bluuebunny/crossref_metadata_2025 huggingface dataset:
Transformation of divacancies to divacancy-oxygen pairs in p-type Czochralski-silicon; mechanism of divacancy diffusion
Authors: Ganagona N. , Vines L. , Monakhov E. V. , Svensson B. G.
Published: January 2014

In this work, a comprehensive study on the transition of divacancy (V2) to divacancy-oxygen (V2O) pairs in p-type silicon has been performed with deep level transient spectroscopy (DLTS). Czochralski grown, boron doped p-type, silicon samples, with a doping concentration of 2 × 1015 cm−3 and oxygen content of 7.0 ± 1.5 × 1017 cm−3, have been irradiated with 1.8 MeV protons. Isothermal annealing at temperatures in the range of 200 °C–300 °C shows a close to one-to-one correlation between the loss in the donor state of V2 and the formation of the donor state of V2O, located at 0.23 eV above the valence band edge. A concurrent transition takes place between the single acceptor states of V2 and V2O, as unveiled by injection of electrons through optical excitation during the trap filling sequence of the DLTS measurements. Applying the theory for diffusion limited reactions, the diffusivity of V2 in the studied p-type samples is determined to be (1.5 ± 0.7) × 10−3exp[−(1.31 ± 0.03) eV/kT] cm2/s, and this represents the neutral charge state of V2. Further, the data seem to favor a two-stage diffusion mechanism involving partial dissociation of V2, although a one-stage process cannot be fully excluded.
A low voltage submillisecond-response polymer network liquid crystal spatial light modulator
Authors: Sun Jie , Wu Shin-Tson , Haseba Yasuhiro
Published: January 2014

We report a low voltage and highly transparent polymer network liquid crystal (PNLC) with submillisecond response time. By employing a large dielectric anisotropy LC host JC-BP07N, we have lowered the V2π voltage to 23 V at λ = 514 nm. This will enable PNLC to be integrated with a high resolution liquid-crystal-on-silicon spatial light modulator, in which the maximum voltage is 24 V. A simple model correlating PNLC performance with its host LC is proposed and validated experimentally. By optimizing the domain size, we can achieve V2π < 15 V with some compromises in scattering and response time.
Study on electrical properties of metal/GaSb junctions using metal-GaSb alloys
Authors: Nishi Koichi , Yokoyama Masafumi , Kim Sanghyeon , Yokoyama Haruki , Takenaka Mitsuru , Takagi Shinichi
Published: January 2014

We study the metal-GaSb alloy formation, the structural properties and the electrical characteristics of the metal-alloy/GaSb diodes by employing metal materials such as Ni, Pd, Co, Ti, Al, and Ta, in order to clarify metals suitable for GaSb p-channel metal-oxide-semiconductor field-effect transistors (pMOSFETs) as metal-GaSb alloy source/drain (S/D). It is found that Ni, Pd, Co, and Ti can form alloy with GaSb by rapid thermal annealing at 250, 250, 350, and 450 °C, respectively. The Ni-GaSb and Pd-GaSb alloy formation temperature of 250 °C is lower than the conventional dopant activation annealing for ion implantation, which enable us to lower the process temperature. The alloy layers show lower sheet resistance (RSheet) than that of p+-GaSb layer formed by ion implantation and activation annealing. We also study the electrical characteristics of the metal-alloy/GaSb junctions. The alloy/n-GaSb contact has large Schottky barrier height (ϕB) for electrons, ∼0.6 eV, and low ϕB for holes, ∼0.2 eV, which enable us to realize high on/off ratio in pMOSFETs. We have found that the Ni-GaSb/GaSb Schottky junction shows the best electrical characteristics with ideal factor (n) of 1.1 and on-current/off-current ratio (Ion/Ioff) of ∼104 among the metal-GaSb alloy/GaSb junctions evaluated in the present study. These electrical properties are also superior to those of a p+-n diode fabricated by Be ion implantation with activation annealing at 350 °C. As a result, the Ni-GaSb alloy can be regarded as one of the best materials to realize metal S/D in GaSb pMOSFETs.
A fast and accurate model for forecasting wind speed and solar radiation time series based on extreme learning machines and principal components analysis
Authors: Bouzgou Hassen
Published: January 2014

