bluuebunny/crossref_metadata_2025 huggingface dataset:
High-intensity power-resolved radiation imaging of an operational nuclear reactor
Authors: Beaumont Jonathan S. , Mellor Matthew P. , Villa Mario , Joyce Malcolm J.
Published: October 2015

Knowledge of the neutron distribution in a nuclear reactor is necessary to ensure the safe and efficient burnup of reactor fuel. Currently these measurements are performed by in-core systems in what are extremely hostile environments and in most reactor accident scenarios it is likely that these systems would be damaged. Here we present a compact and portable radiation imaging system with the ability to image high-intensity fast-neutron and gamma-ray fields simultaneously. This system has been deployed to image radiation fields emitted during the operation of a TRIGA test reactor allowing a spatial visualization of the internal reactor conditions to be obtained. The imaged flux in each case is found to scale linearly with reactor power indicating that this method may be used for power-resolved reactor monitoring and for the assay of ongoing nuclear criticalities in damaged nuclear reactors.
A novel combined RNA-protein interaction analysis distinguishes HIV-1 Gag protein binding sites from structural change in the viral RNA leader
Authors: Kenyon Julia C. , Prestwood Liam J. , Lever Andrew M. L.
Published: October 2015

RNA-protein interactions govern many viral and host cell processes. Conventional ‘footprinting’ to examine RNA-protein complex formation often cannot distinguish between sites of RNA-protein interaction and sites of RNA structural remodelling. We have developed a novel technique combining photo crosslinking with RNA 2′ hydroxyl reactivity (‘SHAPE’) that achieves rapid and hitherto unachievable resolution of both RNA structural changes and the sites of protein interaction within an RNA-protein complex. ‘XL-SHAPE’ was validated using well-characterized viral RNA-protein interactions: HIV-1 Tat/TAR and bacteriophage MS2 RNA/Coat Binding Protein. It was then used to map HIV-1 Gag protein interactions on 2D and 3D models of the viral RNA leader. Distinct Gag binding sites were identified on exposed RNA surfaces corresponding to regions identified by mutagenesis as important for genome packaging. This widely applicable technique has revealed a first view of the stoichiometry and structure of the initial complex formed when HIV captures its genome.
Cord Blood 25-hydroxyvitamin D and Fetal Growth in the China-Anhui Birth Cohort Study
Authors: Zhu Peng , Tong Shi-lu , Hu Wen-biao , Hao Jia-hu , Tao Rui-xue , Huang Kun , Mou Zhe , Zhou Qi-fan , Jiang Xiao-min , Tao Fang-biao
Published: October 2015

We determined the association of cord blood 25-hydroxyvitamin D [25(OH)D] with birth weight and the risk of small for gestational age (SGA). As part of the China-Anhui Birth Cohort (C-ABC) study, we measured cord blood levels of 25(OH)D in 1491 neonates in Hefei, China. The data on maternal sociodemographic characteristics, health status, lifestyle, birth outcomes were prospectively collected. Multiple regression models were used to estimate the association of 25(OH)D levels with birth weight and the risk of SGA. Compared with neonates in the lowest decile of cord blood 25(OH)D levels, neonates in four deciles (the fourth, fifth, sixth and seventh deciles) had significantly increased birth weight and decreased risk of SGA. Multiple linear regression models showed that per 10 nmol/L increase in cord blood 25(OH)D, birth weight increased by 61.0 g (95% CI: 31.9, 89.9) at concentrations less than 40 nmol/L and then decreased by 68.5 g (95% CI: −110.5, −26.6) at concentrations from 40 to 70 nmol/L. This study provides the first epidemiological evidence that there was an inverted U shaped relationship between neonatal vitamin D status and fetal growth and the risk of SGA reduced at moderate concentration.
Photo-reactive charge trapping memory based on lanthanide complex
Authors: Zhuang Jiaqing , Lo Wai-Sum , Zhou Li , Sun Qi-Jun , Chan Chi-Fai , Zhou Ye , Han Su-Ting , Yan Yan , Wong Wing-Tak , Wong Ka-Leung , Roy V. A. L.
Published: October 2015

Traditional utilization of photo-induced excitons is popularly but restricted in the fields of photovoltaic devices as well as photodetectors and efforts on broadening its function have always been attempted. However, rare reports are available on organic field effect transistor (OFET) memory employing photo-induced charges. Here, we demonstrate an OFET memory containing a novel organic lanthanide complex Eu(tta)3ppta (Eu(tta)3 = Europium(III) thenoyltrifluoroacetonate, ppta = 2-phenyl-4,6-bis(pyrazol-1-yl)-1,3,5-triazine), in which the photo-induced charges can be successfully trapped and detrapped. The luminescent complex emits intense red emission upon ultraviolet (UV) light excitation and serves as a trapping element of holes injected from the pentacene semiconductor layer. Memory window can be significantly enlarged by light-assisted programming and erasing procedures, during which the photo-induced excitons in the semiconductor layer are separated by voltage bias. The enhancement of memory window is attributed to the increasing number of photo-induced excitons by the UV light. The charges are stored in this luminescent complex for at least 104 s after withdrawing voltage bias. The present study on photo-assisted novel memory may motivate the research on a new type of light tunable charge trapping photo-reactive memory devices.
A silica coated paper substrate: development and its application in paper spray mass spectrometry for rapid analysis of pesticides in milk
Authors: Wang Qian , Zheng Yajun , Zhang Xiaoling , Han Xiaoxiao , Wang Teng , Zhang Zhiping
Published: October 2015

