bluuebunny/crossref_metadata_2025 huggingface dataset:
Studs Lonigan and the Search for an American Tragedy
Authors: Rosenthal T. G.
Published: February 2011

James T. Farrell was born in 1904 in Chicago, a city which has produced such characteristic American writers as Carl Sandburg, Frank Norris, Theodore Dreiser, Sherwood Anderson, Meyer Levin and Nelson Algren. Like several of his fellow–citizens he has become known, not altogether unjustly, as a ‘one-book writer’. But if there is Justice in the label which has thus been applied to Farrell his ‘one book’ has been less fairly treated and has suffered in reverse much the same wrong-headed fate as that which has over-taken some of the typical English novels of the last decade. While certain novels like John Braine's Room at the Top have been absurdly over-praised because apparent virtues of ‘realism’ and ‘toughness’ have obscured even more apparent literary shortcomings, Studs Lonigan has been under-praised because an extreme aversion to Farrell's undeniable ‘realism’ and ‘toughness’ has resulted in his equally undeniable literary merits being obscured. Studs Lonigan is not a novel to which can be applied R. P. Blackmur's phrase: “one of those books in which everything is undertaken with seriousness except the writing”.
Phase transition in a rechargeable lithium battery
Authors: DREYER W. , GABERŠČEK M. , GUHLKE C. , HUTH R. , JAMNIK J.
Published: February 2011

We discuss the lithium storage process within a single-particle cathode of a lithium-ion battery. The single storage particle consists of a crystal lattice whose interstitial lattice sites may be empty or reversibly filled with lithium atoms. The resulting evolution equations describe diffusion with mechanical coupling and incorporate volume changes, phase transitions and surface tension. In order to simulate the dynamics, we assume spherical symmetry and fast bulk diffusion of the lithium atoms, which lead to a core shell model. We verify the common assumption of phase nucleation at the external boundary of the particle. This model is capable to predict voltage–capacity behaviour. For slow charging rates, we compare the results with experimental voltage–capacity plots exhibiting hysteretic behaviour. We observe that hysteresis cannot be described within the setting of a single-particle cathode. The origin of this fact is discussed in detail. The result is of enormous importance because single-particle models, in particular core shell models, up to now are very popular in the chemical literature.
Almost Isoperimetric Subsets of the Discrete Cube
Authors: ELLIS DAVID
Published: February 2011

We show that a set A ⊂ {0, 1}n with edge-boundary of size at most

can be made into a subcube by at most (2ε/log2(1/ε))|A| additions and deletions, provided ε is less than an absolute constant.

We deduce that if A ⊂ {0, 1}n has size 2t for some t ∈ ℕ, and cannot be made into a subcube by fewer than δ|A| additions and deletions, then its edge-boundary has size at least

provided δ is less than an absolute constant. This is sharp whenever δ = 1/2j for some j ∈ {1, 2, . . ., t}.
IS MORE MEMORY IN EVOLUTIONARY SELECTION (DE)STABILIZING?
Authors: Hommes Cars , Kiseleva Tatiana , Kuznetsov Yuri , Verbic Miroslav
Published: February 2011

We investigate the effects of memory on the stability of evolutionary selection dynamics based on a multinomial logit model in a simple asset pricing model with heterogeneous beliefs. Whether memory is stabilizing or destabilizing depends in general on three key factors: (1) whether or not the weights on past observations are normalized; (2) the ecology or composition of forecasting rules, in particular the average trend extrapolation factor and the spread or diversity in biased forecasts; and (3) whether or not costs for information gathering of economic fundamentals have to be incurred.
Case study of apparent longitudinal differences of spread F occurrence for two midlatitude stations
Authors: Huang W. Q. , Xiao Z. , Xiao S. G. , Zhang D. H. , Hao Y. Q. , Suo Y. C.
Published: February 2011

Spread F is a widely studied subject, and the occurrence of spread F is affected by many factors. One of these factors is acoustic gravity waves (AGWs) which are very important in seeding spread F. Since most of the AGWs in the ionosphere originate from the lower atmosphere, there should be some regional features of spread F due to the different meteorological or ground conditions immediately beneath the local ionosphere. In this paper, a data set with a time coverage of one solar cycle from two Chinese stations located at exactly the same latitude and a 38 degrees separation in longitude, and having sharp contrasts of ground meteorological conditions, are used to make comparisons of spread F occurrence rates. The results showed that the total number of occurrence or occurrence percentage at Changchun station (very near the coast) is always much higher than that at Urumqi station (in the very center of the Europe‐Asia continent). The annual maxima of spread F occurrence are in summer and winter. Other features of spread F occurrence at these two stations are in agreement with known properties of spread F. However, the great difference of occurrence frequency between the two stations is striking and worth further studying.
Lateral transfer of streamwise momentum caused by a roughness transition across a shallow channel
Authors: Vermaas D. A. , Uijttewaal W. S. J. , Hoitink A. J. F.
Published: February 2011

