bluuebunny/crossref_metadata_2025 huggingface dataset:
An integral equation theory for solvation effects on the molecular structural fluctuation
Authors: Matsumura Yoshihiro , Sato Hirofumi
Published: July 2015

A new integral equation theory is proposed, which enables us to efficiently compute conformational distribution of a polyatomic molecule in solution phase. The solvation effect on the intramolecular correlation function is evaluated through a self-consistent procedure. In addition, the analytical expression of solvation free energy is derived, explicitly taking into account the molecular structural fluctuation. The derived equation establishes a direct route between the structural fluctuation and free energy of the molecule. The method was successfully applied to a series of n-alkanes in aqueous solutions to demonstrate the superiority of the proposed theory.
Determining the microwave coupling and operational efficiencies of a microwave plasma assisted chemical vapor deposition reactor under high pressure diamond synthesis operating conditions
Authors: Nad Shreya , Gu Yajun , Asmussen Jes
Published: July 2015

The microwave coupling efficiency of the 2.45 GHz, microwave plasma assisted diamond synthesis process is investigated by experimentally measuring the performance of a specific single mode excited, internally tuned microwave plasma reactor. Plasma reactor coupling efficiencies (η) > 90% are achieved over the entire 100–260 Torr pressure range and 1.5–2.4 kW input power diamond synthesis regime. When operating at a specific experimental operating condition, small additional internal tuning adjustments can be made to achieve η > 98%. When the plasma reactor has low empty cavity losses, i.e., the empty cavity quality factor is >1500, then overall microwave discharge coupling efficiencies (ηcoup) of >94% can be achieved. A large, safe, and efficient experimental operating regime is identified. Both substrate hot spots and the formation of microwave plasmoids are eliminated when operating within this regime. This investigation suggests that both the reactor design and the reactor process operation must be considered when attempting to lower diamond synthesis electrical energy costs while still enabling a very versatile and flexible operation performance.
A new bimetallic plasmonic photocatalyst consisting of gold(core)-copper(shell) nanoparticle and titanium(IV) oxide support
Authors: Sato Yuichi , Naya Shin-ichi , Tada Hiroaki
Published: July 2015

Ultrathin Cu layers (∼2 atomic layers) have been selectively formed on the Au surfaces of Au nanoparticle-loaded rutile TiO2 (Au@Cu/TiO2) by a deposition precipitation-photodeposition technique. Cyclic voltammetry and photochronopotentiometry measurements indicate that the reaction proceeds via the underpotential deposition. The ultrathin Cu shell drastically increases the activity of Au/TiO2 for the selective oxidation of amines to the corresponding aldehydes under visible-light irradiation (λ > 430 nm). Photochronoamperometry measurements strongly suggest that the striking Cu shell effect stems from the enhancement of the charge separation in the localized surface plasmon resonance-excited Au/TiO2.
Designing a tokamak fusion reactor—How does plasma physics fit in?
Authors: Freidberg J. P. , Mangiarotti F. J. , Minervini J.
Published: July 2015

This paper attempts to bridge the gap between tokamak reactor design and plasma physics. The analysis demonstrates that the overall design of a tokamak fusion reactor is determined almost entirely by the constraints imposed by nuclear physics and fusion engineering. Virtually, no plasma physics is required to determine the main design parameters of a reactor: a, R0, B0, Ti, Te, p, n, τE, I. The one exception is the value of the toroidal current I, which depends upon a combination of engineering and plasma physics. This exception, however, ultimately has a major impact on the feasibility of an attractive tokamak reactor. The analysis shows that the engineering/nuclear physics design makes demands on the plasma physics that must be satisfied in order to generate power. These demands are substituted into the well-known operational constraints arising in tokamak physics: the Troyon limit, Greenwald limit, kink stability limit, and bootstrap fraction limit. Unfortunately, a tokamak reactor designed on the basis of standard engineering and nuclear physics constraints does not scale to a reactor. Too much current is required to achieve the necessary confinement time for ignition. The combination of achievable bootstrap current plus current drive is not sufficient to generate the current demanded by the engineering design. Several possible solutions are discussed in detail involving advances in plasma physics or engineering. The main contribution of the present work is to demonstrate that the basic reactor design and its plasma physics consequences can be determined simply and analytically. The analysis thus provides a crisp, compact, logical framework that will hopefully lead to improved physical intuition for connecting plasma physic to tokamak reactor design.
Ionic and viscoelastic mechanisms of a bucky-gel actuator
Authors: Kruusamäe Karl , Sugino Takushi , Asaka Kinji
Published: July 2015

