bluuebunny/crossref_metadata_2025 huggingface dataset:
Copper in Prokaryotes
Authors: Le Brun Nick E.
Published: July 2014

The ability of copper to cycle its oxidation state, and to form high-affinity complexes with a range of biologically relevant ligands, underpins the central role that this metal plays in prokaryotic processes such as respiration, oxidative stress response, the nitrogen cycle and pigmentation. However, the very properties that nature has exploited also mean that copper is extremely toxic. To minimize this toxicity, while also ensuring sufficient supply of the metal, complex systems of trafficking evolved to facilitate transport of copper (as Cu(I)) across membranes and its targeted distribution within the cytoplasm, membrane and periplasm. The past 20 years have seen our understanding of such systems grow enormously, and atomic/molecular and mechanistic detail of many of the major cellular trafficking components is now available. This chapter begins with a discussion of the chemistry of copper that is relevant for understanding the role of this metal throughout life. The subsequent focus is then on current understanding of copper homeostasis in prokaryotes, with eukaryotic copper homeostasis dealt with in the following chapters. The chapter aims to provide a chemical perspective on these complex biological systems, emphasizing the importance of thermodynamic and kinetic properties of copper and the complexes it forms.
Metallothioneins
Authors: Blindauer Claudia A.
Published: July 2014

Metallothioneins (MTs) are small cysteine-rich proteins that bind multiple metal ions in characteristic metal-thiolate clusters. They have been identified and studied in both prokaryotes, where they seem to be limited to a relatively small number of genera, and eukaryotes, where they are nearly ubiquitous. These are the archetypal cytosolic binders and transporters of essential and non-essential d10 metal ions, in particular Zn(II), Cu(I) and Cd(II). The term “metallothioneins” encompasses proteins that are not related through recognizable sequence similarity or even fold similarity, but through an extraordinarily high abundance of cysteine residues, and their metal ion binding ability. Considering the diversity of their primary structures, there is a high likelihood for “metallothioneins” having evolved more than once, i.e. they are thought to constitute a polyphyletic group of proteins. Their structural diversity is accompanied by functional versatility; physiological functions are diverse and include detoxifying and/or trafficking both essential and non-essential metal ions, regulating intracellular availability of Zn or Cu and providing an easily mobilized storage facility for Zn or Cu, depending on the organism concerned. They also can be cellular antioxidants and may link the cellular redox state and Zn status. Depending on organism and tissue, different MTs may have different functions, and even a single MT may perform several of these roles. Indeed, the regulatory DNA sequences of some mammalian MTs harbour not only metal-responsive elements (MREs), but also elements that respond to glucocorticoids (GREs) and oxidative stress (AREs), amongst many other cis-acting elements. This chapter will focus on the structures and in vitro chemistry of metallothioneins from both eukaryotes (including those from vertebrates, invertebrates, plants and fungi) and prokaryotes (including those from cyanobacteria and mycobacteria). The polyphyletic origins of MTs and the resulting diversity of MTs from different phyla in terms of biophysical properties and biological functions emphasize the ongoing need for in-depth studies. It is inappropriate to extrapolate properties and functions from one MT to another.
Fast voltammetry of metals at carbon-fiber microelectrodes: copper adsorption onto activated carbon aids rapid electrochemical analysis
Authors: Pathirathna Pavithra , Samaranayake Srimal , Atcherley Christopher W. , Parent Kate L. , Heien Michael L. , McElmurry Shawn P. , Hashemi Parastoo
Published: July 2014

Fundamental studies of carbon fiber surfaces show that the rapid voltammetric response to trace metals is an adsorption driven process.
Development of an enantiomeric separation of d & l valine as their corresponding isoindole adducts by RP-HPLC for utilization of the l-valine toward pharmaceutically relevant materials
Authors: Denton Justin R. , Dermenjian Renee K. , Mao Bing
Published: July 2014

A RP-HPLC method has been developed for the quantitation of d-valine within l-valine as their corresponding OPA adducts to the 0.05% chiral impurity level.
An overview of analytical methods for monitoring bacterial transglycosylation
Authors: Blanchaert Bart , Adams Erwin , Van Schepdael Ann
Published: July 2014

This review highlights the fluorescence and radioactively labeled assays and high-throughput screens for the search for antibiotics targeting bacterial transglycosylation.
Potassium-induced G-quadruplex DNAzyme as a chemiluminescent sensing platform for highly selective detection of K+
Authors: Wang Hong , Wang Dong Mei , Gao Ming Xuan , Wang Jian , Huang Cheng Zhi
Published: July 2014

A simple and highly selective chemiluminescence (CL) method of K+ detection was firstly developed based on K+-sensitive G-qudruplex DNAzyme in luminol-H2O2 reaction system.
Stimuli-responsive cancer therapy based on nanoparticles
Authors: Yu Jing , Chu Xin , Hou Yanglong
Published: July 2014

Nanoparticle (NP)-based stimuli-sensitive cancer therapy, including pH-, reduction-sensitive NPs and light-, magnetic field-responsive NPs are reviewed.
Direct validation of the restriction of intramolecular rotation hypothesis via the synthesis of novel ortho-methyl substituted tetraphenylethenes and their application in cell imaging
Authors: Zhang Guo-Feng , Chen Ze-Qiang , Aldred Matthew P. , Hu Zhe , Chen Tao , Huang Zhenli , Meng Xianggao , Zhu Ming-Qiang
Published: July 2014

