bluuebunny/crossref_metadata_2025_split huggingface dataset:
Shearing of the CENP-A dimerization interface mediates plasticity in the octameric centromeric nucleosome
Authors: Winogradoff David , Zhao Haiqing , Dalal Yamini , Papoian Garegin A. 
Published: November 2015

AbstractThe centromeric nucleosome is a key epigenetic determinant of centromere identity and function. Consequently, deciphering how CENP-A containing nucleosomes contribute structurally to centromere function is a fundamental question in chromosome biology. Here, we performed microsecond timescale all-atom molecular dynamics (MD) simulations of CENP-A and H3 nucleosomes and report that the octameric CENP-A core particles and nucleosomes display different dynamics from their canonical H3-containing counterparts. The most significant motion observed is within key interactions at the heart of the CENP-A octameric core, wherein shearing of contacts within the CENP-A:CENP-A’ dimerization interface results in a weaker four helix bundle and an extrusion of 10–30 bp of DNA near the pseudo-dyad. Coupled to other local and global fluctuations, the CENP-A nucleosome occupies a more rugged free energy landscape than the canonical H3 nucleosome. Taken together, our data suggest that CENP-A encodes enhanced distortability to the octameric nucleosome, which may allow for enhanced flexing of the histone corein vivo.
Tumor-selective use of DNA base excision repair inhibition in pancreatic cancer using the NQO1 bioactivatable drug, β-lapachone
Authors: Chakrabarti Gaurab , Silvers Molly A. , Ilcheva Mariya , Liu Yuliang , Moore Zachary R. , Luo Xiuquan , Gao Jinming , Anderson Glenda , Liu Lili , Sarode Venetia , Gerber David E. , Burma Sandeep , DeBerardinis Ralph J. , Gerson Stanton L. , Boothman David A. 
Published: November 2015

AbstractBase excision repair (BER) is an essential pathway for pancreatic ductal adenocarcinoma (PDA) survival. Attempts to target this repair pathway have failed due to lack of tumor-selectivity and very limited efficacy. The NAD(P)H:Quinone Oxidoreductase 1 (NQO1) bioactivatable drug, ß-lapachone (ARQ761 in clinical form), can provide tumor-selective and enhanced synergy with BER inhibition. ß-Lapachone undergoes NQO1-dependent futile redox cycling, generating massive intracellular hydrogen peroxide levels and oxidative DNA lesions that stimulate poly(ADP-ribose) polymerase 1 (PARP1) hyperactivation. Rapid NAD+/ATP depletion and programmed necrosis results. To identify BER modulators essential for repair of ß-lapachone-induced DNA base damage, a focused synthetic lethal RNAi screen demonstrated that silencing the BER scaffolding protein, XRCC1, sensitized PDA cells. In contrast, depleting OGG1 N-glycosylase spared cells from ß-lap-induced lethality and blunted PARP1 hyperactivation. Combining ß-lapachone with XRCC1 knockdown or methoxyamine (MeOX), an apyrimidinic/apurinic (AP)-modifying agent, led to NQO1-dependent synergistic killing in PDA, NSCLC, breast and head and neck cancers. OGG1 knockdown, dicoumarol-treatment or NQO1- cancer cells were spared. MeOX + ß-lapachone exposure resulted in elevated DNA double-strand breaks, PARP1 hyperactivation and TUNEL+ programmed necrosis. Combination treatment caused dramatic antitumor activity, enhanced PARP1-hyperactivation in tumor tissue and improved survival of mice bearing MiaPaca2-derived xenografts, with 33% apparent cures. Significance: Targeting base excision repair (BER) alone has limited therapeutic potential for pancreatic or other cancers due to a general lack of tumor-selectivity. Here, we present a treatment strategy that makes BER inhibition tumor-selective and NQO1-dependent for therapy of most solid neoplasms, particularly for pancreatic cancer.
Mesoporous magnetic secondary nanostructures as versatile adsorbent for efficient scavenging of heavy metals
Authors: Bhattacharya Kakoli , Parasar Devaborniny , Mondal Bholanath , Deb Pritam 
Published: November 2015

