bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessing the Hepatic Disposition and Toxicity of Xenobiotics Using Primary Hepatocytes
Authors: Sahi Jasminder , Smith Cornelia , Easterwood LaHoma , Grepper Susan , LeCluyse Edward 
Published: October 2012

AbstractOver the past decade or more, primary hepatocytes have become a standardin vitrotool to evaluate hepatic drug uptake and metabolism, cytochrome P450 (P450) induction, and drug interactions affecting hepatic metabolism and transport. For studies involving short incubation periods, suspensions of isolated hepatocytes have proved very useful for the study of drug uptake mediated via SLC transporters, metabolism mediated by phase I and phase II drug‐metabolizing enzymes and hepatotoxicity, because the incubation medium and cells can be easily separated for analysis of drug metabolites, after which the hepatocytes can be fractionated or extracted. Whole hepatocytes are advantageous for many metabolism‐related experiments because these cells do not require the addition of exogenous cofactors and metabolic enzymes such as is the case for microsomes and recombinant enzymes. Moreover, membrane transporters, which could be rate limiting for uptake of certain compounds, are functional in suspension hepatocytes. When longer‐term incubations are required, for example, for hepatotoxicity or enzyme regulation studies, the cells need to be maintained in primary culture for several days or weeks, hepatocytes can be cultured in 3D configurations or in sandwich culture, which prolongs the longevity of hepatocyte cultures while retaining essential absorption, distribution, metabolism, excretion (ADME)‐related functions. The large number of hepatocytes produced in a single preparation allows for greater data acquisition compared toin situsystems such as isolated perfused liver orin vivoexperiments. Improved isolation and cryopreservation strategies, including pooling and freezing of hepatocytes from multiple donors, have provided a reproducible and constant source of cells, allowing for screening studies using the same hepatocyte preparation(s) over extended periods of time. The enzyme and transporter kinetics and response to treatment with drug candidates/toxins are similar in both fresh and cryopreserved hepatocytes and reflect the enzyme specificity and potency observedin vivoin a species‐specific manner. Overall, the versatility and biological fidelity of primary hepatocytes makes them an excellent tool for preclinical development andin vitro/in vivoextrapolations for drug metabolism and pharmacokinetics (DMPK).
Uniformly Interconnected Silver‐Nanowire Networks for Transparent Film Heaters
Authors: Kim TaeYoung , Kim Yeon Won , Lee Ho Seok , Kim Hyeongkeun , Yang Woo Seok , Suh Kwang S. 
Published: October 2012

AbstractThe fabrication and design principles for using silver‐nanowire (AgNW) networks as transparent electrodes for flexible film heaters are described. For best practice, AgNWs are synthesized with a small diameter and network structures of the AgNW films are optimized, demonstrating a favorably low surface resistivity in transparent layouts with a high figure‐of‐merit value. To explore their potential in transparent electrodes, a transparent film heater is constructed based on uniformly interconnected AgNW networks, which yields an effective and rapid heating of the film at low input voltages. In addition, the AgNW‐based film heater is capable of accommodating a large amount of compressive or tensile strains in a completely reversible fashion, thereby yielding an excellent mechanical flexibility. The AgNW networks demonstrated here possess attractive features for both conventional and emerging applications of transparent flexible electrodes.
Comparative assessment of the sensitivity of localized surface plasmon resonance transducers and interference‐based Fabry‐Pérot transducers
Authors: Kedem O. , Vaskevich A. , Rubinstein I. 
Published: October 2012

AbstractLocalized surface plasmon resonance (LSPR) transducers have been widely investigated for use in sensing applications. An alternative approach based on interference from thin films (Fabry‐Pérot interferometers) has been previously advanced, offering a rather high sensitivity. Both methods involve easily produced substrates and simple optical setups. Here, the sensitivity offered by typical transducers of the two kinds in a usual sensing scenario is compared quantitatively, using experimental and simulated data, and their respective advantages are discussed. To facilitate the comparison a simple sensitivity parameter is proposed. It is concluded that LSPR transducers offer superior sensitivity for analytes and recognition interfaces of small dimensions (up to several nanometers), especially in a wet environment, while the interference transducers become advantageous for thicker layers in dry conditions. For LSPR transducers, significantly higher sensitivity is obtained by using reflection, rather than transmission, measurements.
Synthesis of highly selective spherical caffeine imprinted polymers via ultrasound‐assisted precipitation polymerization
Authors: Phutthawong Nathaporn , Pattarawarapan Mookda 
Published: October 2012