Precise forecasting of renewable energies such as solar and wind is becoming one of the very important concerns in developing modern electrical grids. Hence, establishing appropriate tools of weather forecasting with satisfactory accuracy becomes an essential preoccupation in today's changing power world. In this paper, an approach based on Principal Component Analysis (PCA) and Extreme Learning Machines (ELM) is proposed for the forecasting of time series. The PCA maps the data into a smaller subspace in which the components accounts for as much of the variability in the input space as possible. The variables extracted by the PCA are then introduced to the extreme learning machines, a learning algorithm much faster than the traditional gradient-based learning algorithms. The experiments carried out on three time series lead to: (i) The PCA as variable selection method shows a positive impact on the accuracy of the forecasting process. (ii) ELM model is significantly faster than Multi-Layer Perceptron Network, Radial Basis Function Networks, and Least Squares Support Vector Machines, while preserving the same accuracy level.
Low temperature magnetic behaviour of glass-covered magnetic microwires with gradient nanocrystalline microstructure
Authors: Serrano I. G. , Hernando A. , Marín P.
Published: January 2014

Slow nanocrystallization driving dynamics can be affected by the combination of two factors: sample residual stresses and sample geometry. This effect is evidenced at the initial stages of nanocrystallization of amorphous CoFeSiBCuNb magnetic microwires. Transmission electron microscopy observations indicate how crystallization at temperatures between 730 and 780 K results in a graded microstructure where the crystallization at the surface skin of the microwire, which remains almost amorphous, differs from that of the middle, where elongated grains are observed, and inner regions. However, samples annealed at higher temperatures present a homogeneous microstructure. The effect of gradient microstructure on magnetic properties has been also analyzed and a loss of bistable magnetic behaviour at low temperatures, from that obtained in the amorphous and fully nanocrystallized sample, has been observed and ascribed to changes in sign of magnetostriction for measuring temperatures below 100 K.
A new metric of the low-mode asymmetry for ignition target designs
Authors: Gu Jianfa , Dai Zhensheng , Fan Zhengfeng , Zou Shiyang , Ye Wenhua , Pei Wenbing , Zhu Shaoping
Published: January 2014

In the deuterium-tritium inertial confinement fusion implosion experiments on the National Ignition Facility, the measured neutron yield and hot spot pressure are significantly lower than simulations. Understanding the underlying physics of the deficit is essential to achieving ignition. This paper investigates the low-mode areal density asymmetry in the main fuel of ignition capsule. It is shown that the areal density asymmetry breaks up the compressed shell and significantly reduces the conversion of implosion kinetic energy to hot spot internal energy, leading to the calculated hot spot pressure and neutron yield quite close to the experimental data. This indicates that the low-mode shell areal density asymmetry can explain part of the large discrepancy between simulations and experiments. Since only using the hot spot shape term could not adequately characterize the effects of the shell areal density asymmetry on implosion performance, a new metric of the low-mode asymmetry is developed to accurately measure the probability of ignition.
Conductivity scaling and thermoelectric properties of polyaniline hydrochloride
Authors: Limelette P. , Schmaltz B. , Brault D. , Gouineau M. , Autret-Lambert C. , Roger S. , Grimal V. , Tran Van F.
Published: January 2014