AbstractPorous magnetic secondary nanostructures exhibit high surface area because of the presence of plentiful interparticle spaces or pores. Mesoporous Fe3O4 secondary nanostructures (MFSNs) have been studied here as versatile adsorbent for heavy metal scavenging. The porosity combined with magnetic functionality of the secondary nanostructures has facilitated efficient heavy metal (As, Cu and Cd) remediation from water solution within a short period of contact time. It is because of the larger surface area of MFSNs due to the porous network in addition to primary nanostructures which provides abundant adsorption sites facilitating high adsorption of the heavy metal ions. The brilliance of adsorption property of MFSNs has been realized through comprehensive adsorption studies and detailed kinetics. Due to their larger dimension, MFSNs help in overcoming the Brownian motion which facilitates easy separation of the metal ion sorbed secondary nanostructures and also do not get drained out during filtration, thus providing pure water.
Optically Transparent Microwave Polarizer Based On Quasi-Metallic Graphene
Authors: Grande Marco , Bianco Giuseppe Valerio , Vincenti Maria Antonietta , de Ceglia Domenico , Capezzuto Pio , Scalora Michael , D’Orazio Antonella , Bruno Giovanni 
Published: November 2015

AbstractIn this paper, we report on the engineering and the realization of optically transparent graphene-based microwave devices using Chemical Vapour Deposition (CVD) graphene whose sheet resistance may be tailored down to values below 30 Ω/sq. In particular, we show that the process was successfully used to realize and characterize a simple, optically transparent graphene-based wire-grid polarizer at microwave frequencies (X band). The availability of graphene operating in a quasi-metallic region may allow the integration of graphene layers in several microwave components, thus leading to the realization of fully transparent (and flexible) microwave devices.
Circulating HIV DNA Correlates With Neurocognitive Impairment in Older HIV-infected Adults on Suppressive ART
Authors: Oliveira Michelli Faria de , Murrell Ben , Pérez-Santiago Josué , Vargas Milenka , Ellis Ronald J. , Letendre Scott , Grant Igor , Smith Davey M. , Woods Steven Paul , Gianella Sara 
Published: November 2015

AbstractOlder HIV-infected adults have a higher risk of neurocognitive impairment, but the underlying mechanisms are poorly understood. Here, we investigated the associations between levels of HIV DNA in peripheral blood, soluble markers of inflammation and cellular trafficking in blood and cerebrospinal fluid (CSF) and neurocognitive functioning among 18 younger (22–40 years) and 26 older (50–71 years) HIV-infected subjects, who were administered a comprehensive neurocognitive battery. Older HIV-infected individuals presented higher levels of inflammation in CSF and blood compared to younger individuals, but no difference was observed in HIV DNA levels. Among older participants, higher HIV DNA levels were significantly associated with more severe neurocognitive impairment (p = 0.005), particularly in the Executive Functions domain (p = 0.004). No association was observed between HIV DNA and neurocognition among younger individuals. Despite significantly increased inflammation observed in the older group, none of the inflammatory markers were associated with neurocognitive impairment among older HIV+ individuals (p > 0.05). Our study supports the involvement of peripheral HIV DNA reservoir in the pathogenesis of neurocognitive disorder during suppressive ART. Correlates of neurocognitive impairment might differ between younger and older adults, suggesting that future treatment and prevention strategies for HIV-associated neurocognitive disorders likely need to be tailored based on age.
MacroH2A1 associates with nuclear lamina and maintains chromatin architecture in mouse liver cells
Authors: Fu Yuhua , Lv Pin , Yan Guoquan , Fan Hui , Cheng Lu , Zhang Feng , Dang Yongjun , Wu Hao , Wen Bo 
Published: November 2015

