bluuebunny/crossref_metadata_2025 huggingface dataset:
Low-frequency magnetic fields do not aggravate disease in mouse models of Alzheimer's disease and amyotrophic lateral sclerosis
Authors: Liebl Martina P. , Windschmitt Johannes , Besemer Anna S. , Schäfer Anne-Kathrin , Reber Helmut , Behl Christian , Clement Albrecht M.
Published: February 2015

Low-frequency magnetic fields (LF-MF) generated by power lines represent a potential environmental health risk and are classified as possibly carcinogenic by the World Health Organization. Epidemiological studies indicate that LF-MF might propagate neurodegenerative diseases like Alzheimer's disease (AD) or amyotrophic lateral sclerosis (ALS). We conducted a comprehensive analysis to determine whether long-term exposure to LF-MF (50 Hz, 1 mT) interferes with disease development in established mouse models for AD and ALS, namely APP23 mice and mice expressing mutant Cu/Zn-superoxide dismutase (SOD1), respectively. Exposure for 16 months did not aggravate learning deficit of APP23 mice. Likewise, disease onset and survival of SOD1G85R or SOD1G93A mice were not altered upon LF-MF exposure for ten or eight months, respectively. These results and an extended biochemical analysis of protein aggregation, glial activation and levels of toxic protein species suggests that LF-MF do not affect cellular processes involved in the pathogenesis of AD or ALS.
Nature of charge transport and p-electron ferromagnetism in nitrogen-doped ZrO2: An ab initio perspective
Authors: Zhu Huanfeng , Li Jing , Chen Kun , Yi Xinyu , Cheng Shuai , Gan Fuxi
Published: February 2015

Zirconium dioxide provides an exceptional prototype material for studying the redistribution of the polaron holes and its magnetic coupling with their nearby anions owning to the difference oxygen binding behavior in the monoclinic phase. Here, we perform a comprehensive study of thep-electron magnetism in the nitrogen doped 2 × 2 × 2 monoclinic ZrO2based on spin-polarized density functional theory. Nitrogen substitutions make the system display half-metallic properties and the origin of room temperature ferromagnetism ascribes to thep-pcoupling interaction between N 2pand the host 2pstates. The charge density difference and Mülliken population analyses provide evidences of charge redistributions. Our results reveal that the polaron transfer may alter the magnetic properties and it is greatly facilitated ferromagnetic coupling if the polaron holes are localized around a single anion dopant.
A strategy to design novel structure photochromic sensitizers for dye-sensitized solar cells
Authors: Wu Wenjun , Wang Jiaxing , Zheng Zhiwei , Hu Yue , Jin Jiayu , Zhang Qiong , Hua Jianli
Published: February 2015

Two sensitizers with novel structure were designed and synthetized by introducing photochromic bisthienylethene (BTE) group into the conjugated system. Thanks to the photochromic effect the sensitizers have under ultraviolet and visible light, the conjugated bridge can be restructured and the resulting two photoisomers showed different behaviors in photovoltaic devices. This opens up a new research way for the dye-sensitized solar cells (DSSCs).
Induced pluripotent stem cells as a model for diabetes investigation
Authors: Stepniewski J. , Kachamakova-Trojanowska N. , Ogrocki D. , Szopa M. , Matlok M. , Beilharz M. , Dyduch G. , Malecki M. T. , Jozkowicz A. , Dulak J.
Published: February 2015

Mouse and human induced pluripotent stem cells (iPSCs) may represent a novel approach for modeling diabetes. Taking this into consideration, the aim of this study was to generate and evaluate differentiation potential of iPSCs from lepdb/db (db/db) mice, the model of diabetes type 2 as well as from patients with Maturity Onset Diabetes of the Young 3 (HNF1A MODY). Murine iPSC colonies from both wild type and db/db mice were positive for markers of pluripotency: Oct3/4A, Nanog, SSEA1, CDy1 and alkaline phosphatase and differentiated in vitro and in vivo into cells originating from three germ layers. However, our results suggest impaired differentiation of db/db cells into endothelial progenitor-like cells expressing CD34 and Tie2 markers and their reduced angiogenic potential. Human control and HNF1A MODY reprogrammed cells also expressed pluripotency markers: OCT3/4A, SSEA4, TRA-1–60, TRA-1-81, formed embryoid bodies (EBs) and differentiated into cells of three germ layers. Additionally, insulin expressing cells were obtained from those partially reprogrammed cells with direct as well as EB-mediated differentiation method. Our findings indicate that disease-specific iPSCs may help to better understand the mechanisms responsible for defective insulin production or vascular dysfunction upon differentiation toward cell types affected by diabetes.
Rapid preparation of rare ginsenosides by acid transformation and their structure-activity relationships against cancer cells
Authors: Quan Kai , Liu Qun , Wan Jin-Yi , Zhao Yi-Jing , Guo Ru-Zhou , Alolga Raphael N. , Li Ping , Qi Lian-Wen
Published: February 2015