We report on the thermoelectric properties of the polyaniline hydrochloride as a function of the temperature. In order to stress the influences of both the synthesis and the samples preparation on the thermoelectric efficiency, we have systematically measured the electrical conductivity, the thermopower, and the thermal conductivity. We show that several parameters such as the polymerization temperature and the pressure used to compress powders are crucial in order to optimize the thermoelectric performance. The microscopic origins of the transport coefficients are also discussed. In particular, the overall dataset of the measured electrical conductivity is found to scale onto a master curve involving a unique microscopic length, which coincides with the total bond length of the repeating unit of the polymeric chain. We believe that the drawn conclusions can hold for most of the conducting polymers and are thus potentially generic.
Theoretical condition for transparency in mesoporous layered optical media: Application to switching of hygrochromic coatings
Authors: Deparis O. , Ghazzal M. N. , Simonis P. , Mouchet S. , Kebaili H. , de Coninck J. , Gaigneaux E. M. , Vigneron J. P.
Published: January 2014

Mesoporous Bragg stacks are able to change color upon infiltration or displacement of liquid compounds inside their porous structure. Reversible switching from transparency to coloration offers additional functionality. Based on Bruggeman's effective medium theory, we derive a transparency master equation, which is valid for bilayers of arbitrary host materials and pore-filling compounds. The transparency condition fixes pore volume fractions such that the effective refractive index is homogenized through the bilayer, hence, through arbitrary layered optical media built from this bilayer. This general concept is applied to the case of switching of hygrochromic coatings made of mesoporous mixed oxide Bragg stacks.
Enhancement of band-to-band tunneling in mono-layer transition metal dichalcogenides two-dimensional materials by vacancy defects
Authors: Jiang Xiang-Wei , Gong Jian , Xu Nuo , Li Shu-Shen , Zhang Jinfeng , Hao Yue , Wang Lin-Wang
Published: January 2014

The band-to-band tunneling of monolayer transition metal dichalcogenides nano-junction is investigated using atomistic ab initio quantum transport simulations. From the simulation, it is found that the transition metal vacancy defect in the two-dimensional MX2 (M = Mo,W; X = S,Se) band-to-band tunneling diode can dramatically boost the on-state current up to 10 times while maintaining the device sub-threshold swing. The performance enhancement mechanism is discussed in detail by examining partial density of states of the system. It is found that the transition metal vacancy induces band-gap states, which reduce the effective length of the tunneling transition region.
Dislocation engineering in SiGe on periodic and aperiodic Si(001) templates studied by fast scanning X-ray nanodiffraction
Authors: Mondiali Valeria , Bollani Monica , Cecchi Stefano , Richard Marie-Ingrid , Schülli Tobias , Chahine Gilbert , Chrastina Daniel
Published: January 2014

Fast-scanning X-ray nanodiffraction microscopy is used to directly visualize the misfit dislocation network in a SiGe film deposited on a pit-patterned Si substrate at the beginning of plastic relaxation. X-ray real-space diffracted intensity maps are compared to topographic atomic force microscopy images, in which crosshatch lines can be seen. The change in intensity distribution as a function of the incidence angle shows localized variations in strain within the SiGe film. These variations, which reflect the order imposed by the substrate pattern, are attributed to the presence of both bunches of misfit dislocations and defect-free regions.
Effect of Cr substitution on the magnetic and magnetic-transport properties of Fe2Mn1-xCrxSi alloys
Authors: Pal Lakhan , Gupta Sachin , Suresh K. G. , Nigam A. K.
Published: January 2014

Fe2Mn1-xCrxSi (x = 0, 0.1, and 0.2) alloys were investigated for their magnetic and transport properties in view of the expected half metallicity. It is found that Cr substitution suppresses the antiferromagnetic phase present in parent Fe2MnSi, which completely disappears for x = 0.2. Curie temperature of the alloys increases from 230 K to 299 K as x is increased from 0 to 0.2. The value of the Rhodes-Wohlfarth ratio indicates that the system shows iterant magnetism. Resistivity measurements also show absence of antiferromagnetic phase for x = 0.2. Resistivity data have been fitted by considering the electron-phonon and electron-magnon scattering contributions, which indicates the presence of half metallicity in these compounds. Temperature dependence of resistivity data shows magnetoresistance of −3% and −2.5% at Curie temperature with applied field of 50 kOe for x = 0.1 and 0.2, respectively.
Modulation of amplitude and latency of motor evoked potential by direction of transcranial magnetic stimulation
Authors: Sato Aya , Torii Tetsuya , Iwahashi Masakuni , Itoh Yuji , Iramina Keiji
Published: January 2014