AbstractIn the interphase nucleus, chromatin is organized into three-dimensional conformation to coordinate genome functions. The lamina-chromatin association is important to facilitate higher-order chromatin in mammalian cells, but its biological significances and molecular mechanisms remain poorly understood. One obstacle is that the list of lamina-associated proteins remains limited, presumably due to the inherent insolubility of lamina proteins. In this report, we identified 182 proteins associated with lamin B1 (a constitutive component of lamina) in mouse hepatocytes, by adopting virus-based proximity-dependent biotin identification. These proteins are functionally related to biological processes such as chromatin organization. As an example, we validated the association between lamin B1 and core histone macroH2A1, a histone associated with repressive chromatin. Furthermore, we mapped Lamina-associated domains (LADs) in mouse liver cells and found that boundaries of LADs are enriched for macroH2A. More interestingly, knocking-down of macroH2A1 resulted in the release of heterochromatin foci marked by histone lysine 9 trimethylation (H3K9me3) and the decondensation of global chromatin structure. However, down-regulation of lamin B1 led to redistribution of macroH2A1. Taken together, our data indicated that macroH2A1 is associated with lamina and is required to maintain chromatin architecture in mouse liver cells.
Three-dimensional direct cell patterning in collagen hydrogels with near-infrared femtosecond laser
Authors: Hribar Kolin C. , Meggs Kyle , Liu Justin , Zhu Wei , Qu Xin , Chen Shaochen 
Published: November 2015

AbstractWe report a methodology for three-dimensional (3D) cell patterning in a hydrogel in situ. Gold nanorods within a cell-encapsulating collagen hydrogel absorb a focused near-infrared femtosecond laser beam, locally denaturing the collagen and forming channels, into which cells migrate, proliferate and align in 3D. Importantly, pattern resolution is tunable based on writing speed and laser power and high cell viability (>90%) is achieved using higher writing speeds and lower laser intensities. Overall, this patterning technique presents a flexible direct-write method that is applicable in tissue engineering systems where 3D alignment is critical (such as vascular, neural, cardiac and muscle tissue).
Streptococcus agalactiae Serotype Distribution and Antimicrobial Susceptibility in Pregnant Women in Gabon, Central Africa
Authors: Belard Sabine , Toepfner Nicole , Capan-Melser Mesküre , Mombo-Ngoma Ghyslain , Zoleko-Manego Rella , Groger Mirjam , Matsiegui Pierre-Blaise , Agnandji Selidji T. , Adegnika Ayôla A. , González Raquel , Kremsner Peter G. , Menendez Clara , Ramharter Michael , Berner Reinhard 
Published: November 2015

AbstractNeonatal invasive disease due to Streptococcus agalactiae is life threatening and preventive strategies suitable for resource limited settings are urgently needed. Protective coverage of vaccine candidates based on capsular epitopes will relate to local epidemiology of S. agalactiae serotypes and successful management of critical infections depends on timely therapy with effective antibiotics. This is the first report on serotype distribution and antimicrobial susceptibility of S. agalactiae in pregnant women from a Central African region. Serotypes V, III and Ib accounted for 88/109 (81%) serotypes and all isolates were susceptible to penicillin and clindamycin while 13% showed intermediate susceptibility to erythromycin.
Inhibition of Wnt signalling and breast tumour growth by the multi-purpose drug suramin through suppression of heterotrimeric G proteins and Wnt endocytosis
Authors: Koval Alexey , Ahmed Kamal , Katanaev Vladimir L. 
Published: November 2015

Overactivation of the Wnt signalling pathway underlies oncogenic transformation and proliferation in many cancers, including the triple-negative breast cancer (TNBC), the deadliest form of tumour in the breast, taking about a quarter of a million lives annually worldwide. No clinically approved targeted therapies attacking Wnt signalling currently exist. Repositioning of approved drugs is a promising approach in drug discovery. In the present study we show that a multi-purpose drug suramin inhibits Wnt signalling and proliferation of TNBC cells in vitro and in mouse models, inhibiting a component in the upper levels of the pathway. Through a set of investigations we identify heterotrimeric G proteins and regulation of Wnt endocytosis as the likely target of suramin in this pathway. G protein-dependent endocytosis of plasma membrane-located components of the Wnt pathway was previously shown to be important for amplification of the signal in this cascade. Our data identify endocytic regulation within Wnt signalling as a promising target for anti-Wnt and anti-cancer drug discovery. Suramin, as the first example of such drug or its analogues might pave the way for the appearance of first-in-class targeted therapies against TNBC and other Wnt-dependent cancers.
Competition between spin–orbit interaction and exchange coupling within a honeycomb lattice ribbon
Authors: Su Yu-Hsin , Chen Son-Hsien , Hu C D , Chang Ching-Ray 
Published: November 2015

