bluuebunny/crossref_metadata_2025 huggingface dataset:
Prescriptivism in English literature?
Authors: Tieken-Boon Van Ostade Ingrid
Published: October 2016

One of the things we discovered in the course of the Bridging the Unbridgeable project is that usage guides are predominantly produced by non-specialists. There are linguists, too, who wrote usage guides – David Crystal, for instance, Pam Peters and most recently Stephen Pinker – but authors are very often journalists and novelists. Kingsley Amis (1922–1995), whoseThe King's Englishwas published posthumously in 1997, is a good example, and so is Rebecca Gowers, who revised and updated her great-grandfather'sPlain Wordsin 2014. Examples of journalists-turned-usage-guide-writers are Simon Heffer (Strictly English, 2010) and Oliver Kamm (Accidence Will Happen, 2015). Writing is their job, so it is not surprising that novelists and journalists are drawn to language prescription as well. They may not be linguists in the strict sense, but they should be considered language specialists all the same.
Editorial: Joining the Conversation
Authors: RAE PAUL
Published: October 2016

In my previous editorial, I made reference to what Theresa Lillis and Mary Jane Curry call ‘literacy brokering’ amongst non-native speakers of English who seek to publish in anglophone academic journals. The term ‘literacy’ makes sense in the context, and, as I noted, the practice is hardly exclusive to those whose first language is not English. However, as Aoife Monks of Contemporary Theatre Review and I planned a New Scholars session on academic publishing for this year's annual conference of the International Federation for Theatre Research (IFTR, with which this journal is affiliated), a supplementary way of thinking about academic knowledge production came to mind: as conversation. And it is a conversational mode that wends its way through the articles presented in this issue of Theatre Research International.
From Panic to Reconciliation: Protest Theatre and the State in Zimbabwe, 1999–2012
Authors: CHIKONZO KELVIN
Published: October 2016

Between 1999 and 2008, Zimbabwe was in political and economic crisis. A number of theatre-makers responded by creating several different kinds of protest theatre. They did this to compensate for a media monopoly by the state, to promote active citizen engagement in politics, and to promote political change. This article first surveys developments in protest theatre at this time. It then draws attention to a brand of protest theatre that emerged after the crisis in Zimbabwe, after the formation of a Government of National Unity. Reconciliatory protest theatre, I explain, was concerned with issues of national healing and reconciliation which dominated the post-crisis situation in Zimbabwe. Whilst both the state and protest artists concurred on the fact that the nation ought to be healed and that reconciliation was needed, tensions emerged as to how the processes of healing and reconciliation were to unfold. By looking at two examples in detail, I explain how Zimbabwe's theatre artists viewed this issue, and how the state reacted.
The adaptive calibration model of stress responsivity: An empirical test in the Tracking Adolescents' Individual Lives Survey study
Authors: Ellis Bruce J. , Oldehinkel Albertine J. , Nederhof Esther
Published: October 2016

The adaptive calibration model (ACM) is a theory of developmental programing focusing on calibration of stress response systems and associated life history strategies to local environmental conditions. In this article, we tested some key predictions of the ACM in a longitudinal study of Dutch adolescent males (11–16 years old;N= 351). Measures of sympathetic, parasympathetic, and adrenocortical activation, reactivity to, and recovery from social–evaluative stress validated the four-pattern taxonomy of the ACM via latent profile analysis, though with some deviations from expected patterns. The physiological profiles generally showed predicted associations with antecedent measures of familial and ecological conditions and life stress; as expected, high- and low-responsivity patterns were found under both low-stress and high-stress family conditions. The four patterns were also differentially associated with aggressive/rule-breaking behavior and withdrawn/depressed behavior. This study provides measured support for key predictions of the ACM and highlights important empirical issues and methodological challenges for future research.
The algebra of recursive graph transformation language UnCAL: complete axiomatisation and iteration categorical semantics
Authors: HAMANA MAKOTO , MATSUDA KAZUTAKA , ASADA KAZUYUKI
Published: October 2016

The aim of this paper is to provide mathematical foundations of a graph transformation language, called UnCAL, using categorical semantics of type theory and fixed points. About 20 years ago, Bunemanet al. developed a graph database query language UnQL on the top of a functional meta-language UnCAL for describing and manipulating graphs. Recently, the functional programming community has shown renewed interest in UnCAL, because it provides an efficient graph transformation language which is useful for various applications, such as bidirectional computation.

In order to make UnCAL more flexible and fruitful for further extensions and applications, in this paper, we give a more conceptual understanding of UnCAL using categorical semantics. Our general interest of this paper is to clarify what is the algebra of UnCAL. Thus, we give an equational axiomatisation and categorical semantics of UnCAL, both of which are new. We show that the axiomatisation is complete for the original bisimulation semantics of UnCAL. Moreover, we provide a clean characterisation of the computation mechanism of UnCAL called ‘structural recursion on graphs’ using our categorical semantics. We show a concrete model of UnCAL given by the λG-calculus, which shows an interesting connection to lazy functional programming.
Neuropsychological Functioning in Preterm-Born Twins and Singletons at Preschool Age
Authors: Raz Sarah , Piercy Jamie C. , Heitzer Andrew M. , Peters Brittany N. , Newman Julie Bapp , DeBastos Angela K. , Ofen Noa , Batton Beau , Batton Daniel G.
Published: October 2016