AbstractA facile and efficient method for synthesis of molecularly imprinted polymers via ultrasound‐assisted precipitation polymerization was developed. Caffeine was applied as a model template in the imprinting using methacrylic acid and ethylene glycol dimethacrylate as a functional monomer and a crosslinker, respectively. Polymerization under sonochemical conditions proceeded rapidly (within 3 h at 60°C) to afford polymer microspheres with narrow size distributions in excellent yields while maintaining the binding specificity toward the template. It was found that the imprinted polymer prepared at low initial temperature (40°C) exhibited the best caffeine binding performance in terms of specificity and selectivity. © 2012 Wiley Periodicals, Inc. J. Appl. Polym. Sci., 2013
Resistivity Tomography in the Park of Pratolino at Vaglia (Florence, Italy)
Authors: Cozzolino Marilena , Di Giovanni Elisa , Mauriello Paolo , Vanni Desideri Andrea , Patella Domenico 
Published: October 2012

ABSTRACTWithin this article are the results of a geoelectrical survey performed in the park of Pratolino at Vaglia (Florence, Italy), using the multiple dipole–dipole profile technique. The purpose was to outline the location of the main body of the ancient Villa Medici di Pratolino, of which only a separate building, now known as Villa Demidoff, is visible in its full splendour. The three‐dimensional probability‐based electrical resistivity tomography inversion (PERTI) approach has been adopted. The three‐dimensional resistivity tomography inversion provides evidence at the expected depth of burial of a regular pattern of resistivity relative maxima, mostly distributed along the sides of a mesh closely resembling the structural plan of a building. The almost perfect superposition of the high resistivity source image over an official historical plan of the ancient Villa Medici has allowed the regular mesh of the resistivity maxima to be ascribed to remains of walls. As the Pratolino case‐history is one of the first applications of the PERTI algorithm to real field datasets, its performance has been tested using the well‐known ERTLab commercial software as a benchmark. The comparison has shown a very good agreement between the two inversions and also confirmed the much higher computing speed and greater versatility of the PERTI algorithm, as outlined in a previous paper where only synthetic models were tested. Copyright © 2012 John Wiley & Sons, Ltd.
Using electrophoretic mobility shift assays to measure equilibrium dissociation constants: GAL4‐p53 binding DNA as a model system
Authors: Heffler Michael A. , Walters Ryan D. , Kugel‡ Jennifer F. 
Published: October 2012

AbstractAn undergraduate biochemistry laboratory experiment is described that will teach students the practical and theoretical considerations for measuring the equilibrium dissociation constant (KD) for a protein/DNA interaction using electrophoretic mobility shift assays (EMSAs). An EMSA monitors the migration of DNA through a native gel; the DNA migrates more slowly when bound to a protein. To determine a KD the amount of unbound and protein‐bound DNA in the gel is measured as the protein concentration increases. By performing this experiment, students will be introduced to making affinity measurements and gain experience in performing quantitative EMSAs. The experiment describes measuring the KD for the interaction between the chimeric protein GAL4‐p53 and its DNA recognition site; however, the techniques are adaptable to other DNA binding proteins. In addition, the basic experiment described can be easily expanded to include additional inquiry‐driven experimentation. © 2012 by The International Union of Biochemistry and Molecular Biology
Proteopedia: 3D visualization and annotation of transcription factor–DNA readout modes
Authors: Machado Ana Carolina Dantas , Saleebyan Skyler B. , Holmes Bailey T. , Karelina Maria , Tam Julia , Kim Sharon Y. , Kim Keziah H. , Dror Iris , Hodis Eran , Martz Eric , Compeau Patricia A. , Rohs Remo 
Published: October 2012