Research on lateral exchange of streamwise momentum between parallel flows in open channels has mainly been focused on compound channels composed of a main channel and a floodplain, on mixing layer development downstream of river confluences, and on partially vegetated channels. This study aims to establish the mechanisms responsible for streamwise momentum exchange between concurrent parallel flows subject to different bed roughnesses. The contribution of momentum exchange of each mechanism is determined on the basis of flume experiments. For an initially uniform flow that experiences a bed with two parallel lanes of different roughnesses, three mechanisms for exchange of streamwise momentum can be distinguished: cross‐channel secondary circulations, turbulent mixing resulting from vortices acting in the horizontal plane, and mass transfer from the decelerating flow over the rough‐bottomed lane to the accelerating flow in the parallel smooth‐bottomed lane. The mass transfer and associated momentum transfer across the channel cause a gain in longitudinal momentum. The secondary circulations are driven by turbulence anisotropy and feature a main cell that extends over the full water depth, which is centered at the smooth side of the smooth‐to‐rough transition. The gain of momentum corresponding to the mass transfer in the developing reach is on the same order of magnitude as the momentum exchange by turbulent mixing and of that by secondary circulations in the most downstream position, where the flow is nearly developed. The contribution of the secondary circulations to the exchange of streamwise momentum between the parallel flows gradually becomes dominant over the contribution of turbulent mixing when depth increases.
Prey bacteria shape the community structure of their predators
Authors: Chen Huan , Athar Rana , Zheng Guili , Williams Henry N
Published: February 2011

Although predator–prey interactions among higher organisms have been studied extensively, only few examples are known for microbes other than protists and viruses. Among the bacteria, the most studied obligate predators are the Bdellovibrio and like organisms (BALOs) that prey on many other bacteria. In the macroscopical world, both predator and prey influence the population size of the other's community, and may have a role in selection. However, selective pressures among prey and predatory bacteria have been rarely investigated. In this study, Bacteriovorax, a predator within the group of BALOs, in environmental waters were fed two prey bacteria, Vibrio vulnificus and Vibrio parahaemolyticus. The two prey species yielded distinct Bacteriovorax populations, evidence that selective pressures shaped the predator community and diversity. The results of laboratory experiments confirmed the differential predation of Bacteriovorax phylotypes on the two bacteria species. Not only did Bacteriovorax Cluster IX exhibit the versatility to be the exclusive efficient predator on Vibrio vulnificus, thereby, behaving as a specialist, but was also able to prey with similar efficiency on Vibrio parahaemolyticus, indicative of a generalist. Therefore, we proposed a designation of versatilist for this predator. This initiative should provide a basis for further efforts to characterize the predatory patterns of bacterial predators. The results of this study have revealed impacts of the prey on Bacteriovorax predation and in structuring the predator community, and advanced understanding of predation behavior in the microbial world.
Parental Care in Childhood and Obesity in Adulthood: A Study Among Twins
Authors: Vámosi Marianne Eva , Heitmann Berit L. , Thinggaard Mikael , Kyvik Kyvik O.
Published: February 2011

The purpose of the study was to examine if parental antipathy and neglect during childhood were associated with obesity in adulthood. From the Danish Twin Registry (DTR) 146 adult same‐sexed twin pairs discordant for BMI were identified. Criteria for being discordant were that one of the twins should have a BMI between 20 and 25 kg/m2 (normal weight) and the co‐twin a BMI ≥30 kg/m² (obesity). In total 236 out of 289 (81.7%) eligible twin individuals participated in an interview and a physical examination. A part of the Childhood Experience of Care and Abuse, the parental care and neglect questionnaire, by Bifulco et al., was used to assess perceived parental antipathy and neglect. Data were analyzed by means of intrapair comparisons. Our results showed that recalled maternal antipathy (P = 0.04) and maternal neglect (P = 0.01) were both associated with adult obesity. Paternal neglect and antipathy were not related with adult obesity. The study demonstrates that experience in childhood maternal antipathy and neglect may contribute to the development of obesity at age 20 and later in adulthood.
A functional family-wide screening of SP/KLF proteins identifies a subset of suppressors of KRAS-mediated cell growth
Authors: Fernandez-Zapico Martin E. , Lomberk Gwen A. , Tsuji Shoichiro , DeMars Cathrine J. , Bardsley Michael R. , Lin Yi-Hui , Almada Luciana L. , Han Jing-Jing , Mukhopadhyay Debabrata , Ordog Tamas , Buttar Navtej S. , Urrutia Raul
Published: February 2011

SP/KLF (Specificity protein/Krüppel-like factor) transcription factors comprise an emerging group of proteins that may behave as tumour suppressors. Incidentally, many cancers that display alterations in certain KLF proteins are also associated with a high incidence of KRAS (V-Ki-ras2 Kirsten rat sarcoma viral oncogene homologue) mutations. Therefore in the present paper we investigate whether SP/KLF proteins suppress KRAS-mediated cell growth, and more importantly, the potential mechanisms underlying these effects. Using a comprehensive family-wide screening of the 24 SP/KLF members, we discovered that SP5, SP8, KLF2, KLF3, KLF4, KLF11, KLF13, KLF14, KLF15 and KLF16 inhibit cellular growth and suppress transformation mediated by oncogenic KRAS. Each protein in this subset of SP/KLF members individually inhibits BrdU (5-bromo-2-deoxyuridine) incorporation in KRAS oncogenic-mutant cancer cells. SP5, KLF3, KLF11, KLF13, KLF14 and KLF16 also increase apoptosis in these cells. Using KLF11 as a representative model for mechanistic studies, we demonstrate that this protein inhibits the ability of cancer cells to form both colonies in soft agar and tumour growth in vivo. Molecular studies demonstrate that these effects of KLF11 are mediated, at least in part, through silencing cyclin A via binding to its promoter and leading to cell-cycle arrest in S-phase. Interestingly, similar to KLF11, KLF14 and KLF16 mechanistically share the ability to modulate the expression of cyclin A. Collectively, the present study stringently defines a distinct subset of SP/KLF proteins that impairs KRAS-mediated cell growth, and that mechanistically some members of this subset accomplish this, at least in part, through regulation of the cyclin A promoter.
Phosphorylation of cAMP-specific PDE4A5 (phosphodiesterase-4A5) by MK2 (MAPKAPK2) attenuates its activation through protein kinase A phosphorylation
Authors: MacKenzie Kirsty F. , Wallace Derek A. , Hill Elaine V. , Anthony Diana F. , Henderson David J. P. , Houslay Daniel M. , Arthur J. Simon C. , Baillie George S. , Houslay Miles D.
Published: February 2011

