bluuebunny/crossref_metadata_2025 huggingface dataset:
Calving rates at tidewater glaciers vary strongly with ocean temperature
Authors: Luckman Adrian , Benn Douglas I. , Cottier Finlo , Bevan Suzanne , Nilsen Frank , Inall Mark
Published: October 2015

Rates of ice mass loss at the calving margins of tidewater glaciers (frontal ablation rates) are a key uncertainty in sea level rise projections. Measurements are difficult because mass lost is replaced by ice flow at variable rates, and frontal ablation incorporates sub-aerial calving, and submarine melt and calving. Here we derive frontal ablation rates for three dynamically contrasting glaciers in Svalbard from an unusually dense series of satellite images. We combine ocean data, ice-front position and terminus velocity to investigate controls on frontal ablation. We find that frontal ablation is not dependent on ice dynamics, nor reduced by glacier surface freeze-up, but varies strongly with sub-surface water temperature. We conclude that calving proceeds by melt undercutting and ice-front collapse, a process that may dominate frontal ablation where submarine melt can outpace ice flow. Our findings illustrate the potential for deriving simple models of tidewater glacier response to oceanographic forcing.
Structure and density of basaltic melts at mantle conditions from first-principles simulations
Authors: Bajgain Suraj , Ghosh Dipta B. , Karki Bijaya B.
Published: October 2015

The origin and stability of deep-mantle melts, and the magmatic processes at different times of Earth’s history are controlled by the physical properties of constituent silicate liquids. Here we report density functional theory-based simulations of model basalt, hydrous model basalt and near-MORB to assess the effects of iron and water on the melt structure and density, respectively. Our results suggest that as pressure increases, all types of coordination between major cations and anions strongly increase, and the water speciation changes from isolated species to extended forms. These structural changes are responsible for rapid initial melt densification on compression thereby making these basaltic melts possibly buoyantly stable at one or more depths. Our finding that the melt-water system is ideal (nearly zero volume of mixing) and miscible (negative enthalpy of mixing) over most of the mantle conditions strengthens the idea of potential water enrichment of deep-mantle melts and early magma ocean.
Trends and variability of the atmosphere–ocean turbulent heat flux in the extratropical Southern Hemisphere
Authors: Herman Agnieszka
Published: October 2015

Ocean–atmosphere interactions are complex and extend over a wide range of temporal and spatial scales. Among the key components of these interactions is the ocean–atmosphere (latent and sensible) turbulent heat flux (THF). Here, based on daily optimally-interpolated data from the extratropical Southern Hemisphere (south of 30°S) from a period 1985–2013, we analyze short-term variability and trends in THF and variables influencing it. It is shown that, in spite of climate-change-related positive trends in surface wind speeds over large parts of the Southern Ocean, the range of the THF variability has been decreasing due to decreasing air–water temperature and humidity differences. Occurrence frequency of very large heat flux events decreased accordingly. Remarkably, spectral analysis of the THF data reveals, in certain regions, robust periodicity at frequencies 0.03–0.04 day−1, corresponding exactly to frequencies of the baroclinic annular mode (BAM). Finally, it is shown that the THF is correlated with the position of the major fronts in sections of the Antarctic Circumpolar Current where the fronts are not constrained by the bottom topography and can adjust their position to the atmospheric and oceanic forcing, suggesting differential response of various sections of the Southern Ocean to the changing atmospheric forcing.
Current-limiting challenges for all-spin logic devices
Authors: Su Li , Zhang Youguang , Klein Jacques-Olivier , Zhang Yue , Bournel Arnaud , Fert Albert , Zhao Weisheng
Published: October 2015

All-spin logic device (ASLD) has attracted increasing interests as one of the most promising post-CMOS device candidates, thanks to its low power, non-volatility and logic-in-memory structure. Here we investigate the key current-limiting factors and develop a physics-based model of ASLD through nano-magnet switching, the spin transport properties and the breakdown characteristic of channel. First, ASLD with perpendicular magnetic anisotropy (PMA) nano-magnet is proposed to reduce the critical current (Ic0). Most important, the spin transport efficiency can be enhanced by analyzing the device structure, dimension, contact resistance as well as material parameters. Furthermore, breakdown current density (JBR) of spin channel is studied for the upper current limitation. As a result, we can deduce current-limiting conditions and estimate energy dissipation. Based on the model, we demonstrate ASLD with different structures and channel materials (graphene and copper). Asymmetric structure is found to be the optimal option for current limitations. Copper channel outperforms graphene in term of energy but seriously suffers from breakdown current limit. By exploring the current limit and performance tradeoffs, the optimization of ASLD is also discussed. This benchmarking model of ASLD opens up new prospects for design and implementation of future spintronics applications.
Predominant role of interferon-γ in the host protective effect of CD8+ T cells against Neospora caninum infection
Authors: Correia Alexandra , Ferreirinha Pedro , Botelho Sofia , Belinha Ana , Leitão Catarina , Caramalho Íris , Teixeira Luzia , González-Fernandéz África , Appelberg Rui , Vilanova Manuel
Published: October 2015

