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      • Computational studies of hole/electron transport in positional isomers of linear oligo-thienoacenes: Evaluation of internal reorganization energies using density functional theory

        Thomas, A.,Chitumalla, R.K.,Puyad, A.L.,Mohan, K.V.,Jang, J. Elsevier Scientific Pub. Co 2016 Computational & theoretical chemistry Vol.1089 No.-

        <P>The paper computationally investigates and compares the internal reorganization energies associated with the intermolecular transport of a hole and electron in a series of positional isomers of fused planar acenodithiophenes (S(n)a-c) with those of linear acenes (LA(n)). In particular, it is observed that, amongst the positional isomers, the para isomers (S(n)c) have got ultra-small reorganization energies than the other two positional isomers. The non-bonding character of frontier molecular orbitals (FMO) of these para isomers is the main reason for the existence of this phenomenon. Secondly, the nonbonding character in the FMO of these molecules is mediated by their open shell singlet biradical nature in ground state, as revealed by the Spin-flip time dependent density functional theory analysis. These aforementioned findings and characteristics of S(n)c series of molecules, strongly recommend that these molecules if synthesized will show high charge carrier mobility. Also we have revealed that biradicaloid nature of a molecule is new interesting design factor to achieve low reorganization energies. (C) 2016 Elsevier B.V. All rights reserved.</P>

      • SCIEKCI등재

        At Death's Door: Alternaria Pathogenicity Mechanisms

        Lawrence, Christopher B.,Mitchell, Thomas K.,Craven, Kelly D.,Cho, Yang-Rae,Cramer, Robert A.,Kim, Kwang-Hyung The Korean Society of Plant Pathology 2008 Plant Pathology Journal Vol.24 No.2

        The fungal genus Alternaria is comprised of many saprophytic and endophytic species, but is most well known as containing many notoriously destructive plant pathogens. There are over 4,000 Alternaria/host associations recorded in the USDA Fungal Host Index ranking the genus 10th among nearly 2,000 fungal genera based on the total number of host records. While few Alternaria species appear to have a sexual stage to their life cycles, the majority lack sexuality altogether. Many pathogenic species of Alternaria are prolific toxin producers, which facilitates their necrotrophic lifestyle. Necrotrophs must kill host cells prior to colonization, and thus these toxins are secreted to facilitate host cell death often by triggering genetically programmed apoptotic pathways or by directly causing cell damage resulting in necrosis. While many species of Alternaria produce toxins with rather broad host ranges, a closely-related group of agronomically important Alternaria species produce selective toxins with a very narrow range often to the cultivar level. Genes that code for and direct the biosynthesis of these host-specific toxins for the Alternaria alternata sensu lato lineages are often contained on small, mostly conditionally dispensable, chromosomes. Besides the role of toxins in Alternaria pathogenesis, relatively few genes and/or gene products have been identified that contribute to or are required for pathogenicity. Recently, the completion of the A. brassicicola genome sequencing project has facilitated the examination of a substantial subset of genes for their role in pathogenicity. In this review, we will highlight the role of toxins in Alternaria pathogenesis and the use of A. brassicicola as a model representative for basic virulence studies for the genus as a whole. The current status of these research efforts will be discussed.

      • SCISCIESCOPUS

        The Hexameric Helicase DnaB Adopts a Nonplanar Conformation during Translocation

        Itsathitphaisarn, O.,Wing, Richard A.,Eliason, William K.,Wang, J.,Steitz, Thomas A. Cell Press ; MIT Press 2012 Cell Vol.151 No.2

        DNA polymerases can only synthesize nascent DNA from single-stranded DNA (ssDNA) templates. In bacteria, the unwinding of parental duplex DNA is carried out by the replicative DNA helicase (DnaB) that couples NTP hydrolysis to 5' to 3' translocation. The crystal structure of the DnaB hexamer in complex with GDP-AlF<SUB>4</SUB> and ssDNA reported here reveals that DnaB adopts a closed spiral staircase quaternary structure around an A-form ssDNA with each C-terminal domain coordinating two nucleotides of ssDNA. The structure not only provides structural insights into the translocation mechanism of superfamily IV helicases but also suggests that members of this superfamily employ a translocation mechanism that is distinct from other helicase superfamilies. We propose a hand-over-hand mechanism in which sequential hydrolysis of NTP causes a sequential 5' to 3' movement of the subunits along the helical axis of the staircase, resulting in the unwinding of two nucleotides per subunit.