A novel silica coated paper substrate has been developed, which demonstrated a high capacity for direct analysis of pesticides in paper spray mass spectrometry.
Enzyme-regulated topology of a cyclic peptide brush polymer for tuning assembly
Authors: Wang Zhao , Li Yiwen , Huang Yuran , Thompson Matthew P. , LeGuyader Clare L. M. , Sahu Swagat , Gianneschi Nathan C.
Published: October 2015

Norbornenyl cyclic elastin-like peptides were polymerized via ring opening metathesis polymerization (ROMP) to generate thermally responsive brush polymers.
Pulsed EPR characterization of HIV-1 protease conformational sampling and inhibitor-induced population shifts
Authors: Liu Zhanglong , Casey Thomas M. , Blackburn Mandy E. , Huang Xi , Pham Linh , de Vera Ian Mitchelle S. , Carter Jeffrey D. , Kear-Scott Jamie L. , Veloro Angelo M. , Galiano Luis , Fanucci Gail E.
Published: October 2015

The conformational landscape of HIV-1 protease can be characterized by double electron–electron resonance (DEER) spin-labeling.
Quantifying transient interactions between amide groups and the guanidinium cation
Authors: Balos V. , Bonn M. , Hunger J.
Published: October 2015

The guanidinium cation interacts with amide groups, the interaction strength is – compared to other cations – only intermediate.
A simple aqueous electrochemical method to synthesize TiO2 nanoparticles
Authors: Bezares Ivan , del Campo Adolfo , Herrasti Pilar , Muñoz-Bonilla Alexandra
Published: October 2015

Here, a simple and rapid electrochemical approach to synthesize TiO2 nanoparticles in aqueous solution is reported.
Intramolecular photostabilization via triplet-state quenching: design principles to make organic fluorophores “self-healing”
Authors: van der Velde Jasper H. M. , Uusitalo Jaakko J. , Ugen Lourens-Jan , Warszawik Eliza M. , Herrmann Andreas , Marrink Siewert J. , Cordes Thorben
Published: October 2015

Covalent linkage of fluorophores and photostabilizers was recently revived as a strategy to make organic fluorophores “self-healing” via triplet-state quenching. Although Lüttke and co-workers pioneered this strategy already in the 1980s, the general design principles still remain elusive. In this contribution, we combine experiments and theory to understand what determines the photostabilization efficiency in dye–photostabilizer conjugates. Our results from single-molecule microscopy and molecular dynamics simulations of different Cy5-derivatives suggest that the distance and relative geometry between the fluorophore and photostabilizer are more important than the chemical nature of the photostabilizer, e.g. its redox potential, which is known to influence electron-transfer rates. We hypothesize that the efficiency of photostabilization scales directly with the contact rate of the fluorophore and photostabilizer. This study represents an important step in the understanding of the molecular mechanism of intramolecular photostabilization and can pave the way for further development of stable emitters for various applications.
Biomimetic sensor design
Authors: Lee Ju Hun , Jin Hyo-Eon , Desai Malav S. , Ren Shuo , Kim Soyoun , Lee Seung-Wuk
Published: October 2015

Detection of desired target chemicals in a sensitive and selective manner is critically important to protect human health, environment and national security.
Anodic stripping voltammetry of anti-Vi antibody functionalized CdTe quantum dots for the specific monitoring of Salmonella enterica serovar Typhi
Authors: Pandey Satish K. , Rishi Praveen , Suri C. Raman , Vinayaka Aaydha C.
Published: October 2015

CdTe QD based stripping voltammetry for Vi capsular polysaccharide detection. The technique has provided an insight into the competence of CdTe QD and GNP immuno-conjugates. This is a novel approach to characterize the efficiency of immuno-conjugates of QDs and GNPs.
Fabrication and photoelectrochemical properties of silicon/nickel oxide core/shell nanowire arrays
Authors: Zhang Fu-Qiang , Hu Ya , Meng Xiang-Min , Peng Kui-Qing
Published: October 2015

A photoelectrochemical (PEC) cell made of a silicon nanowire array coated with a thin nickel oxide (NiOx) shell layer for solar water oxidation is presented.
Hierarchical self-assembly of random mica nanosheet-stabilized silver nanoparticles into flower microstructures for highly sensitive SERS substrates
Authors: Chiu Chih-Wei , Lin Po-Hsien
Published: October 2015

The use of self-assembled novel flower-like microstructures as SERS substrates allowed high-efficiency detection of adenine molecules from DNA.
Preparation of PdxAuybimetallic nanostructures with controllable morphologies supported on reduced graphene oxide nanosheets and wrapped in a polypyrrole layer
Authors: Yao Tongjie , Zuo Quan , Wang Hao , Wu Jie , Zhang Xiao , Sun Jianmin , Cui Tieyu
Published: October 2015

A one-step method to prepare reduced graphene oxide/PdxAuy/polypyrrole composites with good catalytic activity was introduced. The morphologies of alloy nanostructures could turn to be spherical, coral-like and porous cluster-like.
Co-operation of α-galactosylceramide-loaded tumour cells and TLR9 agonists induce potent anti-tumour responses in a murine colon cancer model
Authors: Dong Tiangeng , Yi Tuo , Yang Mengxuan , Lin Shengli , Li Wenxiang , Xu Xingyuan , Hu Jianwei , Jia Lijun , Hong Xinqiang , Niu Weixin
Published: October 2015