It is well established that CD8+ T cells play an important role in protective immunity against protozoan infections. However, their role in the course of Neospora caninum infection has not been fully elucidated. Here we report that CD8-deficient mice infected with N. caninum presented higher parasitic loads in the brain and lungs and lower spleen and brain immunity-related GTPases than their wild-type counterparts. Moreover, adoptive transfer of splenic CD8+ T cells sorted from N. caninum-primed immunosufficient C57BL/10 ScSn mice prolonged the survival of infected IL-12-unresponsive C57BL/10 ScCr recipients. In both C57BL/6 and C57BL/10 ScSn mice CD8+ T cells are activated and produce interferon-γ (IFN-γ) upon challenged with N. caninum. The host protective role of IFN-γ produced by CD8+ T cells was confirmed in N. caninum-infected RAG2-deficient mice reconstituted with CD8+ T cells obtained from either IFN-γ-deficient or wild-type donors. Mice receiving IFN-γ-expressing CD8+ T cells presented lower parasitic burdens than counterparts having IFN-γ-deficient CD8+ T cells. Moreover, we observed that N. caninum-infected perforin-deficient mice presented parasitic burdens similar to those of infected wild-type controls. Altogether these results demonstrate that production of IFN-γ is a predominant protective mechanism conferred by CD8+ T cells in the course of neosporosis.
An Intelligent Decision Support System for Leukaemia Diagnosis using Microscopic Blood Images
Authors: Chin Neoh Siew , Srisukkham Worawut , Zhang Li , Todryk Stephen , Greystoke Brigit , Peng Lim Chee , Alamgir Hossain Mohammed , Aslam Nauman
Published: October 2015

This research proposes an intelligent decision support system for acute lymphoblastic leukaemia diagnosis from microscopic blood images. A novel clustering algorithm with stimulating discriminant measures (SDM) of both within- and between-cluster scatter variances is proposed to produce robust segmentation of nucleus and cytoplasm of lymphocytes/lymphoblasts. Specifically, the proposed between-cluster evaluation is formulated based on the trade-off of several between-cluster measures of well-known feature extraction methods. The SDM measures are used in conjuction with Genetic Algorithm for clustering nucleus, cytoplasm and background regions. Subsequently, a total of eighty features consisting of shape, texture and colour information of the nucleus and cytoplasm sub-images are extracted. A number of classifiers (multi-layer perceptron, Support Vector Machine (SVM) and Dempster-Shafer ensemble) are employed for lymphocyte/lymphoblast classification. Evaluated with the ALL-IDB2 database, the proposed SDM-based clustering overcomes the shortcomings of Fuzzy C-means which focuses purely on within-cluster scatter variance. It also outperforms Linear Discriminant Analysis and Fuzzy Compactness and Separation for nucleus-cytoplasm separation. The overall system achieves superior recognition rates of 96.72% and 96.67% accuracies using bootstrapping and 10-fold cross validation with Dempster-Shafer and SVM, respectively. The results also compare favourably with those reported in the literature, indicating the usefulness of the proposed SDM-based clustering method.
The neuropeptide oxytocin modulates consumer brand relationships
Authors: Fürst Andreas , Thron Jesko , Scheele Dirk , Marsh Nina , Hurlemann René
Published: October 2015

Each year, companies invest billions of dollars into marketing activities to embellish brands as valuable relationship partners assuming that consumer brand relationships (CBRs) and interpersonal relationships rest upon the same neurobiological underpinnings. Given the crucial role of the neuropeptide oxytocin (OXT) in social bonding, this study tests whether OXT-based mechanisms also determine the bond between consumers and brands. We conducted a randomized, placebo-controlled study involving 101 subjects and analyzed the effect of intranasal OXT on consumers’ attribution of relationship qualities to brands, brands paired with human celebrity endorsers and familiar persons. OXT indeed promoted the attribution of relationship qualities not only in the case of social and semi-social stimuli, but also brands. Intriguingly, for subjects scoring high on autistic-like traits, the effect of OXT was completely reversed, evident in even lower relationship qualities across all stimulus categories. The importance of OXT in a CBR context is further corroborated by a three-fold increase in endogenous release of OXT following exposure to one’s favorite brand and positive associations between baseline peripheral OXT concentrations and brand relationship qualities. Collectively, our findings indicate that OXT not only plays a fundamental role in developing interpersonal relationships, but also enables relationship formation with objects such as brands.
The transfer and transformation of collective network information in gene-matched networks
Authors: Kitsukawa Takashi , Yagi Takeshi
Published: October 2015

Networks, such as the human society network, social and professional networks and biological system networks, contain vast amounts of information. Information signals in networks are distributed over nodes and transmitted through intricately wired links, making the transfer and transformation of such information difficult to follow. Here we introduce a novel method for describing network information and its transfer using a model network, the Gene-matched network (GMN), in which nodes (neurons) possess attributes (genes). In the GMN, nodes are connected according to their expression of common genes. Because neurons have multiple genes, the GMN is cluster-rich. We show that, in the GMN, information transfer and transformation were controlled systematically, according to the activity level of the network. Furthermore, information transfer and transformation could be traced numerically with a vector using genes expressed in the activated neurons, the active-gene array, which was used to assess the relative activity among overlapping neuronal groups. Interestingly, this coding style closely resembles the cell-assembly neural coding theory. The method introduced here could be applied to many real-world networks, since many systems, including human society and various biological systems, can be represented as a network of this type.
Activation of Mg2+-dependent DNAzymes based on AP site-containing triplex for specific melamine recognition
Authors: Wang Ya , Zhang Junying , Zhu Linling , Lu Linlin , Feng Chongchong , Wang Fengyang , Xu Zhiai , Zhang Wen
Published: October 2015

A novel strategy for melamine recognition based on melamine binding-triggered triplex formation and DNAzyme activity regulation was developed.
Oxide-based nanostructures for photocatalytic and electrocatalytic applications
Authors: Ganguly Aparna , Anjaneyulu Oruganti , Ojha Kasinath , Ganguli Ashok K.
Published: October 2015