Ionic electromechanically active polymers (IEAPs) are considered attractive candidates for soft, miniature, and lightweight actuators. The bucky-gel actuator is a carbonaceous subtype of IEAP that due to its structure (i.e. two highly porous electrodes sandwiching a thin ion-permeable electrolyte layer) and composition (i.e. being composed of soft porous polymer, carbon nanotubes, and ionic liquid) is very similar to an electric double-layer capacitor. In response to the voltage applied between the electrodes of a bucky-gel actuator, the laminar structure bends. The time domain behavior exhibits, however, a phenomenon called the back-relaxation, i.e., after some time the direction of bending is reversed even though voltage remains constant. In spite of the working mechanism of IEAP actuators being generally attributed to the transport of ions within the soft multilayer system, the specific details remain unclear. A so-called two-carrier model proposes that the bending and subsequent back-relaxation are caused by the relocation of two ionic species having different mobilities as they enter and exit the electrode layers. By adopting the two-carrier model for bucky-gel actuators, we see very good agreement between the mathematical representation and the experimental data of the electromechanical behavior. Furthermore, since the bucky-gel actuator is viscoelastic, we propose to use the time domain response of a blocking force as the key parameter related to the inner ionic mechanism. We also introduce a method to estimate the viscoelastic creep compliance function from the time domain responses for curvature and blocking force. This analysis includes four types of bucky-gel actuators of varying composition and structure.
Vapor-liquid-solid epitaxial growth of Si1−xGex alloy nanowires: Composition dependence on precursor reactivity and morphology control for vertical forests
Authors: Choi S. G. , Manandhar P. , Picraux S. T.
Published: July 2015

Growth of high-density group IV alloy nanowire forests is critical for exploiting their unique functionalities in many applications. Here, the compositional dependence on precursor reactivity and optimized conditions for vertical growth are studied for Si1−xGex alloy nanowires grown by the vapor-liquid-solid method. The nanowire composition versus gas partial-pressure ratio for germane-silane and germane-disilane precursor combinations is obtained at 350 °C over a wide composition range (0.05 ≤ x ≤ 0.98) and a generalized model to predict composition for alloy nanowires is developed based on the relative precursor partial pressures and reactivity ratio. In combination with germane, silane provides more precise compositional control at high Ge concentrations (x > 0.7), whereas disilane greatly increases the Si concentration for a given gas ratio and enables more precise alloy compositional control at small Ge concentrations (x < 0.3). Vertically oriented, non-kinking nanowire forest growth on Si (111) substrates is then discussed for silane/germane over a wide range of compositions, with temperature and precursor partial pressure optimized by monitoring the nanowire growth front using in-situ optical reflectance. For high Ge compositions (x ≈ 0.9), a “two-step” growth approach with nucleation at higher temperatures results in nanowires with high-density and uniform vertical orientation. With increasing Si content (x ≈ 0.8), the optimal growth window is shifted to higher temperatures, which minimizes nanowire kinking morphologies. For Si-rich Si1−xGex alloys (x ≈ 0.25), vertical nanowire growth is enhanced by single-step, higher-temperature growth at reduced pressures.
Geodesic acoustic mode in toroidally rotating anisotropic tokamaks
Authors: Ren Haijun
Published: July 2015

Effects of anisotropy on the geodesic acoustic mode (GAM) are analyzed by using gyro-kinetic equations applicable to low-frequency microinstabilities in a toroidally rotating tokamak plasma. Dispersion relation in the presence of arbitrary Mach number M, anisotropy strength σ, and the temperature ration τ is analytically derived. It is shown that when σ is less than 3 + 2τ, the increased electron temperature with fixed ion parallel temperature increases the normalized GAM frequency. When σ is larger than 3 + 2τ, the increasing of electron temperature decreases the GAM frequency. The anisotropy σ always tends to enlarge the GAM frequency. The Landau damping rate is dramatically decreased by the increasing τ or σ.
Cannula-based computational fluorescence microscopy
Authors: Kim Ganghun , Nagarajan Naveen , Capecchi Mario R. , Menon Rajesh
Published: July 2015

We converted a solid-glass cannula into a high-resolution widefield fluorescence microscope. Calibrating the space-variant point-spread functions of the cannula and applying a nonlinear optimization algorithm to reconstruct object details enable this development. The resolution of our system is ∼1 μm, and fluorophore position is determined to a precision of ∼20 nm. Images of microglia from fixed slices of mouse brains at various post-natal development stages were also obtained.
Random exchange interaction effects on the phase transitions in frustrated classical Heisenberg model
Authors: Li W. C. , Song X. , Feng J. J. , Jia X. T. , Zeng M. , Gao X. S. , Qin M. H.
Published: July 2015

In this work, the effects of the random exchange interaction on the phase transitions and phase diagrams of classical frustrated Heisenberg model are investigated by Monte Carlo simulation in order to simulate the chemical doping effect in real materials. It is observed that the antiferromagnetic transitions shift toward low temperature with the increasing magnitude of the random exchange interaction, which can be qualitatively understood from the competitions among local spin states. This study is related to the magnetic properties in the doped iron-based superconductors.
Simultaneous fabrication of nanogap electrodes using field-emission-induced electromigration
Authors: Ito Mitsuki , Yagi Mamiko , Morihara Kohei , Shirakashi Jun-ichi
Published: July 2015

