bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparison of total scattering data from various sources: the case of a nanometric spinel
Authors: Confalonieri Giorgia , Dapiaggi Monica , Sommariva Marco , Gateshki Milen , Fitch Andy N. , Bernasconi Andrea
Published: April 2015

Total scattering data of nanocrystalline gahnite (ZnAl2O4, 2–3 nm) have been collected with three of the most commonly used instruments: (i) ID31 high-resolution diffractometer at the European Synchrotron Radiation Facility (ESRF) (Qmax = 22 Å−1); (ii) ID11 high-energy beamline at the ESRF (Qmax = 26.6 Å−1); and (iii) Empyrean laboratory diffractometer by PANalytical with molybdenum anode X-ray tube (Qmax = 17.1 Å−1). Pair distribution functions (PDFs) for each instrument data-set have been obtained, changing some of the parameters, by PDFgetX3 software, with the aim of testing the software in the treatment of different total scattering data. The material under analysis has been chosen for its nanometric (and possibly disordered) nature, to give rise to a challenge for all the diffractometers involved. None of the latter should have a clear advantage. The PDF and F(Q) functions have been visually compared, and then the three PDF sets have been used for refinements by means of PDFgui suite. All the refinements have been made exactly in the same way for the sake of a fair comparison. Small differences could be observed in the experimental PDFs and the derived results, but none of them seemed to be significant.
New Legal Realism, Empiricism, and Scientism: The Relative Objectivity of Law and Social Science
Authors: LANG ANDREW
Published: April 2015

In this article, I suggest that one of the central characteristics of New Legal Realism is the productive tension between empiricist and pragmatist theories of knowledge which lies at its core. On one side, new realist work in its empiricist posture seeks to use empirical knowledge of the world as the basis on which to design, interpret, apply, and criticize the law. On the other, in its pragmatist moments, it explicitly draws attention to the social and political contingency of any claims to empirical knowledge of the world, including its own. As a consequence, it is distinctive of much scholarship in the New Legal Realist vein that it continually enacts creative syntheses of different philosophies of truth in an attempt to be, in Shaffer's words, ‘positivist . . . interpretivist, and legal realist all at once’. The first part of this article draws on existing historical accounts of legal realism briefly to trace the problematic and ambiguous place of scientism in the legal realist tradition. Then, in the second and more important part of the article, I argue that the ambivalence of the legal realists’ vision has left us, in certain contexts, with a complicated form of mixed legal-scientific governance which has proved remarkably and surprisingly resilient in the face of late twentieth century critiques of scientific objectivity. This may be one of the most enduring legacies of the ‘old’ legal realists for those today who work in the New Legal Realist vein.
Effect of heifer-raising practices onE. coliantimicrobial resistance andSalmonellaprevalence in heifer raisers
Authors: PEREIRA R. V. , SILER J. D. , CUMMINGS K. J. , DAVIS M. A. , WARNICK L. D.
Published: April 2015

Although cattle movement and commingling play an important role in the inter-herd transmission of pathogens, little is known about the effect of commingling of heifers at raising operations. The objective of this study was to compare the resistance ofE. coliand prevalence ofSalmonellafrom pooled faecal pats of heifers raised off-farm at multi-source raisers (MULTI) that raised heifers from at least two farms compared with on-farm raisers (HOME), with heifers from only that farm. MULTI faecal pat samples were collected from pens with animals that had arrived at the farm within the previous 2 months (AP) and from animals that would be departing the heifer raiser in 2–3 months (DP). Corresponding age sampling was conducted at HOME raisers. Odds of ampicillin resistance were 3·0 times greater inE. colicollected from MULTI compared to HOME raisers.E. colifrom AP pens had significantly (P< 0·05) higher odds of resistance to ampicillin, neomycin, streptomycin, and tetracycline compared to DP pens.Salmonellarecovery was not significantly different between heifer-raising systems (P= 0·3). Heifer-raising system did not have a major overall impact on selection of resistantE. coli, which was strongly affected by the age of the animals sampled.
Landscape Setting as Medium of Communication at Chavín de Huántar, Peru
Authors: Contreras Daniel A.
Published: April 2015

The Central Andean ceremonial centre of Chavín de Huántar is situated in a dramatic, mountainous and dynamic environment high on the eastern slope of the Peruvian Andes, yet the site's landscape setting has remained in the shadow of its monumental architecture, complex lithic art and highly elaborated material culture. Nevertheless, that dynamic landscape setting was an integral part of the site's significance as a ceremonial centre and may be read as evidence of the capacity, worldview and message of the site's builders. First, Chavín's setting is evidence of capacity, demonstrating the considerable degree of labour mobilization and organization, as well as expertise, implied by the site's modified landscape. Second, Chavín's landscape, considered in its Central Andean context, provides evidence of worldview, demonstrating that landscape setting was a medium of interest for Chavín's designers. Third, the modified landscape provides evidence of message, allowing exploration of what Chavín's designers were trying to communicate, and to whom. Focusing on these three aspects in reading Chavín's landscape suggests that landscape setting was a vital aspect of Central Andean Middle and Late Formative Period (1000–500 bce) ceremonial centres and argues that emergent elites actively exploited landscape setting as a communicative medium and forum for dissemination of ideology, deliberately communicating to multiple audiences.
Towards a Theory of Landscape Iconoclasm
Authors: González Zarandona José Antonio
Published: April 2015

‘Landscape: the land escapes (1) when we try to seize it with our maps, satellites, geographic information systems and Street Views, land is what evades our surveillance (2) land is the terrain of escape.’ (Cubitt 2012)