The anticancer activities of ginsenosides are widely reported. The structure-activity relationship of ginsenosides against cancer is not well elucidated because of the unavailability of these compounds. In this work, we developed a transformation method to rapidly produce rare dehydroxylated ginsenosides by acid treatment. The optimized temperature, time course and concentration of formic acid were 120°C, 4 h and 0.01%, respectively. From 100 mg of Rh1, 8.3 mg of Rk3 and 18.7 mg of Rh4 can be produced by acid transformation. Similarly, from 100 mg of Rg3, 7.4 mg of Rk1 and 15.1 mg of Rg5 can be produced. From 100 mg of Rh2, 8.3 mg of Rk2 and 12.7 mg of Rh3 can be generated. Next, the structure-activity relationships of 23 ginsenosides were investigated by comparing their cytotoxic effects on six human cancer cells, including HCT-116, HepG2, MCF-7, Hela, PANC-1 and A549. The results showed that: (1) the cytotoxic effect of ginsenosides is inversely related to the sugar numbers; (2) sugar linkages rank as C-3 > C-6 > C-20; (3) the protopanaxadiol-type has higher activities; (4) having the double bond at the terminal C20-21 exhibits stronger activity than that at C20-22; and (5) 20(S)-ginsenosides show stronger effects than their 20(R)-stereoisomers.
An orthogonal C–H borylation – cross-coupling strategy for the preparation of tetrasubstituted “A2B2”-chrysene derivatives with tuneable photophysical properties
Authors: Heard K. W. J. , Morrison J. J. , Weston L. , Lo C. H. , Pirvu L. , Raftery J. , Little M. S. , McDouall J. J. W. , Yeates S. G. , Quayle P.
Published: February 2015

Cl-substituents serve as a functionalisable regiocontrol element for the orthogonal functionalisation of chrysene.
Changes in mangrove species assemblages and future prediction of the Bangladesh Sundarbans using Markov chain model and cellular automata
Authors: Mukhopadhyay Anirban , Mondal Parimal , Barik Jyotiskona , Chowdhury S. M. , Ghosh Tuhin , Hazra Sugata
Published: February 2015

The composition and assemblage of mangroves in the Bangladesh Sundarbans are changing systematically in response to several environmental factors.
N-Branched acyclic nucleoside phosphonates as monomers for the synthesis of modified oligonucleotides
Authors: Hocková Dana , Rosenbergová Šárka , Ménová Petra , Páv Ondřej , Pohl Radek , Novák Pavel , Rosenberg Ivan
Published: February 2015

The solid phase synthesis of nonamers containing a highly flexible acyclic central unit was performed and their hybridization properties were evaluated.
Discovery of new targets of phenolic acids in danshen using a label-free cell phenotypic assay
Authors: Wang Jixia , Hou Tao , Wei Lai , Shi Liying , He Jian , Zhou Nan , Sun Guangwei , Zhang Xiuli , Liang Xinmiao
Published: February 2015

Pharmacological profiling of 10 known phenolic acids in danshen using a label-free cell phenotypic assay in HT-29 and A431 cells revealed that lithospermic acid, salvianolic acid A, B, C and danshensu all displayed agonistic activity towards GPR35.
Novel biobased thermoplastic elastomer consisting of synthetic polyester elastomer and polylactide by in situ dynamical crosslinking method
Authors: Kang Hailan , Hu Xiaoran , Li Manqiang , Zhang Liqun , Wu Youping , Ning Nanying , Tian Ming
Published: February 2015

Owing to the sustainability and environmental friendliness of biobased polymers, a new biobased thermoplastic vulcanizate is produced by in situ dynamic crosslinking of biobased polyester elastomer and polylactide.
Ratiometric fluorescent and chromogenic chemodosimeter for cyanide detection in water and its application in bioimaging
Authors: Mahapatra Ajit Kumar , Maiti Kalipada , Maji Rajkishor , Manna Saikat Kumar , Mondal Sanchita , Ali Syed Samim , Manna Srimanta
Published: February 2015

An indole conjugated thiophene–pyridyl moiety, ITP, has been synthesized and characterized for the selective detection of cyanide with a low detection limit.
Visible-light-controlled homo- and copolymerization of styrenes by a bichromophoric Ir–Pd catalyst
Authors: Murata K. , Saito K. , Kikuchi S. , Akita M. , Inagaki A.
Published: February 2015

Visible-light-controlled polymerization was achieved by a bichromophoric organopalladium catalyst which possesses a naphthyl-substituted cyclometallated Ir(iii) light-absorbing moiety.
Anisotropic particles templated by Janus emulsion
Authors: Ge Lingling , Lu Shuhui , Han Jie , Guo Rong
Published: February 2015

Crescent-to-moon shaped anisotropic particles in both micrometer and nanometer size have been successfully fabricated in batch scale with Janus emulsion as template.
Effects of Sn atoms on formation of ZnO nanorings
Authors: Yousefi Ramin
Published: February 2015

ZnO dual-nanorings were formed as a result of planar defects in nanobelts that were generated due to the presence of Sn atoms.
Use of silane-functionalized graphene oxide in organic photovoltaic cells and organic light-emitting diodes
Authors: Lee Chang Yeong , Le Quyet Van , Kim Cheolmin , Kim Soo Young
Published: February 2015

The silane-functionalized graphene oxide could be used as an interfacial layer in organic devices.
Photon upconversion nanomaterials
Authors: Liu Xiaogang , Yan Chun-Hua , Capobianco John A.
Published: February 2015

Guest editors Xiaogang Liu, Chun-Hua Yan and John A. Capobianco introduce the Photon Upconversion Nanomaterials issue of Chemical Society Reviews.
Exposing the intermolecular nature of the second relaxation pathway in a mononuclear cobalt(ii) single-molecule magnet with positive anisotropy
Authors: Habib Fatemah , Korobkov Ilia , Murugesu Muralee
Published: February 2015