We present a simple technique for simultaneous control of the electrical properties of multiple Ni nanogaps. This technique is based on electromigration induced by a field emission current and is called “activation.” Simultaneous tuning of the tunnel resistance of multiple nanogaps was achieved by passing a Fowler–Nordheim (F-N) field emission current through an initial group of three Ni nanogaps connected in series. The Ni nanogaps, which had asymmetrical shapes with initial gap separations in the 80–110-nm range, were fabricated by electron-beam lithography and a lift-off process. By performing the activation procedure, the current–voltage properties of the series-connected nanogaps were varied simultaneously from “insulating” to “metallic” via “tunneling” properties by increasing the preset current of the activation procedure. We can also simultaneously control the tunnel resistances of the series-connected nanogaps, which range from a resistance of the order of 100 TΩ–100 kΩ, by increasing the preset current from 1 nA to 30 μA. This tendency is quite similar to that of individually activated nanogaps, and the tunnel resistance values of the simultaneously activated nanogaps were almost the same at each preset current. These results clearly imply that the electrical properties of the series-connected nanogaps can be controlled simultaneously via the activation procedure.
DOE: Let’s move accelerator technologies to commercial markets
Authors: Feder Toni
Published: July 2015

Accelerator-based technologies are used in the production and handling of everyday items, from gems to tires to weapons.
Neutrino detector moves from Italy to Illinois
Authors: Feder Toni
Published: July 2015

Liquid argon is selected for next-generation experiments.
A half century of density functional theory
Authors: Zangwill Andrew
Published: July 2015

Today’s most popular method for calculating the electronic structure of atoms, molecules, liquids, solids, and plasmas began as a bold hypothesis: The electron density distribution completely characterizes the ground state of a many-electron system.
Seasonal changes in chlorine and methoxyl content of leaves of deciduous trees and their impact on release of chloromethane and methanol at elevated temperatures
Authors: McRoberts W. Colin , Keppler Frank , Harper David B. , Hamilton John T. G.
Published: July 2015

Environmental context
Chloromethane is the most abundant naturally produced chlorine-containing organic compound, responsible for ~16% of chlorine-catalysed stratospheric ozone destruction. A significant source of this gas is emission from biomass by reaction between chloride ion and methoxyl groups of the biopolymers pectin and lignin. The seasonal changes in the chlorine and methoxyl pools observed in leaves of several deciduous tree species have implications for understanding chlorine volatilisation during biomass burning and estimation of the global chloromethane budget.

Abstract
Atmospheric chloromethane (CH3Cl) plays a role in the destruction of stratospheric ozone. Previous studies suggest an important source of this gas is emission from leaves and leaf litter at ambient and elevated (150–350°C) temperatures. In this study, the total chlorine and OCH3 content of leaves of the deciduous temperate tree species ash, beech, Norway maple and oak were measured throughout the 2004 and 2005 growing seasons. The total chlorine content increased with leaf age. The overall seasonal accumulation varied between five- and twenty-one fold, dependent on both year and species. Throughout the 2004 growing season, the OCH3 pool and the release of CH3Cl and methanol (CH3OH) from leaves of ash and Norway maple were monitored on heating to 350°C. The amounts of CH3Cl released increased linearly as leaf chlorine accumulated whereas emissions of CH3OH did not substantially change. Conversion of chlorine to CH3Cl was lower in the spring than during the summer and autumnal senescence period, ranging from 22 to 58%. No correlation was found between leaf OCH3 content and either CH3Cl or CH3OH release. The percentage conversion of OCH3 to the summed concentrations of CH3OH and CH3Cl ranged from 41 to 66%. The plant components pectin and lignin were identified as two major sources of the CH3 group in CH3Cl and CH3OH and emissions ceased when the OCH3 pool contributing the methyl moiety was exhausted (>350°C). These findings have implications for estimation of CH3Cl release during biomass burning and for our understanding of chlorine volatilisation during energy production from biomass.
DNA barcoding Australian macroinvertebrates for monitoring programs: benefits and current short comings
Authors: Shackleton Michael , Rees Gavin N.
Published: July 2015

Identification of macroinvertebrates is a key component of monitoring programs that seek to understand the condition of aquatic environments. Classical identification approaches underpin such programs, but molecular approaches are gaining recognition as valuable ways to identify organisms for research and monitoring programs. We applied DNA barcoding data to specimens collected as part of monitoring programs in the Murray–Darling Basin, to investigate the possible informational benefits these data may provide. We also tested the performances of two online DNA databases in assigning taxon names to our sequence data. We found that relying on the online databases to determine species identifications was currently problematic for the Australian freshwater fauna because of a lack of available sequence data. However, we also found that collecting and applying barcode data to our monitoring programs gave considerable informational benefits by providing greater resolution of specimen identity, highlighting the presence of potential cryptic species, providing information on larval and adult associations, demonstrating instances where misidentification had occurred though classical approaches, and providing conformation of the performance of diagnostic characters currently used in keys to determine species identities.
100 Years of superphosphate addition to pasture in an acid soil—current nutrient status and future management
Authors: Schefe Cassandra R. , Barlow Kirsten M. , Robinson Nathan J. , Crawford Douglas M. , McLaren Timothy I. , Smernik Ronald J. , Croatto George , Walsh Ronald D. , Kitching Matt
Published: July 2015