RIR hypothesis as the mechanism of aggregation-induced emission phenomenon is validated via the synthesis of ortho-methyl tetraphenylethenes.
Molecular volumes of DOPC and DOPS in mixed bilayers of multilamellar vesicles
Authors: Murugova T. N. , Balgavý P.
Published: July 2014

Specific volume of 1,2-dioleoyl-sn-glycero-3-phosphocholine and 1,2-dioleoyl-sn-glycero-3-phospho-l-serine mixtures in bilayers linearly depends on the molar fraction of the constituents, indicating an ideal volume mixing.
Polyoxometalate based open-frameworks (POM-OFs)
Authors: Miras Haralampos N. , Vilà-Nadal Laia , Cronin Leroy
Published: July 2014

Polyoxometalate-based open frameworks (POM-OFs) are extended architectures incorporating metal-oxide cluster units and comprise an emergent family of materials with a large diversity of topologies, structural flexibility and functionality at the nanoscale.
Triptycene based organometallic complexes: a new class of acceptor synthons for supramolecular ensembles
Authors: Chakraborty Sourav , Mondal Snehasish , Bhowmick Sourav , Ma Jianqiu , Tan Hongwei , Neogi Subhadip , Das Neeladri
Published: July 2014

New triptycene based organometallic complexes have been synthesized and subsequently used for design of the triptycene motif containing nanoscalar trigonal prisms. Flexible 3,3′-bipyridine is employed as a donor unit.
Ruthenium sensitizers having an ortho-dicarboxyl group as an anchoring unit for dye-sensitized solar cells: synthesis, photo- and electrochemical properties, and adsorption behavior to the TiO2 surface
Authors: Ozawa Hironobu , Fukushima Kei , Sugiura Takahito , Urayama Ayako , Arakawa Hironori
Published: July 2014

A novel ruthenium sensitizer with a 3′,4′-dicarboxyterpyridine (TUS-28) has been synthesized as an improved model sensitizer of the dye-sensitized solar cells.
Well-dispersed ultrafine Mn3O4 nanocrystals on reduced graphene oxide with high electrochemical Li-storage performance
Authors: Huang Hui , Zhang Liyuan , Xia Yang , Gan Yongping , Tao Xinyong , Liang Chu , Zhang Wenkui
Published: July 2014

The Mn3O4–reduced graphene oxide composite synthesized by a microexplosion mechanism shows high electrochemical Li-storage performance.
Towards a unified description of the charge transport mechanisms in conductive atomic force microscopy studies of semiconducting polymers
Authors: Moerman D. , Sebaihi N. , Kaviyil S. E. , Leclère P. , Lazzaroni R. , Douhéret O.
Published: July 2014

The nanoscale electrical properties of fibrillate poly-3-hexylthiophene are studied using conducting-AFM. The conditions for the prevalence of either local or bulk resistances dominated regime are identified. As local current is space charge limited, an analytical model is derived to determine locally carrier mobility and density.
Current rectification by nanoparticle blocking in single cylindrical nanopores
Authors: Ali Mubarak , Ramirez Patricio , Nasir Saima , Nguyen Quoc-Hung , Ensinger Wolfgang , Mafe Salvador
Published: July 2014

Charged nanoparticles induce high current rectification ratios in single cylindrical nanopores.
A lysosome-targeted drug delivery system based on sorbitol backbone towards efficient cancer therapy
Authors: Maniganda Santhi , Sankar Vandana , Nair Jyothi B. , Raghu K. G. , Maiti Kaustabh K.
Published: July 2014

A lysosome-targeted drug delivery system utilizing sorbitol scaffold linked to octa-guanidine and to a peptide substrate of lysosomal cysteine protease, cathepsin B.
Facile synthesis of pseudo-peanut shaped hematite iron oxide nano-particles and their promising ethanol and formaldehyde sensing characteristics
Authors: Das P. , Mondal B. , Mukherjee K.
Published: July 2014

Herein, pseudo-peanut shaped hematite iron oxide nano-particles are prepared through a facile cost effective wet chemical synthesis route.
A new C–C bond formation model based on the quantum chemical topology of electron density
Authors: Domingo Luis R.
Published: July 2014

Pseudodiradicalstructures and GEDT involved in the C–C single bond formation in non-polar, polar and ionic organic reactions.
Gold-nanoparticle-modified polyvinylidene fluoride membranes used for western blotting with high sensitivity
Authors: Tang Fengwu , Zhang Sai , Zhala Gahu , Huo Jingrui , Tu Yue , Xu Zhongwei , Fan Rong , Li Wei , Chen Xuyi , Chen Xiaoyi
Published: July 2014

In this study, we report an ultrasensitive western blotting method by introducing gold nanoparticles (AuNPs) onto modified polyvinylidene fluoride (PVDF) membranes via atom transfer radical polymerization (ATRP).
CO2-triggered release from switchable surfactant impregnated liposomes
Authors: Hegh Dylan Y. , Mackay Sean M. , Tan Eng Wui
Published: July 2014

Incorporation of an amidine-based switchable surfactant into the lipid membrane of a liposome produces a system that is capable of triggered release upon in situ exposure to CO2. The amount of liposomal contents released is dependent on the concentration of switchable surfactant incorporated.
Silver catalyzed decarboxylative acylation of pyridine-N-oxides using α-oxocarboxylic acids
Authors: Suresh Rajendran , Kumaran Rajendran Senthil , Senthilkumar Vajiram , Muthusubramanian Shanmugam
Published: July 2014

