bluuebunny/crossref_metadata_2025 huggingface dataset:
Entropic force on granular chains self-extracting from one-dimensional confinement
Authors: Jeng Pei-Ren , Chen KuanHua , Hwang Gwo-jen , Cho Ethan Y. , Lien Chenhsin , To Kiwing , Chou Y. C.
Published: January 2014

The entropic forces on the self-retracting granular chains, which are confined in channels with different widths, are determined. The time dependence of the length of chain remaining in the channel Lin(t) is measured. The entropic force is treated as the only parameter in fitting the solution of the nonlinear equation of motion of Lin(t) to the experimental data. The dependence of the entropic force on the width of the confining channel can be expressed as a power-law with an exponent of 1.3, which is consistent with the previous theoretical predictions for the entropy loss due to confinement.
Pressure effects on magnetic pair-breaking in Mn- and Eu-substituted BaFe2As2
Authors: Rosa P. F. S. , Garitezi T. M. , Adriano C. , Grant T. , Fisk Z. , Urbano R. R. , Fernandes R. M. , Pagliuso P. G.
Published: January 2014

We report a combined study of hydrostatic pressure (P ≤ 25 kbar) and chemical substitution on the magnetic pair-breaking effect in Eu- and Mn-substituted BaFe2As2 single crystals. At ambient pressure, both substitutions suppress the superconducting (SC) transition temperature (Tc) of BaFe2–xCoxAs2 samples slightly under the optimally doped region, indicating the presence of a pair-breaking effect. At low pressures, an increase of Tc is observed for all studied compounds followed by an expected decrease at higher pressures. However, in the Eu dilute system, Tc further increases at higher pressure along with a narrowing of the SC transition, suggesting that a pair-breaking mechanism reminiscent of the Eu Kondo single impurity regime is being suppressed by pressure. Furthermore, Electron Spin Resonance (ESR) measurements indicate the presence of Mn2+ and Eu2+ local moments and the microscopic parameters extracted from the ESR analysis reveal that the Abrikosov–Gor'kov expression for magnetic pair-breaking in a conventional sign-preserving superconducting state cannot describe the observed reduction of Tc.
Reflection type of terahertz imaging system using a high-Tc superconducting oscillator
Authors: Kashiwagi T. , Nakade K. , Marković B. , Saiwai Y. , Minami H. , Kitamura T. , Watanabe C. , Ishida K. , Sekimoto S. , Asanuma K. , Yasui T. , Shibano Y. , Tsujimoto M. , Yamamoto T. , Mirković J. , Kadowaki K.
Published: January 2014

A reflection type of imaging system is shown at sub-terahertz frequencies generated from high-Tc superconducting intrinsic Josephson junction mesa structures fabricated by single crystalline Bi2Sr2CaCu2O8+δ to demonstrate how the sub-terahertz imaging technique using monochromatic radiation is powerful and unique for the variety of practical applications. Several examples are discussed in detail and are compared to other terahertz imaging systems.
Observation of the large magnetocaloric effect and suppression of orbital entropy change in Fe-doped MnV2O4
Authors: Huang Z. H. , Luo X. , Hu L. , Tan S. G. , Liu Y. , Yuan B. , Chen J. , Song W. H. , Sun Y. P.
Published: January 2014

We present the structural and magnetic properties of Mn1−xFexV2O4 (x = 0.1, 0.2, and 0.3), and investigate the magnetocaloric effect in those compounds. The ferrimagnetic spin ordering is enhanced with the Fe doping at Mn site of MnV2O4, while the orbital ordering is suppressed. Large magnetic entropy changes up to 3.8 J/kg K as well as the relative cooling power up to 110 J/kg at the field change of 0-2 T for Mn1−xFexV2O4 are calculated from the isothermal magnetization measurements. The large orbital entropy change of MnV2O4 is suppressed by the Fe doping, while the spin entropy contribution arising from the strong spin-orbit coupling remains. Moreover, the doping of Fe broadens the temperature span of the large magnetic entropy change and increases the relative cooling power of MnV2O4 by 2.4 times.
Electromigration-induced back stress in critical solder length for three-dimensional integrated circuits
Authors: Huang Y. T. , Hsu H. H. , Wu Albert T.
Published: January 2014

Because of the miniaturization of electronic devices, the reliability of electromigration has become a major concern when shrinking the solder dimensions in flip-chip joints. Fast reaction between solders and electrodes causes intermetallic compounds (IMCs) to form, which grow rapidly and occupy entire joints when solder volumes decrease. In this study, U-grooves were fabricated on Si chips as test vehicles. An electrode-solder-electrode sandwich structure was fabricated by using lithography and electroplating. Gaps exhibiting well-defined dimensions were filled with Sn3.5Ag solders. The gaps between the copper electrodes in the test sample were limited to less than 15 μm to simulate microbumps. The samples were stressed at various current densities at 100 °C, 125 °C, and 150 °C. The morphological changes of the IMCs were observed, and the dimensions of the IMCs were measured to determine the kinetic growth of IMCs. Therefore, this study focused on the influence of back stress caused by microstructural evolution in microbumps.
Quantum confinement effect in Bi anti-dot thin films with tailored pore wall widths and thicknesses
Authors: Park Y. , Hirose Y. , Nakao S. , Fukumura T. , Xu J. , Hasegawa T.
Published: January 2014