The enormous efforts on the design of efficient oxide-based materials towards photocatalysis & electrocatalysis have been highlighted in this article with emphasis on their size, structure & morphology.
Oxidative photoreactivity of mono-transition-metal functionalized lacunary Keggin anions
Authors: Dave M. , Streb C.
Published: October 2015

The photooxidative activity of mono-transition-metal functionalized lacunary silicotungstate Keggin anions is reported together with preliminary mechanistic insight into the photoreactivity.
Oxocomplexes of Mo(vi) and W(vi) with 8-hydroxyquinoline-5-sulfonate in solution: structural studies and the effect of the metal ion on the photophysical behaviour
Authors: Luísa Ramos M. , Justino Licínia L. G. , Abreu Paulo E. , Fonseca Sofia M. , Burrows Hugh D.
Published: October 2015

Mo(vi) and W(vi) complexes with 8-HQS show differences in luminescence behaviour, attributed to the relative energies of their LMCT and emitting ligand based levels.
Resolving ambiguities in nanowire field-effect transistor characterization
Authors: Heedt Sebastian , Otto Isabel , Sladek Kamil , Hardtdegen Hilde , Schubert Jürgen , Demarina Natalia , Lüth Hans , Grützmacher Detlev , Schäpers Thomas
Published: October 2015

The profound impact of InAs nanowire surface states on transistor functionality is quantified using a novel dual-gate FET evaluation method in conjunction with finite element method simulations of nanowire electrostatics.
Nano-scale, planar and multi-tiered current pathways from a carbon nanotube–copper composite with high conductivity, ampacity and stability
Authors: Subramaniam Chandramouli , Sekiguchi Atsuko , Yamada Takeo , Futaba Don N. , Hata Kenji
Published: October 2015

The realization of nanoscale, multi-dimensional patternability of CNT–Cu conductive lines which exhibit superior ampacity and high-temperature stability compared to Cu is reported.
Diffraction scattering computed tomography: a window into the structures of complex nanomaterials
Authors: Birkbak M. E. , Leemreize H. , Frølich S. , Stock S. R. , Birkedal H.
Published: October 2015

Diffraction scattering computed tomography allows probing nanoscale materials in 3D while fully reconstructing scattering/diffraction patterns inside the sample.
A fast transfer-free synthesis of high-quality monolayer graphene on insulating substrates by a simple rapid thermal treatment
Authors: Wu Zefei , Guo Yanqing , Guo Yuzheng , Huang Rui , Xu Shuigang , Song Jie , Lu Huanhuan , Lin Zhenxu , Han Yu , Li Hongliang , Han Tianyi , Lin Jiangxiazi , Wu Yingying , Long Gen , Cai Yuan , Cheng Chun , Su Dangsheng , Robertson John , Wang Ning
Published: October 2015

A simple method is developed for the transfer-free synthesis of monolayer graphene on dielectric substrates.
Graphene quantum dots for the inhibition of β amyloid aggregation
Authors: Liu Yibiao , Xu Li-Ping , Dai Wenhao , Dong Haifeng , Wen Yongqiang , Zhang Xueji
Published: October 2015

GQDs, efficient and low-cytotoxicity inhibitors, are reported for their application in inhibiting the aggregation of Aβ peptides.
Solvent-free mechanochemical synthesis of a bicyclononyne tosylate: a fast route towards bioorthogonal clickable poly(2-oxazoline)s
Authors: Glassner Mathias , Maji Samarendra , de la Rosa Victor R. , Vanparijs Nane , Ryskulova Kanykei , De Geest Bruno G. , Hoogenboom Richard
Published: October 2015

The mechanochemical synthesis of a bicyclononyne tosylate (BCN-OTs) and its subsequent use for the CROP of 2-ethyl-2-oxazoline yielding bioorthogonal clickable poly(2-ethyl-2-oxazoline) is presented.
Supramolecular assembly of dipeptide functionalized benzo[ghi]perylene monoimide directs white light emission via donor–acceptor interactions
Authors: Manna Manoj K. , Rasale Dnyaneshwar B. , Das Apurba K.
Published: October 2015

Optical and self-assembly nature of an aromatic dipeptide Phe-Phe (FF) functionalized benzo[ghi]perylene monoimide (BPI) are studied. Acceptor BPI-FF-OMe molecule shows white light emission upon energy transfer from donor pyrenebutyric acid molecule.
Micron-sized flower-like Fe3O4@GMA magnetic porous microspheres for lipase immobilization
Authors: Ali Zafar , Tian Lei , Zhao Panpan , Zhang Baoliang , Nisar Ali , Li Xiangjie , Zhang Hepeng , Zhang Qiuyu
Published: October 2015

Flower-like Fe3O4 microspheres prepared by a fast solvothermal method were selected to fabricate micron-sized Fe3O4@glycidyl methacrylate (GMA) magnetic porous microspheres.
ZnS nanoparticles embedded in porous carbon matrices as anode materials for lithium ion batteries
Authors: Fu Yun , Zhang Zhian , Yang Xing , Gan Yongqin , Chen Wei
Published: October 2015

In situ synthesis of a novel zinc sulfide/porous carbon composite is achieved by virtue of the metal–organic frameworks strategy. The composite exhibits significant electrochemical performance as an anode material for lithium ion batteries.
Low-temperature synthesis of WO3 nanolamella and their sensing properties for xylene
Authors: li Feng , li Yujia , Jing Fuyi , Zhou Jingran , Chen Yu , Sun Dongming , Ruan Shengping
Published: October 2015