Silver catalyzed acylation of pyridine-N-oxides by α-oxocarboxylic acid is demonstrated. This decarboxylative acylation using a metal catalyst takes place at 50 °C via a radical process.
Integrated bioprinting and imaging for scalable, networkable desktop experimentation
Authors: Orloff Nathan D. , Truong Cynthia , Cira Nathan , Koo Stephen , Hamilton Andrea , Choi Sean , Wu Victoria , Riedel-Kruse Ingmar H.
Published: July 2014

A fluid-deposition and imaging platform based on a re-engineered desktop printer and scanner integrated for do-it-yourself research, remote experimentation, and (on-line) education.
Direct observation of the formation and destruction of the inverted continuous oil phase in the micro-outlet region achieved by the confined diluted O/W emulsion stream
Authors: Ma Liran , Xu Xuefeng , Zhang Chenhui , Luo Jianbin
Published: July 2014

We demonstrate a direct observation of the oil-in-water (O/W) emulsion droplets in a confined point contact geometry, to shed new light on the mechanism of the interaction between emulsion and solid surfaces under confinement.
Silver- and sulfadiazine-loaded nanostructured silica materials as potential replacement of silver sulfadiazine
Authors: Szegedi Ágnes , Popova Margarita , Yoncheva Krassimira , Makk Judit , Mihály Judith , Shestakova Pavletta
Published: July 2014

Sulfadiazine-loaded silver nanoporous silica carriers have similar antibacterial properties as silver sulfadiazine.
Fabrication of porous film with controlled pore size and wettability by electric breath figure method
Authors: Zhai Song , Ye Jia-Ru , Wang Nan , Jiang Lin-Hai , Shen Qing
Published: July 2014

A novel electric breath figure (EBF) method was developed by applying an electrostatic generator to assist the common breath figure (BF) method, and it was applied to fabricate polystyrene (PS) film.
Yolk–shell Fe3O4@ZrO2 prepared by a tunable polymer surfactant assisted sol–gel method for high temperature stable microwave absorption
Authors: Yu Meng , Liang Chongyun , Liu Mengmei , Liu Xialin , Yuan Kaiping , Cao Hui , Che Renchao
Published: July 2014

Highly-dispersed Fe3O4@ZrO2 yolk–shell structures with a ZrO2 shell of homogeneous shell thickness was successfully prepared via a polymer surfactant (hydroxypropyl cellulose) assisted sol–gel method.
Endoscopic Procedures in Patients under Clopidogrel or Dual Antiplatelet Therapy: A Survey among German Gastroenterologists and Current Guidelines
Authors: Theilmann L. , Labenz J. , Abdel Samie A. ,   for the ALGK
Published: July 2014

Background: Because of the higher risk of bleeding, guidelines recommend cessation of clopidogrel seven days prior to high-risk endoscopic procedures. However, premature cessation of clopidogrel may lead to catastrophic cardiovascular sequelae due to stent thrombosis. We aimed to assess the current clinical practice among German gastroenterologists regarding endoscopic procedures in patients under clopidogrel/dual antiplatelet therapy.

Methods: A 10-item questionnaire on endoscopic procedures in patients under clopidogrel/dual antiplatelet therapy was sent by e-mail to all 220 members of the ALGK.

Results: 73 (33 %) chief gastroenterologists returned completed questionnaires, 35 (48 %) of whom conduct high-volume endoscopic units performing more than 4000 procedures per annum. 62 (85 %) endoscopic units perform endoscopic biopsies under clopidogrel alone, while just in 30 (41 %) departments biopsies are carried out under dual antiplatelet therapy. In 36 (49 %) GI-units endoscopic polypectomy under clopidogrel monotherapy is performed, in contrast to only 4 (5.5 %) in the case of combined antiplatelet therapy. However, in emergency situations more than 60 % of all participants do perform endoscopic sphincterotomy in patients under clopidogrel/dual antiplatelet therapy. Percutaneous endoscopic gastrostomy is carried out in 32 endoscopic units (44 %) under clopidogrel monotherapy, but only in 4 (5.5 %) under dual antiplatelet therapy.

Conclusion: Current guidelines on endoscopic procedures in patients under clopidogrel/dual antiplatelet therapy are mainly based on expert opinion and therefore, backed by only weak evidence. Our survey shows that in this setting the clinical decision making takes place on an individual basis, as there are no data to support the recommendations of the present guidelines.
Impact of Perioperative Immunosuppressive Medication on Surgical Outcome in Crohn’s Disease (CD)
Authors: Eisner F. , Küper M. A. , Ziegler F. , Zieker D. , Königsrainer A. , Glatzle J.
Published: July 2014

Introduction: Patients with Crohn’s disease [CD] carry an 80 − 90 % lifetime risk of undergoing surgery. Many of these patients are on immunosuppressive medication at the time of surgery. The aim of this study was to evaluate the effect of immunosuppression on the surgical outcome in CD patients.

Methods: We retrospectively analyzed 484 consecutive abdominal operations for CD from 1995 to 2008 for surgical complications.

Results: A total of 241 operations (= 49.8 %) were performed under perioperative immunosuppression (corticoids and thiopurine). The overall complication rate was 18.6 %, the major complication rate was 8.7 % and the anastomotic leakage rate was 3.3 %. No differences were observed between patients without immunosuppression compared to those with immunosuppression. Patients with colo-rectal resections showed a higher complication rate than patients with small bowel resection independently of immunosuppression.