cAMP-specific PDE (phosphodiesterase) 4 isoforms underpin compartmentalized cAMP signalling in mammalian cells through targeting to specific signalling complexes. Their importance is apparent as PDE4 selective inhibitors exert profound anti-inflammatory effects and act as cognitive enhancers. The p38 MAPK (mitogen-activated protein kinase) signalling cascade is a key signal transduction pathway involved in the control of cellular immune, inflammatory and stress responses. In the present study, we show that PDE4A5 is phosphorylated at Ser147, within the regulatory UCR1 (ultraconserved region 1) domain conserved among PDE4 long isoforms, by MK2 (MAPK-activated protein kinase 2, also called MAPKAPK2). Phosphorylation by MK2, although not altering PDE4A5 activity, markedly attenuates PDE4A5 activation through phosphorylation by protein kinase A. This modification confers the amplification of intracellular cAMP accumulation in response to adenylate cyclase activation by attenuating a major desensitization system to cAMP. Such reprogramming of cAMP accumulation is recapitulated in wild-type primary macrophages, but not MK2/3-null macrophages. Phosphorylation by MK2 also triggers a conformational change in PDE4A5 that attenuates PDE4A5 interaction with proteins whose binding involves UCR2, such as DISC1 (disrupted in schizophrenia 1) and AIP (aryl hydrocarbon receptor-interacting protein), but not the UCR2-independent interacting scaffold protein β-arrestin. Long PDE4 isoforms thus provide a novel node for cross-talk between the cAMP and p38 MAPK signalling systems at the level of MK2.
Characterization of a novel JNK (c-Jun N-terminal kinase) inhibitory peptide
Authors: Ngoei Kevin R. W. , Catimel Bruno , Church Nicole , Lio Daisy S. , Dogovski Con , Perugini Matthew A. , Watt Paul M. , Cheng Heung-Chin , Ng Dominic C. H. , Bogoyevitch Marie A.
Published: February 2011

An improved understanding of the roles of protein kinases in intracellular signalling and disease progression has driven significant advances in protein kinase inhibitor discovery. Peptide inhibitors that target the kinase protein substrate-binding site have continued to attract attention. In the present paper, we describe a novel JNK (c-Jun N-terminal kinase) inhibitory peptide PYC71N, which inhibits JNK activity in vitro towards a range of recombinant protein substrates including the transcription factors c-Jun, ATF2 (activating trancription factor 2) and Elk1, and the microtubule regulatory protein DCX (doublecortin). Analysis of cell culture studies confirmed the actions of a cell-permeable version of PYC71 to inhibit c-Jun phosphorylation during acute hyperosmotic stress. The analysis of the in vitro data for the kinetics of this inhibition indicated a substrate–inhibitor complex-mediated inhibition of JNK by PYC71N. Alanine-scanning replacement studies revealed the importance of two residues (PYC71N Phe9 or Phe11 within an FXF motif) for JNK inhibition. The importance of these residues was confirmed through interaction studies showing that each change decreased interaction of the peptide with c-Jun. Furthermore, PYC71N interacted with both non-phosphorylated (inactive) JNK1 and the substrate c-Jun, but did not recognize active JNK1. In contrast, a previously characterized JNK-inhibitory peptide TIJIP [truncated inhibitory region of JIP (JNK-interacting protein)], showed stronger interaction with active JNK1. Competition binding analysis confirmed that PYC71N inhibited the interaction of c-Jun with JNK1. Taken together, the results of the present study define novel properties of the PYC71N peptide as well as differences from the characterized TIJIP, and highlight the value of these peptides to probe the biochemistry of JNK-mediated substrate interactions and phosphorylation.
Substrate specificity of haloalkane dehalogenases
Authors: Koudelakova Tana , Chovancova Eva , Brezovsky Jan , Monincova Marta , Fortova Andrea , Jarkovsky Jiri , Damborsky Jiri
Published: February 2011

An enzyme's substrate specificity is one of its most important characteristics. The quantitative comparison of broad-specificity enzymes requires the selection of a homogenous set of substrates for experimental testing, determination of substrate-specificity data and analysis using multivariate statistics. We describe a systematic analysis of the substrate specificities of nine wild-type and four engineered haloalkane dehalogenases. The enzymes were characterized experimentally using a set of 30 substrates selected using statistical experimental design from a set of nearly 200 halogenated compounds. Analysis of the activity data showed that the most universally useful substrates in the assessment of haloalkane dehalogenase activity are 1-bromobutane, 1-iodopropane, 1-iodobutane, 1,2-dibromoethane and 4-bromobutanenitrile. Functional relationships among the enzymes were explored using principal component analysis. Analysis of the untransformed specific activity data revealed that the overall activity of wild-type haloalkane dehalogenases decreases in the following order: LinB~DbjA>DhlA~DhaA~DbeA~DmbA>DatA~DmbC~DrbA. After transforming the data, we were able to classify haloalkane dehalogenases into four SSGs (substrate-specificity groups). These functional groups are clearly distinct from the evolutionary subfamilies, suggesting that phylogenetic analysis cannot be used to predict the substrate specificity of individual haloalkane dehalogenases. Structural and functional comparisons of wild-type and mutant enzymes revealed that the architecture of the active site and the main access tunnel significantly influences the substrate specificity of these enzymes, but is not its only determinant. The identification of other structural determinants of the substrate specificity remains a challenge for further research on haloalkane dehalogenases.
Expression and functional validation of new p38α transcriptional targets in tumorigenesis
Authors: Swat Aneta , Dolado Ignacio , Igea Ana , Gomez-Lopez Gonzalo , Pisano David G. , Cuadrado Ana , Nebreda Angel R.
Published: February 2011