Tungsten trioxides (WO3) are an important class of n-type semiconductor oxide materials with a wide band-gap.
Structural reliability evaluation of low-k nanoporous dielectric interlayers integrated into microelectronic devices
Authors: Heo Kyuyoung , Ree Brian J. , Choi Kyeung-Keun , Ree Moonhor
Published: October 2015

Structural reliability assessment on the integration of low-k nanoporous dielectrics into a multilayer structure, involving capping, chemical mechanical polishing, post-cleaning, and thermal annealing processes, was successfully demonstrated in a nondestructive manner.
Influence of hybrid nanostructures and its tailoring mechanism on permeability, rheology, conductivity, and adhesion properties of a novel rubber blend nanocomposite
Authors: Sankaran Kumar , Nando Golok B. , Ramachandran Padmanabhan , Nair Sujith , Govindan Unnikrishnan , Arayambath Sreejesh , Chattopadhyay Santanu
Published: October 2015

The development of hybrid nanostructures in the nanocomposite significantly increases the air impermeability, electrical, and thermal conductivity. Interestingly, it bridges to increase the path of diffusion and conduction.
Co-assembly of two types of complementary dendritic units into amphiphilic supramolecular complexes capable of hosting guest molecules
Authors: Liu Yi , Xiao Ting , Xu Li , Liu Xun-Yong
Published: October 2015

Novel amphiphilic supramolecular complexes with two types of complementary dendritic units could encapsulate hydrophilic guests with excellent aggregating encapsulation performances.
Au@Cu7S4 yolk–shell nanoparticles as a 980 nm laser-driven photothermal agent with a heat conversion efficiency of 63%
Authors: Zhang Jing , Liu Guigao , He Fang , Chen Lixia , Huang Yuan
Published: October 2015

Au@Cu7S4 yolk–shell nanoparticles have been prepared via an inward replacement strategy and they exhibit powerful photothermal properties with a heat conversion efficiency up to 63% under 980 nm laser irradiation.
Effect of aggregation behavior and phenolic hydroxyl group content on the performance of lignosulfonate doped PEDOT as a hole extraction layer in polymer solar cells
Authors: Hong Nanlong , Qiu Xueqing , Deng Wanyuan , He Zhicai , Li Yuan
Published: October 2015

Aggregation behaviour and –OH content of lignosulfonate play a key role for the promising performance when PEDOT:LS acts as the HEL in PSCs.
Modelling and optimization of critical parameters by hybrid RSM-GA for the separation of BSA using a tubular configured MFI-type zeolite microfiltration membrane
Authors: Kumar R. Vinoth , Moorthy I. Ganesh , Pugazhenthi G.
Published: October 2015

A tubular MFI-type zeolite membrane exhibited good rejection (82%) of BSA with a permeate flux of 4.63 × 10−5m s−1.
Unprecedentedly targeted customization of molecular energy levels with auxiliary-groups in organic solar cell sensitizers
Authors: Xie Yongshu , Wu Wenjun , Zhu Haibo , Liu Jingchuan , Zhang Weiwei , Tian He , Zhu Wei-Hong
Published: October 2015

Lowering the LUMOs and decreasing energy “waste” is targeted through inserting an auxiliary group from an electron donor or acceptor into D–π–A organic sensitizers, and the photovoltaic efficiency increases 38 fold from 0.24 to 9.46%.
High symmetry or low symmetry, that is the question – high performance Dy(iii) single-ion magnets by electrostatic potential design
Authors: Sun Wen-Bin , Yan Peng-Fei , Jiang Shang-Da , Wang Bing-Wu , Zhang Yi-Quan , Li Hong-Feng , Chen Peng , Wang Zhe-Ming , Gao Song
Published: October 2015

A suitable arrangement of the ligand charge can complement a low symmetry system and induce an excellent unexpected SMM behavior.
Dewetting transition induced by surfactants in sessile droplets at the early evaporation stage
Authors: Zhong Xin , Duan Fei
Published: October 2015

As surfactants are employed to control the wettability of solutions, we observe that the sessile droplet dewetting induced by autophobing exhibits a unique relation with the surfactant concentration.
Molecular assembly of highly symmetric molecules under a hydrogen bond framework controlled by alkyl building blocks: a simple approach to fine-tune nanoscale structures
Authors: Tanphibal Pimsai , Tashiro Kohji , Chirachanchai Suwabun
Published: October 2015

This work shows how the molecular assemblies under the hydrogen bond and weak interactions fine-tune their morphologies through the systematic studies of highly symmetric molecules, i.e. diamine-based benzoxazine dimers.
Entropic forces stabilize diverse emergent structures in colloidal membranes
Authors: Kang Louis , Gibaud Thomas , Dogic Zvonimir , Lubensky T. C.
Published: October 2015

A variety of structures and properties of depletion-induced colloidal membranes can be quantitatively explained by a simple theory that combines Frank elasticity and depletant entropy.
Plasma-grown graphene petals templating Ni–Co–Mn hydroxide nanoneedles for high-rate and long-cycle-life pseudocapacitive electrodes
Authors: Xiong Guoping , He Pingge , Liu Lei , Chen Tengfei , Fisher Timothy S.
Published: October 2015

Ni–Co–Mn triple hydroxide (NCMTH) nanoneedles were coated on plasma-grown graphitic petals (GPs) by a facile one-step hydrothermal method for high-rate and long-cycle-life pseudocapacitive electrodes.
Dual-template synthesis of ordered mesoporous carbon/Fe2O3nanowires: high porosity and structural stability for supercapacitors
Authors: Hu Junkai , Noked Malachi , Gillette Eleanor , Han Fudong , Gui Zhe , Wang Chunsheng , Lee Sang Bok
Published: October 2015