‘Since the middle of the twentieth century, the claim that something is art does not imply what it might have meant at the end of the nineteenth century, when it was made out to be a hallmark of European high and bourgeois society.’ (Heyd 2012, 287)

The destruction of Indigenous rock art sites in the Pilbara district in Western Australia has become a natural sight within the mining landscape of the area. Whilst much of the destruction is explained as acts of vandalism and as a result of the industrial activities that are propelling the Australian economy, I claim that a new theory of iconoclasm is needed to explain fully this disastrous example of heritage conservation. Henceforth, in order to explain the destruction of the Murujuga/Burrup Peninsula petroglyphs, the largest archaeological site in the world, this paper develops the theory of landscape iconoclasm. This theory states that the destruction of Indigenous landscapes can be compared to the destruction of religious images, by analysing the inherent symbolic functions of iconoclasm, together with those of heritage, the better to elucidate the state of affairs in the Murujuga/Burrup Peninsula. Furthermore, by drawing from Aboriginal mythology and art-historical and anthropological theories, the theory of landscape iconoclasm is able to explain the destruction of archaeological sites within a framework that falls outside prevalent discourses of heritage.
Infant Death and the Archaeology of Grief
Authors: Cannon Aubrey , Cook Katherine
Published: April 2015

To build a theoretical and empirical foundation for interpretation of the absence, segregation or simplicity of infant burials in archaeological contexts, we review social theories of emotion, inter-disciplinary views on the relationship between mortality rates and emotional investment, and archaeological interpretations of infant burial patterns. The results indicate a lack of explicit theory in most archaeological accounts and a general lack of consideration for individual variation and the process of change in mortuary practice. We outline the tenets of Bowlby's attachment theory and Stroebe and Schut's dual process model of bereavement to account theoretically for pattern, variation and change in modes of infant burial. We illustrate the value of this psychology-based perspective in an analysis of Victorian gravestone commemorations of infant burials in 35 villages in rural south Cambridgeshire, England, where individual and class-based variation, relative to falling mortality rates, is best explained as a function of coping strategies and contextually based social constraint on the overt representation of grief and loss.
Advances from neuroimaging studies in eating disorders
Authors: Frank Guido K. W.
Published: April 2015

Over the past decade, brain imaging has helped to better define eating disorder–related brain circuitry. Brain research on gray matter (GM) and white matter (WM) volumes had been inconsistent, possibly due to the effects of acute starvation, exercise, medication, and comorbidity, but newer studies have controlled for such effects. Those studies suggest larger left medial orbitofrontal gyrus rectus volume in ill adult and adolescent anorexia nervosa after recovery from anorexia nervosa, and in adult bulimia nervosa. The orbitofrontal cortex is important in terminating food intake, and altered function could contribute to self-starvation. The right insula, which processes taste but also interoception, was enlarged in ill adult and adolescent anorexia nervosa, as well as adults recovered from the illness. The fixed perception of being fat in anorexia nervosa could be related to altered insula function. A few studies investigated WM integrity, with the most consistent finding of reduced fornix integrity in anorexia and bulimia nervosa—a limbic pathway that is important in emotion but also food intake regulation. Functional brain imaging using basic sweet taste stimuli in eating disorders during the ill state or after recovery implicated repeatedly reward pathways, including insula and striatum. Brain imaging that targeted dopamine-related brain activity using taste-reward conditioning tasks suggested that this circuitry is hypersensitive in anorexia nervosa, but hyporesponsive in bulimia nervosa and obesity. Those results are in line with basic research and suggest adaptive reward system changes in the human brain in response to extremes of food intake—changes that could interfere with normalization of eating behavior.
Energy and macronutrient intakes in Brazil: results of the first nationwide individual dietary survey
Authors: Souza Rita AG , Yokoo Edna M , Sichieri Rosely , Pereira Rosangela A
Published: April 2015

Objective

To characterize energy and macronutrient intakes in Brazil and to describe the top food items contributing to energy and macronutrient intakes.

Design

Two non-consecutive 24 h dietary records were collected and energy and macronutrient data were adjusted for usual intake distribution. Descriptive statistics and ANOVA with the Bonferroni post hoc test were analysed using SAS version 9·1. Means and standard deviations were estimated for sex, age and income strata.

Setting

Nationwide cross-sectional survey, 2008–2009.

Subjects

Nationally representative sample of individuals ≥10 years old (n32 749), excluding pregnant and lactating women (n 1254).

Results

The average energy intake was 7958 kJ/d (1902 kcal/d) and mean energy density was 6·82 kJ/g (1·63 kcal/g). Added sugar represented 13 % of total energy intake and animal protein represented 10 %. The mean contribution of total fat to energy intake was 27 %, while the mean saturated fat contribution was 9 %. Compared with the lowest quartile of income, individuals in the highest income quartile had greater mean intakes of energy, added sugar, alcohol, animal protein, total fat, saturated fat, monounsaturated fat and trans fat. Rice, beans, beef, bread and coffee were among the top five foods contributing most to the intakes of energy, carbohydrates, protein, fat and fibre.