The investigation of a pentagonal bipyramidal Co(ii) complex with large positive anisotropy (D ≈ +30 cm−1) revealed field induced Single-Molecule Magnet behaviour with Ueff ≈ 50 K at 1.0 kOe.
Fabrication of ultrathin CoMoO4nanosheets modified with chitosan and their improved performance in energy storage device
Authors: Ramkumar Ramya , Minakshi Manickam
Published: February 2015

Ultrathin nanosheet-assembled cobalt molybdate (CoMoO4) with a mesoporous morphology was synthesized by a urea-assisted solution combustion route at a temperature of 400 °C.
Chemical modification of tannins to elaborate aromatic biobased macromolecular architectures
Authors: Arbenz Alice , Avérous Luc
Published: February 2015

This review presents different chemical modifications of tannins, an abundant source of aromatic biomolecules, to elaborate biobased polymers.
Proteomic analysis of human sonic hedgehog (SHH) medulloblastoma stem-like cells
Authors: Ronci Maurizio , Catanzaro Giuseppina , Pieroni Luisa , Po Agnese , Besharat Zein Mersini , Greco Viviana , Levi Mortera Stefano , Screpanti Isabella , Ferretti Elisabetta , Urbani Andrea
Published: February 2015

First proteomic characterization of sonic hedgehog human medulloblastoma stem-like cells.
Bacterial iron–sulfur cluster sensors in mammalian pathogens
Authors: Miller Halie K. , Auerbuch Victoria
Published: February 2015

We review how iron–sulfur cluster-containing regulators contribute to bacterial pathogenesis through control of gene expression in response to environmental cues.
Au nanoparticle decorated resin microspheres: synthesis and application in electrochemical cytosensors for sensitive and selective detection of lung cancer A549 cells
Authors: Lu Wenbo , Wang Hong-Yin , Wang Man , Wang Ying , Tao Lin , Qian Weiping
Published: February 2015

A novel cytosensor that can sensitively differentiate cancer cells from normal ones is prepared by using antibody-decorated resin microspheres.
Separating isopropanol from its diluted solutions via a process of integrating gas stripping and vapor permeation
Authors: Guan Yu , Hu Song , Wang Ying , Qin Peiyong , Karim M. Nazmul , Tan Tianwei
Published: February 2015

The novel process, integrated gas stripping and vapor permeation, is environmental, energy-efficient and highly selective for isopropanol recovery.
Effect of different morphologies on slow crack growth of high-density polyethylene
Authors: Pan Yuxi , Gao Xueqin , Wang Zhongwu , Lei Jun , Li ZhongMing , Shen KaiZhi
Published: February 2015

We made different morphologies of HDPE using OSIM to increase the resistance to SCG.
Proline-functionalized chitosan–palladium(ii) complex, a novel nanocatalyst for C–C bond formation in water
Authors: Hajipour A. R. , Boostani E. , Mohammadsaleh F.
Published: February 2015

An environmentally friendly palladium-based catalyst supported on proline-functionalized chitosan was successfully prepared and evaluated as a heterogeneous nanocatalyst in the Suzuki cross-coupling reaction of various aryl halides with phenylboronic acid.
Identification of competitive inhibitors for bovine serum albumin from dynamic combinatorial libraries containing a bienzyme system
Authors: He Wei , Fang Zheng , Yang Zhao , Ji Dong , Chen Ketao , Guo Kai
Published: February 2015

Three dynamic combinatorial libraries (DCLs) have been generated by using esterification, combined with a protocol based on size-exclusion chromatography (SEC) and HRMS.
Design, synthesis, biological evaluation and molecular docking of novel dabigatran derivatives as potential thrombin inhibitors
Authors: Li Chun-Lei , Dong Ming-Hui , Ren Yu-Jie , Li Li-Hua
Published: February 2015

A series of dabigatran derivatives were designed and synthesized to discover effective thrombin inhibitors.
Evaluation of different bridged organosilicas as efficient adsorbents for the herbicide S-metolachlor
Authors: López María Isabel , Otero Rocío , Esquivel Dolores , Jiménez-Sanchidrián César , María Fernández José , Romero-Salguero Francisco José
Published: February 2015

The adsorption ofS-metolachlor on (organo)silicas largely depends on their composition and textural properties. Periodic mesoporous benzenesilica was particularly efficient for repetitive adsorption cycles.
Correction: Removal of Cu2+, Pb2+ and Cr6+ from aqueous solutions using a chitosan/graphene oxide composite nanofibrous adsorbent
Authors: Najafabadi Hossein Hadi , Irani Mohammad , Rad Leila Roshanfekr , Sojoudi Amirsalar , Haririan Ismaeil
Published: February 2015

Correction for ‘Removal of Cu2+, Pb2+ and Cr6+ from aqueous solutions using a chitosan/graphene oxide composite nanofibrous adsorbent’ by Hossein Hadi Najafabadi et al., RSC Adv., 2015, 5, 16532–16539.
Resonant two-photon ionization spectroscopy of Al atoms and dimers solvated in helium nanodroplets
Authors: Krasnokutski Serge A. , Huisken Friedrich
Published: February 2015

Resonant two-photon ionization (R2PI) spectroscopy has been applied to investigate the solvation of Al atoms in helium droplets. The R2PI spectra reveal vibrational progressions that can be attributed to Al–Hen vibrations. It is found that small helium droplets have very little chance to pick up an aluminum atom after collision. However, the pick-up probability increases with the size of the helium droplets. The absorption band that is measured by monitoring the ions on the mass of the Al dimer is found to be very little shifted with respect to the Al monomer band (∼400 cm−1). However, using the same laser wavelength, we were unable to detect any Aln photoion with n larger than two.
Charged dendrimers under the action of AC electric fields: Breathing characteristics of molecular size, polarizations, and ion distributions
Authors: Das Ashok K. , Hsiao Pai-Yi
Published: February 2015