Abstract3D visualization assists in identifying diverse mechanisms of protein‐DNA recognition that can be observed for transcription factors and other DNA binding proteins. We used Proteopedia to illustrate transcription factor‐DNA readout modes with a focus on DNA shape, which can be a function of either nucleotide sequence (Hox proteins) or base pairing geometry (p53). © 2012 by The International Union of Biochemistry and Molecular Biology
Synthesis and Photophysical Characterisation of a Fluorescent Nucleoside Analogue that Signals the Presence of an Abasic Site in RNA
Authors: Tanpure Arun A. , Srivatsan Seergazhi G. 
Published: October 2012

AbstractThe synthesis and site‐specific incorporation of an environment‐sensitive fluorescent nucleoside analogue (2), based on a 5‐(benzofuran‐2‐yl)pyrimidine core, into DNA oligonucleotides (ONs), and its photophysical properties within these ONs are described. Interestingly and unlike 2‐aminopurine (a widely used nucleoside analogue probe), when incorporated into an ON and hybridised with a complementary ON, the emissive nucleoside 2 displays significantly higher emission intensity than the free nucleoside. Furthermore, photophysical characterisation shows that the fluorescence properties of the nucleoside analogue within ONs are significantly influenced by flanking bases, especially by guanosine. By utilising the responsiveness of the nucleoside to changes in base environment, a DNA ON reporter labelled with the emissive nucleoside 2 was constructed; this signalled the presence of an abasic site in a model depurinated sarcin/ricin RNA motif of a eukaryotic 28S rRNA.
Extended Model for Theoretical Determination of Mass Transfer Coefficients in Multiphase Flows – Part 1
Authors: John Saskia , Dujardin Viviane , Kück Ulf Daniel , Mießner Ulrich , Räbiger Norbert 
Published: October 2012

AbstractDie Auslegung von Reaktoren mit Mehrphasensystemen und die Steuerung überlagerter chemischer Reaktionen stellen auch heute noch Herausforderungen dar. Neuere, erweiterte Erkenntnisse zur Charakterisierung der Meso‐Ebene in Mehrphasenströmungen weisen vielversprechende Optionen in Hinblick auf eine theoretische Abschätzung von Stoffübergangskoeffizienten auf. Bestehende Modellansätze sind bisher nur für enge Anwendungsbereiche der Mehrphasenströmung gültig. Welche Möglichkeiten sich durch eine, auf den neuen Erkenntnissen basierende Zusammenführung der Modelle für die zukünftige Modellierung und die Berechnung des Stofftransportes ergeben, wird in dem vorliegenden Artikel aufgezeigt.
A new two‐step single slope A/D converter for using in CMOS image sensors
Authors: Teymouri Masood 
Published: October 2012

SUMMARYThis paper presents a high‐speed, high‐resolution column parallel analog‐to‐digital converter (ADC) with global digital error correction. Proposed A/D converter is suitable for using in high‐frame‐rate complementary metal–oxide–semiconductor (CMOS) image sensors. This new method has more advantages than conventional ramp ADC from viewpoint of speed and resolution. A prototype 11‐bit ADC is designed in 0.25‐µm CMOS technology. Moreover, an overall signal‐to‐noise ratio of 63.8 dB can be achieved at 0.5Msample/s. The power dissipation of all 320 column‐parallel ADCs with the peripheral circuits consume 76 mW at 2.5‐V supplies. Copyright © 2012 John Wiley & Sons, Ltd.
Keeping pace with climate change: what is wrong with the evolutionary potential of upper thermal limits?
Authors: Santos Mauro , Castañeda Luis E. , Rezende Enrico L. 
Published: October 2012

AbstractThe potential of populations to evolve in response to ongoing climate change is partly conditioned by the presence of heritable genetic variation in relevant physiological traits. Recent research suggests thatDrosophila melanogasterexhibits negligible heritability, hence little evolutionary potential in heat tolerance when measured under slow heating rates that presumably mimic conditions in nature. Here, we study the effects of directional selection for increased heat tolerance usingDrosophilaas a model system. We combine a physiological model to simulate thermal tolerance assays with multilocus models for quantitative traits. Our simulations show that, whereas the evolutionary response of the genetically determined upper thermal limit (CTmax) is independent of methodological context, the response in knockdown temperatures varies with measurement protocol and is substantially (up to 50%) lower than forCTmax. Realized heritabilities of knockdown temperature may grossly underestimate the true heritability ofCTmax. For instance, assuming that the true heritability ofCTmax in the base population ish2 = 0.25, realized heritabilities of knockdown temperature are around 0.08–0.16 depending on heating rate. These effects are higher in slow heating assays, suggesting that flawed methodology might explain the apparently limited evolutionary potential of cosmopolitanD.melanogaster.
Avoiding minorities: Social invisibility
Authors: Pérez Juan A. , Passini Stefano 
Published: October 2012