      • KCI등재

        Remediation of radioiodine using polyamine anion exchange resins

        Daniel N.T. Barton,Thomas J. Robshaw,Oluwatobi Okusanya,김대근,Sarah E. Pepper,Clint A. Sharrad,이택승,Mark D. Ogden 한국공업화학회 2019 Journal of Industrial and Engineering Chemistry Vol.78 No.-

        Two weak base anion exchange resins, Lewatit A365 and Purolite MTS9850, have been tested for theremoval of aqueous iodide from conditions simulating nuclear waste reprocessing streams. pH variationand relevant co-contaminant addition (nitrate, molybdate and iodine) allowed for assessment of iodideextraction behaviour of each resin. Isotherm experiments were performed and maximum uptakecapacities obtained exceed current industrial adsorbents, such as silver-impregnated zeolites. Maximumloading capacities, determined by Dubinin–Radushkevich isotherm, were 76114 mg g 1 for MTS9850and 589 15 mg g 1 for A365. Uptake for both resins was significantly suppressed by nitrate andmolybdate ions. The presence of dissolved iodine in the raffinate however, was found to increase iodideuptake. This was explained by characterisation of the spent resin surface by infrared and Ramanspectroscopy, which determined the presence of triiodide, indicating charge-transfer complex formationon the surface. Dynamic studies assessed the effect of co-contaminants on iodide uptake in a columnenvironment. Data wasfitted to three dynamic models, with the Dose-Response model providing the bestdescription of breakthrough. In all cases iodide breakthrough was accelerated, indicating suppression ofuptake, but capacity was still significant.

      • KCI등재

        At Death’s Door: Alternaria Pathogenicity Mechanisms

        Christopher B. Lawrence,Thomas K. Mitchell,Kelly D. Craven,Yangrae Cho,Robert A. Cramer Jr,김광형 한국식물병리학회 2008 Plant Pathology Journal Vol.24 No.2

        The fungal genus Alternaria is comprised of many saprophytic and endophytic species, but is most well known as containing many notoriously destructive plant pathogens. There are over 4,000 Alternaria/host associations recorded in the USDA Fungal Host Index ranking the genus 10th among nearly 2,000 fungal genera based on the total number of host records. While few Alternaria species appear to have a sexual stage to their life cycles, the majority lack sexuality altogether. Many pathogenic species of Alternaria are prolific toxin producers, which facilitates their necrotrophic lifestyle. Necrotrophs must kill host cells prior to colonization, and thus these toxins are secreted to facilitate host cell death often by triggering genetically programmed apoptotic pathways or by directly causing cell damage resulting in necrosis. While many species of Alternaria produce toxins with rather broad host ranges, a closelyrelated group of agronomically important Alternaria species produce selective toxins with a very narrow range often to the cultivar level. Genes that code for and direct the biosynthesis of these host-specific toxins for the Alternaria alternata sensu lato lineages are often contained on small, mostly conditionally dispensable, chromosomes. Besides the role of toxins in Alternaria pathogenesis, relatively few genes and/or gene products have been identified that contribute to or are required for pathogenicity. Recently, the completion of the A. brassicicola genome sequencing project has facilitated the examination of a substantial subset of genes for their role in pathogenicity. In this review, we will highlight the role of toxins in Alternaria pathogenesis and the use of A. brassicicola as a model representative for basic virulence studies for the genus as a whole. The current status of these research efforts will be discussed.

      • Calcium-Permeable AMPA Receptors Mediate the Induction of the Protein Kinase A-Dependent Component of Long-Term Potentiation in the Hippocampus

        Park, Pojeong,Sanderson, Thomas M.,Amici, Mascia,Choi, Sun-Lim,Bortolotto, Zuner A.,Zhuo, Min,Kaang, Bong-Kiun,Collingridge, Graham L. Society for Neuroscience 2016 The Journal of neuroscience Vol.36 No.2

        <P>Two forms of NM DA receptor (NMDAR)-dependent long-term potentiation (LIP) at hippocampal CAI synapses can be distinguished based on their sensitivity to inhibitors of protein kinase A (PKA). The PKA-dependent form requires multiple episodes of high-frequency stimulation (HFS) or theta burst stimuli (TBS) with a spacing between episodes in the order of minutes. To investigate the mechanism by which spaced episodes induce the PKA-dependent form of LIP, we have compared, in interleaved experiments, spaced (s) and compressed (c) TBS protocols in the rat CAI synapses. We find that LIP induced by sTBS, but not that induced by cTBS, involves the insertion of calcium-permeable (CP) AMPARs, as assessed using pharmacological and electrophysiological criteria. Furthermore, a single TBS when paired with rolipram [4-(3-(cyclopentyloxy)-4-methoxyphenyl)pyrrolidin-2-one], to activate PKA, generates an LTP that also involves the insertion of CP-AMPARs. These data demonstrate that the involvement of CP-AMPARs in LTP is critically determined by the timing of the induction trigger and is associated specifically with the PKA-dependent form of LIP.</P>