p38α MAPK (mitogen-activated protein kinase) plays an important tumour suppressor role, which is mediated by both its negative effect on cell proliferation and its pro-apoptotic activity. Surprisingly, most tumour suppressor mechanisms co-ordinated by p38α have been reported to occur at the post-translational level. This contrasts with the important role of p38α in the regulation of transcription and the profound changes in gene expression that normally occur during tumorigenesis. We have analysed whole-genome expression profiles of Ras-transformed wild-type and p38α-deficient cells and have identified 202 genes that are potentially regulated by p38α in transformed cells. Expression analysis has confirmed the regulation of these genes by p38α in tumours, and functional validation has identified several of them as probable mediators of the tumour suppressor effect of p38α on Ras-induced transformation. Interestingly, approx. 10% of the genes that are negatively regulated by p38α in transformed cells contribute to EGF (epidermal growth factor) receptor signalling. Our results suggest that inhibition of EGF receptor signalling by transcriptional targets of p38α is an important function of this signalling pathway in the context of tumour suppression.
Evident and latent plasticity across the rice diterpene synthase family with potential implications for the evolution of diterpenoid metabolism in the cereals
Authors: Morrone Dana , Hillwig Matthew L. , Mead Matthew E. , Lowry Luke , Fulton D. Bruce , Peters Reuben J.
Published: February 2011

The evolution of natural product biosynthetic pathways can be envisioned to occur via a number of mechanisms. In the present study we provide evidence that latent plasticity plays a role in such metabolic evolution. In particular, rice (Oryza sativa) produces both ent- and syn-CPP (copalyl diphosphate), which are substrates for downstream diterpene synthases. In the present paper we report that several members of this enzymatic family exhibit dual reactivity with some pairing of ent-, syn- or normal CPP stereochemistry. Evident plasticity was observed, as a previously reported ent-sandaracopimaradiene synthase also converts syn-CPP into syn-labda-8(17),12E,14-triene, which can be found in planta. Notably, normal CPP is not naturally found in rice. Thus the presence of diterpene synthases that react with this non-native metabolite reveals latent enzymatic/metabolic plasticity, providing biochemical capacity for utilization of such a novel substrate (i.e. normal CPP) which may arise during evolution, the implications of which are discussed.
SUMO2 and SUMO3 transcription is differentially regulated by oxidative stress in an Sp1-dependent manner
Authors: Sang Jing , Yang Kai , Sun Yueping , Han Yan , Cang Hui , Chen Yuying , Shi Guiying , Wang Kangmin , Zhou Jie , Wang Xiangrui , Yi Jing
Published: February 2011

Protein SUMOylation (SUMO is small ubiquitin-related modifier) is a dynamic process that is strictly regulated under physiological and pathological conditions. However, little is known about how various intra- or extra-cellular stimuli regulate expression levels of components in the SUMO system. SUMO isoforms SUMO2 and SUMO3 can rapidly convert to be conjugated in response to a variety of cellular stresses. Owing to the limitations of sequence homology, SUMO2 and SUMO3 cannot be differentiated between and are thus referred to as SUMO2/3. Whether these two isoforms are regulated in distinct manners has never been addressed. In the present paper we report that the expression of SUMO3, but not SUMO2, can be down-regulated at the transcription level by cellular oxidative stress. In the present study, we checked SUMO2 and SUMO3 mRNA levels in cells exposed to various doses of H2O2 and in cells bearing different levels of ROS (reactive oxygen species). We found an inverse relationship between SUMO3 transcription and ROS levels. We characterized a promoter region specific for the mouse Sumo3 gene that is bound by the redox-sensitive transcription factor Sp1 (specificity protein 1) and demonstrated oxidation of Sp1, as well as suppression of Sp1–DNA binding upon oxidative stress. This revealed for the first time that the expression of SUMO2 and SUMO3 is regulated differently by ROS. These findings may enhance our understanding about the regulation of SUMOylation and also shed light on the functions of Sp1.
TRPM7 regulates polarized cell movements
Authors: Su Li-Ting , Liu Wei , Chen Hsiang-Chin , González-Pagán Omayra , Habas Raymond , Runnels Loren W.
Published: February 2011

TRPM7 (transient receptor potential melastatin 7) is a Ca2+- and Mg2+-permeant ion channel in possession of its own kinase domain. As a kinase, the protein has been linked to the control of actomyosin contractility, whereas the channel has been found to regulate cell adhesion as well as cellular Mg2+ homoeostasis. In the present study we show that depletion of TRPM7 by RNA interference in fibroblasts alters cell morphology, the cytoskeleton, and the ability of cells to form lamellipodia and to execute polarized cell movements. A pulldown-purification assay revealed that knockdown of TRPM7 prevents cells from activating Rac and Cdc42 (cell division cycle 42) when stimulated to migrate into a cellular wound. Re-expression of TRPM7 reverses these phenotypic changes, as does, unexpectedly, expression of a kinase-inactive mutant of TRPM7. Surprisingly, expression of the Mg2+ transporter SLC41A2 (solute carrier family 41 member 2) is also effective in restoring the change in cell morphology, disruption of the cytoskeleton and directional cell motility caused by depletion of the channel-kinase. The results of the present study uncover an essential role for Mg2+ in the control of TRPM7 over the cytoskeleton and its ability to regulate polarized cell movements.
Molecular interaction and functional regulation of connexin50 gap junctions by calmodulin
Authors: Chen Yanyi , Zhou Yubin , Lin Xianming , Wong Hing-Cheung , Xu Qin , Jiang Jie , Wang Siming , Lurtz Monica M. , Louis Charles F. , Veenstra Richard D. , Yang Jenny J.
Published: February 2011