Pasture-based animal production systems, which occupy a significant proportion of the landscape in Victoria, Australia, have historically been nutrient-limited, with phosphorus (P) often the most limiting nutrient. The Permanent Top-Dressed (PTD) pasture experiment was established in 1914 at the Rutherglen Research Station, Victoria, to investigate the management of this deficiency. The main objective of the PTD experiment was to demonstrate the value of adding P fertiliser at two rates to increase pasture productivity for lamb and wool production. We report on the status of the PTD soils after 100 years, investigating the long-term implications of continuous grazing and fertiliser management (0, 125 and 250 kg/ha of superphosphate every second year) of non-disturbed pasture. We investigated the long-term effects of P fertiliser on the forms and distribution of P and other relevant soil parameters. In the fertilised treatments, P has accumulated in the surface soils (0–10 cm) as both orthophosphate and organic P, with an Olsen P of 16–21 mg P/kg, which is non-limiting for pasture production. In the treatment with 250 kg superphosphate, there has also been movement of P down through the soil profile, probably due to the high sand content of the surface soil and the transfer through the profile of small quantities of water-soluble P and P bound to organic ligands. Over time, the site has continued to acidify (surface 0–10 cm); the soil acidity combined with aluminium (Al) concentrations in the fertilised treatments approach a level that should impact on production and where broadcast lime would be recommended. After 100 years of non-disturbed pasture, the surface soils of these systems would be in a state of quasi-equilibrium, in which the fertilised systems have high levels of carbon (C), nitrogen, P and exchangeable Al. The continued stability of this system is likely dependent upon maintaining the high C status, which is important to nutrient cycling and the prevention of Al phytotoxicity. There are two risks to this system: (i) the declining pH; and (ii) soil disturbance, which may disrupt the equilibrium of these soils and the bio-chemical processes that maintain it.
Human–wildlife interactions in urban areas: a review of conflicts, benefits and opportunities
Authors: Soulsbury Carl D. , White Piran C. L.
Published: July 2015

Wildlife has existed in urban areas since records began. However, the discipline of urban ecology is relatively new and one that is undergoing rapid growth. All wildlife in urban areas will interact with humans to some degree. With rates of urbanisation increasing globally, there is a pressing need to understand the type and nature of human–wildlife interactions within urban environments, to help manage, mitigate or even promote these interactions. Much research attention has focussed on the core topic of human–wildlife conflict. This inherent bias in the literature is probably driven by the ease with which it can be quantified and assessed. Human–wildlife conflicts in terms of disease transmission, physical attack and property damage are important topics to understand. Equally, the benefits of human–wildlife interactions are becoming increasingly recognised, despite being harder to quantify and generalise. Wildlife may contribute to the provision of ecosystem services in urban areas, and some recent work has shown how interactions with wildlife can provide a range of benefits to health and wellbeing. More research is needed to improve understanding in this area, requiring wildlife biologists to work with other disciplines including economics, public health, sociology, ethics, psychology and planning. There will always be a need to control wildlife populations in certain urban situations to reduce human–wildlife conflict. However, in an increasingly urbanised and resource-constrained world, we need to learn how to manage the risks from wildlife in new ways, and to understand how to maximise the diverse benefits that living with wildlife can bring.
Distinct roles for GABA across multiple timescales in mammalian circadian timekeeping
Authors: DeWoskin Daniel , Myung Jihwan , Belle Mino D. C. , Piggins Hugh D. , Takumi Toru , Forger Daniel B.
Published: July 2015

Significance

Each day, over 50 billion synaptic signals, mediated by the neurotransmitter GABA, are sent between neurons in the central circadian pacemaker in the mammalian brain to time and coordinate daily events. Although GABA is the only signaling molecule sent and received by most, if not all of these neurons, its role is not well understood. Past studies have shown paradoxically that GABA can synchronize and desynchronize, as well as excite and inhibit, clock neurons. Through experiments and modeling characterizing the role of GABA in timekeeping, we propose the existence of two types of differentially regulated GABA signaling—fast signaling that regulates neuronal output, and slow signaling that modulates synchrony between neurons—a hypothesis that can explain many previous experimental results.
Delicate conformational balance of the redox enzyme cytochrome P450cam
Authors: Skinner Simon P. , Liu Wei-Min , Hiruma Yoshitaka , Timmer Monika , Blok Anneloes , Hass Mathias A. S. , Ubbink Marcellus
Published: July 2015

Significance

The ubiquitous enzymes called cytochromes P450 catalyze a broad range of chemical reactions using molecular oxygen. For example, in humans, these enzymes are involved in breakdown of foreign compounds, including drugs. The bacterial cytochrome P450cam is thought to open up to allow substrate to enter the active site, and then to close during catalysis to keep reactive intermediates inside. Surprisingly, recent crystal structures suggested that the enzyme is open during the reaction. We have studied the enzyme in solution using paramagnetic NMR spectroscopy, demonstrating that, in fact, the enzyme is closed. This finding indicates that the subtle balance between open and closed is affected by crystallization, which can lead to the wrong conclusions about the protein dynamics.
Structural characterization of the interaction of Ubp6 with the 26S proteasome
Authors: Aufderheide Antje , Beck Florian , Stengel Florian , Hartwig Michaela , Schweitzer Andreas , Pfeifer Günter , Goldberg Alfred L. , Sakata Eri , Baumeister Wolfgang , Förster Friedrich
Published: July 2015