We investigated quantum confinement effects in Bi anti-dot thin films grown on anodized aluminium oxide templates. The pore wall widths (wBi) and thickness (t) of the films were tailored to have values longer or shorter than Fermi wavelength of Bi (λF = ∼40 nm). Magnetoresistance measurements revealed a well-defined weak antilocalization effect below 10 K. Coherence lengths (Lϕ) as functions of temperature were derived from the magnetoresistance vs field curves by assuming the Hikami-Larkin-Nagaoka model. The anti-dot thin film with wBi and t smaller than λF showed low dimensional electronic behavior at low temperatures where Lϕ(T) exceed wBi or t.
Thermoelastic study of nanolayered structures using time-resolved X-ray diffraction at high repetition rate
Authors: Navirian H. A. , Schick D. , Gaal P. , Leitenberger W. , Shayduk R. , Bargheer M.
Published: January 2014

We investigate the thermoelastic response of a nanolayered sample composed of a metallic SrRuO3 electrode sandwiched between a ferroelectric Pb(Zr0.2Ti0.8)O3 film with negative thermal expansion and a SrTiO3 substrate. SrRuO3 is rapidly heated by fs-laser pulses with 208 kHz repetition rate. Diffraction of X-ray pulses derived from a synchrotron measures the transient out-of-plane lattice constant c of all three materials simultaneously from 120 ps to 5 μs with a relative accuracy up to Δc/c = 10−6. The in-plane propagation of sound is essential for understanding the delayed out-of-plane compression of Pb(Zr0.2Ti0.8)O3.
Low-temperature (180 °C) formation of large-grained Ge (111) thin film on insulator using accelerated metal-induced crystallization
Authors: Toko K. , Numata R. , Oya N. , Fukata N. , Usami N. , Suemasu T.
Published: January 2014

The Al-induced crystallization (AIC) yields a large-grained (111)-oriented Ge thin film on an insulator at temperatures as low as 180 °C. We accelerated the AIC of an amorphous Ge layer (50-nm thickness) by initially doping Ge in Al and by facilitating Ge diffusion into Al. The electron backscatter diffraction measurement demonstrated the simultaneous achievement of large grains over 10 μm and a high (111) orientation fraction of 90% in the polycrystalline Ge layer formed at 180 °C. This result opens up the possibility for developing Ge-based electronic and optical devices fabricated on inexpensive flexible substrates.
Partial recovery of the magnetoelectrical properties of AlGaN/GaN-based micro-Hall sensors irradiated with protons
Authors: Abderrahmane A. , Tashiro T. , Takahashi H. , Ko P. J. , Okada H. , Sato S. , Ohshima T. , Sandhu A.
Published: January 2014

The effect of annealing on the magnetoelectrical properties of proton-irradiated micro-Hall sensors at an energy of 380 keV and very high proton fluences was studied. Recovery of the electron mobility and a decrease in the sheet resistance of the annealed micro-Hall sensors, as well as an enhancement in their magnetic sensitivity were reported. Trap removal and an improvement in the crystal quality by removing defects were confirmed through current–voltage measurements and Raman spectroscopy, respectively.
First principles calculations, neutron, and x-ray diffraction investigation of Y3Ni13B2, Y3Co13B2, and Y3Ni10Co3B2
Authors: Plugaru N. , Valeanu M. , Plugaru R. , Campo J.
Published: January 2014

Fully relativistic calculations within the local spin density approximation and the generalized gradient approximation were performed to determine the local spin and orbital magnetic moments, as well as the magnetocrystalline anisotropy energy of Y3Ni13B2, Y3Co13B2, and Y3Ni10Co3B2 compounds. A weak in-plane magnetic anisotropy is determined for Y3Ni13B2, under the assumption of a crystallographic-like magnetic unit cell and collinear magnetic moments. The calculations predict considerable c-axis anisotropy for Y3Co13B2 and Y3Ni10Co3B2, but smaller than that of YCo5. The values of the magnetocrystalline anisotropy energy correlate well with both the magnitude of the orbital magnetic moment and the orbital magnetic moment anisotropy. The mixing between Co or Ni 3d states and B 2p states, observable at the bottom of the valence band of the 3d metal having a boron atom nearest neighbor, decreases the 3d spin and especially, the 3d orbital magnetic moments. Y3Ni13B2 and Y3Ni10Co3B2 were also investigated by powder neutron diffraction experiments, at temperatures between 1.8 and 249 K. The Co and Ni site averaged magnetic moments calculated in the mixed compound are in fair agreement with the values obtained by the refinement of the magnetic contribution to the diffraction pattern.
Communication: Stochastic evaluation of explicitly correlated second-order many-body perturbation energy
Authors: Willow Soohaeng Yoo , Zhang Jinmei , Valeev Edward F. , Hirata So
Published: January 2014

A stochastic algorithm is proposed that can compute the basis-set-incompleteness correction to the second-order many-body perturbation (MP2) energy of a polyatomic molecule. It evaluates the sum of two-, three-, and four-electron integrals over an explicit function of electron-electron distances by a Monte Carlo (MC) integration at an operation cost per MC step increasing only quadratically with size. The method can reproduce the corrections to the MP2/cc-pVTZ energies of H2O, CH4, and C6H6 within a few mEh after several million MC steps. It circumvents the resolution-of-the-identity approximation to the nonfactorable three-electron integrals usually necessary in the conventional explicitly correlated (R12 or F12) methods.
Integrating non-planar metamaterials with magnetic absorbing materials to yield ultra-broadband microwave hybrid absorbers
Authors: Li Wei , Wu Tianlong , Wang Wei , Guan Jianguo , Zhai Pengcheng
Published: January 2014

