bluuebunny/crossref_metadata_2025 huggingface dataset:
Lattice Boltzmann simulations of sedimentation of a single fiber in a weak vertical shear flow
Authors: Qi Dewei , He Guowei , Liu Yingming
Published: September 2013

Instability of a suspension is directly related to the problem of the cross-stream migration of a particle relative to its neighboring particle suspension. Such cross-stream or lateral migration of a single non-spherical particle (fiber) settling in a bounded weak shear flow with vertical streamlines produced by a perturbation to the fiber number density is studied using lattice Boltzmann simulations. The present simulation results demonstrate that at a given shear rate, the lateral migration can be divided into three phases depending on settling Reynolds number Rsd and particle aspect ratio κ. At a low settling Reynolds number Rsd, the suspension becomes more stable in phase 1. As Rsd increases and excesses a critical settling Reynolds number Rsd1, the fiber suspension becomes unstable in phase 2. In phase 3, at an enough large Rsd, the inertia dominates the weak shear flow and it may have little effect on stability. A mechanism of the instability induced by an inertial fiber orientation drift and a shear induced cross-streamline drift, recently proposed by Shin, Koch, and Subramanian [“Structure and dynamics of dilute suspensions of finite reynolds number settling fibers,” Phys. Fluids 21, 123304 (2009)], is examined and confirmed.
Magnetic ramp scale at supercritical perpendicular collisionless shocks: Full particle electromagnetic simulations
Authors: Yang Zhongwei , Lu Quanming , Gao Xinliang , Huang Can , Yang Huigen , Liu Ying , Hu Hongqiao , Han Desheng
Published: September 2013

Supercritical perpendicular collisionless shocks are known to exhibit foot, ramp, and overshoot structures. The shock ramp structure is in a smaller scale in contrast to other microstructures (foot and overshoot) within the shock front. One-dimensional full particle simulations of strictly perpendicular shocks over wide ranges of ion beta βi, Alfvén Mach number MA, and ion-to-electron mass ratio mi/me are presented to investigate the impact of plasma parameters on the shock ramp scale. Main results are (1) the ramp scale can be as small as several electron inertial length. (2) The simulations suggest that in a regime below the critical ion beta value, the shock front undergoes a periodic self-reformation and the shock ramp scale is time-varying. At higher ion beta values, the shock front self-reformation is smeared. At still higher ion beta value, the motion of reflected ions is quite diffuse so that they can lead to a quasi-steady shock ramp. Throughout the above three conditions, the shock ramp thickness increases with βi. (3) The increase (decrease) in Mach number and the decrease (increase) in the beta value have almost equivalent impact on the state (i.e., stationary or nonstationary) of the shock ramp. Both of front and ramp thicknesses are increased with MA.
Interface and thickness tuning for blade coated small-molecule organic light-emitting diodes with high power efficiency
Authors: Chang Yu-Fan , Chiu Yu-Chian , Chang Hao-Wen , Wang Yi-Siang , Shih Yi-Lun , Wu Chih-Hao , Liu Yi-Lun , Lin Yu-Sheng , Meng Hsin-Fei , Chi Yun , Huang Heh-Lung , Tseng Mei-Rurng , Lin Hao-Wu , Zan Hsiao-Wen , Horng Sheng-Fu , Juang Jenh-Yih
Published: September 2013

We developed a general method based on fluorescence microscopy to characterize the interface dissolution in multi-layer organic light-emitting diodes (OLEDs) by blade coating. A sharp bi-layer edge was created before blade coating, with the bottom layer being insoluble and top layer soluble. After blade coating, fluorescence images showed that the edge of the top layer shifted when the layer dissolved completely, whereas the bottom layer's edge remained in place as a positioning mark. The dissolution depth was determined to be 15–20 nm when the emissive-layer host of 2,6-bis (3-(9H-carbazol-9-yl)phenyl) pyridine (26DCzPPy) was coated on the hole-transport layer of N,N′-bis(naphthalen-1-yl)-N,N′-bis(phenyl)-benzidine(NPB), which was consistent with a sudden drop in efficiency of orange OLEDs with layer thickness below 20 nm. Thus, the layer thickness of OLEDs was optimized to stay more than 20 nm for blade coating. For a two-color white OLED with the structure TCTA/26DCzPPy:PO-01-TB:FIrpic/TPBI, efficiency was 24 cd/A and 8.5 lm/W at 1000 cd/m2. For a three-color white OLED with Os(fptz)2(dhpm) added as the emitter, the efficiency was 12.3 cd/A and 3.7 lm/W at 1000 cd/m2. For a green device with the structure TCTA/26DCzPPy:Ir(mppy)3/TPBI, the efficiency was 41.9 cd/A and 23.4 lm/W at 1000 cd/m2.
Optical characterization of individual GaAs quantum dots grown with height control technique
Authors: Sarti F. , Muñoz Matutano G. , Bietti S. , Vinattieri A. , Sanguinetti S. , Gurioli M.
Published: September 2013

We show that the epitaxial growth of height-controlled GaAs quantum dots, leading to the reduction of the inhomogeneous emission bandwidth, produces individual nanostructures of peculiar morphology. Besides the height controlled quantum dots, we observe nanodisks formation. Exploiting time resolved and spatially resolved photoluminescence we establish the decoupling between quantum dots and nanodisks and demonstrate the high optical properties of the individual quantum dots, despite the processing steps needed for height control.
Nanomechanical resonant structures in single-crystal diamond
Authors: Burek Michael J. , Ramos Daniel , Patel Parth , Frank Ian W. , Lončar Marko
Published: September 2013