Significance

In eukaryotic cells the 26S proteasome is responsible for the regulated degradation of intracellular proteins. The function of this large macromolecular machine is regulated by many cofactors, most notably the deubiquitylating enzyme ubiquitin C-terminal hydrolase 6 (Ubp6). Here, we investigate the structure of Ubp6 bound to the 26S proteasome and explore its influence on the conformational landscape of the 26S proteasome. Our structure reveals that Ubp6’s active site may contribute to a large composite active site, also formed by the mouth of the proteasomal ATPase ring and the active site of deubiquitylating enzyme regulatory particle non-ATPase 11. Moreover, Ubp6 modulates the conformational landscape of the proteasome, favoring an intermediate state, which may explain the effects of Ubp6 on proteasomal degradation.
Are you happy yet? Entrepreneurs’ subjective well-being
Authors: Sherman Cynthia L. , Randall Craig , Kauanui Sandra K.
Published: July 2015

This study examines the relationship between entrepreneurs’ subjective well-being and flow, productivity, and intrinsically-based success or extrinsically-based success. Subjective well-being and flow have been studied in educational, health, and work environments; however, only
recently has the Global Entrepreneurship Monitor 2013 examined well-being of entrepreneurs. In entrepreneurs it is particularly important because understanding the relationship between subjective well-being (happiness), and the factors of flow, productivity, and definition of success can influence
entrepreneurial decision-making and overall firm performance. A survey of 191 entrepreneurs in Florida and California was used to collect data that was then analyzed using factor analysis, correlation, and regression. Entrepreneurial well-being was shown to increase with the presence of flow,
intrinsic definitions of success, and productivity in entrepreneurs. Extrinsic factors that entrepreneurs use to define success, however, were negatively linked to well-being.
THE HCN/HNC ABUNDANCE RATIO TOWARD DIFFERENT EVOLUTIONARY PHASES OF MASSIVE STAR FORMATION
Authors: Jin Miwha , Lee Jeong-Eun , Kim Kee-Tae
Published: July 2015

Using the H13CN and HN13C J = 1–0 line observations, the abundance ratio of HCN/HNC has been estimated for different evolutionary stages of massive star formation: infrared dark clouds (IRDCs), high-mass protostellar objects (HMPOs), and ultracompact H ii regions (UCH iis). IRDCs were divided into “quiescent IRDC cores (qIRDCc)” and “active IRDC cores (aIRDCc),” depending on star formation activity. The HCN/HNC ratio is known to be higher at active and high temperature regions related to ongoing star formation, compared to cold and quiescent regions. Our observations toward 8 qIRDCc, 16 aIRDCc, 23 HMPOs, and 31 UCH iis show consistent results; the ratio is 0.97 (±0.10), 2.65 (±0.88), 4.17 (±1.03), and 8.96 (±3.32) in these respective evolutionary stages, increasing from qIRDCc to UCH iis. The change of the HCN/HNC abundance ratio, therefore, seems directly associated with the evolutionary stages of star formation, which have different temperatures. One suggested explanation for this trend is the conversion of HNC to HCN, which occurs effectively at higher temperatures. To test the explanation, we performed a simple chemical model calculation. In order to fit the observed results, the energy barrier of the conversion must be much lower than the value provided by theoretical calculations.
Integrating full spectrum of sequence features into predicting functional microRNA–mRNA interactions
Authors: Wang Zixing , Xu Wenlong , Liu Yin
Published: July 2015

Motivation: MicroRNAs (miRNAs) play important roles in general biological processes and diseases pathogenesis. Identifying miRNA target genes is an essential step to fully understand the regulatory effects of miRNAs. Many computational methods based on the sequence complementary rules and the miRNA and mRNA expression profiles have been developed for this purpose. It is noted that there have been many sequence features of miRNA targets available, including the context features of the target sites, the thermodynamic stability and the accessibility energy for miRNA-mRNA interaction. However, most of current computational methods that combine sequence and expression information do not effectively integrate full spectrum of these features; instead, they perceive putative miRNA–mRNA interactions from sequence-based prediction as equally meaningful. Therefore, these sequence features have not been fully utilized for improving miRNA target prediction.

Results: We propose a novel regularized regression approach that is based on the adaptive Lasso procedure for detecting functional miRNA–mRNA interactions. Our method fully takes into account the gene sequence features and the miRNA and mRNA expression profiles. Given a set of sequence features for each putative miRNA–mRNA interaction and their expression values, our model quantifies the down-regulation effect of each miRNA on its targets while simultaneously estimating the contribution of each sequence feature to predicting functional miRNA–mRNA interactions. By applying our model to the expression datasets from two cancer studies, we have demonstrated our prediction results have achieved better sensitivity and specificity and are more biologically meaningful compared with those based on other methods.

Availability and implementation: The source code is available at: http://nba.uth.tmc.edu/homepage/liu/miRNALasso.

Supplementary information:  Supplementary data are available at Bioinformatics online.

Contact:  Yin.Liu@uth.tmc.edu
Inference of Markovian properties of molecular sequences from NGS data and applications to comparative genomics
Authors: Ren Jie , Song Kai , Deng Minghua , Reinert Gesine , Cannon Charles H. , Sun Fengzhu
Published: July 2015

Motivation: Next-generation sequencing (NGS) technologies generate large amounts of short read data for many different organisms. The fact that NGS reads are generally short makes it challenging to assemble the reads and reconstruct the original genome sequence. For clustering genomes using such NGS data, word-count based alignment-free sequence comparison is a promising approach, but for this approach, the underlying expected word counts are essential.