Conclusions

In general, Brazilians’ dietary intake is compatible with a high risk of obesity and non-communicable chronic diseases, being characterized by high intakes of added sugar and saturated fat. Income may be a major determinant of diet nutritional characteristics.
IMPROPER INTERSECTIONS OF KUDLA–RAPOPORT DIVISORS AND EISENSTEIN SERIES
Authors: Sankaran Siddarth
Published: April 2015

We consider a certain family of Kudla–Rapoport cycles on an integral model of a Shimura variety attached to a unitary group of signature (1, 1), and prove that the arithmetic degrees of these cycles are Fourier coefficients of the central derivative of an Eisenstein series of genus 2. The integral model in question parameterizes abelian surfaces equipped with a non-principal polarization and an action of an imaginary quadratic number ring, and in this setting the cycles are degenerate: they may contain components of positive dimension. This result can be viewed as confirmation, in the degenerate setting and for dimension 2, of conjectures of Kudla and Kudla–Rapoport that predict relations between the intersection numbers of special cycles and the Fourier coefficients of automorphic forms.
LIBERALISM AND HISTORY AFTER THE SECOND WORLD WAR: THE CASE OF JACOB TAUBES
Authors: MARTIN JAMIE
Published: April 2015

Before his death in 1987, Jacob Taubes played an important role in postwar German academic philosophy and religious thought. Best known for his leftist political theology and scholarship on the history of Western eschatology, Taubes's thought was influential on mid-twentieth-century debates in Germany about secularization and modern political theology. Outside his relationship with Carl Schmitt, however, Taubes has received little attention in histories of postwar European thought, and few attempts have been made to understand his idiosyncratic work on its own terms. This essay presents new contexts for understanding Taubes and his political-theological critique of the ideological dominance of liberalism in postwar Germany. By analyzing Taubes's thought through the lens of his intellectual quarrel with Hans Blumenberg over secularization, it reassesses his contributions to postwar debates about the political temporality appropriate to a secular and non-utopian social theory, and the consequences of these debates for broader critiques of political liberalism.
BETWEEN ARISTOTLE AND LUCRETIUS: DISCOURSES OF NATURE AND ROUSSEAU’SDISCOURS SUR L’INEGALITE
Authors: KONOVAL BRANDON
Published: April 2015

In theDiscourse on Inequality, Rousseau presents himself as declaiming in “the Lyceum of Athens” but in the presence of Plato and Xenocrates. Why should Rousseau's arguments be heard in such precincts, and why, moreover, is Aristotle missing from them? Rousseau's response to the topic proposed by the Dijon Academy, on which the Discourse was based, may be correspondingly interpreted as a response to Aristotle's philosophy of nature and of the ways in which that philosophy informs thePoliticsin particular. The critique Rousseau thereby offers of an Aristotelian discourse of nature and society invokes a similar challenge once presented by ancient Epicureanism, and reflects the extraordinary revival of interest in Lucretius’On the Nature of Things, a poem that became the focus of intense critical scrutiny during the Enlightenment. We may therefore understand why theDiscourse on Inequalitywas read as an “Epicurean” text by certain contemporaries, and recognize particular critical objectives served by Epicurean philosophical resources that were further deployed in works like theSocial ContractandLetters Written from the Mountain, reflecting Rousseau's engagement with Genevan reform politics of the 1750s and 1760s.
On Hodgson on property rights
Authors: ALLEN DOUGLAS W.
Published: April 2015

Geoffrey Hodgson has a number of criticisms regarding the ‘economic approach to property rights’ that has been mostly championed by members of the UCLA and Washington departments of economics during the 1960s–1990s. In this short note I address these comments and point out that most are simply a matter of nomenclature. When there are disagreements they stem from Hodgson’s failure to account for positive transaction costs and this literature’s emphasis on operational explanations of organization.
Design of magnetic-resonant wireless power transfer links realized with two coils: comparison of solutions
Authors: Costanzo Alessandra , Dionigi Marco , Mastri Franco , Mongiardo Mauro , Russer Johannes A. , Russer Peter
Published: April 2015

A novel approach for the rigorous design of magnetic resonant wireless power transfer links is introduced. We show how, starting from two coupled inductors and making use of general network theory, it is possible to derive analytic rules for designing the source and load terminations which provide the maximum power transfer efficiency or maximize the received power. We also show that, by adding suitable matching networks to two coupled inductors we can realize a wireless link acting as a 1:n transformer and having the all required tunable reactive elements on the primary side. The proposed topology greatly simplifies the design, since only an inductive coil and a fixed capacitance are required on the secondary side; in addition, when tuning is required due to coils misalignment or to link distance variation, it can be attained by acting on the transmitter side without the need for a feedback communication through the link. Moreover, when the load resistance is designed for maximum output power, its value is fixed and does not depend on the coupling. A numerical and experimental verification of the proposed approach is also presented.
What Will Become of Sweet Briar's Atmospheric Research Station?
Authors: Wendel JoAnna
Published: April 2015

In the middle of the college's financial fight stands an atmospheric research tower with an uncertain future.
Macrophage- and RIP3-dependent inflammasome activation exacerbates retinal detachment-induced photoreceptor cell death
Authors: Kataoka K , Matsumoto H , Kaneko H , Notomi S , Takeuchi K , Sweigard J H , Atik A , Murakami Y , Connor K M , Terasaki H , Miller J W , Vavvas D G
Published: April 2015