The present study analyzed the effects of monophasic magnetic stimulation to the motor cortex. The effects of magnetic stimulation were evaluated by analyzing the motor evoked potentials (MEPs). The amplitude and latency of MEPs on the abductor pollicis brevis muscle were used to evaluate the effects of repetitive magnetic stimulation. A figure eight-shaped flat coil was used to stimulate the region over the primary motor cortex. The intensity of magnetic stimulation was 120% of the resting motor threshold, and the frequency of magnetic stimulation was 0.1 Hz. In addition, the direction of the current in the brain was posterior-anterior (PA) or anterior-posterior (AP). The latency of MEP was compared with PA and AP on initial magnetic stimulation. The results demonstrated that a stimulus in the AP direction increased the latency of the MEP by approximately 2.5 ms. MEP amplitude was also compared with PA and AP during 60 magnetic stimulations. The results showed that a stimulus in the PA direction gradually increased the amplitude of the MEP. However, a stimulus in the AP direction did not modulate the MEP amplitude. The average MEP amplitude induced from every 10 magnetic pulses was normalized by the average amplitude of the first 10 stimuli. These results demonstrated that the normalized MEP amplitude increased up to approximately 150%. In terms of pyramidal neuron indirect waves (I waves), magnetic stimulation inducing current flowing backward to the anterior preferentially elicited an I1 wave, and current flowing forward to the posterior elicited an I3 wave. It has been reported that the latency of the I3 wave is approximately 2.5 ms longer than the I1 wave elicitation, so the resulting difference in latency may be caused by this phenomenon. It has also been reported that there is no alteration of MEP amplitude at a frequency of 0.1 Hz. However, this study suggested that the modulation of MEP amplitude depends on stimulation strength and stimulation direction.
Radiation induced conductivity in space dielectric materials
Authors: Hanna R. , Paulmier T. , Molinie P. , Belhaj M. , Dirassen B. , Payan D. , Balcon N.
Published: January 2014

The radiation-induced conductivity of some polymers was described mainly in literature by a competition between ionization, trapping/detrapping, and recombination processes or by radiation assisted ageing mechanisms. Our aim is to revise the effect of the aforementioned mechanisms on the complex evolution of Teflon® FEP under space representative ionizing radiation. Through the definition of a new experimental protocol, revealing the effect of radiation dose and relaxation time, we have been able to demonstrate that the trapping/recombination model devised in this study agrees correctly with the observed experimental phenomenology at qualitative level and allows describing very well the evolution of radiation induced conductivity with irradiation time (or received radiation dose). According to this model, the complex behavior observed on Teflon® FEP may be basically ascribed to the competition between electron/hole pairs generation and recombination: electrons are deeply trapped and act as recombination centers for free holes. Relaxation effects have been characterized through successive irradiations steps and have been again well described with the defined model at qualitative level: recombination centers created by the irradiation induce long term alteration on the electric properties, especially the effective bulk conductivity. One-month relaxation does not allow a complete recovery of the material initial charging behavior.
Scaling behaviors for resistive memory switching in NiO nanowire devices
Authors: In Kim Sung , Ho Sa Young , Kim Joo-Hyung , Wook Chang Young , Kim Nanmee , Kim Heesang , Yoo Kyung-Hwa
Published: January 2014

We investigated scaling behaviors for NiO nanowire array devices with different nanowire diameters. Plots of the reset current and the third harmonic generation signal as a function of the on-state resistance (R0) show scaling behaviors for all devices, such as NiO film devices. However, the scaling exponents of NiO nanowire devices were different from those of NiO film devices, and hence the fractal dimension estimated from the scaling exponent was smaller for the NiO nanowire devices than for the NiO film devices. This decrease in the fractal dimension was attributed to the confinement of the conducting filaments within each nanowire.
Radio frequency identification and composite container technology demonstration for transporting logistics of wood biomass
Authors: Ranta T. , Föhr J. , Karttunen K. , Knutas A.
Published: January 2014