Dual-templated OMCNWs present the advantages of soft- & hard-template methods, leading to a structure-induced capacitance improvement of Fe2O3nanoparticles.
Sandwich-structured Fe2O3@SiO2@Au nanoparticles with magnetoplasmonic responses
Authors: Cai Zhongyu , Leong Eunice S. P. , Wang Zhigang , Niu Wenxin , Zhang Weiqing , Ravaine Serge , Yakovlev Nikolai L. , Liu Yan Jun , Teng Jinghua , Lu Xianmao
Published: October 2015

We fabricated highly uniform sandwich-structured γ-Fe2O3@SiO2@Au spindle nanoparticles with novel structural and magnetic tunable surface plasmon resonance.
In situ iodoalkane-reduction of graphene oxide in a polymer matrix: an easy and effective approach for the fabrication of conductive composites
Authors: Guo Haiquan , Liu Fangfang , Zhao Jianying , Yao Haibo , Jin Rizhe , Kang Chuanqing , Bian Zheng , Qiu Xuepeng , Gao Lianxun
Published: October 2015

Graphene/polyimide composites with the conductivity of 2.22 S m−1 were fabricated via in situ reduction of graphene oxide by 1,2-diiodoethane.
In search of the boundary between repetitive and non-repetitive protein sequences
Authors: Richard François D. , Kajava Andrey V.
Published: October 2015

Tandem repeats (TRs) are frequently not perfect, containing a number of mutations accumulated during evolution. One of the main problems is to distinguish between the sequences that contain highly imperfect TRs and the aperiodic sequences. The majority of proteins with TRs in sequences have repetitive arrangements in their 3D structures. Therefore, the 3D structures of proteins can be used as a benchmarking criterion for TR detection in sequences. Different TR detection tools use their own scoring procedures to determine the boundary between repetitive and non-repetitive protein sequences. Here we described these scoring functions and benchmark them by using known structural TRs. Our survey shows that none of the existing scoring procedures are able to achieve an appropriate separation between genuine structural TRs and non-TR regions. This suggests that if we want to obtain a collection of structurally and functionally meaningful TRs from a large scale analysis of proteomes, the TR scoring metrics need to be improved.
Two repetitive, biofilm-forming proteins from Staphylococci: from disorder to extension
Authors: Whelan Fiona , Potts Jennifer R.
Published: October 2015

Staphylococcus aureus and Staphylococcus epidermidis are an important cause of medical device-related infections that are difficult to treat with antibiotics. Biofilms, in which bacteria are embedded in a bacterially-produced exopolymeric matrix, form on the surface of the implanted medical device. Our understanding of the molecular mechanisms underlying the initial surface attachment and subsequent intercellular interactions as the biofilm matures is improving. Biofilm accumulation can be mediated by a partially deacetylated form of poly-N-acetylglucosamine (PNAG) but, more recently, the role of bacterial surface proteins is being recognized. Here we describe the structure and function of two S. aureus cell surface proteins, FnBPA and SasG, implicated in host interactions and biofilm accumulation. These multifunctional proteins employ intrinsic disorder for distinct molecular outcomes. In the case of FnBPA, disorder generates adhesive arrays that bind fibronectin (Fn); in the case of SasG, disorder is, counterintuitively, used to maintain a strong extended fold.
A designed repeat protein as an affinity capture reagent
Authors: Speltz Elizabeth B. , Brown Rebecca S.H. , Hajare Holly S. , Schlieker Christian , Regan Lynne
Published: October 2015

Repeat proteins are an attractive target for protein engineering and design. We have focused our attention on the design and engineering of one particular class: tetratricopeptide repeat (TPR) proteins. In previous work, we have shown that the structure and stability of TPR proteins can be manipulated in a rational fashion [Cortajarena (2011) Prot. Sci. 20, 1042–1047; Main (2003) Structure 11, 497–508]. Building on those studies, we have designed and characterized a number of different peptide-binding TPR modules and we have also assembled these modules into supramolecular arrays [Cortajarena (2009) ACS Chem. Biol. 5, 545—552; Cortajarena (2008) ACS Chem. Biol. 3, 161—166; Jackrel (2009) Prot. Sci. 18, 762—774; Kajander (2007) Acta Crystallogr. D Biol. Crystallogr. 63, 800—811]. Here we focus on the development of one such TPR–peptide interaction for a practical application, affinity purification. We illustrate the general utility of our designed protein interaction. Furthermore, this example highlights how basic research on protein–peptide interactions can lead to the development of novel reagents with important practical applications.
ABCA3, a key player in neonatal respiratory transition and genetic disorders of the surfactant system
Authors: Peca Donatella , Cutrera Renato , Masotti Andrea , Boldrini Renata , Danhaive Olivier
Published: October 2015