Objectives: A limited body of research is available on the relationships between multiplicity of birth and neuropsychological functioning in preterm children who were conceived in the age of assisted reproductive technology and served by the modern neonatal intensive care unit. Our chief objective was to evaluate whether, after adjustment for sociodemographic factors and perinatal complications, twin birth accounted for a unique portion of developmental outcome variance in children born at-risk in the surfactant era. Methods: We compared the neuropsychological functioning of 77 twins and 144 singletons born preterm (<34 gestational weeks) and served by William Beaumont Hospital, Royal Oak, MI. Children were evaluated at preschool age, using standardized tests of memory, language, perceptual, and motor abilities. Results: Multiple regression analyses, adjusting for sociodemographic and perinatal variables, revealed no differences on memory or motor indices between preterm twins and their singleton counterparts. In contrast, performance of language and visual processing tasks was significantly lower in twins despite reduced perinatal risk in comparison to singletons. Effect sizes ranged from .33 to .38 standard deviations for global language and visual processing ability indices, respectively. No significant group by sex interactions were observed, and comparison of first-, or second-born twins with singletons yielded medium effect sizes (Cohen’s d=.56 and .40, respectively). Conclusions: The modest twin disadvantage on language and visual processing tasks at preschool-age could not be readily attributable to socioeconomic or perinatal variables. The possibility of biological or social twinning-related phenomena as mechanisms underlying the observed performance gaps are discussed. (JINS, 2016, 22, 865–877)
International historical what?
Authors: Owens Patricia
Published: October 2016

This essay examines the relationship between history and theory through a historical and political analysis of the rise of distinctly social theories, concepts, and practices in the ‘long 19th century’. Sociomania, obsession with things ‘socio’, is a problem in international theory. It is also a serious missed opportunity for Buzan and Lawson’s study of the 19th century. The Global Transformation contributes to international theory in showing how mainstream IR has failed to grasp the full significance of this period. But, in this crucial regard at least, so too have its authors. In adopting rather than fully historicizing the rise and expansion of social theories, works of ‘historical social science’ obscure rather than illuminate the historical and political origins of social forms of governance and thought; underestimate their significance for the history of international theory; and are unable to identify the more fundamental governance form of which the rise of the modern social realm is a concrete historical expression.
The promise of historical dynamism for the American study of international relations
Authors: Braumoeller Bear
Published: October 2016

WhileThe Global Transformationmakes a compelling case for the importance of the oft-ignored 19th century for IR theory, the book also represents an opportunity for an audience for which it was probably not intended: American IR scholars working in the quantitative empirical tradition, whom it should prompt to re-think the question of how the interactions that they seek to understand are conditional on deeper material and ideational dynamics.
Shifting Traction: Differential Treatment and Substantive and Procedural Regard in the International Climate Change Regime
Authors: Huggins Anna , Karim Md Saiful
Published: October 2016

The Paris Agreement to the United Nations Framework Convention on Climate Change (UNFCCC) signifies a shift in how the principle of common but differentiated responsibilities (CBDR) manifests in the international climate change regime. Unlike the UNFCCC and its Kyoto Protocol, the Paris Agreement does not enshrine differentiated substantive mitigation obligations for developed and developing countries. However, an increasingly proceduralized variant of the CBDR principle, which facilitates regard for the interests of developing countries with respect to treaty implementation yet does not guarantee favourable substantive outcomes for these states, is evident in the emerging regime. The experience of the International Maritime Organization’s climate change regime provides a cautionary tale with respect to procedurally oriented differentiation that is not reinforced by effective processes to ensure that developed states honour their finance and technology transfer commitments. Accordingly, this article posits that strong accountability mechanisms are required to transform opportunities for procedural differentiation in the Paris Agreement into a robust framework for procedural regard for the interests of developing states.
‘Dynamic Differentiation’: The Principles of CBDR-RC, Progression and Highest Possible Ambition in the Paris Agreement
Authors: Voigt Christina , Ferreira Felipe
Published: October 2016

The Paris Agreement has struck a careful balance between the need for ambitious and effective climate action and for fair effort sharing among parties based on differentiation. This article provides an overview of the negotiation history of differentiation and analyzes the ‘dynamic differentiation’ as built into the architecture of the Agreement. While being set against the normative background of the United Nations Framework Convention on Climate Change (UNFCCC), the Paris Agreement adopts a more diversified way of differential treatment among parties, approaching it in three complementary ways: firstly, on a principled basis, reflecting common but differentiated responsibilities and respective capabilities (CBDR-RC), in the light of different national circumstances; secondly, in the content of its articles, in particular on mitigation, finance and transparency; and thirdly, on the basis of the principles of progression and highest possible ambition, which represent new and dynamic aspects of differentiation. The authors argue that ‘highest possible ambition’ is reflective of a duty of care that states now need to exercise. It implies a due diligence standard, which requires each government to act in proportion to the risk at stake and to take all appropriate and adequate climate measures according to its responsibility and its best capabilities. By expecting parties to apply this standard at each successive preparation of nationally determined contributions (NDCs), and to progress beyond previous ones, the Paris Agreement has set up reiterative processes, an ‘international normative pull’ and a collective learning environment. This, in turn, creates a reflexive approach to parties’ determination of effort, promoting the evolution of voluntary cooperative behaviour.
‘Common But Differentiated Responsibilities’ in the National Courts: Lessons fromUrgendav.The Netherlands
Authors: Ferreira Patrícia Galvão
Published: October 2016

