bluuebunny/crossref_metadata_2025 huggingface dataset:
Interactions between micro-organisms on skin
Authors: Noble W. C.
Published: March 2014

Synopsis

The mechanisms of interaction are discussed in general terms; this is followed by a review of interaction which may occur in tinea paedis.

The production of penicillin-like and other antibiotics by dermatophyte fungi in lesions of athletes foot may result in the selection of an antibiotic-resistant bacterial flora which, perhaps by production of antibiotic or other secondary metabolites, can reduce the viability of the fungi. The effect on the host is to bring about a change from a fungal skin lesion which is dry and scaly to a bacterial lesion which is macerated and malodorous.
Parasitology
Authors: Burt D. R. R.
Published: March 2014

In Sir John Sinclair's Statistical Account of Scotland (1791–99), we have a very detailed and accurate picture of the conditions prevailing in this country two hundred years ago. There are numerous descriptions of how, during the preceding half-century, the extensive draining of marshes led to the control of malaria, or ague, and the introduction of inoculation almost completely eradicated smallpox; these were important factors which contributed towards the health and prosperity of the country.
A novel microfluidic chip electrophoresis strategy for simultaneous, label-free, multi-protein detection based on a graphene energy transfer biosensor
Authors: Lin Fengming , Zhao Xiaochao , Wang Jianshe , Yu Shiyong , Deng Yulin , Geng Lina , Li HuanJun
Published: March 2014

A new type of parallel, label-free target detection based on the combination of chip electrophoresis and a nanoparticle optical biosensor is reported.
Advancements in solid acid catalysts for biodiesel production
Authors: Su Fang , Guo Yihang
Published: March 2014

Recent advancements in biodiesel synthesis catalyzed by solid acids, particularly novel hybrid organic–inorganic solid acids, are reviewed.
A universal fluorescence sensing strategy based on biocompatible graphene quantum dots and graphene oxide for the detection of DNA
Authors: Qian Z. S. , Shan X. Y. , Chai L. J. , Ma J. J. , Chen J. R. , Feng H.
Published: March 2014

A novel and efficient fluorescence sensing platform based on biocompatible graphene quantum dots and graphene oxide was established.
Plasmonics-enhanced and optically modulated delivery of gold nanostars into brain tumor
Authors: Yuan Hsiangkuo , Wilson Christy M. , Xia Jun , Doyle Sarah L. , Li Shuqin , Fales Andrew M. , Liu Yang , Ozaki Ema , Mulfaul Kelly , Hanna Gabi , Palmer Gregory M. , Wang Lihong V. , Grant Gerald A. , Vo-Dinh Tuan
Published: March 2014

Plasmonics-enhanced optically modulated approach to open blood–brain tumor barrier with high spatial selectivity for gold nanostars delivery into brain tumor.
Oxidation-responsive polymers for biomedical applications
Authors: Song Cheng-Cheng , Du Fu-Sheng , Li Zi-Chen
Published: March 2014

This article summarizes recent progress in the design and synthesis of various oxidation-responsive polymers and their application in biomedical fields.
Non-uniform spatial distribution of tin oxide (SnO2) nanoparticles at the air–water interface
Authors: Jordan Inga , Beloqui Redondo Amaia , Brown Matthew A. , Fodor Daniel , Staniuk Malwina , Kleibert Armin , Wörner Hans Jakob , Giorgi Javier B. , van Bokhoven Jeroen A.
Published: March 2014

Nanoparticle spatial distributions are determined at the air–water interface using X-ray photoelectron spectroscopy combined with a liquid microjet.
A novel porous metal–organic framework from a new bis(acylhydrazone) ligand capable of reversibly adsorbing/desorbing water and small alcohol molecules
Authors: Guo Chun-Li , Li Xiao-Zeng , Zhang Xing-Mei , Wang Lu , Zhu Li-Na
Published: March 2014

Weak coordination and π–π interactions link the metallomacrocycles into two interpenetrating 3D networks to form the material with hydrophilic pores.
Allosteric pathway identification through network analysis: from molecular dynamics simulations to interactive 2D and 3D graphs
Authors: Allain Ariane , Chauvot de Beauchêne Isaure , Langenfeld Florent , Guarracino Yann , Laine Elodie , Tchertanov Luba
Published: March 2014

Allostery is a universal phenomenon that couples the information induced by a local perturbation (effector) in a protein to spatially distant regulated sites. Such an event can be described in terms of a large scale transmission of information (communication) through a dynamic coupling between structurally rigid (minimally frustrated) and plastic (locally frustrated) clusters of residues. To elaborate a rational description of allosteric coupling, we propose an original approach – MOdular NETwork Analysis (MONETA) – based on the analysis of inter-residue dynamical correlations to localize the propagation of both structural and dynamical effects of a perturbation throughout a protein structure. MONETA uses inter-residue cross-correlations and commute times computed from molecular dynamics simulations and a topological description of a protein to build a modular network representation composed of clusters of residues (dynamic segments) linked together by chains of residues (communication pathways). MONETA provides a brand new direct and simple visualization of protein allosteric communication. A GEPHI module implemented in the MONETA package allows the generation of 2D graphs of the communication network. An interactive PyMOL plugin permits drawing of the communication pathways between chosen protein fragments or residues on a 3D representation. MONETA is a powerful tool for on-the-fly display of communication networks in proteins. We applied MONETA for the analysis of communication pathways (i) between the main regulatory fragments of receptors tyrosine kinases (RTKs), KIT and CSF-1R, in the native and mutated states and (ii) in proteins STAT5 (STAT5a and STAT5b) in the phosphorylated and the unphosphorylated forms. The description of the physical support for allosteric coupling by MONETA allowed a comparison of the mechanisms of (a) constitutive activation induced by equivalent mutations in two RTKs and (b) allosteric regulation in the activated and non-activated STAT5 proteins. Our theoretical prediction based on results obtained with MONETA was validated for KIT by in vitro experiments. MONETA is a versatile analytical and visualization tool entirely devoted to the understanding of the functioning/malfunctioning of allosteric regulation in proteins – a crucial basis to guide the discovery of next-generation allosteric drugs.
Synthesis of a doubly thermo-responsive schizophrenic diblock copolymer based on poly[N-(4-vinylbenzyl)-N,N-diethylamine] and its temperature-sensitive flip-flop micellization
Authors: Li Shentong , Huo Fei , Li Quanlong , Gao Chengqiang , Su Yang , Zhang Wangqing
Published: March 2014