Broadening the bandwidth of electromagnetic wave absorbers has greatly challenged material scientists. Here, we propose a two-layer hybrid absorber consisting of a non-planar metamaterial (MM) and a magnetic microwave absorbing material (MAM). The non-planar MM using magnetic MAMs instead of dielectric substrates shows good low frequency absorption and low reflection across a broad spectrum. Benefiting from this and the high frequency strong absorption of the MAM layer, the lightweight hybrid absorber exhibits 90% absorptivity over the whole 2–18 GHz range. Our result reveals a promising and flexible method to greatly extend or control the absorption bandwidth of absorbers.
Tunable millimeter-wave phase shifter based on dielectric elastomer actuation
Authors: Romano P. , Araromi O. , Rosset S. , Shea H. , Perruisseau-Carrier J.
Published: January 2014

A very low-loss tunable millimeter-wave phase shifter driven by dielectric elastomer actuators (DEAs) is presented. The device consists of a fixed coplanar waveguide (CPW) and two metallic loading strips suspended on an elastomer membrane. The horizontal offset between the CPW and the strips is dynamically controlled by integrated DEAs. The variable interaction between the CPW and the loading strips results in a change in the effective permittivity, thereby providing analog-controlled true-time-delay. The design, fabrication, and measurements of this phase shifter based on DEAs are presented, demonstrating state-of-the-art phase shift to loss performance, achieving 235°/dB at 35 GHz.
Evaluation of the spatial distribution of series and shunt resistance of a solar cell using dark lock-in thermography
Authors: Chung Te-yuan , Wang Chung-Hao , Chang Kai-Jay , Chen Szu-Yu , Hsieh Hsin-Hsin , Huang Chao-Ping , Arthur Cheng Ching-Hsiao
Published: January 2014

A theoretical approach of using dark lock-in thermography (DLIT) to resolve series and shunt resistance spatial distribution of a solar cell is derived. The resistance distribution can be represented as a simple function of DLIT temperature amplitude and phase distribution under small signal approximation. DLIT experiment using different solar cells was performed and obtained the temperature amplitude and phase images along with the corresponding resistance images.
Microstructural and crystallographic imperfections of MgB2 superconducting wire and their correlation with the critical current density
Authors: Shahabuddin Mohammed , Alzayed Nasser S. , Oh Sangjun , Choi Seyong , Maeda Minoru , Hata Satoshi , Shimada Yusuke , Hossain Md Shahriar Al , Kim Jung Ho
Published: January 2014

A comprehensive study of the effects of structural imperfections in MgB2 superconducting wire has been conducted. As the sintering temperature becomes lower, the structural imperfections of the MgB2 material are increased, as reflected by detailed X-ray refinement and the normal state resistivity. The crystalline imperfections, caused by lattice disorder, directly affect the impurity scattering between the π and σ bands of MgB2, resulting in a larger upper critical field. In addition, low sintering temperature keeps the grain size small, which leads to a strong enhancement of pinning, and thereby, enhanced critical current density. Owing to both the impurity scattering and the grain boundary pinning, the critical current density, irreversibility field, and upper critical field are enhanced. Residual voids or porosities obviously remain in the MgB2, however, even at low sintering temperature, and thus block current transport paths.
Anomalous magnetism of Pr in PrCoAsO
Authors: Tiwari Brajesh , Pal Anand , Awana V. P. S.
Published: January 2014

Detailed magnetization and magneto-transport measurements studies are carried out to unearth the anomalous magnetism of Pr in PrCoAsO compound. The studied PrCoAsO sample is single phase and crystallized in the tetragonal structure with space group P4/nmm in analogy of ZrCuSiAs type compounds. Detailed magnetization measurements showed that Co moments in PrCoAsO exhibit weakly itinerant ferromagnetic Co spins ordering at below 80 K with a small magnetic moments of ∼ 0.12 μB/f.u. High temperatures Curie-Weiss fit, resulted in effective paramagnetic moment μeff (exp) of 5.91 μB/f.u., which can be theoretically assigned to 3d Co (3.88 μB) and 4f Pr (3.58 μB). Further, a positive Curie-Weiss temperature (Θ) of 136 K is seen, indicating predominant ferromagnetic interactions in PrCoAsO. Detailed transport measurements showed that PrCoAsO exhibit metallic behavior and negative magneto-resistance below ferro-magnetically (FM) ordered state. Surprisingly, the situation of PrCoAsO is similar to non magnetic La containing LaCoAsO and strikingly different than that as reported for magnetic Nd, Sm and Gd i.e., (Nd/Sm/Gd)CoAsO. The magnetic behavior of PrCoAsO being closed to LaCoAsO and strikingly different to that of (Nd/Sm/Gd)CoAsO is unusual.
A Class of Computationally Designed Tri-Coordinate Cyclic Silylenes RSi(µ-R)2AlR2
Authors: Xu Jing , Ding Yi-Hong
Published: January 2014