Conclusion: Nearly 50 % of the patients undergoing abdominal surgery for CD are receiving immunosuppressive medication during surgery. However, perioperative immunosuppression with corticoids, thiopurine or the combination of both does not significantly alter the surgical complication rate. Therefore the decision of a required surgery should not be delayed due to the fact that the patient is under immunosuppressive medication.
Complex absorbing potentials within EOM-CC family of methods: Theory, implementation, and benchmarks
Authors: Zuev Dmitry , Jagau Thomas-C. , Bravaya Ksenia B. , Epifanovsky Evgeny , Shao Yihan , Sundstrom Eric , Head-Gordon Martin , Krylov Anna I.
Published: July 2014

A production-level implementation of equation-of-motion coupled-cluster singles and doubles (EOM-CCSD) for electron attachment and excitation energies augmented by a complex absorbing potential (CAP) is presented. The new method enables the treatment of metastable states within the EOM-CC formalism in a similar manner as bound states. The numeric performance of the method and the sensitivity of resonance positions and lifetimes to the CAP parameters and the choice of one-electron basis set are investigated. A protocol for studying molecular shape resonances based on the use of standard basis sets and a universal criterion for choosing the CAP parameters are presented. Our results for a variety of π* shape resonances of small to medium-size molecules demonstrate that CAP-augmented EOM-CCSD is competitive relative to other theoretical approaches for the treatment of resonances and is often able to reproduce experimental results.
Soft x-ray intensity profile measurements of electron cyclotron heated plasmas using semiconductor detector arrays in GAMMA 10 tandem mirror
Authors: Minami R. , Imai T. , Kariya T. , Numakura T. , Eguchi T. , Kawarasaki R. , Nakazawa K. , Kato T. , Sato F. , Nanzai H. , Uehara M. , Endo Y. , Ichimura M.
Published: July 2014

Temporally and spatially resolved soft x-ray analyses of electron cyclotron heated plasmas are carried out by using semiconductor detector arrays in the GAMMA 10 tandem mirror. The detector array has 16-channel for the measurements of plasma x-ray profiles so as to make x-ray tomographic reconstructions. The characteristics of the detector array make it possible to obtain spatially resolved plasma electron temperatures down to a few tens eV and investigate various magnetohydrodynamic activities. High power electron cyclotron heating experiment for the central-cell region in GAMMA 10 has been started in order to reduce the electron drag by increasing the electron temperature.
On the room-temperature phase diagram of high pressure hydrogen: An ab initio molecular dynamics perspective and a diffusion Monte Carlo study
Authors: Chen Ji , Ren Xinguo , Li Xin-Zheng , Alfè Dario , Wang Enge
Published: July 2014

The finite-temperature phase diagram of hydrogen in the region of phase IV and its neighborhood was studied using the ab initio molecular dynamics (MD) and the ab initio path-integral molecular dynamics (PIMD). The electronic structures were analyzed using the density-functional theory (DFT), the random-phase approximation, and the diffusion Monte Carlo (DMC) methods. Taking the state-of-the-art DMC results as benchmark, comparisons of the energy differences between structures generated from the MD and PIMD simulations, with molecular and dissociated hydrogens, respectively, in the weak molecular layers of phase IV, indicate that standard functionals in DFT tend to underestimate the dissociation barrier of the weak molecular layers in this mixed phase. Because of this underestimation, inclusion of the quantum nuclear effects (QNEs) in PIMD using electronic structures generated with these functionals leads to artificially dissociated hydrogen layers in phase IV and an error compensation between the neglect of QNEs and the deficiencies of these functionals in standard ab initio MD simulations exists. This analysis partly rationalizes why earlier ab initio MD simulations complement so well the experimental observations. The temperature and pressure dependencies for the stability of phase IV were also studied in the end and compared with earlier results.
Classical non-Markovian Boltzmann equation
Authors: Alexanian Moorad
Published: July 2014

The modeling of particle transport involves anomalous diffusion, ⟨x2(t) ⟩ ∝ tα with α ≠ 1, with subdiffusive transport corresponding to 0 < α < 1 and superdiffusive transport to α > 1. These anomalies give rise to fractional advection-dispersion equations with memory in space and time. The usual Boltzmann equation, with only isolated binary collisions, is Markovian and, in particular, the contributions of the three-particle distribution function are neglected. We show that the inclusion of higher-order distribution functions give rise to an exact, non-Markovian Boltzmann equation with resulting transport equations for mass, momentum, and kinetic energy with memory in both time and space. The two- and the three-particle distribution functions are considered under the assumption that the two- and the three-particle correlation functions are translationally invariant that allows us to obtain advection-dispersion equations for modeling transport in terms of spatial and temporal fractional derivatives.
Carrier accumulation near electrodes in ferroelectric films due to polarization boundary conditions
Authors: Misirlioglu I. B. , Yildiz M.
Published: July 2014