Detachment of photoreceptors from the retinal pigment epithelium is seen in various retinal disorders, resulting in photoreceptor death and subsequent vision loss. Cell death results in the release of endogenous molecules that activate molecular platforms containing caspase-1, termed inflammasomes. Inflammasome activation in retinal diseases has been reported in some cases to be protective and in others to be detrimental, causing neuronal cell death. Moreover, the cellular source of inflammasomes in retinal disorders is not clear. Here, we demonstrate that patients with photoreceptor injury by retinal detachment (RD) have increased levels of cleaved IL-1β, an end product of inflammasome activation. In an animal model of RD, photoreceptor cell death led to activation of endogenous inflammasomes, and this activation was diminished by Rip3 deletion. The major source of Il1b expression was found to be infiltrating macrophages in the subretinal space, rather than dying photoreceptors. Inflammasome inhibition attenuated photoreceptor death after RD. Our data implicate the infiltrating macrophages as a source of damaging inflammasomes after photoreceptor detachment in a RIP3-dependent manner and suggest a novel therapeutic target for treatment of retinal diseases.
Generation of neutral and high-density electron–positron pair plasmas in the laboratory
Authors: Sarri G. , Poder K. , Cole J. M. , Schumaker W. , Di Piazza A. , Reville B. , Dzelzainis T. , Doria D. , Gizzi L. A. , Grittani G. , Kar S. , Keitel C. H. , Krushelnick K. , Kuschel S. , Mangles S. P. D. , Najmudin Z. , Shukla N. , Silva L. O. , Symes D. , Thomas A. G. R. , Vargas M. , Vieira J. , Zepf M.
Published: April 2015

Electron–positron pair plasmas represent a unique state of matter, whereby there exists an intrinsic and complete symmetry between negatively charged (matter) and positively charged (antimatter) particles. These plasmas play a fundamental role in the dynamics of ultra-massive astrophysical objects and are believed to be associated with the emission of ultra-bright gamma-ray bursts. Despite extensive theoretical modelling, our knowledge of this state of matter is still speculative, owing to the extreme difficulty in recreating neutral matter–antimatter plasmas in the laboratory. Here we show that, by using a compact laser-driven setup, ion-free electron–positron plasmas with unique characteristics can be produced. Their charge neutrality (same amount of matter and antimatter), high-density and small divergence finally open up the possibility of studying electron–positron plasmas in controlled laboratory experiments.
C-Nap1 mutation affects centriole cohesion and is associated with a Seckel-like syndrome in cattle
Authors: Floriot Sandrine , Vesque Christine , Rodriguez Sabrina , Bourgain-Guglielmetti Florence , Karaiskou Anthi , Gautier Mathieu , Duchesne Amandine , Barbey Sarah , Fritz Sébastien , Vasilescu Alexandre , Bertaud Maud , Moudjou Mohammed , Halliez Sophie , Cormier-Daire Valérie , E.L. Hokayem Joyce , Nigg Erich A. , Manciaux Luc , Guatteo Raphaël , Cesbron Nora , Toutirais Geraldine , Eggen André , Schneider-Maunoury Sylvie , Boichard Didier , Sobczak-Thépot Joelle , Schibler Laurent
Published: April 2015

Caprine-like Generalized Hypoplasia Syndrome (SHGC) is an autosomal-recessive disorder in Montbéliarde cattle. Affected animals present a wide range of clinical features that include the following: delayed development with low birth weight, hind limb muscular hypoplasia, caprine-like thin head and partial coat depigmentation. Here we show that SHGC is caused by a truncating mutation in the CEP250 gene that encodes the centrosomal protein C-Nap1. This mutation results in centrosome splitting, which neither affects centriole ultrastructure and duplication in dividing cells nor centriole function in cilium assembly and mitotic spindle organization. Loss of C-Nap1-mediated centriole cohesion leads to an altered cell migration phenotype. This discovery extends the range of loci that constitute the spectrum of autosomal primary recessive microcephaly (MCPH) and Seckel-like syndromes.
Direct synthesis of imino-C-nucleoside analogues and other biologically active iminosugars
Authors: Bergeron-Brlek Milan , Meanwell Michael , Britton Robert
Published: April 2015

Iminosugars have attracted increasing attention as chemical probes, chaperones and leads for drug discovery. Despite several clinical successes, their de novo synthesis remains a significant challenge that also limits their integration with modern high-throughput screening technologies. Herein, we describe a unique synthetic strategy that converts a wide range of acetaldehyde derivatives into iminosugars and imino-C-nucleoside analogues in two or three straightforward transformations. We also show that this strategy can be readily applied to the rapid production of indolizidine and pyrrolizidine iminosugars. The high levels of enantio- and diastereoselectivity, excellent overall yields, convenience and broad substrate scope make this an appealing process for diversity-oriented synthesis, and should enable drug discovery efforts.
Superlattices assembled through shape-induced directional binding
Authors: Lu Fang , Yager Kevin G. , Zhang Yugang , Xin Huolin , Gang Oleg
Published: April 2015

Organization of spherical particles into lattices is typically driven by packing considerations. Although the addition of directional binding can significantly broaden structural diversity, nanoscale implementation remains challenging. Here we investigate the assembly of clusters and lattices in which anisotropic polyhedral blocks coordinate isotropic spherical nanoparticles via shape-induced directional interactions facilitated by DNA recognition. We show that these polyhedral blocks—cubes and octahedrons—when mixed with spheres, promote the assembly of clusters with architecture determined by polyhedron symmetry. Moreover, three-dimensional binary superlattices are formed when DNA shells accommodate the shape disparity between nanoparticle interfaces. The crystallographic symmetry of assembled lattices is determined by the spatial symmetry of the block’s facets, while structural order depends on DNA-tuned interactions and particle size ratio. The presented lattice assembly strategy, exploiting shape for defining the global structure and DNA-mediation locally, opens novel possibilities for by-design fabrication of binary lattices.
Genome-wide meta-analysis identifies multiple novel associations and ethnic heterogeneity of psoriasis susceptibility
Authors: Yin Xianyong , Low Hui Qi , Wang Ling , Li Yonghong , Ellinghaus Eva , Han Jiali , Estivill Xavier , Sun Liangdan , Zuo Xianbo , Shen Changbing , Zhu Caihong , Zhang Anping , Sanchez Fabio , Padyukov Leonid , Catanese Joseph J. , Krueger Gerald G. , Duffin Kristina Callis , Mucha Sören , Weichenthal Michael , Weidinger Stephan , Lieb Wolfgang , Foo Jia Nee , Li Yi , Sim Karseng , Liany Herty , Irwan Ishak , Teo Yikying , Theng Colin T. S. , Gupta Rashmi , Bowcock Anne , De Jager Philip L. , Qureshi Abrar A. , de Bakker Paul I. W. , Seielstad Mark , Liao Wilson , Ståhle Mona , Franke Andre , Zhang Xuejun , Liu Jianjun
Published: April 2015