Dendritic cells (DCs) and invariant natural killer T (iNKT) cells play important roles in linking innate immunity and adaptive immunity. Mature DCs activated by Toll-like receptor (TLR) agonists directly activate iNKT cells and the iNKT ligand α-galactosylceramide (α-Galcer) can induce DC maturation, resulting in enhanced protective immune responses. In the present study, we aimed to boost anti-tumour immunity in a murine colon cancer model by synergizing DCs and iNKT cells using α-Galcer-loaded tumour cells (tumour–Gal) and the TLR9 agonist cytosine-phosphorothioate-guanine (CpG1826). The vaccine strategy was sufficient to inhibit growth of established tumours and prolonged survival of tumour-bearing mice. Importantly, the immunization induced an adaptive memory immune response as the survivors from primary tumour inoculations were resistant to a tumour re-challenge. Furthermore, injection of tumour–Gal with CpG1826 resulted in iNKT cell activation and DC maturation as defined by interferon (IFN)-γ secretion by iNKT, natural killer (NK) cells and interleukin (IL)-12 by DCs. Immunohistochemistry analysis revealed that cluster of differentiation (CD)4+ T-cells and CD8+ T-cells played important roles in anti-tumour immunity. Additionally, the vaccine redirected Th2 (T-helper cell type 2) responses toward Th1 (T-helper cell type 1) responses with increases in IL-2, IFN-γ expression and decreases in IL-4 and IL-5 expression after immunization with tumour–Gal with CpG1826. Taken together, our results demonstrated a novel vaccination by synergizing tumour–Gal and CpG1826 against murine colon cancer, which can be further developed as tumour-specific immunotherapy against human cancer.
Bespoke RNA recognition by Pumilios
Authors: Edwards Thomas A.
Published: October 2015

Pumilio is an RNA-binding protein originally identified in Drosophila, with a Puf domain made up of eight Puf repeats, three helix bundles arranged in a rainbow architecture, where each repeat recognizes a single base of the RNA-binding sequence. The eight-base recognition sequence can therefore be modified simply via mutation of the repeat that recognizes the base to be changed and this is understood in detail via high-resolution crystal structures. The binding mechanism is also altered in a variety of homologues from different species, with bases flipped out from the binding site to regenerate a consensus sequence. Thus Pumilios can be designed with bespoke RNA recognition sequences and can be fused to nucleases, split GFP, etc. as tools in vitro and in cells.
Creating functional sophistication from simple protein building blocks, exemplified by factor H and the regulators of complement activation
Authors: Makou Elisavet , Herbert Andrew P. , Barlow Paul N.
Published: October 2015

Complement control protein modules (CCPs) occur in numerous functionally diverse extracellular proteins. Also known as short consensus repeats (SCRs) or sushi domains each CCP contains approximately 60 amino acid residues, including four consensus cysteines participating in two disulfide bonds. Varying in length and sequence, CCPs adopt a β-sandwich type fold and have an overall prolate spheroidal shape with N- and C-termini lying close to opposite poles of the long axis. CCP-containing proteins are important as cytokine receptors and in neurotransmission, cell adhesion, blood clotting, extracellular matrix formation, haemoglobin metabolism and development, but CCPs are particularly well represented in the vertebrate complement system. For example, factor H (FH), a key soluble regulator of the alternative pathway of complement activation, is made up entirely from a chain of 20 CCPs joined by short linkers. Collectively, therefore, the 20 CCPs of FH must mediate all its functional capabilities. This is achieved via collaboration and division of labour among these modules. Structural studies have illuminated the dynamic architectures that allow FH and other CCP-rich proteins to perform their biological functions. These are largely the products of a highly varied set of intramolecular interactions between CCPs. The CCP can act as building block, spacer, highly versatile recognition site or dimerization mediator. Tandem CCPs may form composite binding sites or contribute to flexible, rigid or conformationally ‘switchable’ segments of the parent proteins.
The role of TRIB1 in lipid metabolism; from genetics to pathways
Authors: Iwamoto Sadahiko , Boonvisut Supichaya , Makishima Saho , Ishizuka Yuumi , Watanabe Kazuhisa , Nakayama Kazuhiro
Published: October 2015

The plasma concentration of lipids is a heritable risk factor for the development of atherosclerosis and related coronary artery diseases (CAD). Mammalian tribbles homologue 1 (TRIB1) is a human locus, the downstream linkage disequilibrium (LD) block of which affects plasma low-density lipoprotein (LDL)-associated cholesterol, triglyceride (TG) levels and CAD across multiple ethnic groups. In addition, association of TRIB1 with non-alcoholic fatty liver disease (NAFLD) has also been shown. A regulatory sequence that enhances TRIB1 promoter activity was identified in the LD block and the minor allele of a single nt polymorphism (SNP, rs6982502) in this regulatory sequence reduces the activity of the TRIB1 promoter. The minor allele of rs6982502 is a risk allele for increasing plasma lipid levels and NAFLD. Trib1 deficiency increases plasma cholesterol and TGs in mice and overexpression of TRIB1 in mouse liver reduces these factors. Expression of rate-limiting lipogenic enzymes is increased in Trib1-knockout mouse liver and decreased with overexpression. Recently, carbohydrate-responsive element-binding protein (ChREBP) emerged as a novel binding partner of TRIB1. Furthermore, novel binding partner, Sin3A (Swi-independent 3A)-associated protein, 18 kDa, was identified, which activates microsomal TG transfer protein (MTTP) expression by binding with MTTP regulatory elements in co-ordination with mSin3A and TRIB1. Very recently, a small molecular compound that up-regulates TRIB1 expression in HepG2 cells has been discovered. Further exploration of the binding partners of TRIB1 and their involvement in lipid metabolism may aid discovery of novel pharmacological targets for the management of dyslipidaemia and steatosis.
Deciphering the role of TRIB1 in regulatory T-cells
Authors: Danger Richard , Dugast Emilie , Braza Faouzi , Conchon Sophie , Brouard Sophie
Published: October 2015