RFID (Radio Frequency Identification) technology is widely used in industry but thus far has almost no applications for energy biomass logistics. A demonstration study was performed to build a real-time Web-based tracking system, denoted as RfIDER that uses RFID to manage energy biomass logistics. In the demonstration study, the functionality of this system was evaluated and further developed. The demonstration involved trucks carrying both composite and metal interchangeable containers with RFID tags mounted on them. Also, the productivity of all work phases in the transportation chain was examined and the readability of the RFID tags was evaluated. The demonstration study revealed that the RfIDER system enables following containers in real time through the supply chain and both storing and reading information on individual containers reliably, such as biomass owner, origin, destination, content, and quality. The RFID tags' readability was better with composite than metal containers. Potential benefits of the system demonstrated are real-time nature and accuracy of the data gathered and an opportunity to allocate and classify said data on the basis of customer needs. Possible logistical advantages include greater efficiency of unloading operations at the energy plant via use of existing information stored in the system.
Infrared Photodissociation Spectroscopy of Ti+(CO2)2Ar and Ti+(CO2)n (n=3–7) Complexes
Authors: Xing Xiao-peng , Wang Guan-jun , Wang Cai-xia , Zhou Ming-fei
Published: January 2014

Ti+(CO2)2Ar and Ti+(CO2)n (n=3–7) complexes are produced by laser vaporization in a pulsed supersonic expansion. The ion complexes of interest are each mass-selected in a time-of-flight spectrometer, and studied with infrared photodissociation spectroscopy. For each complex, a sharp band in the CO stretching frequency region is observed, which confirms the formation of the OTi+CO(CO2)n−1 oxide-carbonyl species. Small OTi+CO(CO2)n−1 complexes (n≤5) exhibit CO stretching and antisymmetric CO2 stretching vibrational bands that are blue-shifted from those of free CO and CO2. The experimental observations indicate that the coordination number of CO and CO2 molecules around TiO+ is five. Evidence is also observed for the presence of another electrostatic bonding Ti+(CO2)2 structural isomer for the Ti+(CO2)2Ar complex, which is characterized to have a bent OCO-Ti+-OCO structure stabilized by argon coordination.
Thermal-induced Unfolding of β-Crystallin and Disassembly of its Oligomers Revealed by Temperature-Jump Time-Resolved Infrared Spectroscopy
Authors: Li Shan-shan , Yu Ying-ying , Li De-yong , He Xiao-chuan , Bao Yong-zhen , Weng Yu-xiang
Published: January 2014

β-Crystallins are the major structural proteins existing in the vertebrate lens, and their conformational stability is critical in maintaining the life-long transparency and refraction index of the lens. Seven subunits of β-crystallins naturally assemble into various heterogeneous oligomers with different sizes. Here, we systematically investigated the thermal stability of the different secondary structures present in β-crystallins and then the dynamic process for the thermal-induced unfolding of β-crystallins by Fourier transform infrared spectroscopy-monitored thermal titration and temperature-jump nanosecond time-resolved IR difference absorbance spectra. Our results show that the N-terminal anti-parallel β-sheets in β-crystallin are the most unstable with a transition midpoint temperature at 36.0±2.1 °C, leading to the formation of an intermediate consisting vastly of random coil structures. This intermediate structure is temporally assigned to that of the monomer generated by the thermal-induced disassembly of β-crystallin oligomers with a transition midpoint temperature of 40.4±0.7 °C. The global unfolding of β-crystallins that leads to denaturation and aggregation indicated by the formation of intermolecular anti-parallel β-sheets has a transition midpoint temperature determined as 72.4±0.2 °C. Temperature-jump time-resolved IR absorbance difference spectroscopy analysis further reveals that thermal-induced unfolding of β-crystallins occurs firstly in the anti-parallel β-sheets in the N-terminal domains with a time constant of 50 ns.
Bacterial Enzyme Responsive Polymersomes: A Closer Look at the Degradation Mechanism of PEG-block-PLA Vesicles
Authors: Tücking Katrin-Stephanie , Handschuh-Wang Stephan , Schönherr Holger
Published: January 2014