      • Evaluation of imputation-based association in and around the integrin- -M (ITGAM) gene and replication of robust association between a non-synonymous functional variant within ITGAM and systemic lupus erythematosus (SLE)

        Han, S.,Kim-Howard, X.,Deshmukh, H.,Kamatani, Y.,Viswanathan, P.,Guthridge, J. M.,Thomas, K.,Kaufman, K. M.,Ojwang, J.,Rojas-Villarraga, A.,Baca, V.,Orozco, L.,Rhodes, B.,Choi, C.-B.,Gregersen, P. K. Oxford University Press 2009 Human Molecular Genetics Vol.18 No.6

        <P>We recently identified a novel non-synonymous variant, rs1143679, at exon 3 of the ITGAM gene associated with systemic lupus erythematosus (SLE) susceptibility in European-Americans (EAs) and African-Americans. Using genome-wide association approach, three other studies also independently reported an association between SLE susceptibility and ITGAM or ITGAM-ITGAX region. The primary objectives of this study are to assess whether single or multiple causal variants from the same gene or any nearby gene(s) are involved in SLE susceptibility and to confirm a robust ITGAM association across nine independent data sets (n = 8211). First, we confirmed our previously reported association of rs1143679 (risk allele 'A') with SLE in EAs (P = 1.0 x 10(-8)) and Hispanic-Americans (P = 2.9 x 10(-5)). Secondly, using a comprehensive imputation-based association test, we found that ITGAM is one of the major non-human leukocyte antigen susceptibility genes for SLE, and the strongest association for EA is the same coding variant rs1143679 (log(10)Bayes factor=20, P = 6.17 x 10(-24)). Thirdly, we determined the robustness of rs1143679 association with SLE across three additional case-control samples, including UK (P = 6.2 x 10(-8)), Colombian (P = 3.6 x 10(-7)), Mexican (P = 0.002), as well as two independent sets of trios from UK (P(TDT) = 1.4 x 10(-5)) and Mexico (P(TDT) = 0.015). A meta-analysis combing all independent data sets greatly reinforces the association (P(meta) = 7.1 x 10(-50), odds ratio = 1.83, 95% confidence interval = 1.69-1.98, n = 10 046). However, this ITGAM association was not observed in the Korean or Japanese samples, in which rs1143679 is monomorphic for the non-risk allele (G). Taken together along with our earlier findings, these results demonstrate that the coding variant, rs1143679, best explains the ITGAM-SLE association, especially in European- and African-derived populations, but not in Asian populations.</P>

      • SCISCIESCOPUS

        Transient receptor potential vanilloid-1 (TRPV1) is a mediator of lung toxicity for coal fly ash particulate material.

        Deering-Rice, Cassandra E,Johansen, Mark E,Roberts, Jessica K,Thomas, Karen C,Romero, Erin G,Lee, Jeewoo,Yost, Garold S,Veranth, John M,Reilly, Christopher A American Society for Pharmacology and Experimental 2012 Molecular pharmacology Vol.81 No.3

        <P>Environmental particulate matter (PM) pollutants adversely affect human health, but the molecular basis is poorly understood. The ion channel transient receptor potential vanilloid-1 (TRPV1) has been implicated as a sensor for environmental PM and a mediator of adverse events in the respiratory tract. The objectives of this study were to determine whether TRPV1 can distinguish chemically and physically unique PM that represents important sources of air pollution; to elucidate the molecular basis of TRPV1 activation by PM; and to ascertain the contributions of TRPV1 to human lung cell and mouse lung tissue responses exposed to an insoluble PM agonist, coal fly ash (CFA1). The major findings of this study are that TRPV1 is activated by some, but not all of the prototype PM materials evaluated, with rank-ordered responses of CFA1 > diesel exhaust PM > crystalline silica; TRP melastatin-8 is also robustly activated by CFA1, whereas other TRP channels expressed by airway sensory neurons and lung epithelial cells that may also be activated by CFA1, including TRPs ankyrin 1 (A1), canonical 4α (C4α), M2, V2, V3, and V4, were either slightly (TRPA1) or not activated by CFA1; activation of TRPV1 by CFA1 occurs via cell surface interactions between the solid components of CFA1 and specific amino acid residues of TRPV1 that are localized in the putative pore-loop region; and activation of TRPV1 by CFA1 is not exclusive in mouse lungs but represents a pathway by which CFA1 affects the expression of selected genes in lung epithelial cells and airway tissue.</P>