Langevin dynamics simulations are performed to study the response of charged dendrimers in alternating current electric fields in 3:1 salt solutions. Time evolutions of molecular size show breathing characteristics which take saw-tooth-like patterns in square-wave electric fields and undulated sine-function ones in sine-wave fields. Detailed study reveals how the dendrimer and condensed ions oscillate in the electric fields, which result in polarization of the molecule. To effect a significant deformation of the dendrimer, the applied field amplitude must be larger than some critical strength Ecrit and the field frequency smaller than a threshold fcrit. The response behavior is characterized by two relaxation times in square-wave fields, both of which decrease linearly with the strong field strength larger than Ecrit. In sine-wave fields, the molecular size exhibits interesting hysteretic behavior in plotting the curves with the field variation. A Maxwell-Wagner type polarization theory is derived and proved by simulations, which connects fcrit with the strength of the applied electric field.
A correction for the Hartree-Fock density of states for jellium without screening
Authors: Blair Alexander I. , Kroukis Aristeidis , Gidopoulos Nikitas I.
Published: February 2015

We revisit the Hartree-Fock (HF) calculation for the uniform electron gas, or jellium model, whose predictions—divergent derivative of the energy dispersion relation and vanishing density of states (DOS) at the Fermi level—are in qualitative disagreement with experimental evidence for simple metals. Currently, this qualitative failure is attributed to the lack of screening in the HF equations. Employing Slater’s hyper-Hartree-Fock (HHF) equations, derived variationally, to study the ground state and the excited states of jellium, we find that the divergent derivative of the energy dispersion relation and the zero in the DOS are still present, but shifted from the Fermi wavevector and energy of jellium to the boundary between the set of variationally optimised and unoptimised HHF orbitals. The location of this boundary is not fixed, but it can be chosen to lie at arbitrarily high values of wavevector and energy, well clear from the Fermi level of jellium. We conclude that, rather than the lack of screening in the HF equations, the well-known qualitative failure of the ground-state HF approximation is an artifact of its nonlocal exchange operator. Other similar artifacts of the HF nonlocal exchange operator, not associated with the lack of electronic correlation, are known in the literature.
Symmetry breaking and uniqueness for the incompressible Navier-Stokes equations
Authors: Dascaliuc Radu , Michalowski Nicholas , Thomann Enrique , Waymire Edward C.
Published: February 2015

The present article establishes connections between the structure of the deterministic Navier-Stokes equations and the structure of (similarity) equations that govern self-similar solutions as expected values of certain naturally associated stochastic cascades. A principle result is that explosion criteria for the stochastic cascades involved in the probabilistic representations of solutions to the respective equations coincide. While the uniqueness problem itself remains unresolved, these connections provide interesting problems and possible methods for investigating symmetry breaking and the uniqueness problem for Navier-Stokes equations. In particular, new branching Markov chains, including a dilogarithmic branching random walk on the multiplicative group (0, ∞), naturally arise as a result of this investigation.
Estimation of microwave penetration distance and complex permittivity of graphite by measurement of permittivity and direct current conductivity of graphite powder mixtures
Authors: Yoshikawa N. , Kawahira K. , Saito Y. , Todoroki H. , Taniguchi S.
Published: February 2015

Microwave penetration distance into powder mixtures of FeO(OH)/graphite (C) and tri-calciumphosphate/C was studied by changing the fraction of graphite powder and the degree of the compression. They are combined into a parameter of carbon volume fraction [Pct. Vc]. Experimentally, it was shown that the penetration distance decreased at high [Pct. Vc]. Measurement of permittivity became impossible at certain [Pct. Vc], which is related with the abrupt increase in DC conductivity (occurrence of percolation). In this study, dependence of DC conductivity of the mixture on [Pct. Vc] was expressed using generalized effective medium approximation. And then, average permittivity of the mixture below percolation threshold was measured and analyzed using a mixing rule based on effective medium approximation. In this procedure, permittivity of carbon was estimated to fit the data of the measured average permittivity. Transition from the dielectric to the conductive nature of the powder mixture influences the penetration distance; however, it was shown that the predicted penetration distances by equations using conductivity (σ) or complex permittivity (ε) of the mixtures are consistent with each other, namely, their extrapolations are continuous across the transition region of the percolation threshold.
Direct evidence of void passivation in Cu(InGa)(SSe)2 absorber layers
Authors: Lee Dongho , Lee Jaehan , Heo Sung , Park Jong-Bong , Kim Young-Su , Mo Chan B. , Huh Kwangsoo , Yang JungYup , Nam Junggyu , Baek Dohyun , Park Sungchan , Kim ByoungJune , Kim Dongseop , Kang Yoonmook
Published: February 2015

We have investigated the charge collection condition around voids in copper indium gallium sulfur selenide (CIGSSe) solar cells fabricated by sputter and a sequential process of selenization/sulfurization. In this study, we found direct evidence of void passivation by using the junction electron beam induced current method, transmission electron microscopy, and energy dispersive X-ray spectroscopy. The high sulfur concentration at the void surface plays an important role in the performance enhancement of the device. The recombination around voids is effectively suppressed by field-assisted void passivation. Hence, the generated carriers are easily collected by the electrodes. Therefore, when the S/(S + Se) ratio at the void surface is over 8% at room temperature, the device performance degradation caused by the recombination at the voids is negligible at the CIGSSe layer.
Feasibility study of a high-spatial resolution x-ray computed tomography using sub-pixel shift method
Authors: Yoneyama Akio , Baba Rika , Sumitani Kazushi , Hirai Yasuharu
Published: February 2015