A plausible model for this underlying distribution of word counts is given through modeling the DNA sequence as a Markov chain (MC). For single long sequences, efficient statistics are available to estimate the order of MCs and the transition probability matrix for the sequences. As NGS data do not provide a single long sequence, inference methods on Markovian properties of sequences based on single long sequences cannot be directly used for NGS short read data.

Results: Here we derive a normal approximation for such word counts. We also show that the traditional Chi-square statistic has an approximate gamma distribution, using the Lander-Waterman model for physical mapping. We propose several methods to estimate the order of the MC based on NGS reads and evaluate those using simulations. We illustrate the applications of our results by clustering genomic sequences of several vertebrate and tree species based on NGS reads using alignment-free sequence dissimilarity measures. We find that the estimated order of the MC has a considerable effect on the clustering results, and that the clustering results that use an MC of the estimated order give a plausible clustering of the species.

Availability and implementation: Our implementation of the statistics developed here is available as R package ‘NGS.MC’ at http://www-rcf.usc.edu/∼fsun/Programs/NGS-MC/NGS-MC.html.

Contact:  fsun@usc.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Differences Between New Immigrants From the Former Soviet Union and Veteran Residents in Knowledge, Perception, and Risk Factors of Stroke
Authors: Melnikov Semyon , Itzhaki Michal , Koton Silvia
Published: July 2015

Background:

Stroke is the fourth most common cause of death in developed countries and a leading cause of acquired disability in adults. Awareness of risk factors and warning signs for stroke has a considerable impact on early arrival at the hospital and early thrombolytic treatment. Delays in seeking medical treatment following the onset of stroke symptoms have been shown to be more common among ethnic minorities.

Objective:

The aim of the current study was to examine stroke awareness and knowledge among new immigrants from the Former Soviet Union (IFSUs) compared with veteran residents (VRs).

Methods:

The study was conducted by students of the nursing master of arts program. Data were collected during March 2010 and June 2014. Trained registered nurses conducted interviews, using a structured, pretested, open-ended questionnaire. Participants were recruited by a snowball method from among the interviewers’ friends and family members, 40 years or older with no history of stroke.

Results:

A total of 643 Israelis, 420 VRs (65.3%) and 223 IFSUs (34.7%), were interviewed; 40.7% were men, with a mean age of 52.6 (SD, 9.3) years. Compared with VRs, IFSUs were more likely to report previous myocardial infarction (P = .022), hypertension (P < .001), and diabetes (P = .012). The mean number of stroke warning signs reported by IFSUs was higher than that reported by VRs (P = .031). When asked about risk factors for stroke, IFSUs more often stated hypertension (P = .03), whereas VRs more often reported family history (P = .03). Immigrants from the Former Soviet Union were more aware of strategies for the prevention of stroke than VRs (P = .02). The preferred sources of information about stroke for IFSUs, as distinguished from VRs, were personal doctors (P = .001) and radio programs (P = .03).

Conclusions:

Veteran residents showed lower levels of knowledge about stroke. Educational campaigns aimed at increasing knowledge of stroke among Israel’s general population in Israel, as well as culturally targeting specific subgroups, are recommended.
Control of vortex rings for manoeuvrability
Authors: Gemmell Brad J. , Troolin Daniel R. , Costello John H. , Colin Sean P. , Satterlie Richard A.
Published: July 2015

Manoeuvrability is critical to the success of many species. Selective forces acting over millions of years have resulted in a range of capabilities currently unmatched by machines. Thus, understanding animal control of fluids for manoeuvring has both biological and engineering applications. Within inertial fluid regimes, propulsion involves the formation and interaction of vortices to generate thrust. We use both volumetric and planar imaging techniques to quantify how jellyfish (Aurelia aurita) modulate vortex rings during turning behaviour. Our results show that these animals distort individual vortex rings during turns to alter the force balance across the animal, primarily through kinematic modulation of the bell margin. We find that only a portion of the vortex ring separates from the body during turns, which may increase torque. Using a fluorescent actin staining method, we demonstrate the presence of radial muscle fibres lining the bell along the margin. The presence of radial muscles provides a mechanistic explanation for the ability of scyphomedusae to alter their bell kinematics to generate non-symmetric thrust for manoeuvring. These results illustrate the advantage of combining imaging methods and provide new insights into the modulation and control of vorticity for low-speed animal manoeuvring.
An elementary model for autoignition of laminar jets
Authors: Gordon Peter V. , Gotti Daniel J. , Hegde Uday G. , Hicks Michael C. , Kulis Michael J. , Sivashinsky Gregory I.
Published: July 2015

In this paper, we formulate and analyse an elementary model for autoignition of cylindrical laminar jets of fuel injected into an oxidizing ambient at rest. This study is motivated by renewed interest in analysis of hydrothermal flames for which such configuration is common. As a result of our analysis, we obtain a sharp characterization of the autoignition position in terms of the principal physical and geometrical parameters of the problem.
Vibrating barrier: a novel device for the passive control of structures under ground motion
Authors: Cacciola P. , Tombari A.
Published: July 2015