The landmark 2015 decision by the Hague District Court inUrgendav.The Netherlandsrepresents the first time a national court has expressly used the international environmental law (IEL) principle of common but differentiated responsibilities and capabilities (CBDRs) of the climate regime as a complementary tool to interpret the scope of a state’s climate obligations under domestic law. This article highlights that despite the marked engagement of national courts with IEL in recent decades (including engaging with principles such as sustainable development, polluter pays, intergenerational equity, and precaution), until this decision CBDRs had remained outside the purview of environmental law jurisprudence at the national level. The article examines how the Hague Court used CBDRs to help address two common barriers to climate liability: causation and the ‘political question’ doctrine. The article argues that the Court was able to find normative content in a core element of the climate-related CBDRs: the ‘leadership’ role of developed countries in climate action. This core element has remained remarkably consensual throughout the contested history of CBDRs in the climate regime – a history that has gained a new chapter with the signature of the Paris Agreement in December 2015. The article concludes thatUrgendav.The Netherlandsmay serve as a starting point for a more productive and extensive use of CBDRs in climate litigation, provided litigants make more explicit use of the persuasive authority of the principle.
Cooperation for Climate Mitigation in Amazonia: Brazil’s Emerging Role as a Regional Leader
Authors: Tigre Maria Antonia
Published: October 2016

Since their inception, climate change negotiations have stalled because of the scope of parties’ mitigation responsibilities under the United Nations Framework Convention on Climate Change (UNFCCC). The concept of common but differentiated responsibilities and respective capabilities (CBDR-RC) became a core principle of the framework to ensure consensus on a global climate policy in 1992 and to promote differentiation. By letting each country assess its current responsibilities and capacities for climate mitigation through their nationally determined contributions (NDCs), the Paris Agreement has built on the principle of CBDR-RC and promoted self-differentiation. As the concept evolved, the role of emerging economies has been a particular focus of discussions. Academia is still grappling with the revised meaning of CBDR-RC and the newly introduced NDCs. This article contributes to the discussion by analyzing the role of emerging economies in climate governance through the lens of regional responsibility. In particular, it discusses how cooperation can be a more effective way to ensure differentiation, especially by distinguishing emerging economies from other developing countries with fewer capacities. The article uses the Amazon rainforest as a case study, discussing Brazil’s role within the region. Building on lessons from regional schemes that have successfully promoted climate mitigation, the article looks at the Amazon Cooperation Treaty Organization (ACTO) as an avenue for enhanced cooperation at the regional level.
A randomized study of pomalidomide vs placebo in persons with myeloproliferative neoplasm-associated myelofibrosis and RBC-transfusion dependence
Authors:   for the RESUME trialists, Tefferi A , Al-Ali H K , Barosi G , Devos T , Gisslinger H , Jiang Q , Kiladjian J-J , Mesa R , Passamonti F , Ribrag V , Schiller G , Vannucchi A M , Zhou D , Reiser D , Zhong J , Gale R P
Published: October 2016

RBC-transfusion dependence is common in persons with myeloproliferative neoplasm (MPN)-associated myelofibrosis. The objective of this study was to determine the rates of RBC-transfusion independence after therapy with pomalidomide vs placebo in persons with MPN-associated myelofibrosis and RBC-transfusion dependence. Two hundred and fifty-two subjects (intent-to-treat (ITT) population) including 229 subjects confirmed by central review (modified ITT population) were randomly assigned (2:1) to pomalidomide or placebo. Trialists and subjects were blinded to treatment allocation. Primary end point was proportion of subjects achieving RBC-transfusion independence within 6 months. One hundred and fifty-two subjects received pomalidomide and 77 placebo. Response rates were 16% (95% confidence interval (CI), 11, 23%) vs 16% (8, 26%;P=0.87). Response in the pomalidomide cohort was associated with ⩽4 U RBC/28 days (odds ratio (OR)=3.1; 0.9, 11.1), age ⩽65 (OR=2.3; 0.9, 5.5) and type of MPN-associated myelofibrosis (OR=2.6; 0.7, 9.5). Responses in the placebo cohort were associated with ⩽4 U RBC/28 days (OR=8.6; 0.9, 82.3), white blood cell at randomization >25 × 109/l (OR=4.9; 0.8, 28.9) and interval from diagnosis to randomization >2 years (OR=4.9; 1.1, 21.9). Pomalidomide was associated with increased rates of oedema and neutropenia but these adverse effects were manageable. Pomalidomide and placebo had similar RBC-transfusion-independence response rates in persons with MPN-associated RBC-transfusion dependence.
Diversity-oriented synthetic strategy for developing a chemical modulator of protein–protein interaction
Authors: Kim Jonghoon , Jung Jinjoo , Koo Jaeyoung , Cho Wansang , Lee Won Seok , Kim Chanwoo , Park Wonwoo , Park Seung Bum
Published: October 2016

