivatives 6a–j, which are then used in the preparation of the thermosensitive dinucleoside phosphorothioates 7a–j. The negatively charged thiophosphate protecting groups of 7a–b and 7e–j presumably undergo thermolytic cyclodeesterification at elevated temperature under essentially neutral conditions. The thiophosphate protecting groups of 7e and 7f show relatively rapid deprotection kinetics at 37 °C (t½ = 20 and 42 h, respectively) and are therefore suitable for the protection of phosphodiester functions flanking the CpG motifs of immunomodulatory DNA sequences, whereas the thiophosphate protecting groups of 7g–j with thermolytic deprotection half-lives in the range of 94–265 h at 37 °C are more appropriate for the thiophosphate protection of CpG motifs. Furthermore, the thermostability of the group protecting the thiophosphate function of 7a (t½ = 82 min at 90 °C) should offer adequate protection of the 5′- and/or 3′-terminal phosphodiester functions of DNA prodrugs against ubiquitous extracellular and intracellular exonucleases.
Bright Photon Upconversion on Composite Organic Lanthanide Molecules through Localized Thermal Radiation (2017)

Converting low-energy photons via thermal radiation can be a potential approach for utilizing infrared (IR) photons to improve photovoltaic efficiency. Lanthanide-containing materials have achieved great progress in IR-to-visible photon upconversion (UC). Herein, we first report bright photon, tunable wavelength UC through localized thermal radiation at the molecular scale with low excitation power density (<10 W/cm<sup>2</sup>) realized on lanthanide complexes of perfluorinated organic ligands. This is enabled by engineering the pathways of nonradiative de-excitation and energy transfer in a composite of ytterbium and terbium perfluoroimidodiphosphinates. The IR-excited thermal UC and wavelength control is realized through the terbium activators sensitized by the ytterbium sensitizers having high luminescence efficiency. The metallic molecular composite thus can be a potential energy material in the use of the IR solar spectrum for thermal photovoltaic applications.
Pseudomembranous Colitis Caused by a Toxin A − B + Strain of Clostridium difficile (2000)

We report a case of severe pseudomembranous colitis due to a toxin A(-) B(+) strain of Clostridium difficile in an immunosuppressed patient and discuss the implications for diagnostic testing in suspected C. difficile-associated diarrhea.
Identification of a highly conserved sequence element at the 3' terminus of hepatitis C virus genome RNA (1996)

Previous reports suggest that the hepatitis C virus (HCV) genome RNA terminates with homopolymer tracts of either poly(U) or poly(A). By ligation of synthetic oligonucleotides followed by reverse transcription-PCR, cDNA cloning, and sequence analysis, we determined the 3'-terminal sequence of HCV genome RNA. Our results show that the HCV 3' nontranslated region consists of four elements (positive sense, 5' to 3'): (i) a short sequence with significant variability among genotypes, (ii) a homopolymeric poly(U) tract, (iii) a polypyrimidine stretch consisting of mainly U with interspersed C residues, (iv) a novel sequence of 98 bases. This latter nucleotide sequence is not present in human genomic DNA and is highly conserved among HCV genotypes. The 3'-terminal 46 bases are predicted to form a stable stem-loop structure. Using a quantitative-competitive reverse transcription-PCR assay, we show that a substantial fraction of HCV genome RNAs from a high- specific-infectivity inoculum contain this 3'-terminal sequence element. These results indicate that the HCV genome RNA terminates with a highly conserved RNA element which is likely to be required for authentic HCV replication and recovery of infectious RNA from cDNA.