AbstractThree experiments examined how self‐consciousness has an impact on the visual exploration of a social field. The main hypothesis was that merely a photograph of people can trigger a dynamic process of social visual interaction such that minority images are avoided when people are in a state of self‐reflective consciousness. In all three experiments, pairs of pictures—one with characters of social minorities and one with characters of social majorities—were shown to the participants. By means of eye‐tracking technology, the results of Experiment 1 (n = 20) confirmed the hypothesis that in the reflective consciousness condition, people look more at the majority than minority characters. The results of Experiment 2 (n = 89) confirmed the hypothesis that reflective consciousness also induces avoiding reciprocal visual interaction with minorities. Finally, by manipulating the visual interaction (direct vs. non‐direct) with the photos of minority and majority characters, the results of Experiment 3 (n = 56) confirmed the hypothesis that direct visual interaction with minority characters is perceived as being longer and more aversive. The overall conclusion is that self‐reflective consciousness leads people to avoid visual interaction with social minorities, consigning them to social invisibility. Copyright © 2012 John Wiley & Sons, Ltd.
REV1 and DNA polymerase zeta in DNA interstrand crosslink repair
Authors: Sharma Shilpy , Canman Christine E. 
Published: October 2012

AbstractDNA interstrand crosslinks (ICLs) are covalent linkages between two strands of DNA, and their presence interferes with essential metabolic processes such as transcription and replication. These lesions are extremely toxic, and their repair is essential for genome stability and cell survival. In this review, we will discuss how the removal of ICLs requires interplay between multiple genome maintenance pathways and can occur in the absence of replication (replication‐independent ICL repair) or during S phase (replication‐coupled ICL repair), the latter being the predominant pathway used in mammalian cells. It is now well recognized that translesion DNA synthesis (TLS), especially through the activities of REV1 and DNA polymerase zeta (Polζ), is necessary for both ICL repair pathways operating throughout the cell cycle. Recent studies suggest that the convergence of two replication forks upon an ICL initiates a cascade of events including unhooking of the lesion through the actions of structure‐specific endonucleases, thereby creating a DNA double‐stranded break (DSB). TLS across the unhooked lesion is necessary for restoring the sister chromatid before homologous recombination repair. Biochemical and genetic studies implicate REV1 and Polζ as being essential for performing lesion bypass across the unhooked crosslink, and this step appears to be important for subsequent events to repair the intermediate DSB. The potential role of Fanconi anemia pathway in the regulation of REV1 and Polζ‐dependent TLS and the involvement of additional polymerases, including DNA polymerases kappa, nu, and theta, in the repair of ICLs is also discussed in this review. Environ. Mol. Mutagen. 2012. © 2012 Wiley Periodicals, Inc.
DNA polymerase delta in dna replication and genome maintenance
Authors: Prindle Marc J. , Loeb Lawrence A. 
Published: October 2012

AbstractThe eukaryotic genome is in a constant state of modification and repair. Faithful transmission of the genomic information from parent to daughter cells depends upon an extensive system of surveillance, signaling, and DNA repair, as well as accurate synthesis of DNA during replication. Often, replicative synthesis occurs over regions of DNA that have not yet been repaired, presenting further challenges to genomic stability. DNA polymerase δ (pol δ) occupies a central role in all of these processes: catalyzing the accurate replication of a majority of the genome, participating in several DNA repair synthetic pathways, and contributing structurally to the accurate bypass of problematic lesions during translesion synthesis. The concerted actions of pol δ on the lagging strand, pol ϵ on the leading strand, associated replicative factors, and the mismatch repair (MMR) proteins results in a mutation rate of less than one misincorporation per genome per replication cycle. This low mutation rate provides a high level of protection against genetic defects during development and may prevent the initiation of malignancies in somatic cells. This review explores the role of pol δ in replication fidelity and genome maintenance. Environ. Mol. Mutagen. 2012. © 2012 Wiley Periodicals, Inc.
Complex spatial feedbacks of tephra redistribution, ice melt and surface roughness modulate ablation on tephra covered glaciers
Authors: Nield Joanna M. , Chiverrell Richard C. , Darby Stephen E. , Leyland Julian , Vircavs Larisa H. , Jacobs Benjamin 
Published: October 2012