Diversity-oriented synthesis (DOS) can provide a collection of diverse and complex drug-like small molecules, which is critical in the development of new chemical probes for biological research of undruggable targets. However, the design and synthesis of small-molecule libraries with improved biological relevance as well as maximized molecular diversity represent a key challenge. Herein, we employ functional group-pairing strategy for the DOS of a chemical library containing privileged substructures, pyrimidodiazepine or pyrimidine moieties, as chemical navigators towards unexplored bioactive chemical space. To validate the utility of this DOS library, we identify a new small-molecule inhibitor of leucyl-tRNA synthetase–RagD protein–protein interaction, which regulates the amino acid-dependent activation of mechanistic target of rapamycin complex 1 signalling pathway. This work highlights that privileged substructure-based DOS strategy can be a powerful research tool for the construction of drug-like compounds to address challenging biological targets.
Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system
Authors: Anantharaman Karthik , Brown Christopher T. , Hug Laura A. , Sharon Itai , Castelle Cindy J. , Probst Alexander J. , Thomas Brian C. , Singh Andrea , Wilkins Michael J. , Karaoz Ulas , Brodie Eoin L. , Williams Kenneth H. , Hubbard Susan S. , Banfield Jillian F.
Published: October 2016

The subterranean world hosts up to one-fifth of all biomass, including microbial communities that drive transformations central to Earth’s biogeochemical cycles. However, little is known about how complex microbial communities in such environments are structured, and how inter-organism interactions shape ecosystem function. Here we apply terabase-scale cultivation-independent metagenomics to aquifer sediments and groundwater, and reconstruct 2,540 draft-quality, near-complete and complete strain-resolved genomes that represent the majority of known bacterial phyla as well as 47 newly discovered phylum-level lineages. Metabolic analyses spanning this vast phylogenetic diversity and representing up to 36% of organisms detected in the system are used to document the distribution of pathways in coexisting organisms. Consistent with prior findings indicating metabolic handoffs in simple consortia, we find that few organisms within the community can conduct multiple sequential redox transformations. As environmental conditions change, different assemblages of organisms are selected for, altering linkages among the major biogeochemical cycles.
Self-propelling vesicles define glycolysis as the minimal energy machinery for neuronal transport
Authors: Hinckelmann María-Victoria , Virlogeux Amandine , Niehage Christian , Poujol Christel , Choquet Daniel , Hoflack Bernard , Zala Diana , Saudou Frédéric
Published: October 2016

The glycolytic enzyme glyceraldehyde-3-phosphate dehydrogenase (GAPDH) facilitates fast axonal transport in neurons. However, given that GAPDH does not produce ATP, it is unclear whether glycolysis per se is sufficient to propel vesicles. Although many proteins regulating transport have been identified, the molecular composition of transported vesicles in neurons has yet to be fully elucidated. Here we selectively enrich motile vesicles and perform quantitative proteomic analysis. In addition to the expected molecular motors and vesicular proteins, we find an enrichment of all the glycolytic enzymes. Using biochemical approaches and super-resolution microscopy, we observe that most glycolytic enzymes are selectively associated with vesicles and facilitate transport of vesicles in neurons. Finally, we provide evidence that mouse brain vesicles produce ATP from ADP and glucose, and display movement in a reconstituted in vitro transport assay of native vesicles. We conclude that transport of vesicles along microtubules can be autonomous.
Nitrogen fixation in a chemoautotrophic lucinid symbiosis
Authors: König Sten , Gros Olivier , Heiden Stefan E. , Hinzke Tjorven , Thürmer Andrea , Poehlein Anja , Meyer Susann , Vatin Magalie , Mbéguié-A-Mbéguié Didier , Tocny Jennifer , Ponnudurai Ruby , Daniel Rolf , Becher Dörte , Schweder Thomas , Markert Stephanie
Published: October 2016

The shallow water bivalve Codakia orbicularis lives in symbiotic association with a sulfur-oxidizing bacterium in its gills. The endosymbiont fixes CO2 and thus generates organic carbon compounds, which support the host's growth. To investigate the uncultured symbiont's metabolism and symbiont–host interactions in detail we conducted a proteogenomic analysis of purified bacteria. Unexpectedly, our results reveal a hitherto completely unrecognized feature of the C. orbicularis symbiont's physiology: the symbiont's genome encodes all proteins necessary for biological nitrogen fixation (diazotrophy). Expression of the respective genes under standard ambient conditions was confirmed by proteomics. Nitrogenase activity in the symbiont was also verified by enzyme activity assays. Phylogenetic analysis of the bacterial nitrogenase reductase NifH revealed the symbiont's close relationship to free-living nitrogen-fixing Proteobacteria from the seagrass sediment. The C. orbicularis symbiont, here tentatively named ‘Candidatus Thiodiazotropha endolucinida’, may thus not only sustain the bivalve's carbon demands. C. orbicularis may also benefit from a steady supply of fixed nitrogen from its symbiont—a scenario that is unprecedented in comparable chemoautotrophic symbioses.
Early nucleation events in the polymerization of actin, probed by time-resolved small-angle x-ray scattering
Authors: Oda Toshiro , Aihara Tomoki , Wakabayashi Katsuzo
Published: October 2016