With the aim of designing novel low-valent silylenes, herein we report the first systematic investigation of the SiAlR5 system. Based on the ‘topology’ isomeric search strategy, four classes of isomers, i.e. RSi(μ-R)2AlR2 1, R3Si-AlR2 2, R2Si(μ-R)AlR2 3, and R2Si-AlR3 4 were identified. For 12 groups with an electron lone-pair, i.e. R = F, NH2,OH, SH, OMe, PMe2, SMe, OEt, PEt2, SEt, OPh, and PPh2, the tri-coordinate silylene 1 is the most stable structure, which contains two sets of intermolecular donor–acceptor interactions. In accordance with the ‘silylene’ term, the Si-centre can undergo both a nucleophilic reaction and insertion reaction. Moreover, coupling AlR3 (R = OR′ and PR′2) (R′ = H, Me, Et, and Ph) with the known cyclic di-coordinate silylene could lead to stable tri-coordinate silylenes. These novel tri-coordinate silylenes strongly welcome laboratory studies in near future.
Synthesis of Carbohydrate-based Natural Products from Leonurus japonicus and their Biological Evaluation as Anti-oxidants
Authors: Clayton Evette , Hattie Mitchell , Debowski Aleksandra W. , Stubbs Keith A.
Published: January 2014

Natural products are important materials that have found a wide variety of uses, especially in medicine. Traditional Chinese medicine (TCM) has especially taken advantage of natural products and compounds found in Leonurus, a species of herb used extensively in TCM to treat various ailments. Herein we describe the synthesis of three natural products from Leonurus japonicus and our investigation of their hepatoprotective properties.
Characterization of aerobically fit individuals with cardiovascular disease
Authors: Lesser Iris A. , Farias‐Godoy Alejandra , Isserow Saul , Myers Jonathan , Lear Scott A.
Published: January 2014

With an ageing population there is an increased prevalence of individuals living with cardiovascular disease (CVD). Characteristics of older aerobically fit individuals with previously diagnosed CVD have not been studied. Therefore, our knowledge is limited as to how, or if, aerobically fit individuals with CVD attempt to adapt their physical activity and the intensity of their training programmes. The objective of this paper is to characterise the physical activity habits and behaviours of older aerobically fit individuals with CVD. We identified 28 aerobically fit patients with CVD from those who completed a minimum of 15 and 12 min of the Bruce treadmill protocol for men and women, respectively. Consenting participants responded to questionnaires regarding physical activity levels, competitive event participation and self‐monitoring since diagnosis of heart disease. Average age and treadmill time of participants were 56 and 49 years and 15.6 and 13.0 min for males and females, respectively. Data were obtained regarding recent medical history (medical diagnoses, surgeries/procedures). Despite the majority of individuals participating in the same or more activity since their diagnosis, 25% indicated that their condition limited their activity and 39% reported having symptoms during activity. Nearly all participants (93%) indicated that they monitored their heart rate during exercise. However, only 14% of participants stated that their physician advised them on how to exercise safely. It is necessary for physicians and cardiac rehabilitation programmes to be involved in safe and effective exercise programming to allow individuals to return to sport after CVD.
The ShcD signaling adaptor facilitates ligand-independent phosphorylation of the EGF receptor
Authors: Wills Melanie K. B. , Tong Jiefei , Tremblay Sylvie L. , Moran Michael F. , Jones Nina
Published: January 2014

Proto-oncogenic Src homology and collagen (Shc) proteins have been considered archetypal adaptors of epidermal growth factor receptor (EGFR)–mediated signaling. We report that in addition to its role as an EGFR-binding partner and Grb2 platform, ShcD acts noncanonically to promote phosphorylation of select EGFR residues. Unexpectedly, Y1068, Y1148, and Y1173 are subject to ShcD-induced, cell-autonomous hyperphosphorylation in the absence of external stimuli. This response is not elicited by other Shc proteins and requires the intrinsic EGFR kinase, as well as the ShcD phosphotyrosine-binding (PTB) domain. Assessments of Erk, Akt, phospholipase C 1γ, and FAK pathways reveal no apparent distal signaling targets of ShcD. Nevertheless, the capacity of cultured cells to repopulate a wounded monolayer is markedly accelerated by ShcD in an EGFR kinase–dependent manner. Furthermore, detection of overexpressed ShcD coincident with EGFR phosphorylation in human gliomas suggests a clinical application for these findings. We thus demonstrate unique and relevant synergy between ShcD and EGFR that is unprecedented among signaling adaptors.
Critical roles for multiple formins during cardiac myofibril development and repair
Authors: Rosado Michelle , Barber Cynthia F. , Berciu Cristina , Feldman Steven , Birren Susan J. , Nicastro Daniela , Goode Bruce L.
Published: January 2014

Cardiac and skeletal muscle function depends on the proper formation of myofibrils, which are tandem arrays of highly organized actomyosin contractile units called sarcomeres. How the architecture of these colossal molecular assemblages is established during development and maintained over the lifetime of an animal is poorly understood. We investigate the potential roles in myofibril formation and repair of formin proteins, which are encoded by 15 different genes in mammals. Using quantitative real-time PCR analysis, we find that 13 formins are differentially expressed in mouse hearts during postnatal development. Seven formins immunolocalize to sarcomeres in diverse patterns, suggesting that they have a variety of functional roles. Using RNA interference silencing, we find that the formins mDia2, DAAM1, FMNL1, and FMNL2 are required nonredundantly for myofibrillogenesis. Knockdown phenotypes include global loss of myofibril organization and defective sarcomeric ultrastructure. Finally, our analysis reveals an unanticipated requirement specifically for FMNL1 and FMNL2 in the repair of damaged myofibrils. Together our data reveal an unexpectedly large number of formins, with diverse localization patterns and nonredundant roles, functioning in myofibril development and maintenance, and provide the first evidence of actin assembly factors being required to repair myofibrils.
Effect of Simulation Training on Compliance with Difficult Airway Management Algorithms, Technical Ability, and Skills Retention for Emergency Cricothyrotomy
Authors: Hubert Vincent , Duwat Antoine , Deransy Romain , Mahjoub Yazine , Dupont Hervé
Published: January 2014

Background:

The effectiveness of simulation is rarely evaluated. The aim of this study was to assess the impact of a short training course on the ability of anesthesiology residents to comply with current difficult airway management guidelines.