A novel device, called vibrating barrier (ViBa), that aims to reduce the vibrations of adjacent structures subjected to ground motion waves is proposed. The ViBa is a structure buried in the soil and detached from surrounding buildings that is able to absorb a significant portion of the dynamic energy arising from the ground motion. The working principle exploits the dynamic interaction among vibrating structures due to the propagation of waves through the soil, namely the structure–soil–structure interaction. The underlying theoretical aspects of the novel control strategy are scrutinized along with its numerical modelling. Closed-form solutions are also derived to design the ViBa in the case of harmonic excitation. Numerical and experimental analyses are performed in order to investigate the efficiency of the device in mitigating the effects of ground motion waves on the structural response. A significant reduction in the maximum structural acceleration of 87% has been achieved experimentally.
Shape control of slack space reflectors using modulated solar pressure
Authors: Borggräfe Andreas , Heiligers Jeannette , Ceriotti Matteo , McInnes Colin R.
Published: July 2015

The static deflection profile of a large spin-stabilized space reflector because of solar radiation pressure acting on its surface is investigated. Such a spacecraft consists of a thin reflective circular film, which is deployed from a supporting hoop structure in an untensioned, slack manner. This paper investigates the use of a variable reflectivity distribution across the surface to control the solar pressure force and hence the deflected shape. In this first analysis, the film material is modelled as one-dimensional slack radial strings with no resistance to bending or transverse shear, which enables a semi-analytic derivation of the nominal deflection profile. An inverse method is then used to find the reflectivity distribution that generates a specific, for example, parabolic deflection shape of the strings. Applying these results to a parabolic reflector, short focal distances can be obtained when large slack lengths of the film are employed. The development of such optically controlled reflector films enables future key mission applications such as solar power collection, radio-frequency antennae and optical telescopes.
Maximizing negative thermal expansion via rigid unit modes: a geometry-based approach
Authors: Grima J. N. , Bajada M. , Scerri S. , Attard D. , Dudek K. K. , Gatt R.
Published: July 2015

Existent rigid unit mode (RUM) models based on rotating squares, which may explain the phenomenon of negative thermal expansion (NTE), are generalized so as to assess the NTE potential for novel systems made from rectangular or rhombic rigid units. Analytical models for the area coefficients of thermal expansion (CTE) of these innovative networks are derived in an attempt to determine the optimal geometrical parameters and connectivity for maximum NTE. It was found that all systems exhibit NTE, the extent of which is determined by the shape and connectivity of the elemental rigid units (side lengths ratio or internal angle). It was also found that some of the networks proposed here should exhibit significantly superior NTE properties when compared with the well-known network of squares, and that for optimal NTE characteristics, pencil-like rigid units should be used rather than square-shaped ones, as these permit larger pore sizes that are more conducive to NTE. All this compliments earlier work on the negative Poisson's ratio (auxetic) potential of such systems and may provide a route for the design of new materials exhibiting superior thermo-mechanical characteristics including specifically tailored CTEs or giant NTE characteristics.
Reclassification of Actinobacillus muris as Muribacter muris gen. nov., comb. nov.
Authors: Nicklas Werner , Bisgaard Magne , Aalbæk Bent , Kuhnert Peter , Christensen Henrik
Published: July 2015

To reinvestigate the taxonomy of [Actinobacillus] muris, 474 strains, mainly from mice and rats, were characterized by phenotype and 130 strains selected for genotypic characterization by 16S rRNA and partial rpoB gene sequencing. The type strain was further investigated by whole-genome sequencing. Phylogenetic analysis of the DNA sequences showed one monophyletic group with intragroup similarities of 96.7 and 97.2 % for the 16S rRNA and rpoB genes, respectively. The highest 16S rRNA gene sequence similarity to a taxon with a validly published name outside the group was 95.9 %, to the type strain of [Pasteurella] pneumotropica. The closest related taxon based on rpoB sequence comparison was ‘Haemophilus influenzae-murium’, with 88.4 % similarity. A new genus and a new combination, Muribacter muris gen. nov., comb. nov., are proposed based on a distinct phylogenetic position based on 16S rRNA and rpoB gene sequence comparisons, with major divergence from the existing genera of the family Pasteurellaceae. The new genus has the characteristics of [A.] muris with the emendation that acid formation from ( − )-d-mannitol and hydrolysis of aesculin are variable, while the α-glucosidase test is positive. There is no requirement for exogenously supplied NAD (V factor) for the majority of strains investigated; however, one strain was found to require NAD. The major fatty acids of the type strain of Muribacter muris were C14 : 0, C14 : 0 3-OH/iso-C16 : 1 I, C16 : 1ω7c and C16 : 0, which is in line with most genera of the Pasteurellaceae. The type strain of Muribacter muris is CCUG 16938T ( = NCTC 12432T = ATCC 49577T).
Pantoea intestinalis sp. nov., isolated from the human gut
Authors: Prakash Om , Nimonkar Yogesh , Vaishampayan Ankita , Mishra Mrinal , Kumbhare Shreyas , Josef Neetha , Shouche Yogesh S.
Published: July 2015