Nucleators generating new F-actin filaments play important roles in cell activities. Detailed information concerning the events involved in nucleation of actin alone in vitro is fundamental to understanding these processes, but such information has been hard to come by. We addressed the early process of salt-induced polymerization of actin using the time-resolved synchrotron small-angle X-ray scattering (SAXS). Actin molecules in low salt solution maintain a monomeric state by an electrostatic repulsive force between molecules. On mixing with salts, the repulsive force was rapidly screened, causing an immediate formation of many of non-polymerizable dimers. SAXS kinetic analysis revealed that tetramerization gives the highest energetic barrier to further polymerization, and the major nucleation is the formation of helical tetramers. Filaments start to grow rapidly with the formation of pentamers. These findings suggest an acceleration mechanism of actin assembly by a variety of nucleators in cells.
Knowledge-guided fuzzy logic modeling to infer cellular signaling networks from proteomic data
Authors: Liu Hui , Zhang Fan , Mishra Shital Kumar , Zhou Shuigeng , Zheng Jie
Published: October 2016

Modeling of signaling pathways is crucial for understanding and predicting cellular responses to drug treatments. However, canonical signaling pathways curated from literature are seldom context-specific and thus can hardly predict cell type-specific response to external perturbations; purely data-driven methods also have drawbacks such as limited biological interpretability. Therefore, hybrid methods that can integrate prior knowledge and real data for network inference are highly desirable. In this paper, we propose a knowledge-guided fuzzy logic network model to infer signaling pathways by exploiting both prior knowledge and time-series data. In particular, the dynamic time warping algorithm is employed to measure the goodness of fit between experimental and predicted data, so that our method can model temporally-ordered experimental observations. We evaluated the proposed method on a synthetic dataset and two real phosphoproteomic datasets. The experimental results demonstrate that our model can uncover drug-induced alterations in signaling pathways in cancer cells. Compared with existing hybrid models, our method can model feedback loops so that the dynamical mechanisms of signaling networks can be uncovered from time-series data. By calibrating generic models of signaling pathways against real data, our method supports precise predictions of context-specific anticancer drug effects, which is an important step towards precision medicine.
Velocimetry of superconducting vortices based on stroboscopic resonances
Authors: Jelić Ž. L. , Milošević M. V. , Silhanek A. V.
Published: October 2016

An experimental determination of the mean vortex velocity in superconductors mostly relies on the measurement of flux-flow resistance with magnetic field, temperature, or driving current. In the present work we introduce a method combining conventional transport measurements and a frequency-tuned flashing pinning potential to obtain reliable estimates of the vortex velocity. The proposed device is characterized using the time-dependent Ginzburg-Landau formalism, where the velocimetry method exploits the resonances in mean vortex dissipation when temporal commensuration occurs between the vortex crossings and the flashing potential. We discuss the sensitivity of the proposed technique on applied current, temperature and heat diffusion, as well as the vortex core deformations during fast motion.
A programmable metasurface with dynamic polarization, scattering and focusing control
Authors: Yang Huanhuan , Cao Xiangyu , Yang Fan , Gao Jun , Xu Shenheng , Li Maokun , Chen Xibi , Zhao Yi , Zheng Yuejun , Li Sijia
Published: October 2016

Diverse electromagnetic (EM) responses of a programmable metasurface with a relatively large scale have been investigated, where multiple functionalities are obtained on the same surface. The unit cell in the metasurface is integrated with one PIN diode, and thus a binary coded phase is realized for a single polarization. Exploiting this anisotropic characteristic, reconfigurable polarization conversion is presented first. Then the dynamic scattering performance for two kinds of sources, i.e. a plane wave and a point source, is carefully elaborated. To tailor the scattering properties, genetic algorithm, normally based on binary coding, is coupled with the scattering pattern analysis to optimize the coding matrix. Besides, inverse fast Fourier transform (IFFT) technique is also introduced to expedite the optimization process of a large metasurface. Since the coding control of each unit cell allows a local and direct modulation of EM wave, various EM phenomena including anomalous reflection, diffusion, beam steering and beam forming are successfully demonstrated by both simulations and experiments. It is worthwhile to point out that a real-time switch among these functionalities is also achieved by using a field-programmable gate array (FPGA). All the results suggest that the proposed programmable metasurface has great potentials for future applications.
Deep-submicron Graphene Field-Effect Transistors with State-of-Art fmax
Authors: Lyu Hongming , Lu Qi , Liu Jinbiao , Wu Xiaoming , Zhang Jinyu , Li Junfeng , Niu Jiebin , Yu Zhiping , Wu Huaqiang , Qian He
Published: October 2016

In order to conquer the short-channel effects that limit conventional ultra-scale semiconductor devices, two-dimensional materials, as an option of ultimate thin channels, receive wide attention. Graphene, in particular, bears great expectations because of its supreme carrier mobility and saturation velocity. However, its main disadvantage, the lack of bandgap, has not been satisfactorily solved. As a result, maximum oscillation frequency (fmax) which indicates transistors’ power amplification ability has been disappointing. Here, we present submicron field-effect transistors with specially designed low-resistance gate and excellent source/drain contact, and therefore significantly improved fmax. The fabrication was assisted by the advanced 8-inch CMOS back-end-of-line technology. A 200-nm-gate-length GFET achieves fT/fmax = 35.4/50 GHz. All GFET samples with gate lengths ranging from 200 nm to 400 nm possess fmax 31–41% higher than fT, closely resembling Si n-channel MOSFETs at comparable technology nodes. These results re-strengthen the promise of graphene field-effect transistors in next generation semiconductor electronics.
M-DNA/Transition Metal Dichalcogenide Hybrid Structure-based Bio-FET sensor with Ultra-high Sensitivity
Authors: Park Hyung-Youl , Dugasani Sreekantha Reddy , Kang Dong-Ho , Yoo Gwangwe , Kim Jinok , Gnapareddy Bramaramba , Jeon Jaeho , Kim Minwoo , Song Young Jae , Lee Sungjoo , Heo Jonggon , Jeon Young Jin , Park Sung Ha , Park Jin-Hong
Published: October 2016