With its host of outstanding material properties, single-crystal diamond is an attractive material for nanomechanical systems. Here, the mechanical resonance characteristics of freestanding, single-crystal diamond nanobeams fabricated by an angled-etching methodology are reported. Resonance frequencies displayed evidence of significant compressive stress in doubly clamped diamond nanobeams, while cantilever resonance modes followed the expected inverse-length-squared trend. Q-factors on the order of 104 were recorded in high vacuum. Results presented here represent initial groundwork for future diamond-based nanomechanical systems which may be applied in both classical and quantum applications.
Experimental estimates of in-plane thermal conductivity in FePt-C granular thin film heat assisted magnetic recording media using a model layered system
Authors: Ho Hoan , Sharma Abhishek A. , Ong Wee-Liat , Malen Jonathan A. , Bain James A. , Zhu Jian-Gang
Published: September 2013

Cross-plane thermal conductivity kth measurements of vertical stacks of FePt/C were used to estimate the in-plane thermal conductivity of Heat Assisted Magnetic Recording (HAMR) media that consist of columnar FePt grains segregated by thin C grain boundaries. FePt/C multilayers with varied repeat units and FePt layer thicknesses (chosen to represent HAMR media grain sizes) were measured using Frequency-Domain Thermoreflectance to determine kth in the direction normal to the layers. The data suggest that when FePt grains are less than 8 nm in diameter, the in-plane kth for HAMR media is below 1 W/m-K and the anisotropy of kth (cross-plane/in-plane) will exceed 10.
Electric field driven magnetic phase transition in graphene nanoflakes
Authors: Zhou Aiping , Sheng Weidong , Xu S. J.
Published: September 2013

Within the framework of Hubbard model, a bowtie-shaped graphene nanoflake is identified to undergo an electric-field induced phase transition from an antiferromagnetic ground state. Unlike the case of half-metallic graphene nanoribbons, the electric field here leads to a non-magnetic state instead of ferromagnetic state after destructing the antiferromagnetic ordering. Because the spin is polarized on different sublattices of the nanodot in the antiferromagnetic phase, the transition occurs when the applied field breaks the sublattice symmetry and induces enough energy splitting among the originally degenerate zero-energy states.
Synthesis, structure, and magnetic properties of SrFe12O19/La1−xCaxMnO3 hard/soft phase composites
Authors: Hue D. T. M. , Lampen P. , Manh T. V. , Viet V. D. , Chinh H. D. , Srikanth H. , Phan M. H.
Published: September 2013

SrFe12O19/La1−xCaxMnO3 (SFO/LCMO) composites with x = 0.1 and 0.5 were synthesized via a two stage combined citrate precursor sol-gel and hydrothermal method. The structure and composition of the samples were refined from the X-ray diffraction patterns. The morphologies of the composites were investigated using transmission and scanning electron microscopies, which revealed micron-sized hexagonal platelets of SFO with LCMO particles with average diameters of 110–130 nm formed at the surface. An investigation of the temperature and field dependence of the magnetization found that the SFO phase with a ferrimagnetic characteristic up to 720 K dominates the magnetic properties of the composite samples. The SFO/LCMO composite samples showed a reduction in saturation magnetization and coercivity when compared with pure SFO. However, low temperature hysteresis loops recorded after cooling in applied fields up to 5 T revealed the absence of exchange bias in the SFO/LCMO composite, ruling out the possibility of significant interfacial magnetic coupling between SFO and LCMO.
Space charge polarization induced augmented in vitro bioactivity of piezoelectric (Na,K) NbO3
Authors: Dubey Ashutosh Kumar , Yamada Hiroaki , Kakimoto Ken-ichi
Published: September 2013

The present study reports the influence of chemical and electrical treatments (CET) of Li-modified sodium potassium niobate [Li0.06(Na0.5K0.5)0.94NbO3, LNKN] piezo-biomaterial on in vitro bioactivity. The chemical treatment of LNKN substrate was performed by Ti sputtering, followed by immersion in NaOH aqueous solution for various time durations and subsequently, the heat treatment. The chemically treated LNKN substrates were then corona poled. The in vitro biomineralization study suggested that the integrated effect of chemical as well as electrical treatments of LNKN piezoceramics stimulates the early stage apatite crystallization as compared to that of the mere chemical treatment. To reveal the mechanism of polarization on crystal formation, the thermally stimulated depolarization currents (TSDC) were measured before and after the chemically as well as electrically treated substrates being soaked in simulated body fluid for various time durations. It has been observed that the release of surface charge in the low temperature region (∼60 °C) has significant effect on apatite formation and growth. The surface charge density decreases with increase in the soaking period and hence, the influence of surface charge on apatite crystallization can be realized. The dielectric relaxation in the low frequency region as well as TSDC analysis suggests that the space charge polarization is dominant polarization mechanism in the CET piezo-biomaterial.
Magnetic structure and lattice contraction in Mn3NiN
Authors: Wu Meimei , Wang Cong , Sun Ying , Chu Lihua , Yan Jun , Chen Dongfeng , Huang Qingzhen , Lynn Jeffrey W.
Published: September 2013