      • KCI등재

        對話形式과 秘義 : 플라톤의 파이드로스 對話編 解釋과 關聯하여

        Thomas Alexander Szleza´kㆍ임성철 새한철학회 2001 哲學論叢 Vol.23 No.1

        이 論文은 파이드로스편의 마지막 부분에 나타난 哲學의 文字化와 口頭化에 관한 플라톤의 입장을 論究하고 있다. 이 논문의 방법론적인 입장은 무엇보다도 古典 言語學의 기본 원칙인 '플라톤을 플라톤에 의해서' 이해하고자 하는 데 있다. 文字 批判의 중심 개념으로써 boethein to(i) logo(i)는 플라톤의 대화편을 기반으로 해석되어야만 한다. 이 개념과 관련하여 빈번하게 인용된 G. Vlastos(Gnomon 35, 1963, 653f.)의 글은 현대적인 개념에 기초하고 있으며, 결국 플라톤의 대화편이 드러내고 있는 문자 비판의 핵심적인 주장을 우리들에게 이해하도록 만들지 못한다. 다행스럽게도, 우리는 boethein to(i) logo(i)에 관한 플라톤 대화편 안의 例證들을 발견한다(법률편 890d-891e, 국가론 362d, 368bc). 이러한 예들은 플라톤에게 있어서 "로고스를 돕는다"하는 것이 동일한 知的 水準에 관한 동일한 내용들의 반복을 결코 의미하지 않는다는 사실을 지적한다. Boethein to logo라는 개념은 더 원리적인 개념들과 더 상승된 원리들을 통해 arche(원리)에 기반을 두는 최종적인 논증을 향해 논증의 수준을 의도적으로 高揚시키는 데 그 본질을 두고 있는 플라톤 대화편의 구조적인 원리를 표현하는 변증술적 기술이다. 우리는, 진정한 哲學者가 자신의 문자화된 로고스를 자신의 말을 통해 도움을 주게 될 때, 자신의 문자화된 글을 자신의 더 가치 있는 口頭的인 도움과 비교하여(파이드로스 278cd) 별다른 가치가 없는 것으로 증명하는 까닭을 이해할 수 있다. 철학자가 언제나 자신의 글을 도울 수 있는 것처럼, 그는 자신의 문자화된 로고스로부터 口頭的인 도움에 의해서만 사용될 수 있는 것을 항상 간직하고자 한다. 결국, 플라톤적 철학자는 자신이 발견했던 모든 것들을 문자로 남기려 하지 않는다. This article offers a new interpretation of Plato's criticism of writing on the last pages of the "Phaedrus". The method used is the classical philological method: the task is to explain "Plato out of Plato" (following the principle of Alexandrian philology "Homeron ex Homerou"). In the first place, the central concept of the criticism of writing, i.e. "boethein to(i) logo(i)" (to help one's logos), needs an interpretation based on the dialogues. For it can be shown that the much-quoted interpretation of G.Vlastos (Gnomon 35,1963, 653f.) is based on modern conceptions only and that it therefore fails to make the central tenets of the criticism of writing understandable. Fortunately, there is no lack in Plato of instances of "boethein to(i) logo(i)". Some of them are briefly analysed: Laws 890 d - 891 e, Republic 362 d, 368 bc. These sample cases show that "helping the logos" in Plato never means something like "repeating the same things on the same intellectual level, until they become somewhat clearer". Boethein to(i) logo(i) always means the dialogical technique of going beyond what was said in the first argument. To help one's logos is to argue for the same thesis by means of more fundamental concepts and more advanced theories. Now we can understand why Plato wrote that the true philosopher, when helping his written logos by his own word (legon autos), will demonstrate the inferior value of his writing as compared to his more valuable oral help (cf. "tagegrammena phaula apodeixai" vs. "echein timiotera", Phdr. 278 cd). As the philosopher will always be able to help his writing, he will always keep something out of his written logos, which he will use only when oral help is needed. The Platonic philosopher thus will not write down all the truths he has found.

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