Abstract
Spin density patterns of a pinned magnetic impurity that is embedded in a honeycomb lattice with zigzag edges are investigated by employing a mean-field assisted Landauer–Keldysh formalism. Both the intrinsic spin–orbit coupling and the extrinsic localized magnetic moments are considered, and the effects of the pinning directions and the species of the sublattice on the electron spins are analyzed. A local time-reversal symmetry breaking cannot destroy the equilibrium edge-state spin accumulation that is induced by intrinsic spin–orbit coupling when the pinning field lies in the plane of the ribbon and the embedding position is the A-site at the edge. The induced local spin can be either parallel or antiparallel to the localized impurity moment, depending on the location of the pinned impurity, because itinerant electrons are found only at the B-site of the edge, but not at the A-site.
Influence of collisions on parametric instabilities induced by lower hybrid waves in tokamak plasmas
Authors: Castaldo C. , Di Siena A. , Fedele R. , Napoli F. , Amicucci L. , Cesario R. , Schettini G. 
Published: November 2015

Abstract
Parametric instabilities induced at the plasma edge by lower hybrid wave power externally coupled to tokamak plasmas have, via broadening of the antenna spectrum, strong influence on the power deposition and current drive in the core. For modeling the parametric instabilities at the tokamak plasma edge in lower hybrid current drive experiments, the effect of the collisions has been neglected so far. In the present work, a specific collisional parametric dispersion relation, useful to analyze these nonlinear phenomena near the lower hybrid antenna mouth, is derived for the first time, based on a kinetic model. Numerical solutions show that in such cold plasma regions the collisions prevent the onset of the parametric instabilities. This result is important for present lower hybrid current drive experiments, as well as in fusion reactor scenarios.
Dependence of pedestal structure on collisionality at fixed beta in JT-60U
Authors: Urano H. , Aiba N. , Kamiya K. , Kamada Y. 
Published: November 2015

Abstract
The dependence of pedestal structure on collisionality at fixed beta has been investigated in JT-60U. In the ITER-relevant low collisionality regime, the pedestal width does not change with edge collisionality. In the high collisionality regime, the pedestal width broadens with increased edge collisionality. The pedestal pressure gradient and width are not significantly changed when the pedestal is close to an intermediate n peeling-ballooning mode boundary at low collisionality. The experimental result indicates that conventional pedestal models where the pedestal width is independent of collisionality and is determined by

at the pedestal is not a bad assumption in the ITER-relevant low collisionality regime. On the other hand, the pressure gradient decreases and the pedestal width increases at high collisionality. The pedestal broadening becomes significant when the pedestal is marginal to be unstable at the high n ballooning mode in the high collisionality regime.
Influence of plant size on female-biased sex allocation in a single-flowered, nectarless herb
Authors: Xiong Ying-Ze , Xie Meng , Huang Shuang-Quan 
Published: November 2015

Abstract
Relative allocation to female and male function in hermaphroditic species often departs from strict equisexuality. Increased femaleness with plant size in animal-pollinated species has been proposed in theory and demonstrated in empirical studies. However, such size-dependent sex allocation (SDS) has not been observed in some insect-pollinated species, throwing doubt on the generalization of SDS, that large plants have decelerated male function investment. Himalayan mayapple Podophyllum hexandrum (Berberidaceae) produces a single terminal flower and no nectar, providing a simple system for studying SDS without the confounding effects of flower number and nectar production. To investigate the SDS in P. hexandrum , plant size, biomass of floral organs (stamens, pistils and petals) and gamete production (pollen and ovule number) were measured in four populations in Yunnan Province, northwest China. Isometric allocation to female and male function with plant size was found in two populations, but the prediction of SDS was supported in the other two populations. Using pollen and ovule production as the allocation currency, allocation to female and male function was isometric in all studied populations. Resources allocated to attractive (petals) and sexual (pistils and stamens) structures did not show a significantly disproportionate increase with plant size in three of the four studied populations. The general pattern of isometric allocation to female and male function and to attractive and sexual structures could be attributed to the species being capable of automatic self-pollination, related to low pollen loss, minor deleterious effect of selfing and low importance of attractive structures. However, in further studies, careful consideration should be given to the different currencies used to estimate sex allocation.
Rapid evolution of the inter-sexual genetic correlation for fitness inDrosophila melanogaster
Authors: Collet J. M. , Fuentes S. , Hesketh J. , Hill M. S. , Innocenti P. , Morrow E. H. , Fowler K. , Reuter M. 
Published: November 2015