The nuclear and magnetic structures of the cubic antiperovskite compound Mn3NiN are studied using neutron powder diffraction as a function of temperature and applied magnetic field. On cooling in zero field from the paramagnetic state, an anomalous lattice expansion abruptly occurs as the long range antiferromagnetic order first develops below TN = 262 K. The magnetic structure has lower symmetry than the crystal and can be conveniently described by a rhombohedral R-3 symmetry with dimension of √2ac × √2ac × √3ac, where ac is the chemical unit cell. In this description, the magnetic moment of the Mn is restricted to the a-b plane, but continuously rotates from 90° to around 38° as the temperature decreases to ≈120 K, below which the spin directions remain fixed. The combined magnetic and structural transition exhibits a very large magnetovolume effect with an entropy change of ΔS ≈ 54 J/kg K, but the application of a 6 T magnetic field has little effect on the magnetic structure or entropy change. The crystallographic results indicate that the properties can be tailored by small changes in the composition and site vacancies, and the results enrich the understanding of the magnetostrictive effects in antiperovskites.
Low Reynolds number airfoil optimization for wind turbine applications using genetic algorithm
Authors: Ram Krishnil R. , Lal Sunil , Rafiuddin Ahmed M.
Published: September 2013

Optimization of a low Reynolds number airfoil for use in small wind turbines is carried out using a Genetic Algorithm (GA) optimization technique. With the aim of creating a roughness insensitive airfoil for the tip region of turbine blades, a multi-objective genetic algorithm code is developed. A review of existing parameterization and optimization methods is presented along with the strategies applied to optimize the airfoil in this study. A composite Bezier curve is used to parameterize the airfoil. The resulting airfoil, the USPT2 has a maximum thickness of 10% and shows insensitivity to roughness at the optimized angles and at other angles of attack as well. The characteristics of USPT2 are studies by comparing it against the popular SG6043 airfoil. While a slight loss in lift is noticed for both airfoils, the drag increments due to early transition are noticeable as well. The airfoil is also studied using computational fluid dynamics (CFD) and wind tunnel experiments during free and forced transition. The USPT2 airfoil will be useful in small wind turbines for locations where blade soiling is likely or where other flow phenomena may cause early transition of the boundary layer.
Effects of surroundings snow coverage and solar tracking on photovoltaic systems operating in Canada
Authors: Mehrtash Mostafa , Rousse Daniel R. , Quesada Guillermo
Published: September 2013

This paper deals with demonstrating the energy performance of solar tracking photovoltaic (PV) systems in Canada. In this study, a grid connected stand-alone PV system has been designed and coupled with four different tracking systems: fixed horizontal, fixed tilted, single-axis tracking, and dual-axis tracking. The performance analysis of the systems focuses on the variation of array irradiance, electricity generation, and efficiency without considerations for economic impacts at this stage. The simulation results show that the dual-axis tracking array provides the best performance over a year. It receives 33% more solar radiation and generates 36% more electricity than the tilted system. On clear winter days, compared to the tilted system, the dual-axis tracking system produces 32% and 29% more electricity in high albedo and low albedo conditions, respectively. High albedo due to surroundings snow coverage has been found to cause an increase of 3.1%, 5.8%, and 7.9% in electricity production of the tilted, single-axis tracking, and dual-axis tracking system respectively, over a winter. The results of this research support the idea that tracking the sun is effective on clear days and could be counterproductive on overcast days. Therefore, in high albedo conditions, it is recommended to track the sun and stay fixed once the sky becomes overcast.
Variation of pinning mechanism and enhancement of critical current density in MgB2 bulk containing self-generated coherent MgB4 impurity
Authors: Cai Qi , Liu Yongchang , Ma Zongqing , Li Huijun , Yu Liming
Published: September 2013

Bulk MgB2, with self-generated MgB4 pinning centers, have experienced two-step sintering process, initially at 750 °C and then 900–1000 °C. On the contrary to the widely accepted point that MgB4 deteriorates superconductivity, it was found that MgB4 played a significant role in enhancing critical current density. The precipitation pattern of MgB4 was studied from the lattice scale images. It was observed that the initial coherent relation between the MgB4 and the matrix was destroyed to become semi-coherent and even incoherent as the second-step sintering temperature increased. Owing to the lattice distortion caused by the elastic accommodation of the coherent interface, the small-sized MgB4 particles controlled by the sintering temperature, and the fine grain connectivity affected by the porosity, the critical current density was improved over the entire magnetic field. Finally, the dominating pinning mechanism within the crystal was confirmed to be Δκ pinning in the two-step sintered MgB2 sample, where the κ is the Ginzburg-Landau parameter, while the mechanism of one-step sintered sample is surface pinning.
Nonlinear stress-strain behavior of carbon nanotube fibers subject to slow sustained strain rate
Authors: Sun Gengzhi , Wang Dong , Pang John H. L. , Liu Jun , Zheng Lianxi
Published: September 2013