We study the effect of surface polarization on the distribution of free carriers in a wide bandgap semiconductor ferroelectric (FE) film using a thermodynamic approach. We show that free carriers, namely, holes and electrons from ionizable impurities or atomic vacancies can accumulate near the film-electrode interface, if FE polarization profile has a very steep change near the surface that is specified by the extrapolation length. Such an outcome is just the opposite of what happens in a Schottky junction in a partially or fully depleted film. This is also an entirely different effect than what has been often studied in similar structures, where the work function and screening length of the electrode metal determines the electronic character of the interface. Even for low-to-moderate densities of ionizable defects with states within the bandgap close to the band edges, high densities of carriers can localize close to the electrodes in a single domain state FE film when above a critical thickness. For very low densities of such ionizable defects, short extrapolation lengths cause electrical domain formation with minimal carrier accumulation because of the already weak depolarizing fields. This is also true for films below a critical thickness with low-to-moderate densities of ionizable impurities, i.e., electrical domains get stabilized regardless of defect density. The implications of our findings for polarization controlled Schottky to Ohmic-like transition of an interface and experimental results are discussed. It is also found that interfaces of an n-type FE heterostructure can behave like a p-type depending on the barrier heights and impurity density. We conclude that, for low-to-moderate ionizable impurity densities, it is the rate of change of polarization at the interface with position rather than solely its presence that leads to carrier accumulation and that both interfaces can become Ohmic-like with opposite signs of carriers.
Non-ideal optical isotropy of blue phase liquid crystal
Authors: Lan Yi-Fen , Liu Yifan , Huang Pu-Jung , Xu Daming , Tsai Cheng-Yeh , Lin Chin-Haun , Sugiura Norio , Wu Shin-Tson
Published: July 2014

Since 1981, blue phase liquid crystal (BPLC) was regarded as optical isotropy and high contrast ratio (CR) should be achieved easily. However, low CR of BPLC display was reported in all literatures. Here, we show BPLC is non-ideal optical isotropy which leads to poor CR. In our report, BPLC not only revealed primary structure of double-twist cylinder and secondary structure of lattice but also revealed tertiary structure of self-alignment on electrode surface. This finding will be useful to improve CR and inspire researches in display industry and academics.
Coherent lattice dynamics of the topological insulator Bi2Te3 probed by ultrafast spectroscopy
Authors: Flock J. , Dekorsy T. , Misochko O. V.
Published: July 2014

Femtosecond laser pulses have been used to excite coherent optical phonons in single crystalline Bi2Te3. Oscillations from low and high frequency phonons of two A1g and one Eg symmetry modes are observed. In order to clarify the process of coherent phonon generation, the time domain measurements were complemented by spontaneous Raman scattering. The comparison of frequency and time domain results reveals the discrepancies between the time and frequency domain measurements among which the most striking difference is given by the fact that the Eg(I) phonon is missing in the time domain data.
The determination of charge carrier mobility from the current transients in organic field effect transistor
Authors: Juška G. , Nekrašas N. , Genevičius K. , Grigaitis T.
Published: July 2014

In this paper, we present features of current transients in organic field effect transistors obtained by the computer simulation and experimentally. We analyse the influence of the charge carrier reservoir at the organic semiconductor-insulator interface and the load resistance on the current transients. We demonstrate how to determine the amount of charge carriers in the reservoir and how to take it into account when calculating the mobility values estimated from current transients. Such correction reduces the estimated mobility values and changes mobility dependence on the electric field.
Light-induced vibration characteristics of free-standing carbon nanotube films fabricated by vacuum filtration
Authors: Li Junying , Zhu Yong , Wang Xin , Wang Ning , Zhang Jie
Published: July 2014

In this paper, we fabricated carbon nanotube (CNT) films with different thickness by vacuum filtration method, and the films were separated from Mixed Cellulose Ester membranes with burn-off process. The thickness of CNT films with different concentrations of CNTs 50 mg, 100 mg, 150 mg, and 200 mg are 10.36 μm, 20.90 μm, 30.19 μm, and 39.98 μm respectively. The CNT bundles are homogeneously distributed and entangled with each other, and still maintain 2D continuous network structures after burn-off process. The optical absorptivity of the films is between 84% and 99% at wavelengths ranging from 400 nm to 2500 nm. Vibration characteristics were measured with the Fabry-Perot (F-P) interferometer vibration measurement system. CNT films vibrate only under the xenon light irradiating perpendicularly to the surface. Vibration recorded by Fabry-Perot interferometer is considered to be caused by the time-dependent thermal moment, which is due to the temperature differences of two sides of CNT films. The vibration frequency spectrums between 0.1 ∼ 0.5 Hz were obtained by the Fast Fourier Transform spectra from time domain to frequency domain, and showed a linear relationship with films thickness, which is in accordance with theoretical model of thermal induced vibration.
Strain induced low mechanical switching force in ultrathin PbZr0.2Ti0.8O3 films
Authors: Guo E. J. , Roth R. , Das S. , Dörr K.
Published: July 2014

Mechanical force has been found to be an alternative way to non-electrically switch the polarization of ultrathin ferroelectric films owing to the flexoelectric effect. Reducing the required force for switching is desirable for a low risk of damage to both sample and tip. Here, the strain dependence of mechanical threshold force has been studied in ultrathin PbZr0.2Ti0.8O3 films. The mechanical threshold force for polarization reversal reduces remarkably by a factor of ∼5 with decreasing the compressive strain, associated with a reduction of coercivity and tetragonality. We attributed such behavior to the reduction of switching barrier and remnant polarization. Our work provides a route to realize ultra-low mechanical writing force for non-volatile memory applications.
Towards the Synthesis of Guanidinate- and Amidinate-Bridged Dimers of Mn and Ni
Authors: Stokes Francesca A. , Kloo Lars , Harford Philip J. , Peel Andrew J. , Less Robert J. , Wheatley Andrew E. H. , Wright Dominic S.
Published: July 2014