AbstractSexual antagonism (SA) arises when male and female phenotypes are under opposing selection, yet genetically correlated. Until resolved, antagonism limits evolution towards optimal sex-specific phenotypes. Despite its importance for sex-specific adaptation and existing theory, the dynamics of SA resolution are not well understood empirically. Here, we present data fromDrosophila melanogaster, compatible with a resolution of SA. We compared two independent replicates of the ‘LHM’ population in which SA had previously been described. Both had been maintained under identical, controlled conditions, and separated for <250 generations. Although heritabilities of male and female fitness were similar, the inter-sexual genetic correlation differed significantly, being negative in one replicate (indicating SA) but close to zero in the other. Using population sequencing, we show that phenotypic differences were associated with population divergence in allele frequencies at non-random loci across the genome. Large frequency changes were more prevalent in the population without SA and were enriched at loci mapping to genes previously shown to have a sexually antagonistic relationships between expression and fitness. Our data suggest that rapid evolution towards SA resolution has occurred in one of the populations and open avenues towards studying the genetics of SA and its resolution.
Analysis of the optimality of the Standard Genetic Code
Authors: Kumar Balaji , Saini Supreet 
Published: November 2015

AbstractMany theories have been proposed attempting to explain the origin of the genetic code. While strong reasons remain to believe that the genetic code evolved as a frozen accident, at least for the first few amino acids, other theories remain viable. In this work, we test the optimality of the standard genetic code against approximately 17 million genetic codes, and locate 18 which outperform the standard genetic code at the following three criteria: (a) robustness to point mutation; (b) robustness to frameshift mutation; and (c) ability to encode additional information in the coding region. We use a genetic algorithm to generate and score codes from different parts of the associated landscape, and are, as a result presumably more representative of the entire landscape. Our results show that while the genetic code is sub-optimal for robustness to frameshift mutation and the ability to encode additional information in the coding region, it is very strongly selected for robustness to point mutation. This coupled with the observation that the different performance indicator scores for a particular genetic code are seemingly negatively correlated, make the standard genetic code nearly optimal for the three criteria tested in this work.
Teaching poetry to Chinese English majors: a review of articles from 2000-2013
Authors: Cui Lifang , Hubbard Gillian , Gleeson Margaret 
Published: November 2015

Purpose– The purpose of this paper is to survey and consider the implications of the literature justifying the value of teaching poetry. There has been a long tradition of literature education in the English departments of Chinese universities. English Poetry courses are offered within optional literature modules in senior stages of a BA in English language and literature. In 2000, the new national syllabus for tertiary English majors was issued. This syllabus has brought the teaching of English into line with the perceived practical needs of society. As a result, poetry courses have been under threat within the degree. A substantial number of university teachers have responded to this threat with articles arguing the value of teaching of poetry.Design/methodology/approach– The China National Knowledge Infrastructure (CNKI), the largest database of academic journals in China, reveals that from 2000 to 2013, 102 articles about teaching English poetry to Chinese people learning English as a foreign language were published in Chinese academic journals, of which 67 are concerned with English majors. This literature examines these 67 articles.Findings– These articles justify the purpose of teaching English poetry, evaluate the content of poetry courses and share pedagogical strategies. The issues within this discussion fall into three categories: why teach poetry; what to teach in poetry courses; and how to teach poetry. Because the commitment of Chinese teachers to sharing their beliefs about teaching English poetry is positioned in the context of increased advocacy for the creation of inter-disciplinary market-orientated graduates, discomfort, uncertainty and the desire for change emerge in this discussion. On the other hand, teachers looking for change express caution about the costs of changing pedagogical approaches on the development of the skills of close reading and analysis of poetical texts.Originality/value– This investigation of the local Chinese context resonates with and contributes to the wider discussion of the challenges faced by English literature teachers in both second- (L2) and first-language (L1) contexts and warrants examination. It is difficult to say in advance how far such knowledge could contribute to any policy decisions that may be made in the future, but it is important that the voice of teachers contributes to the larger international debate about the value of humanities in tertiary-level education.