Nonlinear stress-strain behavior of carbon nanotube (CNT) fibers is studied based on the test data where fiber strength can be modeled by the Weibull distribution. CNT fibers spun from vertically aligned arrays are tensioned at slow sustained strain rate (0.00001 1/s) to study the tensile strength resulting from sliding-to-failure effects. A model is developed to estimate the Weibull modulus which characterizes the dispersion of fiber strengths in terms of the maximum sustained stress and failure strain of the fibers. The results show that the sliding indeed has great influence on the stress-strain relation of CNT fibers at low strain rate.
Embryo production and gene expression in superovulated goats supplemented with de-oiled castor cake before and after detoxification treatment
Authors: Arruda I. J. , Silva L. M. , Oliveira C. H. A. , Rodrigues F. V. , Silva A. M. , Fernandes C. C. L. , Gomes-Filho M. A. , Araújo A. A. , Silva C. M. G. , Rondina D.
Published: September 2013

The use of alternative protein sources that do not impair animal performance is a feasible option to reduce costs associated with animal supplementation. Previous studies indicate that castor cake has a high protein value and good ruminal degradability, making it an attractive alternative dietary source for ruminants. Thus, the aim of this study was to evaluate the effects from ingestion of castor cake (treatment CC) or detoxified castor cake (treatment DCC) on serum IgG levels, in vivo production of goat embryos, and the expression profile of genes related to embryonic development, metabolism, and oxidative stress. The results showed the presence of IgG against ricin only in animals of the CC group. The ovulation rate and the production of transferable embryos in animals of the CC group were lower (P < 0.05) than in the animals fed without castor cake (WCC), but neither group differed significantly from the DCC group. There was no effect of type of diet on the expression of the IGF-IR, IGF-II, and GLUT-1 genes in goat embryos produced in vivo. However, the relative expression of mRNA for the HSP 70.1 gene was significantly higher (P < 0.05) in the CC group than in the WCC group, but did not differ from that of the DCC group. In conclusion, this study showed that supplementation with detoxified castor cake can be used for goat feeding, but caution is necessary when providing castor bean meal in the feed of superovulated breeding females, because ricin in the diet, even at low concentrations, altered IgG levels and the expression of mRNA for HSP 70.1, effects that were accompanied by a lower rate of transferable embryos.
Response of a cryptic apex predator to a complete urban to forest gradient
Authors: Isaac Bronwyn , White John , Ierodiaconou Daniel , Cooke Raylene
Published: September 2013

Context
Urbanisation is one of the most damaging landscape-scale disturbance processes leading to significant and potentially irreversible changes in biodiversity. How apex predators respond to urbanisation is poorly understood, largely because of their low density and low detectability. Given the important functional roles of apex predators in ecosystems, it is critical that research investigates how they respond to urbanisation, and how urban systems can be designed to better support apex predators.

Aims
The present research aims to examine how an avian apex predator, the powerful owl, responds to a complete urban–forest gradient in southern Victoria, Australia. Specifically, the research aims to understand the environmental attributes that drive habitat suitability for powerful owls across the urban–forest gradient.

Methods
Using a total of 683 independent field- and atlas-derived records of powerful owls across the study site, the research takes a presence-only modelling approach. The presence points were modelled against a series of geospatial variables that were determined a priori on the basis of the known ecology of powerful owls.

Key results
Potential powerful owl habitat declined in a dramatic fashion in response to increasing levels of urbanisation, ranging from 76% of the forest landscape to 21% of the urban landscape. Powerful owl habitat availability across the urban–forest gradient is positively influenced by tree cover, productivity (normalised difference vegetation index) and proximity to river systems and riparian vegetation.

Conclusions
Presence-only modelling has provided a useful way for investigating the response of an apex predator to a gradient of urbanisation. Although powerful owl habitat availability is negatively reduced by urbanisation, there is significant scope to manage urban landscapes to either maintain or improve the availability of habitat across the gradient.

Implications
High resource-requiring species, such as apex predators, have the capacity to be detrimentally affected by urbanisation processes. Presence-only modelling, however, provides a useful tool for investigating how these difficult-to-detect species are affected by urbanisation, and ultimately inform how landscapes can be managed to maximise habitat availability for apex predators.
Indirection and symbol-like processing in the prefrontal cortex and basal ganglia
Authors: Kriete Trenton , Noelle David C. , Cohen Jonathan D. , O’Reilly Randall C.
Published: September 2013

The ability to flexibly, rapidly, and accurately perform novel tasks is a hallmark of human behavior. In our everyday lives we are often faced with arbitrary instructions that we must understand and follow, and we are able to do so with remarkable ease. It has frequently been argued that this ability relies on symbol processing, which depends critically on the ability to represent variables and bind them to arbitrary values. Whereas symbol processing is a fundamental feature of all computer systems, it remains a mystery whether and how this ability is carried out by the brain. Here, we provide an example of how the structure and functioning of the prefrontal cortex/basal ganglia working memory system can support variable binding, through a form of indirection (akin to a pointer in computer science). We show how indirection enables the system to flexibly generalize its behavior substantially beyond its direct experience (i.e., systematicity). We argue that this provides a biologically plausible mechanism that approximates a key component of symbol processing, exhibiting both the flexibility, but also some of the limitations, that are associated with this ability in humans.
Basal variability in CREB phosphorylation predicts trait-like differences in amygdala-dependent memory
Authors: Cowansage Kiriana K. , Bush David E. A. , Josselyn Sheena A. , Klann Eric , LeDoux Joseph E.
Published: September 2013