Stimuli-responsive polymersomes that are selectively cleaved by enzymes of pathogenic bacteria are herein reported. The local disruption of the polyester wall in poly(ethylene glycol)-block-poly(lactic acid) (PEG-b-PLA) polymersomes filled with reporter dyes owing to enzymatic degradation by proteinase K was monitored by fluorescence lifetime imaging microscopy. Capsule opening occurred on timescales of minutes to hours, leading to the release of the dye, followed by a slow capsule disintegration, and finally cleavage into monomeric lactic acid over several weeks. These nanocontainers represent a promising element in novel theranostic systems for potential application in advanced wound dressings.
The Synthesis of Enantiopure α-Fluoro and α,α-Difluoro-β3-Arginine Derivatives
Authors: March Taryn L. , Freemont Jamie A. , Dumsday Geoff , Johnston Martin R. , Duggan Peter J.
Published: January 2014

The synthesis of a set of monofluorinated, difluorinated, and non-fluorinated N-acetylated-β3-arginine esters, potential inhibitors of trypsin-like proteases, is described. Elaboration to the target compounds from previously reported enantiopure precursors derived from 3-hydroxypropanal involved 6–7 steps and was achieved in 48–65 % overall yield. The α,α-difluoro-β3-arginine derivative was found to be particularly prone to hydrolysis. Three β3-arginine derivatives were tested for their ability to inhibit trypsin, the α,α-difluoro compound being assayed in the form of a carboxylate zwitterion.
Characterisation of locoweeds and their effect on livestock production in the western rangelands of China: a review
Authors: Lu Hao , Cao Dan Dan , Ma Feng , Wang Shan Shan , Yang Xiao Wen , Wang Wen Long , Zhou Qi Wu , Zhao Bao Yu
Published: January 2014

The rangelands of China are an important resource for livestock production, and play a strategic role in maintaining ecosystems and protecting the living environment of humans. Drought, overgrazing, infrastructure development, insufficient investment and poor management of rangelands have led to the invasion and spread of poisonous weeds in these rangelands in recent years. The rapid spread of poisonous weeds over the last few decades have caused a series of ecological problems, including a decrease in biological diversity and consequent desertification, and they are seriously affecting the ecological balance of rangelands, and the sustainable livestock production. Locoweeds, which belong to the genera Oxytropis and Astragalus, are an important species of poisonous legumes in the western rangelands of China, causing large economic losses. This review summarises the species and their ecological distribution, the toxic ingredients, the poisoning mechanism of locoweeds and damage control techniques for locoweeds. It attempts to highlight certain issues relating to research on locoweeds and how they are being tackled in order to understand the significance of locoweeds in preserving ecosystem diversity and the steps that require to be taken to control the spread of locoweeds in the western natural rangeland of China.
ChREBP, a glucose-responsive transcriptional factor, enhances glucose metabolism to support biosynthesis in human cytomegalovirus-infected cells
Authors: Yu Yongjun , Maguire Tobi G. , Alwine James C.
Published: January 2014

Significance

Human cytomegalovirus (HCMV)-infected cells and tumor cells produce similar alterations in glucose metabolism, including increasing glucose uptake and glycolysis and redirecting glucose carbon to support synthesis of biomolecules. We show that HCMV infection induces the glucose-responsive transcriptional factor carbohydrate-response element binding protein to reprogram glucose metabolism to support lipid and nucleotide synthesis. This study provides insight into viral mechanisms of pathogenesis.
Acoustic droplet vaporization is initiated by superharmonic focusing
Authors: Shpak Oleksandr , Verweij Martin , Vos Hendrik J. , de Jong Nico , Lohse Detlef , Versluis Michel
Published: January 2014