Reactions of Cp2M (Cp = cyclopentadienyl, M = Mn, Ni) with lithium amidinates and guanidinates are reported. The highly oxophilic nature of Mn leads to the isolation of the interstitial oxide Mn4O(MeN···CH···NMe)6 (4) in preference to the intended paddle-wheel homodimer Mn2(MeN···CH···NMe)4 when employing the sterically uncongested amidinate [MeN···CH···NMe]– ligand. In contrast, an analogous reaction using Cp2Ni yielded Ni2(MeN···CH···NMe)4 (5). The use of monoprotic guanidinate ligands also gave contrasting results for Mn and Ni. In the first case, the highly unusual spirocycle Mn{μ-NC(NMe2)2}4Li2·3THF (6) was produced in low yield. For M = Ni, use of the [hpp]– (1,3,4,6,7,8-hexahydro-2H-pyrimido[1,2-a]pyrimidinate) ligand gives results comparable with the synthesis of 5, with Ni2(hpp)4 (7) isolated. In contrast to recent data obtained using Cp2Cr, the guanidinate ligands do not sequester coformed CpLi. Density functional theory analysis corroborates the view that the intermetal distance in each of the reported dinickel paddle-wheel complexes (2.4846(8) and 2.3753(5) Å in 5 and 7 respectively) is defined by the geometric parameters of the bidentate ligands and that intermetal bonding is not present.
Divergence of
Drosophila melanogaster
repeatomes in response to a sharp microclimate contrast in Evolution Canyon, Israel
Authors: Kim Young Bun , Oh Jung Hun , McIver Lauren J. , Rashkovetsky Eugenia , Michalak Katarzyna , Garner Harold R. , Kang Lin , Nevo Eviatar , Korol Abraham B. , Michalak Pawel
Published: July 2014

Significance

Repeatome, or the ensemble of all repeat sequences, with its enormous variability and internal epigenetic dynamics, emerges as a critical source of potentially adaptive changes and evolutionary novelties. This conclusion is exemplified here by the cosmopolitan
Drosophila melanogaster
from a sharp ecological contrast in North Israel. Flies derived from the opposing sides of this long-studied microsite exhibit a significant difference in the contents and distribution of mobile elements, as well as microsatellite allele frequencies, corresponding well with earlier reported phenotypic patterns of stress resistance and assortative mating in the system.
4D multiple-cathode ultrafast electron microscopy
Authors: Baskin John Spencer , Liu Haihua , Zewail Ahmed H.
Published: July 2014

Significance

Imaging of dynamical processes in materials and biological structures requires resolutions in both space and time. Four-dimensional electron microscopy was developed to image microscopic objects down to the atomic-scale spatial resolution and the femtosecond time resolution. Unlike stroboscopic techniques applied in studies of reversible processes on the femtosecond scale, single-pulse methods have been limited to the nanosecond scale for capturing irreversible processes such as materials phase transformations. In this contribution, we report on 4D multiple-cathode ultrafast electron microscopy, which enables the direct capture with femtosecond time resolution of phenomena at multiple times in their dynamics and in a single frame. The scope of applications is wide ranging.
Acceleration and sprint profiles of a professional elite football team in match play
Authors: Ingebrigtsen Jørgen , Dalen Terje , Hjelde Geir Håvard , Drust Barry , Wisløff Ulrik
Published: July 2014

The aim of this study was to characterise the acceleration and sprint profiles of elite football match play in one Norwegian elite football team (Rosenborg FC). Fifteen professional players in five playing positions took part in the study (n = 101 observations). Player movement was recorded during every domestic home game of one full season (n = 15) by an automatic tracking system based on microwave technology. Each player performed 91 ± 21 accelerations per match, with a lower number in the second compared with the first half (47 ± 12 vs. 44 ± 12). Players in lateral positions accelerated more often compared to players in central positions (98.3 ± 20.5 vs. 85.3 ± 19.5, p < 0.05). Average sprint distance was 213 ± 111 m distributed between 16.6 ± 7.9 sprints, with no differences between first (106 ± 60 m, 8.2 ± 4.2 sprints) and second halves (107 ± 72 m, 8.3 ± 4.8 sprints). Players in lateral positions sprinted longer distances (287 ± 211 m vs. 160 ± 76 m, p < 0.05) and tended to sprint more often (21.6 ± 7.8 vs. 13.0 ± 5.7, p = 0.064) compared to players in central positions. We found more walking and less of the more intense activities during the last third of the season compared to the first. The main finding in this study was that Norwegian elite players had substantially less number of accelerations and fewer but longer sprints than previous studies reported for higher‐ranked leagues. Also, less high‐intensity activity was found towards the end of the season. Ultimately, these data provide useful information for the fitness coach (1) in planning of position‐specific football training and (2) to avoid the decline in high‐intensity activities the last third of the competitive season.
Transcription factor regulation and chromosome dynamics during pseudohyphal growth
Authors: Mayhew David , Mitra Robi D.
Published: July 2014