The role of regulatory T-cells (Tregs) is crucial to maintain immune homoeostasis by controlling peripheral tolerance. A better understanding in the molecular mechanisms involved in the biology of these Tregs could improve their expansion and selection to treat immune-related diseases, achieve immunosuppression-free organ transplantation and to specifically target them in cancer. We reported on the overexpression of tribbles-1 (TRIB1) in Tregs compared with their counterpart naive T-cells and that TRIB1 interacts with the master molecule of Tregs, forkhead box P3 (FOXP3), a transcription factor essential for Treg suppressive activity. We demonstrated that these two molecules interact together in the nucleus of Tregs and TRIB1 overexpression is associated with a decrease in their proliferative capacities. Since TRIB1 was reported to be overexpressed in the blood of renal transplanted patients with chronic antibody-mediated rejection (CAMR), altogether, these results suggest TRIB1 could be linked to the decrease proportion of Tregs in patients exhibiting CAMR and a key player in Tregs through its FOXP3 interaction. In addition, yeast two-hybrid screening experiments highlighted that TRIB1 potentially interacts with molecules playing roles in intracellular events following T-cell activation and particularly cluster of differentiation (CD)4+ T-cells. This suggests still non explored potential links between TRIB1 in Tregs. Our goal is thus to decipher the role of TRIB1 in the Treg biology, notably in pathways known to involved its partner and main transcriptional factor of Tregs, FOXP3 and to determine the role of TRIB1 in immune pathologies.
The CydDC ABC transporter of Escherichia coli: new roles for a reductant efflux pump
Authors: Shepherd Mark
Published: October 2015

The CydDC complex of Escherichia coli is a heterodimeric ATP-binding cassette (ABC) transporter that exports cysteine and glutathione to the periplasm. These reductants are thought to modulate periplasmic redox poise, impacting upon the disulfide folding of periplasmic and secreted proteins involved in bacterial virulence. Diminished CydDC activity abolishes the assembly of functional bd-type respiratory oxidases and perturbs haem ligation during the assembly of c-type cytochromes. The focus herein is upon a newly-discovered interaction of the CydDC complex with a haem cofactor; haem has recently been shown to modulate CydDC activity and structural modelling reveals a potential haem-binding site on the periplasmic surface of the complex. These findings have important implications for future investigations into the potential roles for the CydDC-bound haem in redox sensing and tolerance to nitric oxide (NO).
Dissecting and reprogramming the folding and assembly of tandem-repeat proteins
Authors: Rowling Pamela J.E. , Sivertsson Elin M. , Perez-Riba Albert , Main Ewan R.G. , Itzhaki Laura S.
Published: October 2015

Studying protein folding and protein design in globular proteins presents significant challenges because of the two related features, topological complexity and co-operativity. In contrast, tandem-repeat proteins have regular and modular structures composed of linearly arrayed motifs. This means that the biophysics of even giant repeat proteins is highly amenable to dissection and to rational design. Here we discuss what has been learnt about the folding mechanisms of tandem-repeat proteins. The defining features that have emerged are: (i) accessibility of multiple distinct routes between denatured and native states, both at equilibrium and under kinetic conditions; (ii) different routes are favoured for folding compared with unfolding; (iii) unfolding energy barriers are broad, reflecting stepwise unravelling of an array repeat by repeat; (iv) highly co-operative unfolding at equilibrium and the potential for exceptionally high thermodynamic stabilities by introducing consensus residues; (v) under force, helical-repeat structures are very weak with non-co-operative unfolding leading to elasticity and buffering effects. This level of understanding should enable us to create repeat proteins with made-to-measure folding mechanisms, in which one can dial into the sequence the order of repeat folding, number of pathways taken, step size (co-operativity) and fine-structure of the kinetic energy barriers.
Tribbles in normal and malignant haematopoiesis
Authors: Stein Sarah J. , Mack Ethan A. , Rome Kelly S. , Pear Warren S.
Published: October 2015

The tribbles protein family, an evolutionarily conserved group of pseudokinases, have been shown to regulate multiple cellular events including those involved in normal and malignant haematopoiesis. The three mammalian Tribbles homologues, Trib1, Trib2 and Trib3 are characterized by conserved motifs, including a pseudokinase domain and a C-terminal E3 ligase-binding domain. In this review, we focus on the role of Trib (mammalian Tribbles homologues) proteins in mammalian haematopoiesis and leukaemia. The Trib proteins show divergent expression in haematopoietic cells, probably indicating cell-specific functions. The roles of the Trib proteins in oncogenesis are also varied and appear to be tissue-specific. Finally, we discuss the potential mechanisms by which the Trib proteins preferentially regulate these processes in multiple cell types.
Structures and functions of mitochondrial ABC transporters
Authors: Schaedler Theresia A. , Faust Belinda , Shintre Chitra A. , Carpenter Elisabeth P. , Srinivasan Vasundara , van Veen Hendrik W. , Balk Janneke
Published: October 2015