Significance

Most studies in neuroscience focus on average, or typical, behavior; however, much less is known about how neurobiological differences between individuals contribute to their cognitive and emotional characteristics. In this study, we use outbred rats to investigate if CREB, a key protein required for memory formation, participates in the natural emergence of memory-related individual differences. We show that CREB is activated at lower levels in rats with trait-like deficits in emotional memory. Thus, even in genetically diverse populations, naturally occurring differences in the function of specific proteins may contribute to defining common behavioral traits.
Genetically dictated change in host mucus carbohydrate landscape exerts a diet-dependent effect on the gut microbiota
Authors: Kashyap Purna C. , Marcobal Angela , Ursell Luke K. , Smits Samuel A. , Sonnenburg Erica D. , Costello Elizabeth K. , Higginbottom Steven K. , Domino Steven E. , Holmes Susan P. , Relman David A. , Knight Rob , Gordon Jeffrey I. , Sonnenburg Justin L.
Published: September 2013

Significance

Our data demonstrate that differences in host genotype that affect the carbohydrate landscape of the distal gut interact with diet to alter the composition and function of resident microbes in a diet-dependent manner.
Featureless and nonfractionalized Mott insulators on the honeycomb lattice at 1/2 site filling
Authors: Kimchi Itamar , Parameswaran S. A. , Turner Ari M. , Wang Fa , Vishwanath Ashvin
Published: September 2013

Significance

Symmetries are increasingly shown to play various key roles determining the possible phases in condensed matter systems. We study bosonic particles (including electron Cooper pairs) living on the vertices of a honeycomb lattice at a density of 1/2 per site. Here the honeycomb symmetries forbid the usual fermionic band insulating state, and the conventional Mott (“strongly interacting”) insulator involves a whole number of particles frozen on each site, suggesting that featureless (fully symmetric) insulators might not exist in this system. Nevertheless, we explicitly construct quantum states and demonstrate that they are examples of featureless insulators on the honeycomb lattice at 1/2 site filling, with a procedure generalizing to lattices with symmorphic symmetry groups.
Feynman’s clock, a new variational principle, and parallel-in-time quantum dynamics
Authors: McClean Jarrod R. , Parkhill John A. , Aspuru-Guzik Alán
Published: September 2013

Significance

Methodology for studying quantum ground-state problems is currently more mature than what is available for quantum dynamical problems. Moreover, modern computing architectures demand that new algorithms be able to make use of parallel processing. We introduce a construction inspired by quantum computation that allows one to use virtually any model for a ground-state wavefunction to model quantum many-body dynamics and formulate it in a way that naturally leads to a parallel-in-time algorithm. We show how the elementary ground-state variational principle maps onto a new time-dependent variational principle and demonstrate practical examples of its use.
Epigenetic control of natural killer cell maturation by histone H2A deubiquitinase, MYSM1
Authors: Nandakumar Vijayalakshmi , Chou YuChia , Zang Linda , Huang Xue F. , Chen Si-Yi
Published: September 2013

Significance

Natural killer (NK) cells are lymphocytes that kill virus-infected and tumor cells as well as activate adaptive immunity through cytokine production. Although several transcription factors have been identified as having roles in NK cell development, little is known about the transcriptional control of these transcription factors and the epigenetic control of NK cell development. In this study we identified the importance of MYSM1, a histone H2A deubiquitinase, for NK cell maturation. We found that MYSM1-mediated epigenetic alterations control the expression of an important NK cell transcription factor, inhibitor of DNA-binding protein (ID2). This study unfolds the regulatory events of key transcription factors of NK cell development such as nuclear factor IL-3 and ID2 through an epigenetic mechanism.
Structural insights into proteoglycan-shaped Hedgehog signaling
Authors: Whalen Daniel M. , Malinauskas Tomas , Gilbert Robert J. C. , Siebold Christian
Published: September 2013

Significance

The Hedgehog (Hh) signaling pathway plays key roles during embryonic development and remains active in adults. Mutations in the genes encoding the Hh signaling pathway proteins lead to developmental disorders and cancer. The glycosaminoglycan (GAG) chains of proteoglycans at the cell surface shape Hh gradients and signal transduction. We determined the crystal structures of Hh proteins with two different GAG chains, heparin and chondroitin sulfate. The GAG-binding site we identified in the Hh protein is previously not identified and the majority of Hh residues forming this GAG-binding site have been previously implicated in developmental diseases. Analysis of the crystal packing, combined with biophysical experiments, revealed GAG-dependent Hh multimerization and suggests a unique mechanism of Hh signaling regulation.
Single-molecule FRET and linear dichroism studies of DNA breathing and helicase binding at replication fork junctions
Authors: Phelps Carey , Lee Wonbae , Jose Davis , von Hippel Peter H. , Marcus Andrew H.
Published: September 2013

Significance

Unique single-molecule fluorescence techniques were used to monitor DNA “breathing” at and near the junctions of model DNA replication forks on biologically relevant microsecond-to-millisecond time scales. Experiments performed in the absence and presence of helicase complexes addressed the role of these fluctuations in helicase function during DNA replication. These studies simultaneously monitored single-molecule Förster resonance energy transfer and single-molecule fluorescence linear dichroism of “internal” Cy3/Cy5 labels placed rigidly into the DNA backbones at positions near the fork junction. Our results showed significant breathing at the fork junction that was greatly augmented by the presence of weakly bound helicase, followed by still larger fluctuations and strand separation after full duplex DNA unwinding by the complete tightly bound and processive helicase complex.
X-ray absorption spectroscopic investigation of the electronic structure differences in solution and crystalline oxyhemoglobin
Authors: Wilson Samuel A. , Green Evan , Mathews Irimpan I. , Benfatto Maurizio , Hodgson Keith O. , Hedman Britt , Sarangi Ritimukta
Published: September 2013