Cx50 (connexin50), a member of the α-family of gap junction proteins expressed in the lens of the eye, has been shown to be essential for normal lens development. In the present study, we identified a CaMBD [CaM (calmodulin)-binding domain] (residues 141–166) in the intracellular loop of Cx50. Elevations in intracellular Ca2+ concentration effected a 95% decline in gj (junctional conductance) of Cx50 in N2a cells that is likely to be mediated by CaM, because inclusion of the CaM inhibitor calmidazolium prevented this Ca2+-dependent decrease in gj. The direct involvement of the Cx50 CaMBD in this Ca2+/CaM-dependent regulation was demonstrated further by the inclusion of a synthetic peptide encompassing the CaMBD in both whole-cell patch pipettes, which effectively prevented the intracellular Ca2+-dependent decline in gj. Biophysical studies using NMR and fluorescence spectroscopy reveal further that the peptide stoichiometrically binds to Ca2+/CaM with an affinity of ~5 nM. The binding of the peptide expanded the Ca2+-sensing range of CaM by increasing the Ca2+ affinity of the C-lobe of CaM, while decreasing the Ca2+ affinity of the N-lobe of CaM. Overall, these results demonstrate that the binding of Ca2+/CaM to the intracellular loop of Cx50 is critical for mediating the Ca2+-dependent inhibition of Cx50 gap junctions in the lens of the eye.
Xrel3/XrelA attenuates β-catenin-mediated transcription during mesoderm formation inXenopusembryos
Authors: Kennedy Mark W. L. , Kao Kenneth R.
Published: February 2011

In Xenopus laevis embryonic development, activation of the Wnt/β-catenin pathway promotes mesoderm cell fate determination via Xnr (Xenopus nodal-related) expression. We have demonstrated previously that Rel/NF-κB (nuclear factor κB) proteins expressed in presumptive ectoderm limit the activity of Xnrs to the marginal zone of embryos during mesoderm induction, which assists to distinguish mesoderm from ectoderm. The mechanism of this regulation, however, is unknown. In the present study, we investigated whether Rel/NF-κB proteins are able to modulate mesoderm formation by mediating Wnt/β-catenin signalling. We determined that ectopic expression of XrelA or Xrel3 in the dorsal marginal zone perturbed dorsal mesoderm formation by down-regulating multiple Wnt/β-catenin target genes including Xnr3, Xnr5 and Xnr6. Ventral co-expression of XrelA or Xrel3 with either wild-type β-catenin or constitutively active β-cateninS37A abrogated β-catenin-induced axis duplication and attenuated β-catenin-stimulated reporter transcription. Lastly, we provide evidence that Xrel3, but not XrelA, can interact with β-catenin without affecting the association of β-catenin with other transcriptional co-activators in vitro. Both Xrel3 and XrelA, however, prevented the accumulation, in nuclei, of exogenously expressed and endogenous β-catenin in vivo. These results suggest that Rel proteins are able to bind β-catenin and attenuate β-catenin-mediated transcription by nuclear exclusion.
Transcriptional regulation of the Zrg17 zinc transporter of the yeast secretory pathway
Authors: Wu Yi-Hsuan , Frey Avery G. , Eide David J.
Published: February 2011

The Msc2 and Zrg17 proteins of Saccharomyces cerevisiae are members of the cation diffusion facilitator family of zinc transporters. These proteins form heteromeric complexes that transport zinc into the ER (endoplasmic reticulum). Previous studies suggested that the ZRG17 gene is regulated in response to zinc status by the Zap1 transcription factor. Zap1 activates the expression of many genes in zinc-deficient cells. In the present study, we assessed whether ZRG17 is a direct Zap1 target gene. We showed that ZRG17 mRNA levels were elevated in zinc-limited cells in a Zap1-dependent manner and were also elevated in zinc-replete cells expressing a constitutively active allele of Zap1. Furthermore, Zrg17 protein levels correlated closely with mRNA levels. A candidate Zap1-binding site [ZRE (zinc-responsive element)] in the ZRG17 promoter was required for this induction. Using electrophoretic mobility-shift assays and chromatin immunoprecipitation, we demonstrated that Zap1 binds specifically to the ZRG17 ZRE both in vitro and in vivo. By using a chromosomal ZRG17 mutant with a non-functional ZRE, we found that Zap1 induction of ZRG17 is required for ER function as indicated by elevated ER stress under zinc-limited conditions. Together, these results establish that ZRG17 is a direct Zap1 target gene and its regulation has biological importance in maintaining ER function.
IEX-1 suppresses apoptotic damage in human intestinal epithelial Caco-2 cells induced by co-culturing with macrophage-like THP-1 cells
Authors: Ishimoto Yoko , Satsu Hideo , Totsuka Mamoru , Shimizu Makoto
Published: February 2011