A doubly thermo-responsive schizophrenic diblock copolymer, poly(tert-butyl methacrylate)-block-poly[N-(4-vinylbenzyl)-N,N-diethylamine], was synthesized and its flip-flop micellization was demonstrated.
One-magnon and exciton inelastic light scattering in the antiferromagnet CoF2
Authors: Meloche E. , Cottam M. G. , Lockwood D. J.
Published: March 2014

Experimental data are reported for the temperature and polarization dependence of the one-magnon Raman light scattering in the rutile-structure antiferromagnet CoF2 (Neel temperature TN = 38 K). The low-lying excitons are also investigated at low temperatures and comparisons made with results from earlier Raman, infrared, and neutron scattering work. A detailed analysis of the one-magnon Stokes and anti-Stokes Raman spectra is presented resulting in comprehensive data for the temperature variation up to TN of the one-magnon frequency, line width, and integrated intensity. A theory of the one-magnon scattering and other magnetic transitions is constructed based mainly on a spin S = 3/2 exchange model, extending a simpler effective S = 1/2 approach. The excitation energies and spectral intensities over a broad range of temperatures are obtained using a Green's function equation of motion method that allows for a careful treatment of the single-ion anisotropy. Overall the S = 3/2 theory compares well with the experimental data.
Spin dynamics of antiferromagnets under action of femtosecond laser pulses (Review Article)
Authors: Ivanov B. A.
Published: March 2014

Investigations of excitation of spin dynamics in transparent antiferromagnets (AFM) under the action of femtosecond laser pulses are reviewed. A variety of observed effects is considered in the context of a unified approach. The analysis is based on the nonlinear sigma model for the antiferromagnetism vector L with taking into account effective fields induced in a magnetic material due to the interaction between light and the spin system of the magnetic material. The contributions of various magneto-optical effects (both standard Faraday or Cotton-Mouton (Voigt) effects and specific L-dependent effects for AFM) are considered as characteristic contributions to the effective field within the sigma model. The most typical experimental data for real AFM are discussed.
Perspective: Bimolecular chemical reaction dynamics in liquids
Authors: Orr-Ewing Andrew J.
Published: March 2014

Bimolecular reactions in the gas phase exhibit rich and varied dynamical behaviour, but whether a profound knowledge of the mechanisms of isolated reactive collisions can usefully inform our understanding of reactions in liquid solutions remains an open question. The fluctuating environment in a liquid may significantly alter the motions of the reacting particles and the flow of energy into the reaction products after a transition state has been crossed. Recent experimental and computational studies of exothermic reactions of CN radicals with organic molecules indicate that many features of the gas-phase dynamics are retained in solution. However, observed differences may also provide information on the ways in which a solvent modifies fundamental chemical mechanisms. This perspective examines progress in the use of time-resolved infra-red spectroscopy to study reaction dynamics in liquids, discusses how existing theories can guide the interpretation of experimental data, and suggests future challenges for this field of research.
Scattering problems in the fractional quantum mechanics governed by the 2D space-fractional Schrödinger equation
Authors: Dong Jianping
Published: March 2014

The 2D space-fractional Schrödinger equation in the time-independent and time-dependent cases for the scattering problems in the fractional quantum mechanics is studied. We define the Green's functions for the two cases and give the mathematical expression of them in infinite series form and in terms of some special functions. The asymptotic formulas of the Green's functions are also given, and applied to get the approximate wave functions for the fractional quantum scattering problems. These results contain those in the standard (integer) quantum mechanics as special cases, and can be applied to study the complex quantum systems.
Hetero-epitaxial EuO interfaces studied by analytic electron microscopy
Authors: Mundy Julia A. , Hodash Daniel , Melville Alexander , Held Rainer , Mairoser Thomas , Muller David A. , Kourkoutis Lena F. , Schmehl Andreas , Schlom Darrell G.
Published: March 2014

With nearly complete spin polarization, the ferromagnetic semiconductor europium monoxide could enable next-generation spintronic devices by providing efficient ohmic spin injection into silicon. Spin injection is greatly affected by the quality of the interface between the injector and silicon. Here, we use atomic-resolution scanning transmission electron microscopy in conjunction with electron energy loss spectroscopy to directly image and chemically characterize a series of EuO|Si and EuO|YAlO3 interfaces fabricated using different growth conditions. We identify the presence of europium silicides and regions of disorder at the EuO|Si interfaces, imperfections that could significantly reduce spin injection efficiencies via spin-flip scattering.
Controlling coverage of solution cast materials with unfavourable surface interactions
Authors: Burlakov V. M. , Eperon G. E. , Snaith H. J. , Chapman S. J. , Goriely A.
Published: March 2014