Significance

The electronic structure of oxyhemoglobin has been under intense scrutiny since the geometric structure of this bent, end-on bound Fe-O
2
species was first determined over three decades ago, but a consensus description has not yet been reached. Here, solution and crystalline X-ray absorption spectroscopies have been combined with time-dependent density functional theory calculations to demonstrate the dominantly

(ferric-superoxide) character of solution oxyhemoglobin. It is also shown that,
in crystallo
, a dominantly Fe
2+
-O
2
(ferrous-dioxygen) character is favored, indicating multiconfigurational character, tunable by a change in state.
Expressomal approach for comprehensive analysis and visualization of ligand sensitivities of xenoestrogen responsive genes
Authors: Shioda Toshi , Rosenthal Noël F. , Coser Kathryn R. , Suto Mizuki , Phatak Mukta , Medvedovic Mario , Carey Vincent J. , Isselbacher Kurt J.
Published: September 2013

Significance

Cells change their mRNA expression in response to biologically active substances in a dose-dependent manner. Because different genes in a cell show distinct sensitivities to the same substance, changes in the genome-wide mRNA expression profile induced by low and high doses of a substance are essentially different, but this notion has been commonly overlooked in previously published studies. Using a human cell culture model and microarray, we performed genome-wide determinations of gene sensitivities to hormonally active substances with statistically rigorous approaches. Our study provides a conceptual and methodological framework for the systematic examination of gene sensitivities and demonstrates effective detection of nonmonotonic dose-dependent responses, introducing the importance of gene sensitivity analysis to pharmacogenomic and toxicogenomic research.
Differential effect of aneuploidy on the X chromosome and genes with sex-biased expression inDrosophila
Authors: Sun Lin , Johnson Adam F. , Li Jilong , Lambdin Aaron S. , Cheng Jianlin , Birchler James A.
Published: September 2013

Significance

This study demonstrates a global impact of genomic imbalance on gene expression and the generality of the inverse dosage effect and aneuploid dosage compensation. The study indicates that sex chromosomes and genes with sex-biased expression evolve distinctly in response to dosage-sensitive regulation.
How does typeface familiarity affect reading performance and reader preference?
Authors: Beier Sofie , Larson Kevin
Published: September 2013

Some typographers have proposed that typeface familiarity is defined by the amount of time that a reader has been exposed to a typeface design, while other typographers have proposed that familiarity is defined by the commonalities in letter shapes. These two hypotheses were tested by measuring the reading speed and preferences of participants. Participants were tested twice with common and uncommon letter shapes, once before and once after spending 20 minutes reading a story with the font. The results indicate that the exposure period has an effect on the speed of reading, but the uncommon letter shapes did not. Readers did not like the uncommon letter shapes. This has implications for the selection of type and the design of future typefaces.
Read&Answer: An application to study task-oriented reading situations
Authors: Vidal-Abarca Eduardo , Cerdán Raquel
Published: September 2013

People often read to fulfill the requirement of a task that demands comprehension, which can be called task-oriented reading. Task- oriented reading activities are associated with reading literacy competencies promoted by international reading literacy assessment programs and definitions of reading skills that emphasize the role of the reader, the tasks, and the social context in reading. Task- oriented reading situations place specific self-regulatory demands on readers that go beyond the scope of comprehension processes considered by current theories and models of comprehension.
Read&Answer is an application developed to record actions and reading time on task-oriented situations in an electronic environment. In this paper we describe Read&Answer and summarize studies on the impact that tasks of different nature have on how readers interact with a text and their final performance, as well as some strategies specific to task-oriented reading situations.
Stochastic association of neighboring replicons creates replication factories in budding yeast
Authors: Saner Nazan , Karschau Jens , Natsume Toyoaki , Gierliński Marek , Retkute Renata , Hawkins Michelle , Nieduszynski Conrad A. , Blow J. Julian , de Moura Alessandro P.S. , Tanaka Tomoyuki U.
Published: September 2013

Inside the nucleus, DNA replication is organized at discrete sites called replication factories, consisting of DNA polymerases and other replication proteins. Replication factories play important roles in coordinating replication and in responding to replication stress. However, it remains unknown how replicons are organized for processing at each replication factory. Here we address this question using budding yeast. We analyze how individual replicons dynamically organized a replication factory using live-cell imaging and investigate how replication factories were structured using super-resolution microscopy. Surprisingly, we show that the grouping of replicons within factories is highly variable from cell to cell. Once associated, however, replicons stay together relatively stably to maintain replication factories. We derive a coherent genome-wide mathematical model showing how neighboring replicons became associated stochastically to form replication factories, which was validated by independent microscopy-based analyses. This study not only reveals the fundamental principles promoting replication factory organization in budding yeast, but also provides insight into general mechanisms by which chromosomes organize sub-nuclear structures.
Recognition of gut microbiota by NOD2 is essential for the homeostasis of intestinal intraepithelial lymphocytes
Authors: Jiang Wei , Wang Xiaqiong , Zeng Benhua , Liu Lei , Tardivel Aubry , Wei Hong , Han Jiahuai , MacDonald H. Robson , Tschopp Jurg , Tian Zhigang , Zhou Rongbin
Published: September 2013