A small number of physiologically important ATP-binding cassette (ABC) transporters are found in mitochondria. Most are half transporters of the B group forming homodimers and their topology suggests they function as exporters. The results of mutant studies point towards involvement in iron cofactor biosynthesis. In particular, ABC subfamily B member 7 (ABCB7) and its homologues in yeast and plants are required for iron-sulfur (Fe-S) cluster biosynthesis outside of the mitochondria, whereas ABCB10 is involved in haem biosynthesis. They also play a role in preventing oxidative stress. Mutations in ABCB6 and ABCB7 have been linked to human disease. Recent crystal structures of yeast Atm1 and human ABCB10 have been key to identifying substrate-binding sites and transport mechanisms. Combined with in vitro and in vivo studies, progress is being made to find the physiological substrates of the different mitochondrial ABC transporters.
Homology modelling of human P-glycoprotein
Authors: Domicevica Laura , Biggin Philip C.
Published: October 2015

P-glycoprotein (P-gp) is an ATP-binding cassette transporter that exports a huge range of compounds out of cells and is thus one of the key proteins in conferring multi-drug resistance in cancer. Understanding how it achieves such a broad specificity and the series of conformational changes that allow export to occur form major, on-going, research objectives around the world. Much of our knowledge to date has been derived from mutagenesis and assay data. However, in recent years, there has also been great progress in structural biology and although the structure of human P-gp has not yet been solved, there are now a handful of related structures on which homology models can be built to aid in the interpretation of the vast amount of experimental data that currently exists. Many models for P-gp have been built with this aim, but the situation is complicated by the apparent flexibility of the system and by the fact that although many potential templates exist, there is large variation in the conformational state in which they have been crystallized. In this review, we summarize how homology modelling has been used in the past, how models are typically selected and finally illustrate how MD simulations can be used as a means to give more confidence about models that have been generated via this approach.
Learning from each other: ABC transporter regulation by protein phosphorylation in plant and mammalian systems
Authors: Aryal Bibek , Laurent Christophe , Geisler Markus
Published: October 2015

The ABC (ATP-binding cassette) transporter family in higher plants is highly expanded compared with those of mammalians. Moreover, some members of the plant ABC subfamily B (ABCB) display very high substrate specificity compared with their mammalian counterparts that are often associated with multi-drug resistance phenomena. In this review, we highlight prominent functions of plant and mammalian ABC transporters and summarize our knowledge on their post-transcriptional regulation with a focus on protein phosphorylation. A deeper comparison of regulatory events of human cystic fibrosis transmembrane conductance regulator (CFTR) and ABCB1 from the model plant Arabidopsis reveals a surprisingly high degree of similarity. Both physically interact with orthologues of the FK506-binding proteins that chaperon both transporters to the plasma membrane in an action that seems to involve heat shock protein (Hsp)90. Further, both transporters are phosphorylated at regulatory domains that connect both nt-binding folds. Taken together, it appears that ABC transporters exhibit an evolutionary conserved but complex regulation by protein phosphorylation, which apparently is, at least in some cases, tightly connected with protein–protein interactions (PPI).
A fresh look at the photoelectron spectrum of bromobenzene: A third-order non-Dyson electron propagator study
Authors: Schneider M. , Soshnikov D. Yu. , Holland D. M. P. , Powis I. , Antonsson E. , Patanen M. , Nicolas C. , Miron C. , Wormit M. , Dreuw A. , Trofimov A. B.
Published: October 2015

The valence-shell ionization spectrum of bromobenzene, as a representative halogen substituted aromatic, was studied using the non-Dyson third-order algebraic-diagrammatic construction [nD-ADC(3)] approximation for the electron propagator. This method, also referred to as IP-ADC(3), was implemented as a part of the Q-Chem program and enables large-scale calculations of the ionization spectra, where the computational effort scales as n5 with respect to the number of molecular orbitals n. The IP-ADC(3) scheme is ideally suited for investigating low-lying ionization transitions, so fresh insight could be gained into the cationic state manifold of bromobenzene. In particular, the present IP-ADC(3) calculations with the cc-pVTZ basis reveal a whole class of low-lying low-intensity two-hole-one-particle (2h-1p) doublet and quartet states, which are relevant to various photoionization processes. The good qualitative agreement between the theoretical spectral profile for the valence-shell ionization transitions generated with the smaller cc-pVDZ basis set and the experimental photoelectron spectrum measured at a photon energy of 80 eV on the PLÉIADES beamline at the Soleil synchrotron radiation source allowed all the main features to be assigned. Some theoretical aspects of the ionization energy calculations concerning the use of various approximation schemes and basis sets are discussed.
Tunability of multichannel optical filter based on magnetized one-dimensional plasma photonic crystal
Authors: Jamshidi-Ghaleh K. , Karami-Garehgeshlagi F. , Mazloom A. A.
Published: October 2015