Pseudohyphal growth is a developmental pathway seen in some strains of yeast in which cells form multicellular filaments in response to environmental stresses. We used multiplexed transposon “Calling Cards” to record the genome-wide binding patterns of 28 transcription factors (TFs) in nitrogen-starved yeast. We identified TF targets relevant for pseudohyphal growth, producing a detailed map of its regulatory network. Using tools from graph theory, we identified 14 TFs that lie at the center of this network, including Flo8, Mss11, and Mfg1, which bind as a complex. Surprisingly, the DNA-binding preferences for these key TFs were unknown. Using Calling Card data, we predicted the in vivo DNA-binding motif for the Flo8-Mss11-Mfg1 complex and validated it using a reporter assay. We found that this complex binds several important targets, including FLO11, at both their promoter and termination sequences. We demonstrated that this binding pattern is the result of DNA looping, which regulates the transcription of these targets and is stabilized by an interaction with the nuclear pore complex. This looping provides yeast cells with a transcriptional memory, enabling them more rapidly to execute the filamentous growth program when nitrogen starved if they had been previously exposed to this condition.
Catastrophic Outpatient Health Payments and Health Payment‐induced Poverty under China's New Rural Cooperative Medical Scheme
Authors: Yang Wei
Published: July 2014

In 2003, the New Rural Cooperative Medical Scheme (NCMS) was initiated in China to provide rural inhabitants with financial protection against health risks. The benefit package was extended to outpatient care in 2007. Using the China Health and Nutrition Survey of 2009, this paper examines the relationship between the households participating in the NCMS and the level and distribution of catastrophic health payments and health payment‐induced poverty resulting from outpatient care. The study finds no significant difference in terms of catastrophic health payments and health payment‐induced poverty before and after NCMS reimbursement. The out‐of‐pocket payments (OOP) are concentrated disproportionately among the poor even after the insurance reimbursement. This heavy burden of OOP payments has become a poverty trap for the poor. This study calls for a more comprehensive insurance and effective insurance package.
mcmc_clib
–an advanced MCMC sampling package for
ode
models
Authors: Kramer Andrei , Stathopoulos Vassilios , Girolami Mark , Radde Nicole
Published: July 2014

Summary : We present a new C implementation of an advanced Markov chain Monte Carlo (MCMC) method for the sampling of ordinary differential equation (ode) model parameters. The software mcmc_clib uses the simplified manifold Metropolis-adjusted Langevin algorithm (SMMALA), which is locally adaptive; it uses the parameter manifold’s geometry (the Fisher information) to make efficient moves. This adaptation does not diminish with MC length, which is highly advantageous compared with adaptive Metropolis techniques when the parameters have large correlations and/or posteriors substantially differ from multivariate Gaussians. The software is standalone (not a toolbox), though dependencies include the GNU scientific library and sundials libraries for ode integration and sensitivity analysis.

Availability and implementation : The source code and binary files are freely available for download at http://a-kramer.github.io/mcmc_clib/ . This also includes example files and data. A detailed documentation, an example model and user manual are provided with the software.

Contact : andrei.kramer@ist.uni-stuttgart.de
Improving peak detection in high-resolution LC/MS metabolomics data using preexisting knowledge and machine learning approach
Authors: Yu Tianwei , Jones Dean P.
Published: July 2014

Motivation: Peak detection is a key step in the preprocessing of untargeted metabolomics data generated from high-resolution liquid chromatography-mass spectrometry (LC/MS). The common practice is to use filters with predetermined parameters to select peaks in the LC/MS profile. This rigid approach can cause suboptimal performance when the choice of peak model and parameters do not suit the data characteristics.

Results: Here we present a method that learns directly from various data features of the extracted ion chromatograms (EICs) to differentiate between true peak regions from noise regions in the LC/MS profile. It utilizes the knowledge of known metabolites, as well as robust machine learning approaches. Unlike currently available methods, this new approach does not assume a parametric peak shape model and allows maximum flexibility. We demonstrate the superiority of the new approach using real data. Because matching to known metabolites entails uncertainties and cannot be considered a gold standard, we also developed a probabilistic receiver-operating characteristic (pROC) approach that can incorporate uncertainties.

Availability and implementation: The new peak detection approach is implemented as part of the apLCMS package available at http://web1.sph.emory.edu/apLCMS/

Contact:  tyu8@emory.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Different on the inside: extreme swimbladder sexual dimorphism in the South Asian torrent minnows
Authors: Conway Kevin W. , Britz Ralf , Siegel Dustin S.
Published: July 2014

The swimbladder plays an important role in buoyancy regulation but is typically reduced or even absent in benthic freshwater fishes that inhabit fast flowing water. Here, we document, for the first time, a remarkable example of swimbladder sexual dimorphism in the highly rheophilic South Asian torrent minnows (
Psilorhynchus
). The male swimbladder is not only much larger than that of the female (up to five times the diameter and up to 98 times the volume in some cases), but is also structurally more complex, with multiple internal septa dividing it into smaller chambers. Males also exhibit a strange organ of unknown function or homology in association with the swimbladder that is absent in females. Extreme sexual dimorphism of non-gonadal internal organs is rare among vertebrates and the swimbladder sexual dimorphisms that we describe for
Psilorhynchus
are unique among fishes.
What big eyes you have: the ecological role of giant pterygotid eurypterids
Authors: Anderson Ross P. , McCoy Victoria E. , McNamara Maria E. , Briggs Derek E. G.
Published: July 2014