NOD2 functions as an intracellular sensor for microbial pathogen and plays an important role in epithelial defense. The loss-of-function mutation of NOD2 is strongly associated with human Crohn’s disease (CD). However, the mechanisms of how NOD2 maintains the intestinal homeostasis and regulates the susceptibility of CD are still unclear. Here we found that the numbers of intestinal intraepithelial lymphocytes (IELs) were reduced significantly in Nod2−/− mice and the residual IELs displayed reduced proliferation and increased apoptosis. Further study showed that NOD2 signaling maintained IELs via recognition of gut microbiota and IL-15 production. Notably, recovery of IELs by adoptive transfer could reduce the susceptibility of Nod2−/− mice to the 2,4,6-trinitrobenzene sulfonic acid (TNBS)–induced colitis. Our results demonstrate that recognition of gut microbiota by NOD2 is important to maintain the homeostasis of IELs and provide a clue that may link NOD2 variation to the impaired innate immunity and higher susceptibility in CD.
Central Line–Associated Bloodstream Infection in Neonatal Intensive Care Units
Authors: Blanchard Ana C. , Fortin Elise , Rocher Isabelle , Moore Dorothy L. , Frenette Charles , Tremblay Claude , Quach Caroline
Published: September 2013

Objective.

Describe the epidemiology of central line-associated bloodstream infections (CLABSIs) in neonatal intensive care units (NICUs) participating in a standardized and mandatory CLABSI surveillance program.

Design.

Retrospective cohort.

Setting.

We included patients admitted (April 2007-March 2011) to 7 level II/III NICUs who developed a CLABSI (as defined by the National Healthcare Safety Network).

Methods

. CLABSIs/1,000 central line–days and device utilization ratio were calculated;x2test, Studentttest, Kruskal-Wallis, and Poisson regression were used.

Results.

Overall, 191 patients had 202 CLABSI episodes for a pooled mean rate of 4.0 CLABSIs/1,000 central line-days and a device utilization ratio of 0.20. Annual pooled mean CLABSI rates increased from 3.6 in 2007-2008 to 5.1 CLABSIs/1,000 central line-days in 2010-2011 (P= .01). The all-cause 30-day case fatality proportion was 8.9% (n = 17) and occurred a median of 8 days after CLABSI. Coagulase-negativeStaphylococcuswas identified in 112 (50.5%) cases.Staphylococcus aureuswas identified in 22 cases, and 3 (13.6%) were resistant to methicillin. An underlying intra-abdominal pathology was found in 20% (40/202) of CLABSI cases, 50% of which were reported in the last year of study. When adjusted for mean birth weight, annual CLABSI incidence rates were independently associated with the proportion of intra-abdominal pathology (P= .007) and the proportion of pulmonary pathology (P= .016) reported.

Conclusion.

The increase in CLABSI rates in Quebec NICUs seems to be associated with an increased proportion of cases with underlying intra-abdominal and pulmonary pathologies, which needs further investigation.
Characterization of Acute and Chronic Neuropathies Induced by Oxaliplatin in Mice and Differential Effects of a Novel Mitochondria-targeted Antioxidant on the Neuropathies
Authors: Toyama Satoshi , Shimoyama Naohito , Ishida Yasuo , Koyasu Takayoshi , Szeto Hazel H. , Shimoyama Megumi
Published: September 2013

Background:

Oxaliplatin, a chemotherapeutic agent used for the treatment of colorectal cancer, induces dose-limiting neuropathy that compromises quality of life. This study aimed to reproduce, in mice, patients’ symptoms of oxaliplatin-induced neuropathy and to observe effects of SS-31, a mitochondria-targeted antioxidant on the neuropathy.

Methods:

Neuropathy was induced by single or repeated injections of oxaliplatin. Cold and mechanical hypersensitivities were assessed by 15°C-cold plate, temperature preference, and von Frey tests. Morphology of peripheral nerves and dorsal root ganglions, expression of spinal cord c-Fos, density of intraepidermal nerve fibers, and levels of dorsal root ganglion–reactive oxygen/nitrogen species were examined. SS-31 was administered concomitantly or after oxaliplatin injections.

Results:

Single injection of oxaliplatin induced cold hypersensitivity in forepaws but not in hind paws which resolved within days (maximal forepaw shakes: 28 ± 1.5 vs. 9.3 ± 1.6/150 s, mean ± SEM, P < 0.001, n = 6 per group). Oxaliplatin-administered mice disfavored 10° and 15°C plates more than control. Paw stimulation at 15°C induced c-Fos–positive cells within superficial laminae of the dorsal horn in C7-T1 segments. Weekly administrations induced gradual development of persistent mechanical allodynia in the hind paws (minimal mechanical threshold: 0.19 ± 0.08 vs. 0.93 ± 0.11 g, P < 0.001, n = 10 per group). Microscopy revealed no overt morphological changes in peripheral nerves and dorsal root ganglions. Concomitant SS-31 administration with repeated oxaliplatin administration attenuated both cold and mechanical hypersensitivity. Decrease in intraepidermal nerve fibers and increase in dorsal root ganglion–reactive oxygen/nitrogen species were also attenuated. Acute SS-31 administration after symptoms were established reversed only cold hypersensitivity.