Psoriasis is a common inflammatory skin disease with complex genetics and different degrees of prevalence across ethnic populations. Here we present the largest trans-ethnic genome-wide meta-analysis (GWMA) of psoriasis in 15,369 cases and 19,517 controls of Caucasian and Chinese ancestries. We identify four novel associations at LOC144817, COG6, RUNX1 and TP63, as well as three novel secondary associations within IFIH1 and IL12B. Fine-mapping analysis of MHC region demonstrates an important role for all three HLA class I genes and a complex and heterogeneous pattern of HLA associations between Caucasian and Chinese populations. Further, trans-ethnic comparison suggests population-specific effect or allelic heterogeneity for 11 loci. These population-specific effects contribute significantly to the ethnic diversity of psoriasis prevalence. This study not only provides novel biological insights into the involvement of immune and keratinocyte development mechanism, but also demonstrates a complex and heterogeneous genetic architecture of psoriasis susceptibility across ethnic populations.
A dominant role for the methyl-CpG-binding protein Mbd2 in controlling Th2 induction by dendritic cells
Authors: Cook Peter C. , Owen Heather , Deaton Aimée M. , Borger Jessica G. , Brown Sheila L. , Clouaire Thomas , Jones Gareth-Rhys , Jones Lucy H. , Lundie Rachel J. , Marley Angela K. , Morrison Vicky L. , Phythian-Adams Alexander T. , Wachter Elisabeth , Webb Lauren M. , Sutherland Tara E. , Thomas Graham D. , Grainger John R. , Selfridge Jim , McKenzie Andrew N. J. , Allen Judith E. , Fagerholm Susanna C. , Maizels Rick M. , Ivens Alasdair C. , Bird Adrian , MacDonald Andrew S.
Published: April 2015

Dendritic cells (DCs) direct CD4+ T-cell differentiation into diverse helper (Th) subsets that are required for protection against varied infections. However, the mechanisms used by DCs to promote Th2 responses, which are important both for immunity to helminth infection and in allergic disease, are currently poorly understood. We demonstrate a key role for the protein methyl-CpG-binding domain-2 (Mbd2), which links DNA methylation to repressive chromatin structure, in regulating expression of a range of genes that are associated with optimal DC activation and function. In the absence of Mbd2, DCs display reduced phenotypic activation and a markedly impaired capacity to initiate Th2 immunity against helminths or allergens. These data identify an epigenetic mechanism that is central to the activation of CD4+ T-cell responses by DCs, particularly in Th2 settings, and reveal methyl-CpG-binding proteins and the genes under their control as possible therapeutic targets for type-2 inflammation.
Optofluidic fabrication for 3D-shaped particles
Authors: Paulsen Kevin S. , Di Carlo Dino , Chung Aram J.
Published: April 2015

Complex three-dimensional (3D)-shaped particles could play unique roles in biotechnology, structural mechanics and self-assembly. Current methods of fabricating 3D-shaped particles such as 3D printing, injection moulding or photolithography are limited because of low-resolution, low-throughput or complicated/expensive procedures. Here, we present a novel method called optofluidic fabrication for the generation of complex 3D-shaped polymer particles based on two coupled processes: inertial flow shaping and ultraviolet (UV) light polymerization. Pillars within fluidic platforms are used to deterministically deform photosensitive precursor fluid streams. The channels are then illuminated with patterned UV light to polymerize the photosensitive fluid, creating particles with multi-scale 3D geometries. The fundamental advantages of optofluidic fabrication include high-resolution, multi-scalability, dynamic tunability, simple operation and great potential for bulk fabrication with full automation. Through different combinations of pillar configurations, flow rates and UV light patterns, an infinite set of 3D-shaped particles is available, and a variety are demonstrated.
100-nm-sized magnetic domain reversal by the magneto-electric effect in self-assembled BiFeO3/CoFe2O4 bilayer films
Authors: Sone Keita , Naganuma Hiroshi , Ito Masaki , Miyazaki Takamichi , Nakajima Takashi , Okamura Soichiro
Published: April 2015

A (001)-epitaxial-BiFeO3/CoFe2O4 bilayer was grown by self-assembly on SrTiO3 (100) substrates by just coating a mixture precursor solution. The thickness ratio of the bilayer could be controlled by adjusting the composition ratio. For example, a BiFeOx:CoFe2Ox = 4:1 (namely Bi4CoFe6Ox) mixture solution could make a total thickness of 110nm divided into 85-nm-thick BiFeO3 and 25-nm-thick CoFe2O4. Self-assembly of the bilayer occurred because the perovskite BiFeO3 better matched the lattice constant (misfit approximately 1%) and crystal symmetry of the perovskite SrTiO3 than the spinel CoFe2O4 (misfit approximately 7%). The magnetic domains of the hard magnet CoFe2O4 were switched by the polarization change of BiFeO3 due to an applied vertical voltage and the switched magnetic domain size was approximately 100nm in diameter. These results suggest that self-assembled BiFeO3/CoFe2O4 bilayers are interesting in voltage driven nonvolatile memory with a low manufacturing cost.
Temperature Dependence of Electric Transport in Few-layer Graphene under Large Charge Doping Induced by Electrochemical Gating
Authors: Gonnelli R. S. , Paolucci F. , Piatti E. , Sharda Kanudha , Sola A. , Tortello M. , Nair Jijeesh R. , Gerbaldi C. , Bruna M. , Borini S.
Published: April 2015