Eurypterids are a group of extinct chelicerates that ranged for over 200 Myr from the Ordovician to the Permian. Gigantism is common in the group; about 50% of families include taxa over 0.8 m in length. Among these were the pterygotids (Pterygotidae), which reached lengths of over 2 m and were the largest arthropods that ever lived. They have been interpreted as highly mobile visual predators on the basis of their large size, enlarged, robust chelicerae and forward-facing compound eyes. Here, we test this interpretation by reconstructing the visual capability ofAcutiramus cummingsi(Pterygotidae) and comparing it with that of the smallerEurypterussp. (Eurypteridae), which lacked enlarged chelicerae, and other arthropods of similar geologic age. InA. cummingsi, there is no area of lenses differentiated to provide increased visual acuity, and the interommatidial angles (IOA) do not fall within the range of high-level modern arthropod predators. Our results show that the visual acuity ofA. cummingsiis poor compared with that of co-occurringEurypterussp. The ecological role of pterygotids may have been as predators on thin-shelled and soft-bodied prey, perhaps in low-light conditions or at night.
Allan Charles Wilson. 18 October 1934 — 21 July 1991
Authors: Cann Rebecca L.
Published: July 2014

Allan Charles Wilson was born on 18 October 1934 at Ngaruawahia, New Zealand. He died in Seattle, Washington, on 21 July 1991 while undergoing treatment for leukaemia. Allan was known as a pioneering and highly innovative biochemist, helping to define the field of molecular evolution and establish the use of a molecular clock to measure evolutionary change between living species. The molecular clock, a method of measuring the timescale of evolutionary change between two organisms on the basis of the number of mutations that they have accumulated since last sharing a common genetic ancestor, was an idea initially championed by Émile Zuckerkandl and Linus Pauling (Zuckerkandl & Pauling 1962), on the basis of their observations that the number of changes in an amino acid sequence was roughly linear with time in the aligned haemoglobin proteins of animals. Although it is now not unusual to see the words ‘molecular evolution’ and ‘molecular phylogeny’ together, when Allan formed his own biochemistry laboratory in 1964 at the University of California, Berkeley, many scientists in the field of evolutionary biology considered these ideas complete heresy. Allan’s death at the relatively young age of 56 years left behind his wife, Leona (deceased in 2009), a daughter, Ruth (b. 1961), and a son, David (b. 1964), as well his as mother, Eunice (deceased in 2002), a younger brother, Gary Wilson, and a sister, Colleen Macmillan, along with numerous nieces, nephews and cousins in New Zealand, Australia and the USA. In this short span of time, he trained more than 55 doctoral students and helped launch the careers of numerous postdoctoral fellows.
David Alan Walker. 18 August 1928 — 13 February 2012
Authors: Horton Peter
Published: July 2014

David Alan Walker was born in Kingston upon Hull, England. He entered King’s College, Newcastle, then part of the University of Durham, where he received his BSc, and subsequently his PhD under Meirion Thomas FRS in 1958. Later, in 1968 he was awarded a DSc at the University of Newcastle in recognition of his exceptional contributions of published work in his field. In 1991 he received a Humboldt Research Prize, and in 2004 the inaugural Communications Award from the International Society of Photosynthesis Research. He was the author of more than 230 publications, including several books. He made important contributions to the understanding of photosynthesis, in particular the fixation of carbon dioxide by the biochemical transformations of the Benson–Calvin cycle in the stroma of chloroplasts of higher plants. Based on the meticulous attention to detail and technical prowess derived from his earlier training as an enzymologist, his work prompted totally new thinking about how this cycle was regulated and how it interfaced with the synthesis of ATP and NADPH in the light reactions of photosynthesis. Later, he was one of a very small group of people to recognize that this regulation was observable in whole leaves through the changes in chlorophyll fluorescence, helping to open the door to one of the most widely used tools in plant physiology. After periods at Newcastle, Purdue, Cambridge, Queen Mary College and Imperial College, London, he spent the largest part of his academic career as a professor at the University of Sheffield. There he established a world-renowned photosynthesis research group that grew into one of the university’s first semi-autonomous research institutes, the Research Institute for Photosynthesis, later renamed the Robert Hill Institute. This legacy persists more than 30 years later. He also distinguished himself in the wider aspects of being a scientist: long before it became fashionable, he wrote about the issues of food, energy and global change in his 1992 book
Energy, plants and man
. His enthusiasm for communicating both the joy of science and these serious issues led to many other imaginative schemes and endeavours, again long before the need for greater ‘public understanding of science’ became recognized.
Droplet interface bilayer reconstitution and activity measurement of the mechanosensitive channel of large conductance from
Escherichia coli
Authors: Barriga Hanna M. G. , Booth Paula , Haylock Stuart , Bazin Richard , Templer Richard H. , Ces Oscar
Published: July 2014

Droplet interface bilayers (DIBs) provide an exciting new platform for the study of membrane proteins in stable bilayers of controlled composition. To date, the successful reconstitution and activity measurement of membrane proteins in DIBs has relied on the use of the synthetic lipid 1,2-diphytanoyl-
sn
-glycero-3-phosphocholine (DPhPC). We report the functional reconstitution of the mechanosensitive channel of large conductance (MscL) into DIBs composed of 1,2-dioleoyl-
sn
-glycero-3-phosphocholine (DOPC), a lipid of significantly greater biological relevance than DPhPC. MscL functionality has been demonstrated using a fluorescence-based assay, showing that dye flow occurs across the DIB when MscL is gated by the cysteine reactive chemical 2-(trimethylammonium)ethyl methane thiosulfonate bromide (MTSET). MscL has already been the subject of a number of studies investigating its interaction with the membrane. We propose that this method will pave the way for future MscL studies looking in detail at the effects of controlled composition or membrane asymmetry on MscL activity using biologically relevant lipids and will also be applicable to other lipid–protein systems, paving the way for the study of membrane proteins in DIBs with biologically relevant lipids.