We have reported previously that apoptosis of intestinal epithelial Caco-2 cells is induced by co-culturing with human macrophage-like THP-1 cells, mainly via the action of TNFα (tumour necrosis factor α) secreted from THP-1 cells [Satsu, Ishimoto, Nakano, Mochizuki, Iwanaga and Shimizu (2006) Exp. Cell Res. 312, 3909–3919]. Our recent DNA microarray analysis of co-cultured Caco-2 cells showed that IEX-1 (immediate early-response gene X-1) is the most significantly increased gene during co-culture [Ishimoto, Nakai, Satsu, Totsuka and Shimizu (2010) Biosci. Biotechnol. Biochem. 74, 437–439]. Hence, we investigated the role of IEX-1 in the co-culture-induced damage of Caco-2 cells. We showed that IEX-1 expression induced in Caco-2 cells was suppressed by anti-TNFα antibody treatment. Experiments using IEX-1-overexpressing and -knockdown Caco-2 cells suggested that IEX-1 was involved in the suppression of Caco-2 cell damage. Increases in caspase 3 activity and TNFR1 (TNF receptor 1) mRNA expression were shown in IEX-1-knockdown Caco-2 cells, suggesting that IEX-1 plays a role in the suppression of apoptosis and protects cells by controlling sensitivity to TNFα under both normal and inflammatory conditions.
Purification and characterization of a Ca2+-dependent novel lectin from Nymphaea nouchali tuber with antiproliferative activities
Authors: Kabir Syed Rashel , Zubair Md. Abu , Nurujjaman Md. , Haque Md. Azizul , Hasan Imtiaj , Islam Md. Farhadul , Hossain Md. Tanvir , Hossain Md. Anowar , Rakib Md. Abdur , Alam Mohammad Taufiq , Shaha Ranajit Kumar , Hossain Md. Tofazzal , Kimura Yoshinobu , Absar Nurul
Published: February 2011

A lectin (termed NNTL) was purified from the extracts of Nymphaea nouchali tuber followed by anion-exchange chromatography on DEAE-cellulose, hydrophobic chromatography on HiTrap Phenyl HP and by repeated anion-exchange chromatography on HiTrap Q FF column. The molecular mass of the purified lectin was 27.0 ± 1.0 kDa, as estimated by SDS/PAGE both in the presence and in the absence of 2-mercaptoethanol. NNTL was an o-nitrophenyl β-D-galactopyranoside sugar-specific lectin that agglutinated rat, chicken and different groups of human blood cells and exhibited high agglutination activity over the pH range 5–9 and temperatures of 30–60°C. The N-terminal sequence of NNTL did not show sequence similarity with any other lectin and the amino acid analysis revealed that NNTL was rich in leucine, methionine and glycine residues. NNTL was a glycoprotein containing 8% neutral sugar and showed toxicity against brine shrimp nauplii with an LC50 value of 120 ± 29 μg/ml and exerted strong agglutination activity against four pathogenic bacteria (Bacillus subtilis, Sarcina lutea, Shigella shiga and Shigella sonnei). In addition, antiproliferative activity of this lectin against EAC (Ehrlich ascites carcinoma) cells showed 56% and 76% inhibition in vivo in mice at 1.5 and 3 mg·kg−1·day−1 respectively. NNTL was a divalent ion-dependent glycoprotein, which lost its activity markedly in the presence of denaturants. Furthermore, measurement of fluorescence spectra in the presence and absence of urea and CaCl2 indicated the requirement of Ca2+ for the stability of NNTL.
Is the beneficial effect of prior exercise on postprandial lipaemia partly due to redistribution of blood flow?
Authors: Hurren Nicholas M. , Balanos George M. , Blannin Andrew K.
Published: February 2011

Preprandial aerobic exercise lowers postprandial lipaemia (a risk factor for coronary heart disease); however, the mechanisms responsible are still not clear. The present study investigated whether blood flow to skeletal muscle and/or the liver was increased in the postprandial period after exercise, relative to a control trial, and whether this resulted from increased cardiac output or redistribution of flow. Eight overweight inactive males, aged 49.4±10.5 years (mean±S.D.), acted as their own controls in a counterbalanced design, either walking briskly for 90 min at 60% V̇O2max (maximal oxygen uptake), or resting in the lab, on the evening of day 1. The following morning, a fasting blood sample was collected, participants consumed a high-fat breakfast, and further venous blood samples were drawn hourly for 6 h. Immediately after blood sampling, Doppler ultrasound was used to measure cardiac output and blood flow through both the femoral artery of one leg and the hepatic portal vein, with the ultrasonographer blinded to trial order. The total postprandial triacylglycerol response was 22% lower after exercise (P=0.001). Blood flow through the femoral artery and the hepatic portal vein was increased by 19% (P<0.001) and 16% (P=0.033), respectively, during the 6-h postprandial period following exercise; however, postprandial cardiac output did not differ between trials (P=0.065). Redistribution of blood flow, to both exercised skeletal muscle and the liver, may therefore play a role in reducing the plasma triacylglycerol response to a high-fat meal on the day after an exercise bout.
C-terminal provasopressin (copeptin) as a prognostic marker after acute non-ST elevation myocardial infarction: Leicester Acute Myocardial Infarction Peptide II (LAMP II) study
Authors: Narayan Hafid , Dhillon Onkar S. , Quinn Pauline A. , Struck Joachim , Squire Iain B. , Davies Joan E. , Ng Leong L.
Published: February 2011