Genetic disorders of the surfactant system are rare diseases with a broad range of clinical manifestations, from fatal respiratory distress syndrome (RDS) in neonates to chronic interstitial lung disease (ILD) in children and adults. ABCA3 [ATP-binding cassette (ABC), subfamily A, member 3] is a lung-specific phospholipid transporter critical for intracellular surfactant synthesis and storage in lamellar bodies (LBs). Its expression is developmentally regulated, peaking prior to birth under the influence of steroids and transcription factors. Bi-allelic mutations of the ABCA3 gene represent the most frequent cause of congenital surfactant deficiency, indicating its critical role in lung function. Mutations affect surfactant lipid and protein processing and LBs’ morphology, leading to partial or total surfactant deficiency. Approximately 200 mutations have been reported, most of which are unique to individuals and families, which makes diagnosis and prognosis challenging. Various types of mutations, affecting different domains of the protein, account in part for phenotype diversity. Disease-causing mutations have been reported in most coding and some non-coding regions of the gene, but tend to cluster in the first extracellular loop and the second nucleotide-binding domain (NBD), leading to defective glycosylation and trafficking defects and interfering with ATP binding and hydrolysis respectively. Mono-allelic damaging and benign variants are often subclinical but may act as disease modifiers in lung diseases such as RDS of prematurity or associate with mutations in other surfactant-related genes. Diagnosis is complex but essential and should combine pathology and ultrastructure studies on lung biopsy with broad-spectrum genetic testing of surfactant-related genes, made possible by recent technology advances in the massive parallel sequencing technology.
The role of Trib1 in myeloid leukaemogenesis and differentiation
Authors: Nakamura Takuro
Published: October 2015

Tribbles homolog 1 (Trib1) was identified as a common integration site of the Homeobox a9 (Hoxa9)/murine ecotropic virus integration site 1 (Meis1) retrovirus in acute myeloid leukaemia (AML). Trib1 is by itself a transforming gene for myeloid cells but also significantly accelerates progression of Hoxa9/Meis1-induced AML. The strong transforming activity of Trib1 depends on its bi-directional function in CCAAT/enhancer-binding protein (C/EBPα) degradation and MAPK/ERK kinase (MEK)/extracellular-signal-regulated kinase (ERK) activation. TRIB1 is also involved in a certain type of human AML and a TRIB1 somatic point mutation R107L was identified in a case of Down syndrome (DS)-related acute megakaryocytic leukaemia. Although Trib1 knockout (KO) did not suppress haematopoiesis in mouse bone marrow significantly, increase in mature granulocytes was observed and promotion of myeloid differentiation was associated with the increased C/EBPα protein. Trib1 thus plays an important role in myeloid cell development and transformation.
ABCB1 in children's brain tumours
Authors: Coyle Beth , Kessler Maya , Sabnis Durgagauri H. , Kerr Ian D.
Published: October 2015

Tumours of the central nervous system are the most common solid tumour, accounting for a quarter of the 1500 cases of childhood cancer diagnosed each year in the U.K. They are the most common cause of cancer-related death in children. Treatment consists of surgery followed by adjuvant chemotherapy and/or radiotherapy. Survival rates have generally increased, but many survivors suffer from radiotherapy-related neurocognitive and endocrine side effects as well as an increased risk of secondary cancer. Adjuvant chemotherapy is normally given in combination to circumvent chemoresistance, but several studies have demonstrated it to be ineffective in the absence of radiotherapy. The identification of children with drug-resistant disease at the outset could allow stratification of those that are potentially curable by chemotherapy alone. Ultimately, however, what is required is a means to overcome this drug resistance and restore the effectiveness of chemotherapy. Medulloblastomas and ependymomas account for over 30% of paediatric brain tumours. Advances in neurosurgery, adjuvant radiotherapy and chemotherapy have led to improvements in 5-year overall survival rates. There remain, however, significant numbers of medulloblastoma patients that have intrinsically drug-resistant tumours and/or present with disseminated disease. Local relapse in ependymoma is also common and has an extremely poor prognosis with only 25% of children surviving first relapse. Each of these is consistent with the acquisition of drug and radiotherapy resistance. Since the majority of chemotherapy drugs currently used to treat these patients are transport substrates for ATP-binding cassette sub-family B member 1 (ABCB1) we will address the hypothesis that ABCB1 expression underlies this drug resistance.
ABC transporter research: going strong 40 years on
Authors: Theodoulou Frederica L. , Kerr Ian D.
Published: October 2015

In most organisms, ABC transporters constitute one of the largest families of membrane proteins. In humans, their functions are diverse and underpin numerous key physiological processes, as well as being causative factors in a number of clinically relevant pathologies. Advances in our understanding of these diseases have come about through combinations of genetic and protein biochemical investigations of these transporters and the power of in vitro and in vivo investigations is helping to develop genotype–phenotype understanding. However, the importance of ABC transporter research goes far beyond human biology; microbial ABC transporters are of great interest in terms of understanding virulence and drug resistance and industrial biotechnology researchers are exploring the potential of prokaryotic ABC exporters to increase the capacity of synthetic biology systems. Plant ABC transporters play important roles in transport of hormones, xenobiotics, metals and secondary metabolites, pathogen responses and numerous aspects of development, all of which are important in the global food security area. For 3 days in Chester, this Biochemical Society Focused Meeting brought together researchers with diverse experimental approaches and with different fundamental questions, all of which are linked by the commonality of ABC transporters.
Watching conformational dynamics of ABC transporters with single-molecule tools
Authors: Husada Florence , Gouridis Giorgos , Vietrov Ruslan , Schuurman-Wolters Gea K. , Ploetz Evelyn , de Boer Marijn , Poolman Bert , Cordes Thorben
Published: October 2015