Here, we report a high performance biosensor based on (i) a Cu2+-DNA/MoS2 hybrid structure and (ii) a field effect transistor, which we refer to as a bio-FET, presenting a high sensitivity of 1.7 × 103 A/A. This high sensitivity was achieved by using a DNA nanostructure with copper ions (Cu2+) that induced a positive polarity in the DNA (receptor). This strategy improved the detecting ability for doxorubicin-like molecules (target) that have a negative polarity. Very short distance between the biomolecules and the sensor surface was obtained without using a dielectric layer, contributing to the high sensitivity. We first investigated the effect of doxorubicin on DNA/MoS2 and Cu2+-DNA/MoS2 nanostructures using Raman spectroscopy and Kelvin force probe microscopy. Then, we analyzed the sensing mechanism and performance in DNA/MoS2- and Cu2+-DNA/MoS2-based bio-FETs by electrical measurements (ID-VG at various VD) for various concentrations of doxorubicin. Finally, successful operation of the Cu2+-DNA/MoS2 bio-FET was demonstrated for six cycles (each cycle consisted of four steps: 2 preparation steps, a sensing step, and an erasing step) with different doxorubicin concentrations. The bio-FET showed excellent reusability, which has not been achieved previously in 2D biosensors.
Substitution rate and natural selection in parvovirus B19
Authors: Stamenković Gorana G. , Ćirković Valentina S. , Šiljić Marina M. , Blagojević Jelena V. , Knežević Aleksandra M. , Joksić Ivana D. , Stanojević Maja P.
Published: October 2016

The aim of this study was to estimate substitution rate and imprints of natural selection on parvovirus B19 genotype 1. Studied datasets included 137 near complete coding B19 genomes (positions 665 to 4851) for phylogenetic and substitution rate analysis and 146 and 214 partial genomes for selection analyses in open reading frames ORF1 and ORF2, respectively, collected 1973–2012 and including 9 newly sequenced isolates from Serbia. Phylogenetic clustering assigned majority of studied isolates to G1A. Nucleotide substitution rate for total coding DNA was 1.03 (0.6–1.27) x 10−4 substitutions/site/year, with higher values for analyzed genome partitions. In spite of the highest evolutionary rate, VP2 codons were found to be under purifying selection with rare episodic positive selection, whereas codons under diversifying selection were found in the unique part of VP1, known to contain B19 immune epitopes important in persistent infection. Analyses of overlapping gene regions identified nucleotide positions under opposite selective pressure in different ORFs, suggesting complex evolutionary mechanisms of nucleotide changes in B19 viral genomes.
HDL Cholesterol Level Is Associated with Contrast Induced Acute Kidney Injury in Chronic Kidney Disease Patients Undergoing PCI
Authors: Park Hoon Suk , Kim Chan Joon , Hwang Byung-Hee , Kim Tae-Hoon , Koh Yoon Seok , Park Hun-Jun , Her Sung-Ho , Jang Sung Won , Park Chul-Soo , Lee Jong Min , Kim Hee-Yeol , Jeon Doo Soo , Kim Pum-Joon , Yoo Ki-Dong , Chang Kiyuk , Jin Dong Chan , Seung Ki-Bae
Published: October 2016

Chronic kidney disease (CKD) is a significant risk factor for contrast induced acute kidney injury (CI-AKI) after percutaneous coronary intervention (PCI). This study included 1592 CKD patients extracted from a prospective multicenter, all comer-based registry of patients undergoing PCI. In multivariate logistic analysis for CI-AKI development, a significant linear trend was observed between the quartiles of HDL-C (quartile 1 vs. 2: odds ratio [OR], 0.716; 95% confidence interval [CI], 0.421–1.219; quartile 1 vs. 3: OR, 0.534; 95% CI, 0.301–0.947; quartile 1 vs. 4: OR, 0.173; 95% CI, 0.079–0.377; P for trend < 0.001). HDL-C quartiles were also negatively correlated with the incidence of CI-AKI; 19.0%, 12.1%, 8.7%, and 3.7% for quartile 1(Q1) (<34 mg/dL), Q2 (34–40 mg/dL), Q3 (40–48 mg/dL), and Q4 (>48 mg/dL) respectively (P < 0.001 overall and for the trend). Multivariate Cox regression analysis for the long term mortality, the highest HDL-C quartile was associated with decreased mortality compared with the lowest HDL-C quartile (hazard ratio [HR] 0.516, 95% CI, 0.320–0.832, P = 0.007). Our study suggests more intensive strategies should be considered for preventing CI-AKI in CKD patients with low serum HDL-C level who is planned for PCI.
Male food defence as a by-product of intersexual cooperation in a non-human primate
Authors: Arseneau-Robar T. Jean M. , Müller Eliane , Taucher Anouk L. , van Schaik Carel P. , Willems Erik P.
Published: October 2016