A high-spatial resolution X-ray computed tomography (CT) adopting a sub-pixel shift method has been developed. By calculating sectional images, using plural CT datasets obtained by scanning the X-ray imager, the spatial resolution can be reduced relative to the sub-pixel size of an X-ray imager. Feasibility observations of a biomedical sample were performed using 12-keV monochromatic synchrotron radiation and a photon-counting X-ray imager 174-μm pixels in size. Four CT measurements were performed to obtain datasets at different positions of the X-ray imager. Fine sectional images were obtained successfully, and the spatial resolution was estimated as 80-μm, which corresponds to just under half the pixel size of the imager. In addition, a fine 3D image was also obtained by scanning the imager two-dimensionally.
Viscous and acoustic losses in length-extensional microplate resonators in liquid media
Authors: Ruiz-Díez Víctor , Hernando-García Jorge , Manzaneque Tomás , Kucera Martin , Schmid Ulrich , Sánchez-Rojas José Luis
Published: February 2015

Damping mechanisms in the length-extensional mode of rectangular, mid-point supported microplate resonators immersed in liquid are studied. Piezoelectrically excited structures with different lengths and thicknesses were designed, fabricated, and characterized both optically and electrically in isopropanol. The experimental quality factors were compared to the results of Finite Element Method (FEM) simulations and the two main mechanisms of losses, i.e., acoustic and viscous losses, were identified. Analytical models for those two mechanisms are presented and the effects of the geometry on the in-liquid performance of the resonators are discussed. By applying these models, we found that for a given thickness, a maximum quality factor is reached at a critical length, resulting from the balance between acoustic and viscous losses. To further increase quality factors, a quarter wavelength fluid cavity was implemented, thereby reducing acoustic losses; an increase over 40% in the quality factor was predicted by a 2D FEM model including the cavity, and a quality factor as high as 145 was measured for a 3 mm long and 93 μm thick resonator in this configuration.
Low-loss metamaterial electromagnetically induced transparency based on electric toroidal dipolar response
Authors: Li Hai-ming , Liu Shao-bin , Liu Si-yuan , Wang Shen-yun , Ding Guo-wen , Yang Hua , Yu Zhi-yang , Zhang Hai-feng
Published: February 2015

In this paper, a low-loss and high transmission analogy of electromagnetically induced transparency based on electric toroidal dipolar response is numerically and experimentally demonstrated. It is obtained by the excitation of the low-loss electric toroidal dipolar response, which confines the magnetic field inside a dielectric substrate with toroidal geometry. The metamaterial electromagnetically induced transparency (EIT) structure is composed of the cut wire and asymmetric split-ring resonators. The transmission level is as high as 0.88, and the radiation loss is greatly suppressed, which can be proved by the surface currents distributions, the magnetic field distributions, and the imaginary parts of the effective permeability and permittivity. It offers an effective way to produce low-loss and high transmission metamaterial EIT.
Evolution of dielectric and ferroelectric relaxor states in Al3+-doped BaTiO3
Authors: Vani K. , Kumar Viswanathan
Published: February 2015

In ferroelectric BaTiO3, we report the evolution of the Dielectric Relaxor and Ferroelectric Relaxor states as a function of B-site doped Al3+ concentration. The relaxor states occur after the paraelectric-ferroelectric phase transition upon cooling. Two different mechanisms are proposed; one based on migration of oxygen vacancies for symmetry-confirmation and the other based on disruption of long-range ferroelectric order by high concentrations of Al3+ ions at the B-site.
DENND2B activates Rab13 at the leading edge of migrating cells and promotes metastatic behavior
Authors: Ioannou Maria S. , Bell Emily S. , Girard Martine , Chaineau Mathilde , Hamlin Jason N.R. , Daubaras Mark , Monast Anie , Park Morag , Hodgson Louis , McPherson Peter S.
Published: February 2015

The small guanosine triphosphatase Rab13 functions in exocytic vesicle trafficking in epithelial cells. Alterations in Rab13 activity have been observed in human cancers, yet the mechanism of Rab13 activation and its role in cancer progression remain unclear. In this paper, we identify the DENN domain protein DENND2B as the guanine nucleotide exchange factor for Rab13 and develop a novel Förster resonance energy transfer–based Rab biosensor to reveal activation of Rab13 by DENND2B at the leading edge of migrating cells. DENND2B interacts with the Rab13 effector MICAL-L2 at the cell periphery, and this interaction is required for the dynamic remodeling of the cell’s leading edge. Disruption of Rab13-mediated trafficking dramatically limits the invasive behavior of epithelial cells in vitro and the growth and migration of highly invasive cancer cells in vivo. Thus, blocking Rab13 activation by DENND2B may provide a novel target to limit the spread of epithelial cancers.
Both tails and the centromere targeting domain of CENP-A are required for centromere establishment
Authors: Logsdon Glennis A. , Barrey Evelyne J. , Bassett Emily A. , DeNizio Jamie E. , Guo Lucie Y. , Panchenko Tanya , Dawicki-McKenna Jennine M. , Heun Patrick , Black Ben E.
Published: February 2015