Methods:

Twenty-seven third-year anesthesiology residents were assessed on a simulator in a “can’t intubate, can’t ventilate” scenario before the training (the pretest) and then randomly 3, 6, or 12 months after training (the posttest). The scenario was built so that the resident was prompted to perform a cricothyrotomy. Compliance with airway management guidelines and the cricothyrotomy’s duration and technical quality were assessed as a checklist score [0 to 10] and a global rating scale [7 to 35].

Results:

After training, all 27 residents (100%) complied with the airway management guidelines, compared with 17 (63%) in the pretest (P < 0.005). In the pretest and the 3-, 6-, and 12-month posttests, the median [range] duration of cricothyrotomy was respectively 117 s [70 to 184], 69 s [43 to 97], 52 s [43 to 76], and 62 s [43 to 74] (P < 0.0001 vs. in the pretest), the median [range] checklist score was 3 [0 to 7], 10 [8 to 10], 9 [6 to 10], and 9 [4 to 10] (P < 0.0001 vs. in the pretest) and the median [range] global rating scale was 12 [7 to 22], 30 [20 to 35], 33 [23 to 35], and 31 [18 to 33] (P < 0.0001 vs. in the pretest). There were no significant differences between performance levels achieved in the 3-, 6-, and 12-month posttests.

Conclusion:

The training session significantly improved the residents’ compliance with guidelines and their performance of cricothyrotomy.
Development of a 4-valent genotyping assay for direct identification of the most frequent Pseudomonas aeruginosa serotypes from respiratory specimens of pneumonia patients
Authors: Koch Holger , Emrich Thomas , Jampen Sandra , Wyss Marianne , Gafner Verena , Lazar Hedvika , Rudolf Michael P.
Published: January 2014

Pseudomonas aeruginosa is a common cause of nosocomial infections and is associated with high rates of mortality. In order to facilitate rapid and sensitive identification of the most prevalent serotypes of P. aeruginosa, we have developed a 4-valent real-time PCR-based assay using oligonucleotides specific for open-reading frames constituting the O-antigen-specific lipopolysaccharide loci of P. aeruginosa. The assay simultaneously detects and differentiates between each of the four serotypes IATS-O1, -O6, -O11 and serogroup 2 (IATS-O2, -O5, and -O16) with high sensitivity and specificity in a single-tube reaction. No cross-reactivity was observed with other serotypes of P. aeruginosa or other microbial species, and reproducibility was demonstrated regardless of template, i.e. purified DNA, bacterial culture and clinical specimens (broncho-alveolar lavage). The limit of detection of the assay was approximately 100 copies per reaction for IATS-O1, -O2 and -O11, and 50 copies per reaction for IATS-O6. Comparison of the assay specificity with a commercially available slide agglutination kit showed consistent results; however, the number of non-typable isolates was reduced by 15 % using the genotyping assay. Use of the 4-valent genotyping assay in the context of a clinical trial resulted in identification of pneumonia patients positive for the IATS-O11 serotype, and hence eligible for therapy with panobacumab (an investigational monoclonal antibody against the O-polysaccharide of serotype IATS-O11).
Quantitative evaluation of the host-colonizing capabilities of the enteric bacterium Pantoea using plant and insect hosts
Authors: Nadarasah Geetanchaly , Stavrinides John
Published: January 2014

The genusPantoeais a highly diverse group comprising free-living, and both pathogenic and non-pathogenic host-associating species. Pathogenic isolates have been found to infect insects, plants and humans, yet it is unclear whether these isolates have similar pathogenic potential to the free-living environmental populations. Using MLSA of six housekeeping genes, we evaluated the phylogenetic relationships among 115 environmental and clinical (human) isolates representing 11Pantoeaspecies. An overlay of the location of isolation onto the resulting tree revealed that clinical and environmental isolates are interspersed, and do not form distinctive groups. We then conducted quantitative growth assays of our isolates using maize, onion and fruit flies as hosts. Notably, most clinical isolates were able to grow in both plant hosts often comparably or even better than the environmental isolates. There were no obvious growth or host colonization patterns that could distinguish those isolates with clinical potential. Growth of an isolate in one host could not be predicted based on its performance in another host, nor could host growth be predicted by phylogeny or source of isolation. This work demonstrates that the host-colonizing capabilities of allPantoeaspecies groups is unpredictable, indicating a broader host range and pathogenic potential than currently assumed.
The Toxoplasma Acto-MyoA Motor Complex Is Important but Not Essential for Gliding Motility and Host Cell Invasion
Authors: Egarter Saskia , Andenmatten Nicole , Jackson Allison J , Whitelaw Jamie A , Pall Gurmann , Black Jennifer A , Ferguson David JP , Tardieux Isabelle , Mogilner Alex , Meissner Markus
Published: January 2014