The temperature dependence of electric transport properties of single-layer and few-layer graphene at large charge doping is of great interest both for the study of the scattering processes dominating the conductivity at different temperatures and in view of the theoretically predicted possibility to reach the superconducting state in such extreme conditions. Here we present the results obtained in 3-, 4- and 5-layer graphene devices down to 3.5 K, where a large surface charge density up to about 6.8·1014 cm−2 has been reached by employing a novel polymer electrolyte solution for the electrochemical gating. In contrast with recent results obtained in single-layer graphene, the temperature dependence of the sheet resistance between 20 K and 280 K shows a low-temperature dominance of a T2 component – that can be associated with electron-electron scattering – and, at about 100 K, a crossover to the classic electron-phonon regime. Unexpectedly, this crossover does not show any dependence on the induced charge density, i.e. on the large tuning of the Fermi energy.
Loss of PTPRM Associates with the Pathogenic Development of Colorectal Adenoma-Carcinoma Sequence
Authors: Sudhir Putty-Reddy , Lin Shiu-Ting , Chia-Wen Chien , Yang Shung-Haur , Li Anna Fen-Yau , Lai Rai-Hua , Wang Mei-Jung , Chen Yuan-Tsong , Chen Chian-Feng , Jou Yuh-Shan , Chen Jeou-Yuan
Published: April 2015

Identification and functional analysis of genes from genetically altered chromosomal regions would suggest new molecular targets for cancer diagnosis and treatment. Here we performed a genome-wide analysis of chromosomal copy number alterations (CNAs) in matching sets of colon mucosa-adenoma-carcinoma samples using high-throughput oligonucleotide microarray analysis. In silico analysis of NCBI GEO and TCGA datasets allowed us to uncover the significantly altered genes (p ≤ 0.001) associated with the identified CNAs. We performed quantitative PCR analysis of the genomic and complementary DNA derived from primary mucosa, adenoma and carcinoma samples and confirmed the recurrent loss and down-regulation of PTPRM in colon adenomas and carcinomas. Functional characterization demonstrated that PTPRM negatively regulates cell growth and colony formation, whereas loss of PTPRM promotes oncogenic cell growth. We further showed that, in accordance to Knudson's two-hit hypothesis, inactivation of PTPRM in colon cancer was mainly attributed to loss of heterozygosity and promoter hypermethylation. Taken together, this study demonstrates a putative tumor suppressive role for PTPRM and that genetic and epigenetic alterations of PTPRM may contribute to early step of colorectal tumorigenesis.
A modelling methodology to assess the effect of insect pest control on agro-ecosystems
Authors: Wan Nian-Feng , Ji Xiang-Yun , Jiang Jie-Xian , Li Bo
Published: April 2015

The extensive use of chemical pesticides for pest management in agricultural systems can entail risks to the complex ecosystems consisting of economic, ecological and social subsystems. To analyze the negative and positive effects of external or internal disturbances on complex ecosystems, we proposed an ecological two-sidedness approach which has been applied to the design of pest-controlling strategies for pesticide pollution management. However, catastrophe theory has not been initially applied to this approach. Thus, we used an approach of integrating ecological two-sidedness with a multi-criterion evaluation method of catastrophe theory to analyze the complexity of agro-ecosystems disturbed by the insecticides and screen out the best insect pest-controlling strategy in cabbage production. The results showed that the order of the values of evaluation index (RCC/CP) for three strategies in cabbage production was “applying frequency vibration lamps and environment-friendly insecticides 8 times” (0.80) < “applying trap devices and environment-friendly insecticides 9 times” (0.83) < “applying common insecticides 14 times” (1.08). The treatment “applying frequency vibration lamps and environment-friendly insecticides 8 times” was considered as the best insect pest-controlling strategy in cabbage production in Shanghai, China.
A multi-functional bubble-based microfluidic system
Authors: Khoshmanesh Khashayar , Almansouri Abdullah , Albloushi Hamad , Yi Pyshar , Soffe Rebecca , Kalantar-zadeh Kourosh
Published: April 2015

Recently, the bubble-based systems have offered a new paradigm in microfluidics. Gas bubbles are highly flexible, controllable and barely mix with liquids and thus can be used for the creation of reconfigurable microfluidic systems. In this work, a hydrodynamically actuated bubble-based microfluidic system is introduced. This system enables the precise movement of air bubbles via axillary feeder channels to alter the geometry of the main channel and consequently the flow characteristics of the system. Mixing of neighbouring streams is demonstrated by oscillating the bubble at desired displacements and frequencies. Flow control is achieved by pushing the bubble to partially or fully close the main channel. Patterning of suspended particles is also demonstrated by creating a large bubble along the sidewalls. Rigorous analytical and numerical calculations are presented to describe the operation of the system. The examples presented in this paper highlight the versatility of the developed bubble-based actuator for a variety of applications; thus providing a vision that can be expanded for future highly reconfigurable microfluidics.
Mechanisms of 2-Oxoglutarate-Dependent Oxygenases: The Hydroxylation Paradigm and Beyond
Authors: Bollinger Jr. J. Martin , Chang Wei-chen , Matthews Megan L. , Martinie Ryan J. , Boal Amie K. , Krebs Carsten
Published: April 2015