A one dimensional plasma photonic crystal (1DPPC) structure was proposed to design a tunable compressing/broadening multi-channel optical filter with external controllability. The 1DPPC with arrangement of (AP)nD(PA)n, where A and D are the dielectric materials, P is a magnetized plasma layer and n is the number of the periodicity, was proposed. The well-known transfer matrix method was employed for analysis. In linear transmittance spectrum, n − 1 defect modes were appeared inside the photonic band gap. The results were shown that by increasing the applied magnetic field intensity and its direction, a red-shift and blue-shift were, respectively, observed in defect mode frequencies. On the other hand, the modes were compressed and broadened with increasing the intensity and the direction of the applied magnetic field, respectively. Externally controllable defect modes can be useful in designing a multichannel tunable optical filter.
Electric polarizability of lipid bilayers: The influence of the structure
Authors: Soussi J. , Chalopin Y.
Published: October 2015

We have calculated the electric polarizability of two types of lipid bilayers, formed by 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) and 1-palmitoyl-2- oleoyl-sn-glycero-3-phosphocholine (POPC) lipids. We demonstrate that despite the very similar chemical structures, the bilayers exhibit dramatically different terahertz infrared (IR) properties. We demonstrate that the chemical structure of the lipids influences the morphology of the bilayers, which in turn impacts their IR responses: interestingly, both structures exhibit a non-uniform absorption. For the case of DPPC, the infrared absorption is mostly driven by the hydrophilic heads, whereas for the POPC lipids, the absorption occurs predominately at the hydrophobic tails.
TIGER2 with solvent energy averaging (TIGER2A): An accelerated sampling method for large molecular systems with explicit representation of solvent
Authors: Li Xianfeng , Snyder James A. , Stuart Steven J. , Latour Robert A.
Published: October 2015

The recently developed “temperature intervals with global exchange of replicas” (TIGER2) accelerated sampling method is found to have inaccuracies when applied to systems with explicit solvation. This inaccuracy is due to the energy fluctuations of the solvent, which cause the sampling method to be less sensitive to the energy fluctuations of the solute. In the present work, the problem of the TIGER2 method is addressed in detail and a modification to the sampling method is introduced to correct this problem. The modified method is called “TIGER2 with solvent energy averaging,” or TIGER2A. This new method overcomes the sampling problem with the TIGER2 algorithm and is able to closely approximate Boltzmann-weighted sampling of molecular systems with explicit solvation. The difference in performance between the TIGER2 and TIGER2A methods is demonstrated by comparing them against analytical results for simple one-dimensional models, against replica exchange molecular dynamics (REMD) simulations for sampling the conformation of alanine dipeptide and the folding behavior of (AAQAA)3 peptide in aqueous solution, and by comparing their performance in sampling the behavior of hen egg–white lysozyme in aqueous solution. The new TIGER2A method solves the problem caused by solvent energy fluctuations in TIGER2 while maintaining the two important characteristics of TIGER2, i.e., (1) using multiple replicas sampled at different temperature levels to help systems efficiently escape from local potential energy minima and (2) enabling the number of replicas used for a simulation to be independent of the size of the molecular system, thus providing an accelerated sampling method that can be used to efficiently sample systems considered too large for the application of conventional temperature REMD.
Particle transport and heat loads in NIO1
Authors: Fonnesu N. , Cavenago M. , Serianni G. , Veltri P.
Published: October 2015

NIO1 is a compact radio frequency ion source designed to generate a 60 kV-135 mA hydrogen negative ion beam and it aims at continuous operation, which implies a detailed thermo-mechanical analysis of the beam-facing components, in particular, the accelerator grids. A 3D analysis of the entire NIO1 beam has been performed for the first time with a fully 3D version of EAMCC, a relativistic particle tracking code for the calculation of the grid power deposition induced by particle impacts. According to the results presented in this paper, secondary and co-extracted electrons cause a non-negligible heat load on the grids, where different high-power density regions, within reasonable sustainable standard limits, are calculated.
How well do static electronic dipole polarizabilities from gas-phase experiments compare with density functional and MP2 computations?
Authors: Thakkar Ajit J. , Wu Taozhe
Published: October 2015

Static electronic dipole polarizabilities for 135 molecules are calculated using second-order Møller-Plesset perturbation theory and six density functionals recently recommended for polarizabilities. Comparison is made with the best gas-phase experimental data. The lowest mean absolute percent deviations from the best experimental values for all 135 molecules are 3.03% and 3.08% for the LC-τHCTH and M11 functionals, respectively. Excluding the eight extreme outliers for which the experimental values are almost certainly in error, the mean absolute percent deviation for the remaining 127 molecules drops to 2.42% and 2.48% for the LC-τHCTH and M11 functionals, respectively. Detailed comparison enables us to identify 32 molecules for which the discrepancy between the calculated and experimental values warrants further investigation.
Scattering for the nonlinear Schrödinger equation with a general one-dimensional confinement
Authors: Carles Rémi , Gallo Clément
Published: October 2015

We consider the defocusing nonlinear Schrödinger equation in several space dimensions in the presence of an external potential depending on only one space variable. This potential is bounded from below and may grow arbitrarily fast at infinity. We prove existence and uniqueness in the associated Cauchy problem, in a suitable functional framework, as well as the existence of wave operators when the power of the nonlinearity is sufficiently large. Asymptotic completeness then stems from at least two approaches, which are briefly recalled.
Shear moduli in bcc-fcc structure transition of colloidal crystals
Authors: Zhou Hongwei , Xu Shenghua , Sun Zhiwei , Zhu Ruzeng
Published: October 2015