Copeptin, the 39-amino-acid C-terminal portion of provasopressin, has been shown to be an independent predictor for adverse events following STEMI (ST elevation myocardial infarction). We hypothesized that plasma copeptin was an independent predictor for adverse outcomes following acute NSTEMI (non-STEMI) and evaluated whether copeptin added prognostic information to the GRACE (Global Registry of Acute Coronary Events) score compared with NT-proBNP (N-terminal pro-B-type natriuretic peptide). Plasma copeptin and NT-proBNP were measured in 754 consecutive patients admitted to the hospital with chest pain and diagnosed as having NSTEMI in this prospective observational study. The end point was all-cause mortality at 6 months. Upper median levels of copeptin were strongly associated with all-cause mortality at 6 months. Copeptin was a significant predictor of time to mortality {HR (hazard ratio), 5.98 [95% CI (confidence interval, 3.75–9.53]; P<0.0005} in univariate analysis and remained a significant predictor in multivariate analysis [HR, 3.03 (05% CI, 1.32–6.98); P=0.009]. There were no significant differences between the area under ROC (receiver operating characteristic) curves of copeptin, NT-proBNP and the GRACE score. Copeptin improved accuracy of risk classification when used in combination with the GRACE score as determined by net reclassification improvement, whereas NT-proBNP did not. The relative utility of the GRACE score was increased more by copeptin than by NT-proBNP over a wide range of risks. Plasma copeptin is elevated after NSTEMI, and higher levels are associated with worse outcomes. Copeptin used in conjunction with the GRACE score improves risk stratification enabling more accurate identification of high-risk individuals.
Mixed time slicing in path integral simulations
Authors: Steele Ryan P. , Zwickl Jill , Shushkov Philip , Tully John C.
Published: February 2011

A simple and efficient scheme is presented for using different time slices for different degrees of freedom in path integral calculations. This method bridges the gap between full quantization and the standard mixed quantum-classical (MQC) scheme and, therefore, still provides quantum mechanical effects in the less-quantized variables. Underlying the algorithm is the notion that time slices (beads) may be “collapsed” in a manner that preserves quantization in the less quantum mechanical degrees of freedom. The method is shown to be analogous to multiple-time step integration techniques in classical molecular dynamics. The algorithm and its associated error are demonstrated on model systems containing coupled high- and low-frequency modes; results indicate that convergence of quantum mechanical observables can be achieved with disparate bead numbers in the different modes. Cost estimates indicate that this procedure, much like the MQC method, is most efficient for only a relatively few quantum mechanical degrees of freedom, such as proton transfer. In this regime, however, the cost of a fully quantum mechanical simulation is determined by the quantization of the least quantum mechanical degrees of freedom.
Topography evolution mechanism on fused silica during low-energy ion beam sputtering
Authors: Völlner J. , Ziberi B. , Frost F. , Rauschenbach B.
Published: February 2011

In this study, the topography evolution of fused silica surfaces during low-energy ion beam erosion has been investigated depending on the ion incidence angle and with focus on the importance of the initial surface topography. Ripple prepattern, also prepared by ion beam erosion, that exhibits an anisotropic surface with adjustable surface amplitudes and gradients was utilized. Based on experimental results that confirm smoothing and patterning behavior, gradient-dependent sputtering is identified being the dominant topography evolution mechanism.
Note: In situ cleavage of crystallographic oriented tips for scanning probe microscopy
Authors: Wutscher T. , Giessibl F. J.
Published: February 2011

We report an in situ method of preparing tips for scanning probe microscopy (SPM). Oriented single-crystal nickel oxide (NiO) rods were diced, using a wafer saw, to prepare artificial breaking points. Two geometries, a single rod and a two-sided cut rod were fabricated. The cleavable tips were mounted to a force sensor based on a quartz tuning fork and cleaved using the coarse approach of the SPM. Atomically resolved force microscopy images of NiO (001) were taken with these NiO tips.
Electron correlation effects on the first hyperpolarizability of push–pull π-conjugated systems
Authors: de Wergifosse Marc , Champagne Benoît
Published: February 2011

The first hyperpolarizability (β) of representative push–pull π-conjugated compounds has been calculated at several levels of approximation to assess the effects of electron correlation. First, the 6-31+G(d) basis set has been shown to give the best balance between accuracy and computational resources for a polyene linker whereas for polyyne linker, the 6-31G(d) basis set is already an optimal choice. As a result of cancellations between higher order contributions, the MP2 method turns out to be the method of choice to predict β of push–pull π-conjugated systems since it closely reproduces the values obtained with the reference CCSD(T) scheme. Moreover, the SDQ-MP4 and CCSD approaches provide rarely improved estimates over MP2 while the MP4 method does not represent an improvement over MP4-SDQ or the SCS-MP2 method, over MP2. Among density functional theory exchange-correlation functionals, LC-BLYP is reliable when characterizing the changes of first hyperpolarizability upon enlarging the π-conjugated linker or upon changing the polyyne linker into a polyene segment. Nevertheless, its reliability is very similar to what can be achieved with the Hartree–Fock method and the MP2 scheme is by far more accurate. On the other hand, the BLYP, B3LYP, and BHandHLYP functionals perform quantitatively better in a number of cases but the trends are poorly described. This is also the case of the B2-PLYP and mPW2-PLYP functionals, which are often the most accurate, though they underestimate the increase of β when going from polyyne to polyene linkers and overestimate the enhancement of β with chain length.
Photopyroelectric response of PTCa/PEEK composite
Authors: Estevam Giuliano Pierre , de Melo Washington Luiz Barros , Sakamoto Walter Katsumi
Published: February 2011

A pyroelectric composite made of calcium modified lead titanate ceramic and polyether–ether–ketone high performance polymer was obtained in the film form by hot pressing the ceramic/polymer mixture into the desired composition. After polarization with a suitable electric field, a ceramic composite film (60% vol.) exhibited a pyroelectric figure of merit three times higher than that of a lead zirconate titanate ceramic. The material was used as infrared radiation sensor. The voltage responsivity decreases with the inverse of the frequency showing the same behavior of the thermally thick sensor. The reproducibility of the sensor responses was observed.
Energy spectra in a helical vortex breakdown
Authors: Di Pierro Bastien , Abid Malek
Published: February 2011