ATP-binding cassette (ABC) transporters play crucial roles in cellular processes, such as nutrient uptake, drug resistance, cell-volume regulation and others. Despite their importance, all proposed molecular models for transport are based on indirect evidence, i.e. functional interpretation of static crystal structures and ensemble measurements of function and structure. Thus, classical biophysical and biochemical techniques do not readily visualize dynamic structural changes. We recently started to use single-molecule fluorescence techniques to study conformational states and changes of ABC transporters in vitro, in order to observe directly how the different steps during transport are coordinated. This review summarizes our scientific strategy and some of the key experimental advances that allowed the substrate-binding mechanism of prokaryotic ABC importers and the transport cycle to be explored. The conformational states and transitions of ABC-associated substrate-binding domains (SBDs) were visualized with single-molecule FRET, permitting a direct correlation of structural and kinetic information of SBDs. We also delineated the different steps of the transport cycle. Since information in such assays are restricted by proper labelling of proteins with fluorescent dyes, we present a simple approach to increase the amount of protein with FRET information based on non-specific interactions between a dye and the size-exclusion chromatography (SEC) column material used for final purification.
Adaptive double‐integral‐sliding‐mode‐maximum‐power‐point tracker for a photovoltaic system
Authors: Subudhi Bidyadhar , Pradhan Raseswari
Published: October 2015

This study proposed an adaptive double‐integral‐sliding‐mode‐controller‐maximum‐power‐point tracker (DISMC‐MPPT) for maximum‐power‐point (MPP) tracking of a photovoltaic (PV) system. The objective of this study is to design a DISMC‐MPPT with a new adaptive double‐integral‐sliding surface in order that MPP tracking is achieved with reduced chattering and steady‐state error in the output voltage or current. The proposed adaptive DISMC‐MPPT possesses a very simple and efficient PWM‐based control structure that keeps switching frequency constant. The controller is designed considering the reaching and stability conditions to provide robustness and stability. The performance of the proposed adaptive DISMC‐MPPT is verified through both MATLAB/Simulink simulation and experiment using a 0.2 kW prototype PV system. From the obtained results, it is found out that this DISMC‐MPPT is found to be more efficient compared with that of Tan's and Jiao's DISMC‐MPPTs.
The influence of the bromine atom Cooper minimum on the photoelectron angular distributions and branching ratios of the four outermost bands of bromobenzene
Authors: Powis I. , Holland D. M. P. , Antonsson E. , Patanen M. , Nicolas C. , Miron C. , Schneider M. , Soshnikov D. Yu. , Dreuw A. , Trofimov A. B.
Published: October 2015

Angle resolved photoelectron spectra of the X̃2B1, Ã2A2, B̃2B2, and C̃2B1 states of bromobenzene have been recorded over the excitation range 20.5-94 eV using linearly polarized synchrotron radiation. The photoelectron anisotropy parameters and electronic branching ratios derived from these spectra have been compared to theoretical predictions obtained with the continuum multiple scattering approach. This comparison shows that ionization from the 8b2 orbital and, to a lesser extent, the 4b1 orbital is influenced by the Cooper minimum associated with the bromine atom. The 8b2 and 4b1 orbitals are nominally bromine lone-pairs, but the latter orbital interacts strongly with the π-orbitals in the benzene ring and this leads to a reduced atomic character. Simulations of the X̃2B1, B̃2B2, and C̃2B1 state photoelectron bands have enabled most of the vibrational structures appearing in the experimental spectra to be assigned. Many of the photoelectron peaks exhibit an asymmetric shape with a tail towards low binding energy. This asymmetry has been examined in the simulations of the vibrationally unexcited peak, due mainly to the adiabatic transition, in the X̃2B1 state photoelectron band. The simulations show that the asymmetric profile arises from hot-band transitions. The inclusion of transitions originating from thermally populated levels results in a satisfactory agreement between the experimental and simulated peak shapes.
Overview of the negative ion based neutral beam injectors for ITER
Authors: Schunke B. , Boilson D. , Chareyre J. , Choi C.-H. , Decamps H. , El-Ouazzani A. , Geli F. , Graceffa J. , Hemsworth R. , Kushwah M. , Roux K. , Shah D. , Singh M. , Svensson L. , Urbani M.
Published: October 2015

The ITER baseline foresees 2 Heating Neutral Beams (HNB’s) based on 1 MeV 40 A D− negative ion accelerators, each capable of delivering 16.7 MW of deuterium atoms to the DT plasma, with an optional 3rd HNB injector foreseen as a possible upgrade. In addition, a dedicated diagnostic neutral beam will be injecting ≈22 A of H0 at 100 keV as the probe beam for charge exchange recombination spectroscopy. The integration of the injectors into the ITER plant is nearly finished necessitating only refinements. A large number of components have passed the final design stage, manufacturing has started, and the essential test beds—for the prototype route chosen—will soon be ready to start.
Cavitation erosion prediction based on analysis of flow dynamics and impact load spectra
Authors: Mihatsch Michael S. , Schmidt Steffen J. , Adams Nikolaus A.
Published: October 2015

Cavitation erosion is the consequence of repeated collapse-induced high pressure-loads on a material surface. The present paper assesses the prediction of impact load spectra of cavitating flows, i.e., the rate and intensity distribution of collapse events based on a detailed analysis of flow dynamics. Data are obtained from a numerical simulation which employs a density-based finite volume method, taking into account the compressibility of both phases, and resolves collapse-induced pressure waves. To determine the spectrum of collapse events in the fluid domain, we detect and quantify the collapse of isolated vapor structures. As reference configuration we consider the expansion of a liquid into a radially divergent gap which exhibits unsteady sheet and cloud cavitation. Analysis of simulation data shows that global cavitation dynamics and dominant flow events are well resolved, even though the spatial resolution is too coarse to resolve individual vapor bubbles. The inviscid flow model recovers increasingly fine-scale vapor structures and collapses with increasing resolution. We demonstrate that frequency and intensity of these collapse events scale with grid resolution. Scaling laws based on two reference lengths are introduced for this purpose. We show that upon applying these laws impact load spectra recorded on experimental and numerical pressure sensors agree with each other. Furthermore, correlation between experimental pitting rates and collapse-event rates is found. Locations of high maximum wall pressures and high densities of collapse events near walls obtained numerically agree well with areas of erosion damage in the experiment. The investigation shows that impact load spectra of cavitating flows can be inferred from flow data that captures the main vapor structures and wave dynamics without the need for resolving all flow scales.
Particle-driven gravity currents in non-rectangular cross section channels
Authors: Zemach T.
Published: October 2015