Shear moduli variation in the metastable-stable structure transition of charged colloidal crystals was investigated by the combination techniques of torsional resonance spectroscopy and reflection spectrometer. Modulus of the system increases with the proceeding of the transition process and it finally reaches the maximum value at the end of the transition. For colloidal crystals in stable state, the experimental moduli show good consistence with theoretical expectations. However, in the transition process, the moduli are much smaller than theoretical ones and this can be chalked up to crystalline imperfection in the transition state.
Pump polarization dependent ultrafast carrier dynamics and two-photon absorption in an a-plane ZnO epitaxial film
Authors: Lin Ja-Hon , Su Hsing-Jung , Lu Chia-Hui , Chang Chun-peng , Liu Wei-Rein , Hsieh Wen-Feng
Published: October 2015

The ultrafast carrier dynamics of non-polar a-plane ZnO epi-film, with the energy difference between the A- and C-valence bands of about 23 meV, grown on r-plane sapphire were investigated using the reflection type pump-probe technique under two perpendicular polarized pumps. By exciting the electron from A-valence band through pump polarization perpendicular to the c-axis of a-ZnO (Epu ⊥ c), the TDR trace revealed two photon absorption (TPA), band filling (BF) and bandgap renormalization (BGR) effects that can be reasonably explained by the electron dynamics in the conduction band. By exciting the electron from C-valence band through parallel pump polarization (Epu∥c), only the BF effect was observed in the TDR trace owing to the hole dynamics in the valence bands. The occurrence of TPA was determined by the pump efficiency depending on the energy difference between the pump photon and the intermediate exciton resonance state.
Terahertz generation by relativistic ponderomotive focusing of two co-axial Gaussian laser beams propagating in ripple density plasma
Authors: Kumar Subodh , Singh Ram Kishor , Sharma R. P.
Published: October 2015

Terahertz (THz) generation by beating of two co-axial Gaussian laser beams, propagating in ripple density plasma, has been studied when both ponderomotive and relativistic nonlinearities are operative. When the two lasers co-propagate in rippled density plasma, electrons acquire a nonlinear velocity at beat frequency in the direction transverse to the direction of propagation. This nonlinear oscillatory velocity couples with the density ripple to generate a nonlinear current, which in turn generates THz radiation at the difference frequency. The necessary phase matching condition is provided by the density ripple. Relativistic ponderomotive focusing of the two lasers and its effects on yield of the generated THz amplitude have been discussed. Numerical results show that conversion efficiency of the order of 10−3 can be achieved in the terahertz radiation generation with relativistic ponderomotive focusing.
When losing your nuts increases your reproductive success: sandalwood (Santalum spicatum) nut caching by the woylie (Bettongia penicillata)
Authors: Murphy Marie , Howard Kay , Hardy Giles E. St J. , Dell Bernard
Published: October 2015

To regenerate sandalwood (Santalum spicatum) stands in south-western Australia it is necessary to understand the complex relationship between woylies (Bettongia penicillata ogilbyi) and sandalwood. Sandalwood requires a seed disperser for successful recruitment and in the past the critically endangered woylie played an important role in dispersing and caching seeds, but it is not clear whether this mutualistic and antagonistic relationship is beneficial to regeneration efforts. An enclosure in a woodland and 46Scandium-labelled seeds, enabled study of the in situ predation of seeds, caching, the fate of cached seeds, the detection of cached seeds and predation of germinated seeds. Woylies preferentially cached sandalwood, then S. acuminatum seeds, before any interest was shown in Acacia acuminata and Gastrolobium microcarpum seeds, which were virtually all eaten in situ. Of a further 500 radiolabelled and individually numbered sandalwood seeds deployed, 42.2% were eaten in situ, 20.8% had an unknown fate and 37% were cached, with some seeds being recached up to four times. After nine months, only four cached seeds remained undisturbed. Olfaction appeared to be the primary method of cache detection. To examine the recruitment rate of cached seeds, the fate of 89 transplanted sandalwood seedlings at two study sites was followed. After one month 38% were intact and growing, but half of the transplanted seedlings were dug up and the remaining endosperm was eaten in situ or taken away. The results highlight the potential of providing seed supplies, including sandalwood seeds and seeds of their hosts, to seed-dispersal marsupials for passive ecosystem repair.
IL-7R signaling in regulatory T cells maintains peripheral and allograft tolerance in mice
Authors: Schmaler Mathias , Broggi Maria A. S. , Lagarde Nadège , Stöcklin Benjamin F. , King Carolyn G. , Finke Daniela , Rossi Simona W.
Published: October 2015

Significance

In mammals, regulatory T cells establish and maintain immune responses toward self- and non–self-antigens by suppression of specific T cells. Several mechanisms of suppression were previously described including starvation for IL-2, a cytokine required for T-cell expansion. Here we show that regulatory T cells (Treg) respond to IL-7, a T-cell survival factor produced by lymph node fibroblast reticular cells, by enhancing their IL-2 sensitivity, thereby limiting expansion of reactive T cells during inflammation. These findings highlight a previously unidentified and unexpected mechanism by which IL-7R signaling in Tregcells maintains peripheral and allograft tolerance. This work may contribute to design new therapeutic approaches using lower IL-2 doses in humans by enhancing the functional competence of regulatory T cells with IL-7.
Group 3 innate lymphoid cells: regulating host–commensal bacteria interactions in inflammation and cancer
Authors: Goc Jeremy , Hepworth Matthew R. , Sonnenberg Gregory F.
Published: October 2015