Creating uniform coatings of a solution-cast material is of central importance to a broad range of applications. Here, a robust and generic theoretical framework for calculating surface coverage by a solid film of material de-wetting a substrate is presented. Using experimental data from semiconductor thin films as an example, we calculate surface coverage for a wide range of annealing temperatures and film thicknesses. The model generally predicts that for each value of the annealing temperature there is a range of film thicknesses leading to poor surface coverage. The model accurately reproduces solution-cast thin film coverage for organometal halide perovskites, key modern photovoltaic materials, and identifies processing windows for both high and low levels of surface coverage.
A long-lived optical waveguide made out of thin air
Authors: Wilson R. Mark
Published: March 2014

Sound and heat in the wake of a femtosecond laser pulse can produce a refractive-index gradient that channels subsequent higher-power pulses.
Whipping up sand dunes from scratch
Authors: Smart Ashley G.
Published: March 2014

A theory of how shifting winds shape sandy terrain has passed a long-awaited experimental test.
Digging into the past without a spade
Authors: Guinnessy Paul K.
Published: March 2014

In a collaboration between geophysicists and archaeologists, large areas of Turkey are being surveyed for archaeological ruins, on a time scale of weeks, not years.
Taiwan’s science miracle
Authors: Feder Toni
Published: March 2014

In the past two decades, a flourishing economy and maturing infrastructure have Taiwanese physicists both staying home more and engaging internationally.
Predicting impacts of global climate change on intraspecific genetic diversity benefits from realistic dispersal estimates
Authors: Duckett Paul E. , Stow Adam J.
Published: March 2014

Global climates are rapidly changing, which for many species will require dispersal to higher altitudes and latitudes to maintain favourable conditions. Changes in distribution for less mobile species is likely to be associated with losses to genetic diversity, yet this cannot be quantified without understanding which parts of a species distribution will colonise favourable regions in the future. To address this we adopted a realistic estimate of dispersal with predicted changes in species distributions to estimate future levels of intraspecific genetic diversity. Using 740 geckos (Gehyra variegata) collected across their distribution in central and eastern inland Australia, we predict genetic loss within phylogenetically distinct units at both mtDNA and microsatellite markers between 2010 and 2070. We found that using a quantified and realistic estimate of dispersal resulted in significant declines to allelic richness (5.114 to 4.052), haplotype richness (7.215 to 4.589) and phylogenetic diversity (0.012 to 0.005) (P < 0.01). In comparison, predicted losses were substantially over- or underestimated when commonly applied dispersal scenarios were utilised. Using biologically relevant estimates of dispersal will help estimate losses of intraspecific genetic diversity following climate change impacts. This approach will provide critical information for the management of species in the near future.
BAT3 modulates p300-dependent acetylation of p53 and autophagy-related protein 7 (ATG7) during autophagy
Authors: Sebti Salwa , Prébois Christine , Pérez-Gracia Esther , Bauvy Chantal , Desmots Fabienne , Pirot Nelly , Gongora Céline , Bach Anne-Sophie , Hubberstey Andrew V. , Palissot Valérie , Berchem Guy , Codogno Patrice , Linares Laetitia K. , Liaudet-Coopman Emmanuelle , Pattingre Sophie
Published: March 2014

Significance

Autophagy allows the lysosomal degradation of intracellular material. It is a tightly regulated process controlled by the tumor-suppressor gene p53, among others. Here we report a unique regulator of autophagy, BAT3, which modulates the intracellular localization of the enzyme p300, an enzyme that adds some acetyl residues on targets proteins (acetylation) to modulate their activity. To stimulate autophagy, BAT3 allows the acetylation of p53 by p300 in the nucleus, but limits the p300-dependent acetylation of ATG7, a protein specific for autophagy, in the cytosol. Thus, BAT3 acts on both the cytosol and the nucleus to tightly modulate autophagy.
Understanding the antagonism of retinoblastoma protein dephosphorylation by PNUTS provides insights into the PP1 regulatory code
Authors: Choy Meng S. , Hieke Martina , Kumar Ganesan Senthil , Lewis Greyson R. , Gonzalez-DeWhitt Kristofer R. , Kessler Rene P. , Stein Benjamin J. , Hessenberger Manuel , Nairn Angus C. , Peti Wolfgang , Page Rebecca
Published: March 2014

Significance

Dephosphorylation of the tumor-suppressor retinoblastoma protein (Rb) leads to its activation. Our structure of the protein phosphatase 1 (PP1) nuclear targeting subunit (PNUTS):PP1 holoenzyme reveals how this reaction is regulated: PNUTS and Rb compete for an identical binding site on PP1. Because PP1 binds PNUTS 400-fold more strongly than Rb, when PNUTS is present, Rb is not dephosphorylated. However, when PNUTS levels are reduced, PP1 binds and dephosphorylates Rb, leading to its activation. This structure also led to the identification of additional common PP1 binding motifs, allowing us to predict how a quarter of the known PP1 regulators bind to PP1. This result is a key advance for understanding the regulation of PP1, which controls >50% of all dephosphorylation reactions.
Graph-based sampling for approximating global helical topologies of RNA
Authors: Kim Namhee , Laing Christian , Elmetwaly Shereef , Jung Segun , Curuksu Jeremy , Schlick Tamar
Published: March 2014