Conclusion:

This model of oxaliplatin-induced neuropathy mimicked patients’ conditions. SS-31 has potentials to prevent both acute and chronic neuropathies but is only helpful in treatment of acute neuropathy. (Anesthesiology 2014; 120:459-73)
Interaction between bud-site selection and polarity-establishment machineries in budding yeast
Authors: Wu Chi-Fang , Savage Natasha S. , Lew Daniel J.
Published: September 2013

Saccharomyces cerevisiae
yeast cells polarize in order to form a single bud in each cell cycle. Distinct patterns of bud-site selection are observed in haploid and diploid cells. Genetic approaches have identified the molecular machinery responsible for positioning the bud site: during bud formation, specific locations are marked with immobile landmark proteins. In the next cell cycle, landmarks act through the Ras-family GTPase Rsr1 to promote local activation of the conserved Rho-family GTPase, Cdc42. Additional Cdc42 accumulates by positive feedback, creating a concentrated patch of GTP-Cdc42, which polarizes the cytoskeleton to promote bud emergence. Using time-lapse imaging and mathematical modelling, we examined the process of bud-site establishment. Imaging reveals unexpected effects of the bud-site-selection system on the dynamics of polarity establishment, raising new questions about how that system may operate. We found that polarity factors sometimes accumulate at more than one site among the landmark-specified locations, and we suggest that competition between clusters of polarity factors determines the final location of the Cdc42 cluster. Modelling indicated that temporally constant landmark-localized Rsr1 would weaken or block competition, yielding more than one polarity site. Instead, we suggest that polarity factors recruit Rsr1, effectively sequestering it from other locations and thereby terminating landmark activity.
The PAR network: redundancy and robustness in a symmetry-breaking system
Authors: Motegi Fumio , Seydoux Geraldine
Published: September 2013

To become polarized, cells must first ‘break symmetry’. Symmetry breaking is the process by which an unpolarized, symmetric cell develops a singularity, often at the cell periphery, that is used to develop a polarity axis. TheCaenorhabditis eleganszygote breaks symmetry under the influence of the sperm-donated centrosome, which causes the PAR polarity regulators to sort into distinct anterior and posterior cortical domains. Modelling analyses have shown that cortical flows induced by the centrosome combined with antagonism between anterior and posterior PARs (mutual exclusion) are sufficient, in principle, to break symmetry, provided that anterior and posterior PAR activities are precisely balanced. Experimental evidence indicates, however, that the system is surprisingly robust to changes in cortical flows, mutual exclusion and PAR balance. We suggest that this robustness derives from redundant symmetry-breaking inputs that engage two positive feedback loops mediated by the anterior and posterior PAR proteins. In particular, the PAR-2 feedback loop stabilizes the polarized state by creating a domain where posterior PARs are immune to exclusion by anterior PARs. The two feedback loops in the PAR network share characteristics with the two feedback loops in the Cdc42 polarization network ofSaccharomyces cerevisiae.
Breaking the epithelial polarity barrier in cancer: the strange case of LKB1/PAR-4
Authors: Partanen Johanna I. , Tervonen Topi A. , Klefström Juha
Published: September 2013

The PAR clan of polarity regulating genes was initially discovered in a genetic screen searching for genes involved in asymmetric cell divisions in theCaenorhabditis elegansembryo. Today, investigations in worms, flies and mammals have established PAR proteins as conserved and fundamental regulators of animal cell polarization in a broad range of biological phenomena requiring cellular asymmetries. The human homologue of invertebrate PAR-4, a serine–threonine kinase LKB1/STK11, has caught attention as a gene behind Peutz–Jeghers polyposis syndrome and as a bona fide tumour suppressor gene commonly mutated in sporadic cancer. LKB1 functions as a master regulator of AMP-activated protein kinase (AMPK) and 12 other kinases referred to as the AMPK-related kinases, including four human homologues of PAR-1. The role of LKB1 as part of the energy sensing LKB1-AMPK module has been intensively studied, whereas the polarity function of LKB1, in the context of homoeostasis or cancer, has gained less attention. Here, we focus on the PAR-4 identity of LKB1, discussing the weight of evidence indicating a role for LKB1 in regulation of cell polarity and epithelial integrity across species and highlight recent investigations providing new insight into the old question: does the PAR-4 identity of LKB1 matter in cancer?
Adaptive molecular networks controlling chemotactic migration: dynamic inputs and selection of the network architecture
Authors: Chang Hao , Levchenko Andre
Published: September 2013

Eukaryotic signalling networks underlying the cell's ability to sense the gradient of chemotactic cues frequently have the dual property of perfect adaptation to spatially homogeneous inputs, and persistent activation by inputs that are spatially graded. This property is also shared by bacterial chemotaxis networks, raising the question of whether these two types of chemotactic processes also have similar organization of the underlying biomolecular processes. Interestingly, perfect adaptation can only be achieved robustly by a handful of mechanisms, and while eukaryotic chemotactic networks appear to rely on one of these—the incoherent feed-forward loop, bacterial chemotaxis depends on another—the negative feedback loop. In this review, we discuss how this conclusion can be reached even if the details of the molecular networks are incompletely understood. Furthermore, we argue that the use of distinct network architectures is not accidental and may be a consequence of the nature of the signalling inputs and the limitations of the sensory properties of different cell types.