A novel bacterial strain, 29Y89BT, was isolated from a faecal sample of a healthy human subject. Cells were Gram-stain-negative, motile, non-spore-forming and rod-shaped. Strain 29Y89BT formed cream-coloured colonies 2 mm in diameter on trypticase soy agar and showed optimum growth at 35 °C. Strain 29Y89BT showed highest 16S rRNA gene sequence similarity to Pantoea gaviniae A18/07T (98.4 %) followed by Pantoea calida 1400/07T (97.2 %). Multi-locus sequence analysis using atpD (ATP synthase β subunit), gyrB (DNA gyrase), infB (initiation translation factor 2) and rpoB (RNA polymerase β subunit) genes also supported the result of 16S rRNA gene sequence based phylogeny. Strain 29Y89BT showed 62 and 40.7 % DNA–DNA relatedness with P. calida DSM 22759T and P. gaviniae DSM 22758T. Strain 29Y89BT contained C17 
: 0 cyclo, C19 
: 0 cyclo ω8c, C16 : 0, C14 : 0 and C12 : 0 as predominant fatty acids. In addition, strain 29Y89BT showed physiological and phenotypic differences from its closest relatives P. gaviniae DSM 22758T and P. calida DSM 22759T. The polar lipid profile mainly comprised phospholipids. The DNA G+C content was 59.1 mol%. Thus, based on the findings of the current study, strain 29Y89BT showed clear delineations from its closest relatives P. gaviniae DSM 22758T and P. calida DSM 22759T, and is thus considered to represent a novel species of the genus Pantoea, for which the name Pantoea intestinalis sp. nov. is proposed. The type strain is 29Y89BT ( = DSM 28113T = MCC 2554T).
SARTools: a DESeq2- and edgeR-based R pipeline for comprehensive differential analysis of RNA-Seq data
Authors: Varet Hugo , Coppée Jean-Yves , Dillies Marie-Agnès
Published: July 2015

Background

Several R packages exist for the detection of differentially expressed genes from RNA-Seq data. The analysis process includes three main steps, namely normalization, dispersion estimation and test for differential expression. Quality control steps along this process are recommended but not mandatory, and failing to check the characteristics of the dataset may lead to spurious results. In addition, normalization methods and statistical models are not exchangeable across the packages without adequate transformations the users are often not aware of. Thus, dedicated analysis pipelines are needed to include systematic quality control steps and prevent errors from misusing the proposed methods.

Results

SARTools is an R pipeline for differential analysis of RNA-Seq count data. It can handle designs involving two or more conditions of a single biological factor with or without a blocking factor (such as a batch effect or a sample pairing). It is based on DESeq2 and edgeR and is composed of an R package and two R script templates (for DESeq2 and edgeR respectively). Tuning a small number of parameters and executing one of the R scripts, users have access to the full results of the analysis, including lists of differentially expressed genes and a HTML report that (i) displays diagnostic plots for quality control and model hypotheses checking and (ii) keeps track of the whole analysis process, parameter values and versions of the R packages used.

Conclusions

SARTools provides systematic quality controls of the dataset as well as diagnostic plots that help to tune the model parameters. It gives access to the main parameters of DESeq2 and edgeR and prevents untrained users from misusing some functionalities of both packages. By keeping track of all the parameters of the analysis process it fits the requirements of reproducible research.
Germline mutation rates and the long-term phenotypic effects of mutation accumulation in wild-type laboratory mice and mutator mice
Authors: Uchimura Arikuni , Higuchi Mayumi , Minakuchi Yohei , Ohno Mizuki , Toyoda Atsushi , Fujiyama Asao , Miura Ikuo , Wakana Shigeharu , Nishino Jo , Yagi Takeshi
Published: July 2015

The germline mutation rate is an important parameter that affects the amount of genetic variation and the rate of evolution. However, neither the rate of germline mutations in laboratory mice nor the biological significance of the mutation rate in mammalian populations is clear. Here we studied genome-wide mutation rates and the long-term effects of mutation accumulation on phenotype in more than 20 generations of wild-type C57BL/6 mice and mutator mice, which have high DNA replication error rates. We estimated the base-substitution mutation rate to be 5.4 × 10−9(95% confidence interval = 4.6 × 10−9–6.5 × 10−9) per nucleotide per generation in C57BL/6 laboratory mice, about half the rate reported in humans. The mutation rate in mutator mice was 17 times that in wild-type mice. Abnormal phenotypes were 4.1-fold more frequent in the mutator lines than in the wild-type lines. After several generations, the mutator mice reproduced at substantially lower rates than the controls, exhibiting low pregnancy rates, lower survival rates, and smaller litter sizes, and many of the breeding lines died out. These results provide fundamental information about mouse genetics and reveal the impact of germline mutation rates on phenotypes in a mammalian population.
Whole-Exome Enrichment with the Agilent SureSelect Human All Exon Platform
Authors: Chen Rui , Im Hogune , Snyder Michael
Published: July 2015

There are multiple platforms available for whole-exome enrichment and sequencing (WES). This protocol is based on the Agilent SureSelect Human All Exon platform, which targets ∼50 Mb of the human exonic regions. The SureSelect system uses ∼120-base RNA probes to capture known coding DNA sequences (CDS) from the NCBI Consensus CDS Database as well as other major RNA coding sequence databases, such as Sanger miRBase. The protocol can be performed at the benchside without the need for automation, and the resulting library can be used for targeted next-generation sequencing on an Illumina HiSeq 2000 sequencer.