Significance

RNA molecules are important components of the cellular machinery and perform many essential roles, including catalysis, transcription, and regulation. Because the structural features are intimately connected to their biological functions, there is great interest in predicting RNA structure from sequence. Present RNA 3D folding algorithms are limited to small RNA structures due to inefficient sampling of RNA structure space. We report a computational approach to predict RNA 3D topologies based on hierarchical sampling of RNA 3D candidate topologies represented as 3D graphs guided by geometrical measures based on known structures. The combination of tools shows great promise for assembling global features of RNA architecture. Applications to RNA design can be envisioned.
Dendritic cell fate is determined by BCL11A
Authors: Ippolito Gregory C. , Dekker Joseph D. , Wang Yui-Hsi , Lee Bum-Kyu , Shaffer Arthur L. , Lin Jian , Wall Jason K. , Lee Baeck-Seung , Staudt Louis M. , Liu Yong-Jun , Iyer Vishwanath R. , Tucker Haley O.
Published: March 2014

Significance

This work demonstrates a key role of the B lymphocyte transcription factor BCL11A in dendritic cell (DC) development. Two major DC subsets—the plasmacytoid DC (pDC) and the conventional DC (cDC)—are believed to arise from a shared precursor called the common DC progenitor (CDP). Potential precursor differences between cDC and pDC generation might nevertheless remain to be elucidated. Here, we show that mutant mice can generate CDPs and cDCs in the absence of BCL11A, whereas pDCs (and also B cells) are abolished. This study also identifies and validates BCL11A target genes using a variety of techniques, and provides a molecular model for BCL11A activity in the B lymphocyte and pDC lineages.
Ena/VASP Enabled is a highly processive actin polymerase tailored to self-assemble parallel-bundled F-actin networks with Fascin
Authors: Winkelman Jonathan D. , Bilancia Colleen G. , Peifer Mark , Kovar David R.
Published: March 2014

Significance

Enabled/vasodilator-stimulated phosphoprotein (Ena/VASP) proteins are required for the formation and maintenance of filopodia, finger-like projections at the leading edge of migrating cells that are composed of parallel actin filaments bundled by Fascin. We imaged individual fluorescently labeled
Drosophila
Ena molecules on both single and Fascin-bundled actin filaments in vitro. Ena stimulates actin assembly by remaining continuously associated with the barbed end and increasing the elongation rate by approximately two- to threefold. Remarkably, the frequency and length of Ena’s processive runs are enhanced on filaments within a Fascin bundle, which drives a positive feedback cycle that allows the assembly of uniformly thick filopodia-like F-actin bundles composed of multiple filaments with aligned ends.
Blood–spinal cord barrier disruption contributes to early motor-neuron degeneration in ALS-model mice
Authors: Winkler Ethan A. , Sengillo Jesse D. , Sagare Abhay P. , Zhao Zhen , Ma Qingyi , Zuniga Edward , Wang Yaoming , Zhong Zhihui , Sullivan John S. , Griffin John H. , Cleveland Don W. , Zlokovic Berislav V.
Published: March 2014

Significance

The blood–spinal cord barrier (BSCB) is damaged in human ALS and rodents expressing ALS-associated superoxide dismutase mutations. The role of BSCB breakdown in disease pathogenesis remains, however, unclear. Early motor-neuron dysfunction and injury are now shown to be proportional to the degree of BSCB disruption, and early protection of the BSCB integrity with an activated protein C analog is found to delay onset of motor-neuron impairment and degeneration. Altogether, these findings in mice show that BSCB breakdown plays a role in early-stage disease pathogenesis and that restoring BSCB integrity retards the disease process. These findings are relevant to the corresponding disease mechanism in human ALS in which ALS-associated vascular pathology is associated.
The emergence of Dutch
Authors: de Vaan Michiel
Published: March 2014

In discussions on the history of Dutch phonology, vowels have played a more prominent role than consonants. In some recent and forthcoming publications (de Vaan 2012, forthcoming a, forthcoming b), I show that the consonants also hold important clues for language history in the Low Countries. The present article is a survey of the main pre-1200 consonant changes affecting the dialects of what eventually became the Dutch language. As far as possible, I add the relative or absolute chronology of the changes involved.
Methodological reflections on the emergence of Old Frisian
Authors: Versloot Arjen
Published: March 2014

The question addressed in this article is whether it is possible to identify the time of the emergence of Frisian from the rest of West Germanic. Some of the criteria used in determining the chronology of Frisian language history are evaluated in terms of their temporal and spatial aspects. Phonological features that appear to differentiate languages from a present-day perspective disappear in a haze of synchronic and diatopic allophonic alternations. Reconstructions of the order of phonological developments often turn out to be best-fit interpretations of changes whose precise character, age and location are hard to determine. Besides, reconstructions of regional distribution are obscured by subsequent migrations and dialect shifts. Consequently, the splits in a language family tree are not bifurcations, but bushes of variation, where only hindsight allows an identification of the chronology and the decisive factors involved.
Shorter Survival in Familial versus Idiopathic Pulmonary Arterial Hypertension is Associated with Hemodynamic Markers of Impaired Right Ventricular Function
Authors: Brittain Evan L. , Pugh Meredith E. , Wheeler Lisa A. , Robbins Ivan M. , Loyd James E. , Newman John H. , Larkin Emma K. , Austin Eric D. , Hemnes Anna R.
Published: March 2014