We consider a high-Reynolds-number gravity current generated by suspension of heavier particles in fluid of density ρi, propagating along a channel into an ambient fluid of the density ρa. The bottom and top of the channel are at z = 0, H, and the cross section is given by the quite general −f1(z) ≤ y ≤ f2(z) for 0 ≤ z ≤ H. The flow is modeled by the one-layer shallow-water equations obtained for the time-dependent motion which is produced by release from rest of a fixed volume of mixture from a lock. We solve the problem by the finite-difference numerical code to present typical height h(x, t), velocity u(x, t), and volume fraction of particles (concentration) ϕ(x, t) profiles. The methodology is illustrated for flow in typical geometries: power-law (f(z) = zα and f(z) = (H − z)α, where α is positive constant), trapezoidal, and circle. In general, the speed of propagation of the flows driven by suspensions decreases compared with those driven by a reduced gravity in homogeneous currents. However, the details depend on the geometry of the cross section. The runout length of suspensions in channels of power-law cross sections is analytically predicted using a simplified depth-averaged “box” model. The present approach is a significant generalization of the classical gravity current problem. The classical formulation for a rectangular channel is now just a particular case, f(z) = const., in the wide domain of cross sections covered by this new model.
Extending the applicability of an open-ring trap to perform experiments with a single laser-cooled ion
Authors: Cornejo J. M. , Colombano M. , Doménech J. , Block M. , Delahaye P. , Rodríguez D.
Published: October 2015

A special ion trap was initially built up to perform β-ν correlation experiments with radioactive ions. The trap geometry is also well suited to perform experiments with laser-cooled ions, serving for the development of a new type of Penning trap, in the framework of the project TRAPSENSOR at the University of Granada. The goal of this project is to use a single 40Ca+ ion as detector for single-ion mass spectrometry. Within this project and without any modification to the initial electrode configuration, it was possible to perform Doppler cooling on 40Ca+ ions, starting from large clouds and reaching single ion sensitivity. This new feature of the trap might be important also for other experiments with ions produced at radioactive ion beam facilities. In this publication, the trap and the laser system will be described, together with their performance with respect to laser cooling applied to large ion clouds down to a single ion.
On the accuracy of commonly used density functional approximations in determining the elastic constants of insulators and semiconductors
Authors: Råsander M. , Moram M. A.
Published: October 2015

We have performed density functional calculations using a range of local and semi-local as well as hybrid density functional approximations of the structure and elastic constants of 18 semiconductors and insulators. We find that most of the approximations have a very small error in the lattice constants, of the order of 1%, while the errors in the elastic constants and bulk modulus are much larger, at about 10% or better. When comparing experimental and theoretical lattice constants and bulk modulus we have included zero-point phonon effects. These effects make the experimental reference lattice constants 0.019 Å smaller on average while making the bulk modulus 4.3 GPa stiffer on average. According to our study, the overall best performing density functional approximations for determining the structure and elastic properties are the PBEsol functional, the two hybrid density functionals PBE0 and HSE (Heyd, Scuseria, and Ernzerhof), as well as the AM05 functional.
Free volume under shear
Authors: Maiti Moumita , Vinutha H. A. , Sastry Srikanth , Heussinger Claus
Published: October 2015

Using an athermal quasistatic simulation protocol, we study the distribution of free volumes in sheared hard-particle packings close to, but below, the random-close packing threshold. We show that under shear, and independent of volume fraction, the free volumes develop features similar to close-packed systems — particles self-organize in a manner as to mimick the isotropically jammed state. We compare athermally sheared packings with thermalized packings and show that thermalization leads to an erasure of these structural features. The temporal evolution in particular the opening-up and the closing of free-volume patches is associated with the single-particle dynamics, showing a crossover from ballistic to diffusive behavior.
Surface modification of ferritic steels using MEVVA and duoplasmatron ion sources
Authors: Kulevoy Timur V. , Chalyhk Boris B. , Fedin Petr A. , Sitnikov Alexey L. , Kozlov Alexander V. , Kuibeda Rostislav P. , Andrianov Stanislav L. , Orlov Nikolay N. , Kravchuk Konstantin S. , Rogozhkin Sergey V. , Useinov Alexey S. , Oks Efim M. , Bogachev Alexey A. , Nikitin Alexander A. , Iskandarov Nasib A. , Golubev Alexander A.
Published: October 2015

Metal Vapor Vacuum Arc (MEVVA) ion source (IS) is a unique tool for production of high intensity metal ion beam that can be used for material surface modification. From the other hand, the duoplasmatron ion source provides the high intensity gas ion beams. The MEVVA and duoplasmatron IS developed in Institute for Theoretical and Experimental Physics were used for the reactor steel surface modification experiments. Response of ferritic-martensitic steel specimens on titanium and nitrogen ions implantation and consequent vacuum annealing was investigated. Increase in microhardness of near surface region of irradiated specimens was observed. Local chemical analysis shows atom mixing and redistribution in the implanted layer followed with formation of ultrafine precipitates after annealing.