Apicomplexan parasites are thought to actively invade the host cell by gliding motility. This movement is powered by the parasite own actomyosin system and depends on the regulated polymerisation and depolymerisation of actin to generate the force for gliding and host cell penetration. Recent studies demonstrated that Toxoplasma gondii can invade the host cell in the absence of several core components of the invasion machinery, such as the motor protein myosin A (MyoA), the microneme proteins MIC2 and AMA1 and actin, indicating the presence of alternative invasion mechanisms. Here the roles of MyoA, MLC1, GAP45 and Act1, core components of the gliding machinery, are re-dissected in detail. Although important roles of these components for gliding motility and host cell invasion are verified, mutant parasites remain invasive and do not show a block of gliding motility, suggesting that other mechanisms must be in place to enable the parasite to move and invade the host cell. A novel, hypothetical model for parasite gliding motility and invasion is presented based on osmotic forces generated in the cytosol of the parasite that are converted into motility. Now published as: PLOS One, doi:10.1371/journal.pone.0091819
The emergence of the rescue effect from explicit within- and between-patch dynamics in a metapopulation
Authors: Eriksson Anders , Elías-Wolff Federico , Mehlig Bernhard , Manica Andrea
Published: January 2014

Immigration can rescue local populations from extinction, helping to stabilise a metapopulation. Local population dynamics is important for determining the strength of this rescue effect, but the mechanistic link between local demographic parameters and the rescue effect at the metapopulation level has received very little attention by modellers. We develop an analytical framework that allows us to describe the emergence of the rescue effect from interacting local stochastic dynamics. We show this framework to be applicable to a wide range of spatial scales, providing a powerful and convenient alternative to individual-based models for making predictions concerning the fate of metapopulations. We show that the rescue effect plays an important role in minimising the increase in local extinction probability associated with high demographic stochasticity, but its role is more limited in the case of high local environmental stochasticity of recruitment or survival. While most models postulate the rescue effect, our framework provides an explicit mechanistic link between local dynamics and the emergence of the rescue effect, and more generally the stability of the whole metapopulation. Now published as: Proceedings of the Royal Society B, 2014, 281(1780):20133127 doi:10.1098/rspb.2013.3127
The role of rewarding and novel events in facilitating memory persistence in a separate spatial memory task
Authors: Salvetti Beatrice , Morris Richard G.M. , Wang Szu-Han
Published: January 2014

Many insignificant events in our daily life are forgotten quickly but can be remembered for longer when other memory-modulating events occur before or after them. This phenomenon has been investigated in animal models in a protocol in which weak memories persist longer if exploration in a novel context is introduced around the time of memory encoding. This study aims to understand whether other types of rewarding or novel tasks, such as rewarded learning in a T-maze and novel object recognition, can also be effective memory-modulating events. Rats were trained in a delayed matching-to-place task to encode and retrieve food locations in an event arena. Weak encoding with only one food pellet at the sample location induced memory encoding but forgetting over 24 h. When this same weak encoding was followed by a rewarded task in a T-maze, the memory persisted for 24 h. Moreover, the same persistence of memory over 24 h could be achieved by exploration in a novel box or by a rewarded T-maze task after a “non-rewarded” weak encoding. When the one-pellet weak encoding was followed by novel object exploration, the memory did not persist at 24 h. Together, the results confirm that place encoding is possible without explicit reward, and that rewarded learning in a separate task lacking novelty can be an effective memory-modulating event. The behavioral and neurobiological implications are discussed.
Structural insights into the catalytic mechanism of human squalene synthase
Authors: Liu Chia-I , Jeng Wen-Yih , Chang Wei-Jung , Shih Min-Fang , Ko Tzu-Ping , Wang Andrew H.-J.
Published: January 2014

Squalene synthase (SQS) is a divalent metal-ion-dependent enzyme that catalyzes the two-step reductive `head-to-head' condensation of two molecules of farnesyl pyrophosphate to form squalene using presqualene diphosphate (PSPP) as an intermediate. In this paper, the structures of human SQS and its mutants in complex with several substrate analogues and intermediates coordinated with Mg2+or Mn2+are presented, which stepwise delineate the biosynthetic pathway. Extensive study of the SQS active site has identified several critical residues that are involved in binding reduced nicotinamide dinucleotide phosphate (NADPH). Based on mutagenesis data and a locally closed (JK loop-in) structure observed in thehSQS-(F288L)–PSPP complex, an NADPH-binding model is proposed for SQS. The results identified four major steps (substrate binding, condensation, intermediate formation and translocation) of the ordered sequential mechanisms involved in the `1′–1' isoprenoid biosynthetic pathway. These new findings clarify previous hypotheses based on site-directed mutagenesis and biochemical analysis.
Structural basis for DNA-mediated allosteric regulation facilitated by the AAA+module of Lon protease
Authors: Lee Alan Yueh-Luen , Chen Yu-Da , Chang Yu-Yung , Lin Yu-Ching , Chang Chi-Fon , Huang Shing-Jong , Wu Shih-Hsiung , Hsu Chun-Hua
Published: January 2014