Males in a number of group-living species fight in intergroup conflicts to defend access to food resources, a seemingly paradoxical behaviour, given that this resource does not usually limit male fitness directly. We investigated the mechanism(s) driving apparent male food defence in wild vervet monkeys (Chlorocebus aethiops pygerythrus) by testing the effect that female resource access, and female audience size and activity had on the response of focal males during simulated intergroup encounters. Males do not appear to defend food to increase the reproductive success of female group members because their response was not influenced by the presence of provisioning boxes that only females could access. Female audience size was also unimportant, suggesting males do not participate in intergroup encounters to advertise their quality to potential mates. However, focal males almost always followed/supported female group members who initiated an approach towards simulated intruders, supporting that male participation largely functions to gain status as a cooperative group member, and that apparent male food defence in this species arises as a by-product of intersexual cooperation. Our study highlights that considering audience composition and activity can reveal the presence of social incentives and illuminate the evolutionary mechanism(s) promoting joint action in intergroup aggression.
Transstadial Transmission and Long-term Association of Crimean-Congo Hemorrhagic Fever Virus in Ticks Shapes Genome Plasticity
Authors: Xia Han , Beck Andrew S. , Gargili Aysen , Forrester Naomi , Barrett Alan D. T. , Bente Dennis A.
Published: October 2016

The trade-off hypothesis, the current paradigm of arbovirus evolution, proposes that cycling between vertebrate and invertebrate hosts presents significant constraints on genetic change of arboviruses. Studying these constraints in mosquito-borne viruses has led to a new understanding of epizootics. The trade-off hypothesis is assumed to be applicable to tick-borne viruses too, although studies are lacking. Tick-borne Crimean-Congo hemorrhagic fever virus (CCHFV), a member of the family Bunyaviridae, is a major cause of severe human disease worldwide and shows an extraordinary amount of genetic diversity compared to other arboviruses, which has been linked to increased virulence and emergence in new environments. Using a transmission model for CCHFV, utilizing the main vector tick species and mice plus next generation sequencing, we detected a substantial number of consensus-level mutations in CCHFV recovered from ticks after only a single transstadial transmission, whereas none were detected in CCHFV obtained from the mammalian host. Furthermore, greater viral intra-host diversity was detected in the tick compared to the vertebrate host. Long-term association of CCHFV with its tick host for 1 year demonstrated mutations in the viral genome become fixed over time. These findings suggest that the trade-off hypothesis may not be accurate for all arboviruses.
Different responses of rhizosphere and non-rhizosphere soil microbial communities to consecutive Piper nigrum L. monoculture
Authors: Li Zhigang , Zu Chao , Wang Can , Yang Jianfeng , Yu Huan , Wu Huasong
Published: October 2016

Soil microorganisms have important influences on plant growth and health. In this study, four black pepper fields consecutively monocultured for 12, 18, 28 and 38 years were selected for investigating the effect of planting age on rhizosphere and non-rhizosphere soil microbial communities and soil physicochemical properties. The results revealed that the relative abundance of the dominant bacterial phyla in rhizosphere soil increased considerably with long-term consecutive monoculture but decreased in non-rhizosphere soil with a significant decline in Firmicutes. For fungi, an increasing trend over time was observed in both rhizosphere and non-rhizosphere soils, with the abundance of the pathogenic fungi Fusarium increasing significantly accompanied by a decrease in the bacteria Pseudomonas and Bacillus that is beneficial for black pepper. Consecutive monoculture, especially for 38 years, considerably decreased soil microbial diversity. Additionally, the rhizosphere soil pH and organic matter and available K contents decreased with increasing planting duration, though available N and P increased. All soil nutrient contents and microbial diversity indices were higher in rhizosphere soil compared to non-rhizosphere soil. The results suggest that long-term consecutive monoculture leads to variations in soil microbial community composition and physicochemical properties in both rhizosphere and non-rhizosphere soils, thus inhibiting the black pepper growth.
Comparison of incubation period distribution of human infections with MERS-CoV in South Korea and Saudi Arabia
Authors: Virlogeux Victor , Fang Vicky J. , Park Minah , Wu Joseph T. , Cowling Benjamin J.
Published: October 2016

The incubation period is an important epidemiologic distribution, it is often incorporated in case definitions, used to determine appropriate quarantine periods, and is an input to mathematical modeling studies. Middle East Respiratory Syndrome coronavirus (MERS) is an emerging infectious disease in the Arabian Peninsula. There was a large outbreak of MERS in South Korea in 2015. We examined the incubation period distribution of MERS coronavirus infection for cases in South Korea and in Saudi Arabia. Using parametric and nonparametric methods, we estimated a mean incubation period of 6.9 days (95% credibility interval: 6.3–7.5) for cases in South Korea and 5.0 days (95% credibility interval: 4.0–6.6) among cases in Saudi Arabia. In a log-linear regression model, the mean incubation period was 1.42 times longer (95% credibility interval: 1.18–1.71) among cases in South Korea compared to Saudi Arabia. The variation that we identified in the incubation period distribution between locations could be associated with differences in ascertainment or reporting of exposure dates and illness onset dates, differences in the source or mode of infection, or environmental differences.
Direct observation of photocarrier electron dynamics in C60 films on graphite by time-resolved two-photon photoemission
Authors: Shibuta Masahiro , Yamamoto Kazuo , Ohta Tsutomu , Nakaya Masato , Eguchi Toyoaki , Nakajima Atsushi
Published: October 2016