The centromere—defined by the presence of nucleosomes containing the histone H3 variant, CENP-A—is the chromosomal locus required for the accurate segregation of chromosomes during cell division. Although the sequence determinants of human CENP-A required to maintain a centromere were reported, those that are required for early steps in establishing a new centromere are unknown. In this paper, we used gain-of-function histone H3 chimeras containing various regions unique to CENP-A to investigate early events in centromere establishment. We targeted histone H3 chimeras to chromosomally integrated Lac operator sequences by fusing each of the chimeras to the Lac repressor. Using this approach, we found surprising contributions from a small portion of the N-terminal tail and the CENP-A targeting domain in the initial recruitment of two essential constitutive centromere proteins, CENP-C and CENP-T. Our results indicate that the regions of CENP-A required for early events in centromere establishment differ from those that are required for maintaining centromere identity.
Collapsing modular counting in bounded arithmetic and constant depth propositional proofs
Authors: Buss Samuel , Kołodziejczyk Leszek , Zdanowski Konrad
Published: February 2015

Jeřábek introduced fragments of bounded arithmetic which are axiomatized with weak surjective pigeonhole principles and support a robust notion of approximate counting. We extend these fragments to accommodate modular counting quantifiers. These theories can formalize and prove the relativized versions of Toda’s theorem on the collapse of the polynomial hierarchy with modular counting. We introduce a version of the Paris-Wilkie translation for converting formulas and proofs of bounded arithmetic with modular counting quantifiers into constant depth propositional logic with modular counting gates. We also define Paris-Wilkie translations to Nullstellensatz and polynomial calculus refutations. As an application, we prove that constant depth propositional proofs that use connectives AND, OR, and mod p gates, for

p
p

a prime, can be translated, with quasipolynomial increase in size, into propositional proofs containing only propositional formulas of depth three in which the top level is Boolean, the middle level consists of mod p gates, and the bottom level subformulas are small conjunctions. These results are improved to depth two by using refutations from the weak surjective pigeonhole principles.
Crucial role for the LSP1–myosin1e bimolecular complex in the regulation of Fcγ receptor–driven phagocytosis
Authors: Maxeiner Sebastian , Shi Nian , Schalla Carmen , Aydin Guelcan , Hoss Mareike , Vogel Simon , Zenke Martin , Sechi Antonio S.
Published: February 2015

Actin cytoskeleton remodeling is fundamental for Fcγ receptor–driven phagocytosis. In this study, we find that the leukocyte-specific protein 1 (LSP1) localizes to nascent phagocytic cups during Fcγ receptor–mediated phagocytosis, where it displays the same spatial and temporal distribution as the actin cytoskeleton. Down-regulation of LSP1 severely reduces the phagocytic activity of macrophages, clearly demonstrating a crucial role for this protein in Fcγ receptor–mediated phagocytosis. We also find that LSP1 binds to the class I molecular motor myosin1e. LSP1 interacts with the SH3 domain of myosin1e, and the localization and dynamics of both proteins in nascent phagocytic cups mirror those of actin. Furthermore, inhibition of LSP1–myosin1e and LSP1–actin interactions profoundly impairs pseudopodial formation around opsonized targets and their subsequent internalization. Thus the LSP1–myosin1e bimolecular complex plays a pivotal role in the regulation of actin cytoskeleton remodeling during Fcγ receptor–driven phagocytosis.
Microtubule-dependent transport and dynamics of vimentin intermediate filaments
Authors: Hookway Caroline , Ding Liya , Davidson Michael W. , Rappoport Joshua Z. , Danuser Gaudenz , Gelfand Vladimir I.
Published: February 2015

We studied two aspects of vimentin intermediate filament dynamics—transport of filaments and subunit exchange. We observed transport of long filaments in the periphery of cells using live-cell structured illumination microscopy. We studied filament transport elsewhere in cells using a photoconvertible-vimentin probe and total internal reflection microscopy. We found that filaments were rapidly transported along linear tracks in both anterograde and retrograde directions. Filament transport was microtubule dependent but independent of microtubule polymerization and/or an interaction with the plus end–binding protein APC. We also studied subunit exchange in filaments by long-term imaging after photoconversion. We found that converted vimentin remained in small clusters along the length of filaments rather than redistributing uniformly throughout the network, even in cells that divided after photoconversion. These data show that vimentin filaments do not depolymerize into individual subunits; they recompose by severing and reannealing. Together these results show that vimentin filaments are very dynamic and that their transport is required for network maintenance.
specL—an R/Bioconductor package to prepare peptide spectrum matches for use in targeted proteomics
Authors: Panse Christian , Trachsel Christian , Grossmann Jonas , Schlapbach Ralph
Published: February 2015

Motivation: Targeted data extraction methods are attractive ways to obtain quantitative peptide information from a proteomics experiment. Sequential Window Acquisition of all Theoretical Spectra (SWATH) and Data Independent Acquisition (DIA) methods increase reproducibility of acquired data because the classical precursor selection is omitted and all present precursors are fragmented. However, especially for targeted data extraction, MS coordinates (retention time information precursor and fragment masses) are required for the particular entities (peptide ions). These coordinates are usually generated in a so-called discovery experiment earlier on in the project if not available in public spectral library repositories. The quality of the assay panel is crucial to ensure appropriate downstream analysis. For that, a method is needed to create spectral libraries and to export customizable assay panels.

Results: Here, we present a versatile set of functions to generate assay panels from spectral libraries for use in targeted data extraction methods (SWATH/DIA) in the area of proteomics.

Availability and implementation: specL is implemented in the R language and available under an open-source license (GPL-3) in Bioconductor since BioC 3.0 (R-3.1) http://www.bioconductor.org (Trachsel et al., 2015). A vignette with a complete tutorial describing data import/export and analysis is included in the package and can also be found as supplement material of this article.