Lon belongs to a unique group of AAA+proteases that bind DNA. However, the DNA-mediated regulation of Lon remains elusive. Here, the crystal structure of the α subdomain of the Lon protease fromBrevibacillus thermoruber(Bt-Lon) is presented, together with biochemical data, and the DNA-binding mode is delineated, showing that Arg518, Arg557 and Arg566 play a crucial role in DNA binding. Electrostatic interactions contributed by arginine residues in the AAA+module are suggested to be important to DNA binding and allosteric regulation of enzymatic activities. Intriguingly, Arg557, which directly binds DNA in the α subdomain, has a dual role in the negative regulation of ATPase stimulation by DNA and in the domain–domain communication in allosteric regulation of Bt-Lon by substrate. In conclusion, structural and biochemical evidence is provided to show that electrostatic interaction in the AAA+module is important for DNA binding by Lon and allosteric regulation of its enzymatic activities by DNA and substrate.
Weak data do not make a free lunch, only a cheap meal
Authors: Luo Zhipu , Rajashankar Kanagalaghatta , Dauter Zbigniew
Published: January 2014

Four data sets were processed at resolutions significantly exceeding the criteria traditionally used for estimating the diffraction data resolution limit. The analysis of these data and the corresponding model-quality indicators suggests that the criteria of resolution limits widely adopted in the past may be somewhat conservative. Various parameters, such asRmergeandI/σ(I), optical resolution and the correlation coefficients CC1/2and CC*, can be used for judging the internal data quality, whereas the reliability factorsRandRfreeas well as the maximum-likelihood target values and real-space map correlation coefficients can be used to estimate the agreement between the data and the refined model. However, none of these criteria provide a reliable estimate of the data resolution cutoff limit. The analysis suggests that extension of the maximum resolution by about 0.2 Å beyond the currently adopted limit where theI/σ(I) value drops to 2.0 does not degrade the quality of the refined structural models, but may sometimes be advantageous. Such an extension may be particularly beneficial for significantly anisotropic diffraction. Extension of the maximum resolution at the stage of data collection and structure refinement is cheap in terms of the required effort and is definitely more advisable than accepting a too conservative resolution cutoff, which is unfortunately quite frequent among the crystal structures deposited in the Protein Data Bank.
(E)-1-[(5-Chloro-3-methyl-1-phenyl-1H-pyrazol-4-yl)methylidene]-2-phenylhydrazine: sheets built from π-stacked hydrogen-bonded chains
Authors: Trilleras Jorge , Utria Michael , Cobo Justo , Glidewell Christopher
Published: January 2014

The reaction between 5-chloro-3-methyl-1-phenyl-1H-pyrazole-4-carbaldehyde and phenylhydrazine proceedsviacondensation to provide the title compound, C17H15ClN4, (I), rather thanviathe alternative routes of simple nucleophilic substitution or cyclocondensation. With the exception of the phenyl group bonded directly to the pyrazole ring, the non-H atoms of (I) are nearly coplanar, with an r.m.s. deviation of 0.058 Å. The molecules are linked intoC(7) chains by a single N—H...N hydrogen bond, and the chains are linked by π–π stacking interactions to form sheets.
Behavioural and physiological responses of limpet prey to a seastar predator and their transmission to basal trophic levels
Authors: Manzur Tatiana , Vidal Francisco , Pantoja José F. , Fernández Miriam , Navarrete Sergio A.
Published: January 2014

Besides the well‐documented behavioural changes induced by predators on prey, predator‐induced stress can also include a suite of biochemical, neurological and metabolic changes that may represent important energetic costs and have long‐lasting effects on individuals and on the demography of prey populations. The rapid transmission of prey behavioural changes to lower trophic levels, usually associated with alteration of feeding rates, can substantially change and even reverse direction over the long term as prey cope with the energetic costs associated with predation‐induced stress. It is therefore critical to evaluate different aspects and assess the costs of non‐consumptive predator effects on prey.

We investigated the behavioural and physiological responses of an herbivorous limpet, Fissurella limbata, to the presence of chemical cues and direct non‐lethal contact by the common seastar predator, Heliaster helianthus. We also evaluated whether the limpets feeding behaviour was modified by the predator and whether this translated into positive or negative effects on biomass of the green alga, Ulva sp.

Our experimental results show the presence of Heliaster led to increased movement activity, increased distances travelled, changes in time budget over different environmental conditions and increased feeding rate in the keyhole limpets. Moreover, additional experiments showed that, beyond the increased metabolic rate associated with limpet increased activity, predator chemical cues heighten metabolic rate as part of the induced stress response.

Changes in individual movement and displacement distances observed through the 9‐day experiment can be interpreted as part of the escape response exhibited by limpets to reduce the risk of being captured by the predator. Increased limpet feeding rate on algae can be visualized as a way individuals compensate for the elevated energetic costs of movement and heightened metabolic rates produced by the predator‐induced stress, which can lead to negative effects on abundance of the lower trophic level.

We suggest that in order to understand the total non‐consumptive effect of predators in natural communities, it is necessary to evaluate not only short‐term behavioural responses, but also the costs associated with the multiple interdependent pathways triggered by predator‐induced stress, and determine how individuals cope with these costs in the long term.
Characterizing microbial communities and processes in a modern stromatolite (SharkBay) using lipid biomarkers and two‐dimensional distributions of porewater solutes
Authors: Pagès Anais , Grice Kliti , Vacher Michael , Welsh David T. , Teasdale Peter R. , Bennett William W. , Greenwood Paul
Published: January 2014