In humans, Fe(ii)- and 2-oxoglutarate-dependent (Fe/2OG) oxygenases are generally of the dioxygenase subclass and mediate hydroxylation of unactivated aliphatic carbon centres. Plants and microbes also employ Fe/2OG hydroxylases and, through investigations of the microbial enzymes, the mechanism of hydroxylation has been established to proceed via a potent high-spin (S = 2) Fe(iv)–oxo (ferryl) complex, which abstracts a hydrogen atom (H˙) from the substrate. Bacteria have further co-opted this central ferryl intermediate for a remarkable array of divergent reactivities, including olefin epoxidations, aliphatic halogenations, olefin-installing 1,2-dehydrogenations, oxacycle-installing 1,3- and 1,5-dehydrogenations, and a redox-neutral stereoinversion. An understanding of the mechanisms leading to this manifold of transformations, and the means by which the individual enzymes direct them, has potential to guide the design of new chemical catalysts and the development of novel bacterially- or chemo-enzymatically-derived drug compounds. In this chapter, we first summarize our understanding of hydroxylation reactions mediated by Fe/2OG hydroxylases and then review recent advances in the elucidation of two of the ‘alternative’ reactivities (halogenation and stereoinversion). Finally, we discuss the remaining, less well understood dehydrogenation reactions, highlighting possible problems with published mechanistic proposals, presenting alternatives to these published mechanisms, and briefly outlining experiments by which the operant mechanisms might be established.
JmjC Lysine Demethylases
Authors: Cheng Xiaodong , Trievel Raymond C.
Published: April 2015

Among the most fundamental questions in the regulation of gene expression in mammals is how epigenetic methylation patterns of histone lysine residues are established, recognized and erased. This chapter reviews recent studies on, and discusses the resulting biochemical and structural insights into, the Jumonji C (JmjC)-containing lysine demethylases (KDMs), focusing on their biological functions, three-dimensional structures, mechanism and substrate specificities.
The TET/JBP Family of Nucleic Acid Base-Modifying 2-Oxoglutarate and Iron-Dependent Dioxygenases
Authors: Aravind L. , Zhang Dapeng , Iyer Lakshminarayan M.
Published: April 2015

The TET/JBP family of enzymes includes 2-oxoglutarate- and Fe(ii)-dependent dioxygenases that oxidize 5-methylpyrimidines in nucleic acids. They include euglenozoan JBP enzymes that catalyse the first step in the biosynthesis of the hypermodified thymine, base J, and metazoan TET enzymes that generate oxidized 5-methylcytosines (hydroxy-, formyl- and carboxymethylcytosine) in DNA. Recent studies suggest that these modified bases function as epigenetic marks and/or as potential intermediates for DNA demethylation during resetting of epigenetic 5mC marks upon zygote formation and in primordial germ cell development. Studies in mammalian models also point to an important role for these enzymes in haematopoiesis, tumour suppression, cell differentiation and neural behavioural adaptation. The TET/JBP family has undergone extensive gene expansion in fungi, such as mushrooms, in conjunction with a novel class of transposons and might play a role in genomic plasticity and speciation. Certain versions from stramenopiles and chlorophytes are likely to modify RNA and often show fusions to other RNA-modifying enzymatic domains. The ultimate origin of the TET/JBP family lies in bacteriophages where the enzymes are likely to catalyse formation of modified bases with key roles in DNA packaging and evasion of host restriction.
Gibberellin Metabolism
Authors: Hedden Peter , Phillips Andrew L.
Published: April 2015

The gibberellin (GA) plant hormones are diterpenoid carboxylic acids that regulate growth and development throughout the life cycle of flowering plants, but are also present in some species of lower plants, fungi and bacteria. The latter stages of their biosynthesis in flowering plants involve the activities of two main families of 2-oxoglutarate-dependent dioxygenases (ODDs): GA 20-oxidases, which oxidize the C-10 methyl group to the aldehyde and then cleave it to form the C19-GAs, and GA 3-oxidases, which introduce a 3β-hydroxyl group as the final step in the formation of the biologically active hormones. Oxidation on C-2 by other ODD families (GA 2-oxidases) that act on C19-GAs or their C20-GA precursors serves as an inactivation mechanism. A further family of ODDs with a restricted species distribution, the GA 7-oxidases, convert the early precursor GA12-aldehyde to GA12, a reaction that is also catalysed by cytochrome P450 monooxygenases. Members of the ODD gene families are major sites of regulation for GA biosynthesis and catabolism, responding to developmental and environmental signals. The paralogues have distinct but often overlapping expression domains, and differ also in levels of expression and regulation. These enzymes have proved to be useful targets for the introduction of beneficial traits into crop species, while the acylcyclohexanedione inhibitors of the GA 3-oxidases have found important application in agriculture as growth retardants.
Isopenicillin N Synthase
Authors: Rutledge Peter J.
Published: April 2015