ABSTRACTTephra fallout from the 2011 Grímsvötn eruption onto Svínafellsjökull, Iceland, created an ice‐ash landscape of a type that is rarely studied but is nevertheless common in glacio‐volcanic regions. We used terrestrial laser scanning (TLS) to measure ice surface topography and absorption at high spatial resolution, confirming ablation rates either reduce or increase under thick (insulating) and thin (reduced albedo) ash deposits, respectively. Fourier transform analysis of the TLS data identified that a three‐fold increase in aerodynamic roughness was attributable to an increase in larger (> 0·2 m) surface features. Moreover, TLS measurements revealed the importance of ash redistribution by meltwater in generating differential melting which modifies roughness and ash patchiness, such that the net effect of these spatial ash–ice feedbacks was to reduce ablation rates by up to 59%. The modulating effects of these previously undocumented feedbacks on ablation rates are, therefore, significant and must be correctly parameterized if ash‐covered glacier mass balances are to be predicted correctly. Copyright © 2012 John Wiley & Sons, Ltd.
Toxicity of sediments potentially contaminated by coal mining and natural gas extraction to unionid mussels and commonly tested benthic invertebrates
Authors: Wang Ning , Ingersoll Christopher G. , Kunz James L. , Brumbaugh William G. , Kane Cindy M. , Evans R. Brian , Alexander Steven , Walker Craig , Bakaletz Steve 
Published: October 2012

Abstract
Sediment toxicity tests were conducted to assess potential effects of contaminants associated with coal mining or natural gas extraction activities in the upper Tennessee River basin and eastern Cumberland River basin in the United States. Test species included two unionid mussels (rainbow mussel, Villosa iris, and wavy-rayed lampmussel, Lampsilis fasciola, 28-d exposures), and the commonly tested amphipod, Hyalella azteca (28-d exposure) and midge, Chironomus dilutus (10-d exposure). Sediments were collected from seven test sites with mussel communities classified as impacted and in proximity to coal mining or gas extraction activities, and from five reference sites with mussel communities classified as not impacted and no or limited coal mining or gas extraction activities. Additional samples were collected from six test sites potentially with high concentrations of polycyclic aromatic hydrocarbons (PAHs) and from a test site contaminated by a coal ash spill. Mean survival, length, or biomass of one or more test species was reduced in 10 of 14 test samples (71%) from impacted areas relative to the response of organisms in the five reference samples. A higher proportion of samples was classified as toxic to mussels (63% for rainbow mussels, 50% for wavy-rayed lampmussels) compared with amphipods (38%) or midge (38%). Concentrations of total recoverable metals and total PAHs in sediments did not exceed effects-based probable effect concentrations (PECs). However, the survival, length, or biomasses of the mussels were reduced significantly with increasing PEC quotients for metals and for total PAHs, or with increasing sum equilibrium-partitioning sediment benchmark toxic units for PAHs. The growth of the rainbow mussel also significantly decreased with increasing concentrations of a major anion (chloride) and major cations (calcium and magnesium) in sediment pore water. Results of the present study indicated that (1) the findings from laboratory tests were generally consistent with the field observations of impacts on mussel populations; (2) total recoverable metals, PAHs, or major ions, or all three in sediments might have contributed to the sediment toxicity; (3) the mussels were more sensitive to the contaminants in sediments than the commonly tested amphipod and midge; and (4) a sediment toxicity benchmark of 1.0 based on PECs may not be protective of mussels. Environ. Toxicol. Chem. 2013;32:207–221. © 2012 SETAC