A delicate balance exists between the mammalian immune system and normally beneficial commensal bacteria that colonize the gastrointestinal tract, which is necessary to maintain tissue homeostasis. Dysregulation of these interactions between the host and commensal bacteria is causally associated with chronic inflammation and the development of cancer. In contrast, recent reports have highlighted that commensal bacteria also play an essential role in promoting anti-tumor immune responses in several contexts, highlighting a paradox whereby interactions between the host and commensal bacteria can influence both pro- and anti-tumor immunity. Given the critical roles for group 3 innate lymphoid cells (ILC3s) in regulating inflammation, tissue repair and host–microbe interactions in the intestine, here we discuss new evidence that ILC3s may profoundly influence the development, progression and control of tumors. In this review, we provide an overview of recent advances in understanding the impact of commensal bacteria on tumorigenesis, discuss recent findings identifying ILC3s as critical regulators of host–microbe interactions and highlight the emerging role of this immune cell population in cancer and their potential implication as a therapeutic target.
Cancer Classification by Correntropy-Based Sparse Compact Incremental Learning Machine
Authors: Nayyeri Mojtaba , Sharifi Noghabi Hossein
Published: October 2015

Cancer prediction is of great importance and significance and it is crucial to provide researchers and scientists with novel, accurate and robust computational tools for this issue. Recent technologies such as Microarray and Next Generation Sequencing have paved the way for computational methods and techniques to play critical roles in this regard. Many important problems in cell biology require the dense nonlinear interactions between functional modules to be considered. The importance of computer simulation in understanding cellular processes is now widely accepted, and a variety of simulation algorithms useful for studying certain subsystems have been designed. In this article, a Sparse Compact Incremental Learning Machine (SCILM) is proposed for cancer classification problem on microarray gene expression data which take advantage of Correntropy cost that makes it robust against diverse noises and outliers. Moreover, since SCILM uses l1-norm of the weights, it has sparseness which can be applied for gene selection purposes as well. Finally, due to compact structure, the proposed method is capable of performing classification tasks in all of the cases with only one neuron in its hidden layer. The experimental analysis is performed on 26 well known microarray datasets regarding diverse kinds of cancers and the results show that the proposed method not only achieved significantly high accuracy but also because of its sparseness, final connectivity weights determined the value and effectivity of each gene regarding the corresponding cancer.
An extended family of novel vertebrate photopigments is widely expressed and displays a diversity of function
Authors: Davies Wayne I.L. , Tamai T. Katherine , Zheng Lei , Fu Josephine K. , Rihel Jason , Foster Russell G. , Whitmore David , Hankins Mark W.
Published: October 2015

Light affects animal physiology and behavior more than simply through classical visual, image-forming pathways. Nonvisual photoreception regulates numerous biological systems, including circadian entrainment, DNA repair, metabolism, and behavior. However, for the majority of these processes, the photoreceptive molecules involved are unknown. Given the diversity of photophysiological responses, the question arises whether a single photopigment or a greater diversity of proteins within the opsin superfamily detect photic stimuli. Here, a functional genomics approach identified the full complement of photopigments in a highly light-sensitive model vertebrate, the zebrafish (Danio rerio), and characterized their tissue distribution, expression levels, and biochemical properties. The results presented here reveal the presence of 42 distinct genes encoding 10 classical visual photopigments and 32 nonvisual opsins, including 10 novel opsin genes comprising four new pigment classes. Consistent with the presence of light-entrainable circadian oscillators in zebrafish, all adult tissues examined expressed two or more opsins, including several novel opsins. Spectral and electrophysiological analyses of the new opsins demonstrate that they form functional photopigments, each with unique chromophore-binding and wavelength specificities. This study has revealed a remarkable number and diversity of photopigments in zebrafish, the largest number so far discovered for any vertebrate. Found in amphibians, reptiles, birds, and all three mammalian clades, most of these genes are not restricted to teleosts. Therefore, nonvisual light detection is far more complex than initially appreciated, which has significant biological implications in understanding photoreception in vertebrates.
Characterization of the fracture behaviour of X42 microalloyed pipeline steel
Authors: Ünal Halil Ibrahim , Atapek Hakan , Beleli Baran Gürkan , Polat Seyda , Gümüs Serap , Erisir Ersoy
Published: October 2015

Purpose

– The purpose of this paper is to investigate the fracture of grade X42 microalloyed steel used as pipe material after tensile test at room temperature and impact tests at 0, −20 and −40°C, respectively.

Design/methodology/approach

– In the first stage of the study, X42 steels in the form of sheet and pipe materials were selected and etched samples were characterized using light microscope. In the second stage, mechanical properties of steels were obtained by microhardness measurements, static tensile and impact tests and all the broken surfaces were examined by scanning electron microscope to determine the fracture type as a function of both microstructure and loading.

Findings

– The examinations revealed that: first, the sheet material had a typical ferritic-pearlitic matrix, second, the transverse section of the sheet steel exhibited a matrix consisting of polygonal ferrite-aligned pearlite colonies and the longitudinal one had elongated ferrite phase and pearlite colonies in the direction of rolling, third, ferrite and pearlite distribution was different from the sheet material due to multiaxial deformation in the pipe material, fourth, tensile fracture surfaces of the steels had typical dimple fracture induced by microvoid coalescence, fifth, impact fracture surfaces of the steels changed as a function of the test temperature and cleavage fracture mode of ferritic-pearlitic matrix became more dominant as the temperature decreased, and sixth, grain morphology had an effect on the fracture behavior of the steels.

Originality/value

– The paper explains the fracture behaviour of X42 microalloyed pipeline steel and its fractographical analysis.