Modern microbial mats are highly complex and dynamic ecosystems. Diffusive equilibration in thin films (DET) and diffusive gradients in thin films (DGT) samplers were deployed in a modern smooth microbial mat from Shark Bay in order to observe, for the first time, two‐dimensional distributions of porewater solutes during day and night time. Two‐dimensional sulfide and alkalinity distributions revealed a strong spatial heterogeneity and a minor contribution of sulfide to alkalinity. Phosphate distributions were also very heterogeneous, while iron(II) distributions were quite similar during day and night with a few hotspots of mobilization. Lipid biomarkers from the three successive layers of the mat were also analysed in order to characterize the microbial communities regulating analyte distributions. The major hydrocarbon products detected in all layers includedn‐alkanes and isoprenoids, whilst other important biomarkers included hopanoids. Phospholipid fatty acid profiles revealed a decrease in cyanobacterial markers with depth, whereas sulfate‐reducing bacteria markers increased in abundance in accordance with rising sulfide concentrations with depth. Despite the general depth trends in community structure and physiochemical conditions within the mat, two‐dimensional solute distributions showed considerable small‐scale lateral variability, indicating that the distributions and activities of the microbial communities regulating these solute distributions were equally heterogeneous and complex.
Metagenomic characterization of ‘Candidatus Defluviicoccus tetraformis strain TFO71’, a tetrad‐forming organism, predominant in an anaerobic–aerobic membrane bioreactor with deteriorated biological phosphorus removal
Authors: Nobu Masaru K. , Tamaki Hideyuki , Kubota Kengo , Liu Wen‐Tso
Published: January 2014

In an acetate‐fed anaerobic–aerobic membrane bioreactor with deteriorated enhanced biological phosphorus removal (EBPR), Defluviicoccus‐related tetrad‐forming organisms (DTFO) were observed to predominate in the microbial community. Using metagenomics, a partial genome of the predominant DTFO, ‘Candidatus Defluviicoccus tetraformis strain TFO71’, was successfully constructed and characterized. Examining the genome confirmed the presence of genes related to the synthesis and degradation of glycogen and polyhydroxyalkanoate (PHA), which function as energy and carbon storage compounds. TFO71 and ‘Candidatus Accumulibacter phosphatis’ (CAP) UW‐1 and CAP UW‐2, representative polyphosphate‐accumulating organisms (PAO), have PHA metabolism‐related genes with high homology, but TFO71 has unique genes for PHA synthesis, gene regulation and granule management. We further discovered genes encoding DTFO polyphosphate (polyP) synthesis, suggesting that TFO71 may synthesize polyP under untested conditions. However, TFO71 may not activate these genes under EBPR conditions because the retrieved genome does not contain all inorganic phosphate transporters that are characteristic of PAOs (CAP UW‐1, CAP UW‐2, Microlunatus phosphovorus NM‐1 and Tetrasphaera species). As a first step in characterizing EBPR‐associated DTFO metabolism, this study identifies important differences between DTFO and PAO that may contribute to EBPR community competition and deterioration.
The CarD/CarG regulatory complex is required for the action of several members of the large set of Myxococcus xanthus extracytoplasmic function σ factors
Authors: Abellón‐Ruiz Javier , Bernal‐Bernal Diego , Abellán María , Fontes Marta , Padmanabhan S. , Murillo Francisco J. , Elías‐Arnanz Montserrat
Published: January 2014

Extracytoplasmic function (ECF) σ factors are critical players in signal transduction networks involved in bacterial response to environmental changes. The Myxococcus xanthus genome reveals ∼45 putative ECF‐σ factors, but for the overwhelming majority, the specific signals or mechanisms for selective activation and regulation remain unknown. One well‐studied ECF‐σ, CarQ, binds to its anti‐σ, CarR, and is inactive in the dark but drives its own expression from promoter PQRS on illumination. This requires the CarD/CarG complex, the integration host factor (IHF) and a specific CarD‐binding site upstream of PQRS. Here, we show that DdvS, a previously uncharacterized ECF‐σ, activates its own expression in a CarD/CarG‐dependent manner but is inhibited when specifically bound to the N‐terminal zinc‐binding anti‐σ domain of its cognate anti‐σ, DdvA. Interestingly, we find that the autoregulatory action of 11 other ECF‐σ factors studied here depends totally or partially on CarD/CarG but not IHF. In silico analysis revealed possible CarD‐binding sites that may be involved in direct regulation by CarD/CarG of target promoter activity. CarD/CarG‐linked ECF‐σ regulation likely recurs in other myxobacteria with CarD/CarG orthologous pairs and could underlie, at least in part, the global regulatory effect of the complex on M. xanthus gene expression.
Clustering of fungal community internal transcribed spacer sequence data obscures taxonomic diversity
Authors: Yamamoto Naomichi , Bibby Kyle
Published: January 2014

Next‐generation DNA sequencing has enabled a rapid expansion in the size of molecular fungal ecology studies employing the nuclear internal transcribed spacer (ITS) region. Many sequence‐processing pipelines and protocols require sequence clustering to generate operational taxonomic units (OTUs) based on sequence similarity as a step to reduce total data quantity and complexity prior to taxonomic assignment. However, the consequences of ITS sequence clustering in regard to sample taxonomic coverage have not been carefully examined. Here we demonstrate that typically used clustering thresholds for fungal ITS sequences result in statistically significant losses in taxonomic coverage. Analyses using environmentally derived fungal sequences indicated an average of 3.1% of species went undetected (P < 0.05) if the sequences were denoised and clustered at a 97% threshold prior to taxonomic assignment. Additionally, an in silico analysis using a reference fungal ITS database suggested that approximately 25% of species went undetected if the sequences were clustered prior to taxonomic assignment. Finally, analysis of sequences derived from pure‐cultured fungal isolates of known identity indicated sequence denoising and clustering were not critical in improving identification accuracy.