Isopenicillin N synthase (IPNS) catalyses the oxidative bicyclization of δ-(l-α-aminoadipoyl)-l-cysteinyl-d-valine (ACV) to form isopenicillin N (IPN), a conversion that is essential in the biosynthesis of penicillin and cephalosporin antibiotics. IPNS uses the full oxidizing potential of molecular oxygen to drive this reaction, forming new C–N and C–S bonds and reducing O2 to two molecules of water. IPNS does not use 2-oxoglutarate (2OG) or any co-substrate other than O2, but has sequence homology along with structural and mechanistic similarities to the 2OG-dependent oxygenase family. The chemically challenging reaction that IPNS catalyses and the central role it plays in antibiotic biosynthesis mean that IPNS has been studied extensively over many years. Crystal structures for the substrate-free enzyme, enzyme–substrate and enzyme–product complexes have all been described, and key intermediates have been trapped chemically and characterized crystallographically as well. This structural information combines with a diverse array of solution phase turnover experiments and spectroscopic studies to provide a detailed picture of IPNS catalysis.
1-Aminocyclopropane-1-Carboxylic Acid Oxidase
Authors: Simaan A. Jalila , Réglier Marius
Published: April 2015

1-Aminocyclopropane carboxylic acid (ACC) oxidase (ACCO) catalyses the final step in ethylene biosynthesis, a key hormone in plant development, stress responses and defence. The substrate, ACC, is converted into ethylene in the presence of dioxygen and a reductant. ACCO also requires carbon dioxide (or bicarbonate) for activity. The crystal structure of ACCO from Petunia hybrida reveals a core folded into a distorted jelly-roll motif (double-stranded β-helix fold) and an active site composed of a single Fe(ii) coordinated by the side chains of two histidines and one aspartate in a 2-His, 1-Asp facial triad. ACCO is related to the 2-oxoglutarate (2OG)-dependent oxygenases although using carbon dioxide and ascorbate rather than 2OG for activity. The present chapter summarizes the advances towards understanding this intriguing enzyme and current hypotheses on the active conformation of the protein, its interaction with substrates and cofactors, the role of CO2/bicarbonate as a cofactor, and its catalytic mechanism.
4-Hydroxyphenylpyruvate Dioxygenase and Hydroxymandelate Synthase: 2-Oxo Acid-Dependent Oxygenases of Importance to Agriculture and Medicine
Authors: Shah Dhara D. , Moran Graham R.
Published: April 2015

Despite a separate evolutionary lineage, 4-hydroxyphenylpyruvate dioxygenase (HPPD) and hydroxymandelate synthase (HMS) are appropriately grouped with the 2-oxo acid-dependent oxygenase (2OADO) family of enzymes. HPPD and HMS accomplish highly similar overall chemistry to that observed in the majority of 2OADOs but require only two substrates rather than three. 2OADOs typically use the 2-oxo acid of 2-oxoglutarate (2OG) as a source of electrons to reduce and activate dioxygen in order to oxidize a third specific substrate. HPPD and HMS use instead the pyruvate substituent of 4-hydroxyphenylpyruvate to activate dioxygen and then proceed to also hydroxylate this substrate, each yielding a distinctly different aromatic product. HPPD catalyses the second and committed step of tyrosine catabolism, a pathway common to nearly all aerobes. Plants require the HPPD reaction to biosynthesize plastoquinones and therefore HPPD inhibitors can have potent herbicidal activity. The ubiquity of the HPPD reaction, however, has meant that HPPD-specific molecules developed as herbicides have other uses in different forms of life. In humans herbicidal HPPD inhibitors can be used therapeutically to alleviate specific inborn defects and also to retard the progress of certain bacterial and fungal infections. This review is intended as a concise overview of the contextual and catalytic chemistries of HPPD and HMS.
N-doped TiO2 based visible light activated label-free photoelectrochemical biosensor for detection of Hg2+ through quenching of photogenerated electrons
Authors: Han Qianqian , Wang Kewei , Xu Lijun , Yan Xiang , Zhang Kunchi , Chen Xing , Wang Qinglin , Zhang Lan , Pei Renjun
Published: April 2015

A photoelectrochemical biosensor was fabricated using T-rich DNA on N-doped TiO2 to detect Hg2+ through quenching of photogenerated electrons.
Surface invasive cleavage assay on a maskless light-directed diamond DNA microarray for genome-wide human SNP mapping
Authors: Nie Bei , Yang Min , Fu Weiling , Liang Zhiqing
Published: April 2015

Fabrication of a dual-probe invasive DNA array on a diamond thin film.
An arginine-functionalized stationary phase for hydrophilic interaction liquid chromatography
Authors: Wu Shengjie , Li Xiuling , Zhang Feifang , Jiang Ge , Liang Xinmiao , Yang Bingcheng
Published: April 2015

A arginine-functionalized HILIC stationary phase has been prepared for the first time by clicking arginine onto silica gel. As an HPLC column, it offered the efficient separation of highly polar analytes. As a SPE sorbent, it exhibited excellent selectivity and enrichment toward acidic glycopeptides.
Molecularly imprinted surface plasmon resonance (SPR) based sensing of bisphenol A for its selective detection in aqueous systems
Authors: Shaikh Huma , Sener Gulsu , Memon Najma , Bhanger Muhammad Iqbal , Nizamani Shafi Muhammad , Üzek Recep , Denizli Adil
Published: April 2015

Bisphenol A (BPA) imprinted poly(ethylene glycol dimethacrylate-N-methacryloyl-l-phenylalanine-vinyl imidazole) [poly(EGDMA-MAPA-VI)] film deposition on a SPR sensor with improved efficiency is described in this paper.
1,8-Naphthyridinic fluorescent ‘turn-on’ and ‘turn-off’ chemosensors for detection of F−and Hg2+ions mimicking INHIBIT molecular logic behaviour
Authors: Chahal Mandeep K. , Sankar Muniappan
Published: April 2015

Naphthyridine-based fluorescent chemosensors were prepared. They exhibited a selective dual-channel response to detect F−and Hg2+ions with lower detection limits (0.5–2 ppm range).