Although individuals with familial pulmonary arterial hypertension (FPAH) have more severe hemodynamics, compared to individuals with idiopathic PAH (IPAH), it is unclear whether this translates into a survival difference. The influence of right ventricular (RV) function on survival in these groups is also unknown. We reviewed hemodynamic data and health information from a prospective institutional database of 57 FPAH and 66 IPAH patients registered with the Vanderbilt Pulmonary Hypertension Research Cohort. We compared hemodynamics at the time of diagnosis between the two groups and calculated pulmonary arteriolar capacitance (PC) and RV stroke work index (RVSWI). Using survival analysis, we compared freedom from a 5‐year composite of death or lung transplantation in FPAH and IPAH patients. The composite outcome of death or transplant at 5 years from diagnosis was significantly increased in FPAH (log rank P < 0.001). PC and RVSWI were significantly decreased in FPAH, compared to IPAH (P < 0.001 for both). In univariate analysis, PC (odds ratio [OR]: 0.17 [95% confidence interval (95% CI): 0.03–0.83]) and RVSWI (OR: 0.86 [95% CI: 0.77–0.95]) were predictors of mortality, as were cardiac index (OR: 0.17 [95% CI: 0.06–0.51]) and PVR (OR: 1.1 [95% CI: 1.01–1.12]). Among FPAH patients, RVSWI was lower in those who died or received a transplant than in survivors (P = 0.006), while PC was not (P = 0.5). We found significantly worse event‐free survival and significantly lower PC and RVSWI in FPAH than in IPAH. In FPAH patients who died or underwent transplantation, RVSWI was lower than that in survivors, suggesting disproportionate RV dysfunction.
Challenges in RNA virus bioinformatics
Authors: Marz Manja , Beerenwinkel Niko , Drosten Christian , Fricke Markus , Frishman Dmitrij , Hofacker Ivo L. , Hoffmann Dieter , Middendorf Martin , Rattei Thomas , Stadler Peter F. , Töpfer Armin
Published: March 2014

Motivation: Computer-assisted studies of structure, function and evolution of viruses remains a neglected area of research. The attention of bioinformaticians to this interesting and challenging field is far from commensurate with its medical and biotechnological importance. It is telling that out of >200 talks held at ISMB 2013, the largest international bioinformatics conference, only one presentation explicitly dealt with viruses. In contrast to many broad, established and well-organized bioinformatics communities (e.g. structural genomics, ontologies, next-generation sequencing, expression analysis), research groups focusing on viruses can probably be counted on the fingers of two hands.

Results: The purpose of this review is to increase awareness among bioinformatics researchers about the pressing needs and unsolved problems of computational virology. We focus primarily on RNA viruses that pose problems to many standard bioinformatics analyses owing to their compact genome organization, fast mutation rate and low evolutionary conservation. We provide an overview of tools and algorithms for handling viral sequencing data, detecting functionally important RNA structures, classifying viral proteins into families and investigating the origin and evolution of viruses.

Contact:  manja@uni-jena.de

Supplementary information:  Supplementary data are available at Bioinformatics online. The references for this article can be found in the Supplementary Material.
Interaction between plastid and mitochondrial retrograde signalling pathways during changes to plastid redox status
Authors: Blanco Nicolás E. , Guinea-Díaz Manuel , Whelan James , Strand Åsa
Published: March 2014

Mitochondria and chloroplasts depend upon each other; photosynthesis provides substrates for mitochondrial respiration and mitochondrial metabolism is essential for sustaining photosynthetic carbon assimilation. In addition, mitochondrial respiration protects photosynthesis against photoinhibition by dissipating excess redox equivalents from the chloroplasts. Genetic defects in mitochondrial function result in an excessive reduction and energization of the chloroplast. Thus, it is clear that the activities of mitochondria and plastids need to be coordinated, but the manner by which the organelles communicate to coordinate their activities is unknown. The
regulator of alternative oxidase
(
rao1)
mutant was isolated as a mutant unable to induce
AOX1a
expression in response to the inhibitor of the mitochondrial cytochrome
c
reductase (complex III), antimycin A.
RAO1
encodes the nuclear localized cyclin-dependent kinase E1 (CDKE1). Interestingly, the
rao1
mutant demonstrates a genome uncoupled phenotype also in response to redox changes in the photosynthetic electron transport chain. Thus, CDKE1 was shown to regulate both
LIGHT HARVESTING COMPLEX B
(
LHCB
) and
ALTERNATIVE OXIDASE 1
(
AOX1a
) expression in response to retrograde signals. Our results suggest that CDKE1 is a central nuclear component integrating mitochondrial and plastid retrograde signals and plays a role in regulating energy metabolism during the response to stress.
Signalling crosstalk in light stress and immune reactions in plants
Authors: Trotta Andrea , Rahikainen Moona , Konert Grzegorz , Finazzi Giovanni , Kangasjärvi Saijaliisa
Published: March 2014