Time-resolved two-photon photoemission (TR-2PPE) spectroscopy is employed to probe the electronic states of a C60 fullerene film formed on highly oriented pyrolytic graphite (HOPG), acting as a model two-dimensional (2D) material for multi-layered graphene. Owing to the in-plane sp2-hybridized nature of the HOPG, the TR-2PPE spectra reveal the energetics and dynamics of photocarriers in the C60 film: after hot excitons are nascently formed in C60 via intramolecular excitation by a pump photon, they dissociate into photocarriers of free electrons and the corresponding holes, and the electrons are subsequently detected by a probe photon as photoelectrons. The decay rate of photocarriers from the C60 film into the HOPG is evaluated to be 1.31 × 1012 s−1, suggesting a weak van der Waals interaction at the interface, where the photocarriers tentatively occupy the lowest unoccupied molecular orbital (LUMO) of C60. The photocarrier electron dynamics following the hot exciton dissociation in the organic thin films has not been realized for any metallic substrates exhibiting strong interactions with the overlayer. Furthermore, the thickness dependence of the electron lifetime in the LUMO reveals that the electron hopping rate in C60 layers is 3.3 ± 1.2 × 1013 s−1.
Basal Tumor Cell Isolation and Patient-Derived Xenograft Engraftment Identify High-Risk Clinical Bladder Cancers
Authors: Skowron K. B. , Pitroda S. P. , Namm J. P. , Balogun O. , Beckett M. A. , Zenner M. L. , Fayanju O. , Huang X. , Fernandez C. , Zheng W. , Qiao G. , Chin R. , Kron S. J. , Khodarev N. N. , Posner M. C. , Steinberg G. D. , Weichselbaum R. R.
Published: October 2016

Strategies to identify tumors at highest risk for treatment failure are currently under investigation for patients with bladder cancer. We demonstrate that flow cytometric detection of poorly differentiated basal tumor cells (BTCs), as defined by the co-expression of CD90, CD44 and CD49f, directly from patients with early stage tumors (T1-T2 and N0) and patient-derived xenograft (PDX) engraftment in locally advanced tumors (T3-T4 or N+) predict poor prognosis in patients with bladder cancer. Comparative transcriptomic analysis of bladder tumor cells isolated from PDXs indicates unique patterns of gene expression during bladder tumor cell differentiation. We found cell division cycle 25C (CDC25C) overexpression in poorly differentiated BTCs and determined that CDC25C expression predicts adverse survival independent of standard clinical and pathologic features in bladder cancer patients. Taken together, our findings support the utility of BTCs and bladder cancer PDX models in the discovery of novel molecular targets and predictive biomarkers for personalizing oncology care for patients.
Fucoidan inhibits CCL22 production through NF-κB pathway in M2 macrophages: a potential therapeutic strategy for cancer
Authors: Sun Jia , Sun Jintang , Song Bingfeng , Zhang Lin , Shao Qianqian , Liu Yanguo , Yuan Daoying , Zhang Yun , Qu Xun
Published: October 2016

In tumor microenvironment, macrophages as a polarized M2 population promote tumor progression via releasing multiple cytokines and chemokines. A brown seaweed fucose-rich polysaccharide, fucoidan has antitumor activity and immune modulation through affecting tumor cells and lymphocytes. Here, we focused on the effect of fucoidan on macrophages especially M2 subtype. Our results demonstrated that fucoidan down-regulated partial cytokines and chemokines, especially a M2-type chemokine CCL22. Furthermore, fucoidan inhibited tumor cells migration and CD4+ T lymphocytes, especially Treg cells, recruitment induced by M2 macrophages conditioned medium through suppression of CCL22. Mechanismly, fucoidan inhibited CCL22 via suppressing p65-NF-κB phosphorylation and nuclear translocation. In addition, p38-MAPK and PI3K-AKT also affected the expression of CCL22 through differential modulation of NF-κB transcriptional activity. Taken together, we reveal an interesting result that fucoidan can inhibit tumor cell migration and lymphocytes recruitment by suppressing CCL22 in M2 macrophages via NF-κB-dependent transcription, which may be a novel and promising mechanism for tumor immunotherapy.
Gentamicin removal in submerged fermentation using the novel fungal strain Aspergillus terreus FZC3
Authors: Liu Yuanwang , Chang Huiqing , Li Zhaojun , Zhang Cheng , Feng Yao , Cheng Dengmiao
Published: October 2016

Social concern and awareness of the potential risk posed by environmental residues of antibiotics such as gentamicin in the development of antibiotic resistance genes have increased. The present study used laboratory-scale experiments to develop methods for gentamicin removal from the environment. A fungus, strain FZC3, which could remove gentamicin in submerged fermentation, was isolated from solid waste and sewage water from a gentamicin production factory. The fungus was identified as Aspergillus terreus by sequencing the PCR-amplified ITS fragments of its rRNA-coding genes and by its morphology. The gentamicin removal efficiency exceeded 95% by day 7 under optimized culture conditions. The results showed that both biosorption and biodegradation were involved. We speculated that Aspergillus terreus FZC3 absorbed gentamicin and subsequently degraded it. We also found that Aspergillus terreus FZC3 survived and maintained a high bioremediation efficiency over a wide pH range, indicating its potential for future use in the large-scale bioremediation of gentamicin.