Contact:  cp@fgcz.ethz.ch or jg@fgcz.ethz.ch

Supplementary information:  Supplementary data are available at Bioinformatics online.
LCR-eXXXplorer: a web platform to search, visualize and share data for low complexity regions in protein sequences
Authors: Kirmitzoglou Ioannis , Promponas Vasilis J.
Published: February 2015

Motivation: Local compositionally biased and low complexity regions (LCRs) in amino acid sequences have initially attracted the interest of researchers due to their implication in generating artifacts in sequence database searches. There is accumulating evidence of the biological significance of LCRs both in physiological and in pathological situations. Nonetheless, LCR-related algorithms and tools have not gained wide appreciation across the research community, partly due to the fact that only a handful of user-friendly software is currently freely available.

Results: We developed LCR-eXXXplorer, an extensible online platform attempting to fill this gap. LCR-eXXXplorer offers tools for displaying LCRs from the UniProt/SwissProt knowledgebase, in combination with other relevant protein features, predicted or experimentally verified. Moreover, users may perform powerful queries against a custom designed sequence/LCR-centric database. We anticipate that LCR-eXXXplorer will be a useful starting point in research efforts for the elucidation of the structure, function and evolution of proteins with LCRs.

Availability and implementation: LCR-eXXXplorer is freely available at the URL http://repeat.biol.ucy.ac.cy/lcr-exxxplorer.

Contact:  vprobon@ucy.ac.cy

Supplementary information:  Supplementary data are available at Bioinformatics online.
EpiToolKit—a web-based workbench for vaccine design
Authors: Schubert Benjamin , Brachvogel Hans-Philipp , Jürges Christopher , Kohlbacher Oliver
Published: February 2015

Summary: EpiToolKit is a virtual workbench for immunological questions with a focus on vaccine design. It offers an array of immunoinformatics tools covering MHC genotyping, epitope and neo-epitope prediction, epitope selection for vaccine design, and epitope assembly. In its recently re-implemented version 2.0, EpiToolKit provides a range of new functionality and for the first time allows combining tools into complex workflows. For inexperienced users it offers simplified interfaces to guide the users through the analysis of complex immunological data sets.

Availability and implementation:  http://www.epitoolkit.de

Contact:  schubert@informatik.uni-tuebingen.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
Automated benchmarking of peptide-MHC class I binding predictions
Authors: Trolle Thomas , Metushi Imir G. , Greenbaum Jason A. , Kim Yohan , Sidney John , Lund Ole , Sette Alessandro , Peters Bjoern , Nielsen Morten
Published: February 2015

Motivation: Numerous in silico methods predicting peptide binding to major histocompatibility complex (MHC) class I molecules have been developed over the last decades. However, the multitude of available prediction tools makes it non-trivial for the end-user to select which tool to use for a given task. To provide a solid basis on which to compare different prediction tools, we here describe a framework for the automated benchmarking of peptide-MHC class I binding prediction tools. The framework runs weekly benchmarks on data that are newly entered into the Immune Epitope Database (IEDB), giving the public access to frequent, up-to-date performance evaluations of all participating tools. To overcome potential selection bias in the data included in the IEDB, a strategy was implemented that suggests a set of peptides for which different prediction methods give divergent predictions as to their binding capability. Upon experimental binding validation, these peptides entered the benchmark study.

Results: The benchmark has run for 15 weeks and includes evaluation of 44 datasets covering 17 MHC alleles and more than 4000 peptide-MHC binding measurements. Inspection of the results allows the end-user to make educated selections between participating tools. Of the four participating servers, NetMHCpan performed the best, followed by ANN, SMM and finally ARB.

Availability and implementation: Up-to-date performance evaluations of each server can be found online at http://tools.iedb.org/auto_bench/mhci/weekly. All prediction tool developers are invited to participate in the benchmark. Sign-up instructions are available at http://tools.iedb.org/auto_bench/mhci/join.

Contact:  mniel@cbs.dtu.dk or bpeters@liai.org

Supplementary information:  Supplementary data are available at Bioinformatics online.
A new method to improve network topological similarity search: applied to fold recognition
Authors: Lhota John , Hauptman Ruth , Hart Thomas , Ng Clara , Xie Lei
Published: February 2015

Motivation: Similarity search is the foundation of bioinformatics. It plays a key role in establishing structural, functional and evolutionary relationships between biological sequences. Although the power of the similarity search has increased steadily in recent years, a high percentage of sequences remain uncharacterized in the protein universe. Thus, new similarity search strategies are needed to efficiently and reliably infer the structure and function of new sequences. The existing paradigm for studying protein sequence, structure, function and evolution has been established based on the assumption that the protein universe is discrete and hierarchical. Cumulative evidence suggests that the protein universe is continuous. As a result, conventional sequence homology search methods may be not able to detect novel structural, functional and evolutionary relationships between proteins from weak and noisy sequence signals. To overcome the limitations in existing similarity search methods, we propose a new algorithmic framework—Enrichment of Network Topological Similarity (ENTS)—to improve the performance of large scale similarity searches in bioinformatics.

Results: We apply ENTS to a challenging unsolved problem: protein fold recognition. Our rigorous benchmark studies demonstrate that ENTS considerably outperforms state-of-the-art methods. As the concept of ENTS can be applied to any similarity metric, it may provide a general framework for similarity search on any set of biological entities, given their representation as a network.