The evolutionary history of plants is tightly connected with the evolution of microbial pathogens and herbivores, which use photosynthetic end products as a source of life. In these interactions, plants, as the stationary party, have evolved sophisticated mechanisms to sense, signal and respond to the presence of external stress agents. Chloroplasts are metabolically versatile organelles that carry out fundamental functions in determining appropriate immune reactions in plants. Besides photosynthesis, chloroplasts host key steps in the biosynthesis of amino acids, stress hormones and secondary metabolites, which have a great impact on resistance against pathogens and insect herbivores. Changes in chloroplast redox signalling pathways and reactive oxygen species metabolism also mediate local and systemic signals, which modulate plant resistance to light stress and disease. Moreover, interplay among chloroplastic signalling networks and plasma membrane receptor kinases is emerging as a key mechanism that modulates stress responses in plants. This review highlights the central role of chloroplasts in the signalling crosstalk that essentially determines the outcome of plant–pathogen interactions in plants.
Tetra-μ3-iodido-tetrakis[(tri-n-butylphosphane-κP)copper(I)]
Authors: Klenk Simon , Frey Wolfgang , Bubrin Martina , Laschat Sabine
Published: March 2014

The title complex, [Cu4I4(C12H27P)4], crystallizes with six molecules in the unit cell and with three independent one-third molecule fragments, completed by application of the relevant symmetry operators, in the asymmetric unit. The tetranuclear copper core shows a tetrahedral geometry (site symmetry 3..). The I atoms also form a tetrahedron, with I...I distances of 4.471 (1) Å. Both tetrahedra show an orientation similar to that of a pair of self-dual platonic bodies. The edges of the I-tetrahedral structure are capped to the face centers of the Cu-tetrahedron andvice versa. The Cuface...I distances are 2.18 Å (averaged) and the Iface...Cu distances are 0.78 Å (averaged). As a geometric consequence of these properties there are eight distorted trigonal–bipyramidal polyhedra evident, wherein each trigonal face builds up the equatorial site and the opposite Cu...I positions form the axial site. As expected, then-butyl moieties are highly flexible, resulting in large elongations of their anisotropic displacement parameters. Some C atoms of then-butyl groups were needed to fix alternative discrete disordered positions.
2,6-Dihydroxy-4-oxo-2-(pyridin-1-ium-3-yl)-4H-1,3,2-benzodioxaborinin-2-ide 0.67-hydrate
Authors: Garcia-Grajeda Blanca A. , Höpfl Herbert , Guerrero-Alvarez Jorge A. , Campos-Gaxiola José J. , Cruz-Enríquez Adriana
Published: March 2014

The asymmetric unit of the title compound, C12H10BNO5·0.67H2O, contains three independent pyridinylboronic acid esters adopting zwitterionic forms and two water molecules. The six-membered heterocyclic rings in the boronic esters have half-chair conformations and the deviations of the B atoms from the boronate mean planes range from 0.456 (3) to 0.657 (3) Å. All of the B atoms have tetrahedral coordination environments, with B—O and B—C bond lengths of 1.446 (4)–1.539 (3) and 1.590 (5)–1.609 (5) Å, respectively. In the crystal, the ester and water molecules are linked into a three-dimensional network by a large number of O—H...O, N—H...O and C—H...O hydrogen bonds. The crystal packing is further accomplished by π–π interactions, with centroid–centroid distances of 3.621 (4)–3.787 (4) Å.
(μ-Acetato-κ2O:O′)[μ-2,6-bis({bis[(pyridin-2-yl-κN)methyl]amino-κN}methyl)-4-methylphenolato-κ2O:O](methanol-κO)dizinc bis(perchlorate)
Authors: Das Biswanath , Haukka Matti , Nordlander Ebbe
Published: March 2014

The binuclear title complex, [Zn2(C33H33N6O)(CH3COO2)(CH3OH)](ClO4)2, was synthesized by the reaction between 2,6-bis({[bis(pyridin-2-yl)methyl]amino}methyl)-4-methylphenol (H-BPMP), Zn(OAc)2and NaClO4. The two ZnIIions are bridged by the phenolate O atom of the octadentate ligand and the acetate group. An additional methanol ligand is terminally coordinated to one of the ZnIIions, rendering the whole structure unsymmetric. Other symmetric dizinc complexes of BPMP have been reported. However, to the best of our knowledge, the present structure, in which the two ZnIIions are distinguishable by the number of coordinating ligands and the coordination geometries (octahedral and square-pyramidal), is unique. The dizinc complex is a dication, and two perchlorate anions balance the charge. The –OH group of the coordinating methanol solvent molecule forms a hydrogen bond with a perchlorate counter-anion. One of the anions is disordered over two sets of sites with an occupancy ratio of 0.734 (2):0.266 (2).
Accessibility of Apple iPad for partially sighted users: pilot study
Authors: Hewett Rachel , Torgerson Carole , Douglas Graeme
Published: March 2014

Purpose

– The purpose of this paper is to present the results of a pilot trial, investigating the accessibility provided by a tablet computer (Apple iPad) to individuals with visual impairment. The study was designed around an N-of-1 randomised controlled trial (RCT), which was replicated for 12 participants. It served as an opportunity to evaluate the use N-of-1 trials in studies involving people who are visually impaired.

Design/methodology/approach

– The study centred round an N-of-1 RCT, comparing the accessibility provided by control equipment (Windows computer) against the intervention equipment (Apple iPad). Twelve participants conducted six tests on the equipment as per randomisation, followed by a quantitative-based evaluation and short interviews.