Using spectrally accurate, direct numerical simulations, we show that vortices with axial flows (without an imposed strain) generate small scales, i.e., breakdown, when they are randomly perturbed. We show that the breakdown that occurs without the necessity of a stagnation point in the flow is nonlinear and that energy spectra of the breakdown present a range of a k−5/3 scaling (k being a wavenumber). These features are the same for centrifugally stable and unstable azimuthal velocities. However, centrifugally unstable azimuthal velocities promote mixing in vortices with an axial flow. We also find that vortex breakdown could be a physical mechanism against a finite time singularity in Navier–Stokes equations. Contrarily, we do not observe a breakdown using spectrally truncated Euler equations. For these equations we find a scaling of the energy spectra compatible with the existence of a finite time singularity.
Numerical study of efficiency for a 670 GHz gyrotron
Authors: Pu Ruifeng , Nusinovich Gregory S. , Sinitsyn Oleksandr V. , Antonsen Thomas M.
Published: February 2011

In this paper, the results of the efficiency study of a 670 GHz gyrotron operating at TE31,8-mode are presented. Calculations are performed by using the self-consistent nonstationary code MAGY. Three cavity configurations were examined. The effects of ohmic losses and electron velocity spread were included in the simulation. The results show that the output efficiency can reach 35% and the velocity spread in the electron beam does not degrade the operation significantly. Furthermore, we verified that the smoothing of the sharp corners for a small tapering angle would reduce mode conversion; the parasitic excitation of neighboring radial modes is less than 1% of the amplitude of the operating mode and the effect on efficiency is small. Lastly, the simulation results show that the after-cavity interaction causes only slight variations in the efficiency.
Modulational instability of ion-acoustic waves in a plasma with a q-nonextensive electron velocity distribution
Authors: Bains A. S. , Tribeche Mouloud , Gill T. S.
Published: February 2011

The modulational instability (MI) of ion-acoustic waves (IAWs) in a two-component plasma is investigated in the context of the nonextensive statistics proposed by Tsallis [J. Stat. Phys. 52, 479 (1988)]. Using the reductive perturbation method, the nonlinear Schrödinger equation (NLSE) which governs the MI of the IAWs is obtained. The presence of the nonextensive electron distribution is shown to influence the MI of the waves. Three different ranges of the nonextensive q-parameter are considered and in each case the MI sets in under different conditions. Furthermore, the effects of the q-parameter on the growth rate of MI are discussed in detail.
Compact formulas for guiding-center orbits in axisymmetric tokamak geometry
Authors: Brizard Alain J.
Published: February 2011

Compact formulas for trapped-particle and passing-particle guiding-center orbits in axisymmetric tokamak geometry are given in terms of the Jacobi elliptic functions and complete elliptic integrals. These formulas can find applications in bounce-center kinetic theory as well as guiding-center Fokker–Planck kinetic theory.
Nitrous oxide tetramer has two highly symmetric isomers
Authors: Oliaee J. Norooz , Dehghany M. , Moazzen-Ahmadi N. , McKellar A. R. W.
Published: February 2011

Infrared spectra of the nitrous oxide tetramer, (N2O)4, are studied in the region of the N2O ν1 fundamental band (∼2200 cm−1). The spectra are observed using a tunable diode laser to probe a pulsed supersonic jet expansion. Parallel (ΔK = 0) bands are observed for the previously observed isomer of (N2O)4, which is confirmed by isotopic substitution to have an oblate symmetric rotor structure with D2d symmetry. A distinct new isomer of (N2O)4 is observed by means of a perpendicular (ΔK = ±1) band. It has a prolate symmetric rotor structure with S4 symmetry. These isomers represent two distinct, but almost equally favorable, ways of bringing together a pair of nonpolar N2O dimers to form a tetramer. It is not clear at present which one represents the true ground state.
Method for probing the magnetic state of nanomaterials encapsulated in carbon nanotubes
Authors: Konabe Satoru , Okada Susumu
Published: February 2011

We propose a method for optically probing the magnetic states of metallic atoms encapsulated in single-walled carbon nanotubes. The absorption spectrum is calculated by solving the Bethe–Salpeter equation, which includes the effects of magnetic atoms, under the tight-binding approximation. Due to the exchange interaction between excitons and polarized spins in ferromagnets, triplet excitons acquire a finite oscillator strength and can thus be excited by light. This mechanism is promising for detecting magnetic ordering of materials encapsulated in carbon nanotubes.
Balanced carrier transport in organic solar cells employing embedded indium-tin-oxide nanoelectrodes
Authors: Hsu Min-Hsiang , Yu Peichen , Huang Jen-Hsien , Chang Chia-Hua , Wu Chien-Wei , Cheng Yu-Chih , Chu Chih-Wei
Published: February 2011

In this paper, we present evidence of balanced electron and hole transport in polymer-fullerene based solar cells by means of embedded indium-tin-oxide nanoelectrodes. Enabled by a controllable electrochemical deposition, the individual nanoelectrodes are uniformly enclosed by a poly(3,4-ethylenedioxythiophene) hole-conducting layer, allowing a relatively short route for holes to reach the anode and hence increasing the effective hole mobility. Consequently, the power conversion efficiency and photogenerated current are maximized with a deposition condition of 50 μC, where the ratio of the electron to hole mobility is nearly unity.
Reactivity of HO2/O−2 Radicals in Aqueous Solution
Authors: Bielski Benon H. J. , Cabelli Diane E. , Arudi Ravindra L. , Ross Alberta B.
Published: February 2011

Kinetic data for the superoxide radical (HO2⇄O−2 +H+, pK=4.8) in aqueous solution have been critically assessed. Rate constants for reactions of O−2 and HO2 with more than 300 organic and inorganic ions, molecules and other transient species have been tabulated.