Availability and implementation: Source code freely available upon request

Contact: lxie@iscb.org
Individual specialization on fishery discards by lesser black-backed gulls (Larus fuscus)
Authors: Tyson Chris , Shamoun-Baranes Judy , Van Loon E. Emiel , Camphuysen Kees (C. J.) , Hintzen Niels T.
Published: February 2015

While seabird–fishery associations are well documented, this research primarily comes from ship-based surveys and consequently individual level responses to discard availability are largely unknown. As part of a long-term study on lesser black-backed gulls (Larus fuscus) in the Netherlands, the fine-scale movements of adults were tracked with GPS tags throughout the breeding period. The aim of this study was to determine if lesser black-backed gulls were utilizing fishery discards in the Wadden Sea and to examine possible consequences of this behaviour. Within the Wadden Sea during weekdays, tracked birds predominately associated with zones where fishing vessels are known to operate (deep gullies). Across all individuals combined (n = 40), there was a significantly reduced use of the Wadden Sea during weekends when the fleets were not operating. Eight females, who markedly increased their use of the Wadden Sea during weekdays throughout the breeding period, were largely responsible for this pattern. The loss of discard resources on weekends primarily resulted in these eight individuals switching to terrestrial foraging areas. Nest attendance and total foraging time were consistent between weekdays and weekends, suggesting that resource shifts on weekends did not impact daily time budgets. As such, it appears that lesser black-backed gulls specializing on discard utilization are able to flexibly respond to the temporary loss of discards by switching to alternative resources.
Selection between foreground models for global 21-cm experiments
Authors: Harker Geraint J. A.
Published: February 2015

The precise form of the foregrounds for sky-averaged measurements of the 21-cm line during and before the epoch of reionization is unknown. We suggest that the level of complexity in the foreground models used to fit global 21-cm data should be driven by the data, under a Bayesian model selection methodology. A first test of this approach is carried out by applying nested sampling to simplified models of global 21-cm data to compute the Bayesian evidence for the models. If the foregrounds are assumed to be polynomials of order n in log–log space, we can infer the necessity to use n = 4 rather than n = 3 with <2 h of integration with limited frequency coverage, for reasonable values of the n = 4 coefficient. Using a higher order polynomial does not necessarily prevent a significant detection of the 21-cm signal. Even for n = 8, we can obtain very strong evidence distinguishing a reasonable model for the signal from a null model with 128 h of integration. More subtle features of the signal may, however, be lost if the foregrounds are this complex. This is demonstrated using a simpler model for the signal that only includes absorption. The results highlight some pitfalls in trying to quantify the significance of a detection from errors on the parameters of the signal alone.
George Fu Gao: the past and future of Ebola
Authors: Poo Mu-ming , Wang Ling
Published: February 2015

Newly returned from the frontline of the battle against Ebola in West Africa, Dr George Fu Gao talked to NSR on this largest Ebola epidemic in history. As Deputy Director-General of the Chinese Center for Disease Control and Prevention (China CDC), an Academician of the Chinese Academy of Sciences and a fellow of the Third World Academy of Sciences (TWAS), Dr Gao has been personally involved in the fight against acute infectious diseases both on the laboratory bench and in the field for many years. Recalling the sight of an Ebola-infected young man stumbling to his death on the street and observing the continuing climb of patient statistics, he anxiously calls for larger global help to affected countries. The help provided by the world community to West Africa was ‘too late and insufficient’, and in this age of globalization ‘no country can care only for herself alone’. In this interview, Dr Gao also reviews the history, progression, and prognosis of the Ebola epidemic, the cause of failure in the early prevention and containment of the disease, the role of government policies and public health systems, and global prospects and strategies for similar acute infectious diseases in the future.
High dispersion spectroscopy of solar-type superflare stars. I. Temperature, surface gravity, metallicity, and vsin i
Authors: Notsu Yuta , Honda Satoshi , Maehara Hiroyuki , Notsu Shota , Shibayama Takuya , Nogami Daisaku , Shibata Kazunari
Published: February 2015

We conducted high-dispersion spectroscopic observations of 50 superflare stars with Subaru High Dispersion Spectrograph (HDS), and measured the stellar parameters of them. These 50 targets were selected from the solar-type (G-type main sequence) superflare stars that we had discovered from the Kepler photometric data. As a result of these spectroscopic observations, we found that more than half (34) of our 50 targets have no evidence of binary systems. We then estimated the effective temperature (Teff), surface gravity (log g), metallicity ([Fe/H]), and projected rotational velocity (vsin i) of these 34 superflare stars on the basis of our spectroscopic data. The accuracy of our estimations is higher than that of the Kepler Input Catalog (KIC) values, and the differences between our values and KIC values [(ΔTeff)rms ∼ 219 K, (Δlog g)rms ∼ 0.37 dex, and (Δ[Fe/H])rms ∼ 0.46 dex] are comparable to the large uncertainties and systematic differences of KIC values reported by the previous researchers. We confirmed that the estimated Teff and log g values of the 34 superflare stars are roughly in the range of solar-type stars. In particular, these parameters and the brightness variation period (P0) of nine of the stars are in the range of “Sun-like” stars (5600 ≤ Teff ≤ 6000 K, log g ≥ 4.0, and P0 > 10 d). Five of the 34 target stars are fast rotators (vsin i ≥ 10 km s−1), while 22 stars have relatively low vsin i values (vsin i < 5 km s−1). These results suggest that stars that have spectroscopic properties similar to the Sun can have superflares, and this supports the hypothesis that the Sun might cause a superflare.