Findings

– One-sided individual randomisation tests showed a significant result for overall satisfaction in favour of the tablet at the 0.05 significance level for seven of the participants. Participants identified several strengths of the iPad in helping a partially sighted user in accessing the internet: inbuilt zoom and magnification options; increased control as a result of the touch screen; and accessibility tools being built into the operating system. The main limitation suggested was the way the zoom function operates by enlarging the onscreen keyboard. This caused difficulties for those with more severe visual impairments using this function in inputting text.

Originality/value

– There has been limited research to substantiate positive reviews of the tablet computer for low-vision users. The results of this pilot study gives evidence in support of these potential benefits, and demonstrates the importance of a more thorough investigation.
Fabrication and characterisation of PCL and PCL/PLA scaffolds for tissue engineering
Authors: Patrício T. , Domingos M. , Gloria A. , D'Amora U. , Coelho J.F. , Bártolo P.J.
Published: March 2014

Purpose

– The main purpose of this research work is to study the effect of poly lactic acid (PLA) addition into poly (e-caprolactone) (PCL) matrices, as well the influence of the mixing process on the morphological, thermal, chemical, mechanical and biological performance of the 3D constructs produced with a novel biomanufacturing device (BioCell Printing).

Design/methodology/approach

– Two mixing processes are used to prepare PCL/PLA blends, namely melt blending and solvent casting. PCL and PCL/PLA scaffolds are produced via BioCell Printing using a 300-μm nozzle, 0/90° lay down pattern and 350-μm pore size. Several techniques such as scanning electron microscopy (SEM), simultaneous thermal analyzer (STA), nuclear magnetic resonance (NMR), static compression analysis and Alamar BlueTM are used to evaluate scaffold's morphological, thermal, chemical, mechanical and biological properties.

Findings

– Results show that the addition of PLA to PCL scaffolds strongly improves the biomechanical performance of the constructs. Additionally, polymer blends obtained by solvent casting present better mechanical and biological properties, compared to blends prepared by melt blending.

Originality/value

– This paper undertakes a detailed study on the effect of the mixing process on the biomechanical properties of PCL/PLA scaffolds. Results will enable to prepare customized PCL/PLA scaffolds for tissue engineering applications with improved biological and mechanical properties, compared to PCL scaffolds alone. Additionally, the accuracy and reproducibility of by the BioCell Printing enables to modulate the micro/macro architecture of the scaffolds enhancing tissue regeneration.
A comparison of aphasia therapy outcomes before and after a Very Early Rehabilitation programme following stroke
Authors: Godecke Erin , Ciccone Natalie A. , Granger Andrew S. , Rai Tapan , West Deborah , Cream Angela , Cartwright Jade , Hankey Graeme J.
Published: March 2014

Background

Very early aphasia rehabilitation studies have shown mixed results. Differences in therapy intensity and therapy type contribute significantly to the equivocal results.

Aims

To compare a standardized, prescribed very early aphasia therapy regimen with a historical usual care control group at therapy completion (4–5 weeks post‐stroke) and again at follow‐up (6 months).

Methods & Procedures

This study compared two cohorts from successive studies conducted in four Australian acute/sub‐acute hospitals. The studies had near identical recruitment, blinded assessment and data‐collection protocols. The Very Early Rehabilitation (VER) cohort (N = 20) had mild–severe aphasia and received up to 20 1‐h sessions of impairment‐based aphasia therapy, up to 5 weeks. The control cohort (n = 27) also had mild–severe aphasia and received usual care (UC) therapy for up to 4 weeks post‐stroke. The primary outcome measure was the Aphasia Quotient (AQ) and a measure of communicative efficiency (DA) at therapy completion. Outcomes were measured at baseline, therapy completion and 6 months post‐stroke and were compared using Generalised Estimating Equations (GEE) models.

Outcomes & Results

After controlling for initial aphasia and stroke disability, the GEE models demonstrated that at the primary end‐point participants receiving VER achieved 18% greater recovery on the AQ and 1.5% higher DA scores than those in the control cohort. At 6 months, the VER participants maintained a 16% advantage in recovery on the AQ and 0.6% more on DA scores over the control cohort participants.

Conclusions & Implications

A prescribed, impairment‐based aphasia therapy regimen, provided daily in very early post‐stroke recovery, resulted in significantly greater communication gains in people with mild–severe aphasia at completion of therapy and at 6 months, when compared with a historical control cohort. Further research is required to demonstrate large‐scale and long‐term efficacy.
Does East Asia Have a Working Financial Safety Net?
Authors: Menon Jayant , Hill Hal
Published: March 2014

Financial safety nets in Asia have come a long way since the Asian financial crisis (AFC) of 1997/1998. With Asian countries not wanting to rely solely on the IMF again, the Chiang Mai Initiative (CMI) was created in 2000. When the CMI also proved inadequate following the global financial crisis, it was first multilateralized (CMIM), and then doubled in size to US$240bn, while the IMF de‐linked portion was increased to 30 percent of the available country quotas. A surveillance unit, the ASEAN+3 Macroeconomic Research Office, was set up in 2001. These are impressive developments, but are they enough to make the CMIM workable? Without clear and rapid‐response procedures to handle a fast‐developing financial emergency, we argue that it is unlikely that the CMIM will be used even as a complement to the IMF. To serve as a stand‐alone option, however, its size or the IMF de‐linked portion of funds needs to be further increased, as does its membership, to add diversity. Only if the ASEAN+3 Macroeconomic Research Office can develop into an independent and credible surveillance authority would it then perhaps be in a position to lead the next rescue.
Uncoupling protein‐2 mediates the protective action of berberine against oxidative stress in rat insulinoma INS‐1E cells and in diabetic mouse islets
Authors: Liu Limei , Liu Jian , Gao Yuansheng , Yu Xiaoxing , Xu Gang , Huang Yu
Published: March 2014

Background and Purpose

Uncoupling protein‐2 (UCP2) may regulate glucose‐stimulated insulin secretion. The current study investigated the effects of berberine, an alkaloid found in many medicinal plants, on oxidative stress and insulin secretion through restoration of UCP2 expression in high glucose (HG)‐treated INS‐1E cells and rat islets or in db/db mouse islets.

Experimental Approach

Mouse and rat pancreatic islets were isolated. Nitrotyrosine, superoxide dismutase (SOD)‐1 and UCP2 expression and AMPK phosphorylation were examined by Western blotting. Insulin secretion was measured by elisa. Mitochondrial reactive oxygen species (ROS) production was detected by confocal microscopy.

Key Results

Incubation of INS‐1E cells and rat islets with HG (30 mmol·L−1; 8 h) elevated nitrotyrosine level, reduced SOD‐1 and UCP2 expression and AMPK phosphorylation, and inhibited glucose‐stimulated insulin secretion. HG also increased mitochondrial ROS in INS‐1E cells. Co‐treatment with berberine inhibited such effects. The AMPK inhibitor compound C, the UCP2 inhibitor genipin and adenovirus ucp2 shRNA inhibited these protective effects of berberine. Furthermore, compound C normalized berberine‐stimulated UCP2 expression but genipin did not affect AMPK phosphorylation. Islets from db/db mice exhibited elevated nitrotyrosine levels, reduced expression of SOD‐1 and UCP2 and AMPK phosphorylation, and decreased insulin secretion compared with those from db/m+ mice. Berberine also improved these defects in diabetic islets and genipin blocked the effects of berberine.

Conclusions and Implications

Berberine inhibited oxidative stress and restored insulin secretion in HG‐treated INS‐IE cells and diabetic mouse islets by activating AMPK and UCP2. UCP2 is an important signalling molecule in mediating anti‐diabetic effects of berberine.
KIBS and innovation: The geographic dynamics of innovation in Quebec
Authors: Plassart Mathilde , Shearmur Richard
Published: March 2014

The question we address in this article concerns the possible existence of specifically geographic processes that influence the propensity of Québec City knowledge‐intensive business services (KIBS) firms to innovate. In other words, after controlling for factors of innovation that are internal to the firm, does their neighbourhood‐level environment within the Quebec census metropolitan area partly determine their propensity to innovate? More specifically, this study looks at whether proximity to certain types of economic activity —measured by their employment levels— is connected with innovation. We show that proximity effects do exist, but that these differ according to the type of innovation considered and according to the type of activity to which proximity is measured. Our results indicate that clusters including KIBS, manufacturing, and technical KIBS seem to benefit innovation. Service establishments are, however, more innovative when they are close to the centre of Quebec City, and remote from professional services and government. The nature of these results differs somewhat from those for Montreal—in particular there is no tendency for innovation to increase with the distance to the central business district (CBD). This suggests that the connection between intra‐metropolitan location and KIBS innovation is dependent on specific metropolitan context, and does not therefore reflect easily generalisable processes.
Collagen-induced arthritis: severity and immune response attenuation using multivalent N-acetyl glucosamine
Authors: Richter J , Čapková K , Hříbalová V , Vannucci L , Danyi I , Malý M , Fišerová A
Published: March 2014

Rheumatoid arthritis is an autoimmunity leading to considerable impairment of quality of life. N-acetyl glucosamine (GlcNAc) has been described previously as a potent modulator of experimental arthritis in animal models and is used for osteoarthritis treatment in humans, praised for its lack of adverse effects. In this study we present a comprehensive immunological analysis of multivalent GlcNAc-terminated glycoconjugate (GC) application in the treatment of collagen-induced arthritis (CIA) and its clinical outcome. We used immunohistochemistry and FACS to describe conditions on the inflammation site. Systemic and clinical effects were evaluated by FACS, cytotoxicity assay, ELISA, cytometric bead array (CBA), RT–PCR and clinical scoring. We found reduced inflammatory infiltration, NKG2D expression on NK and suppression of T, B and antigen-presenting cells (APC) in the synovia. On the systemic level, GCs prevented the activation of monocyte- and B cell-derived APCs, the rise of TNF-α and IFN-γ levels, and subsequent type II collagen (CII)-specific IgG2a formation. Moreover, we detected an increase of anti-inflammatory IL-4 mRNA in the spleen. Similar to the synovia, the GCs caused a significant reduction of NKG2D-expressing NK cells in the spleen without influencing their lytic function. GCs effectively postponed the onset of arthritic symptoms, reduced their severity and in 18% (GN8P) and 31% (GN4C) of the cases completely prevented their appearance. Our data prove that GlcNAc glycoconjugates prevent the inflammatory response, involving proinflammatory cytokine rise, APC activation and NKG2D expression, leading to the attenuation of clinical symptoms. These results support the glycobiological approach to the treatment of collagen-induced arthritis/rheumatoid arthritis (CIA/RA) as a way of bringing new prospects for more effective therapeutic interventions.