Significance

This work explains the long-standing puzzle of the physical mechanisms underlying acoustic droplet vaporization (ADV). ADV makes use of low-boiling-point perfluorocarbon droplets that become metastable once injected into the body, where they can be activated by high-intensity ultrasound. How ultrasound can physically trigger the vaporization remained elusive, also given the large mismatch between the ultrasound wavelength and the droplet size. Here we show that vaporization is preceded by nonlinear propagation of the ultrasound wave generating superharmonics. These high-frequency waves focus efficiently within the droplet, triggering vaporization. ADV shows great potential for advanced medical diagnosis and therapy. Our new understanding allows for further reduction of the required pressure amplitudes, thereby minimizing the adverse effects on healthy tissue.
China’s international trade and air pollution in the United States
Authors: Lin Jintai , Pan Da , Davis Steven J. , Zhang Qiang , He Kebin , Wang Can , Streets David G. , Wuebbles Donald J. , Guan Dabo
Published: January 2014

Significance

International trade affects global air pollution and transport by redistributing emissions related to production of goods and services and by potentially altering the total amount of global emissions. Here we analyze the trade influences by combining an economic-emission analysis on China’s bilateral trade and atmospheric chemical transport modeling. Our focused analysis on US air quality shows that Chinese air pollution related to production for exports contributes, at a maximum on a daily basis, 12–24% of sulfate pollution over the western United States. The US outsourcing of manufacturing to China might have reduced air quality in the western United States with an improvement in the east, due to the combined effects of changes in emissions and atmospheric transport.
Self-replicating colloidal clusters
Authors: Zeravcic Zorana , Brenner Michael P.
Published: January 2014

Significance

One of the hallmarks of living systems is self-replication. Mimicking nature’s ability to self-replicate would not only give more insight into biological mechanisms of self-replication but also could potentially revolutionize material science and nanotechnology. Over the past 60 y, much research, both theoretical and experimental, has been focused on understanding and realizing self-replicating systems. However, artificial systems that efficiently self-replicate remained elusive. In this paper, we construct schemes for self-replication of small clusters of isotropic particles. By manipulating the energy landscape of the process, we show how exponential replication can be achieved. As a proof of principle, we show exponential self-replication of an octahedral cluster using finite-temperature computer simulations.
Chiral symmetry breaking and surface faceting in chromonic liquid crystal droplets with giant elastic anisotropy
Authors: Jeong Joonwoo , Davidson Zoey S. , Collings Peter J. , Lubensky Tom C. , Yodh A. G.
Published: January 2014

Significance

Lyotropic chronomic liquid crystals (LCLCs) are water-based systems consisting of planar molecules that form aligned stacks in the nematic phase that develop two-dimensional crystalline order upon cooling to the columnar phase. They are characterized by an unusually small resistance to twist distortions. This work explores the interplay of giant elastic anisotropy and geometrical frustration imposed by boundary conditions in droplets, demonstrating, in particular, spontaneous formation in the nematic phase of chiral patterns from achiral building blocks and of central line defects and surface faceting in the columnar phase. Because LCLCs are water-loving, these findings about the combined effects of anisotropic elasticity, confinement, and frustration take steps toward tapping applications for liquid crystals in aqueous environments.
Artificial riboswitches for gene expression and replication control of DNA and RNA viruses
Authors: Ketzer Patrick , Kaufmann Johanna K. , Engelhardt Sarah , Bossow Sascha , von Kalle Christof , Hartig Jörg S. , Ungerechts Guy , Nettelbeck Dirk M.
Published: January 2014

Significance

Riboswitches are short RNA sequences for ligand-dependent modulation of gene expression
in cis
. This study demonstrates that an artificial riboswitch, a ligand-dependent self-cleaving ribozyme (aptazyme), can knockdown expression of an adeno- (DNA) virus early and a measles (RNA) virus structural gene, impacting biological outcomes, i.e. inhibiting viral genome replication and infectivity, respectively. It is the first report of riboswitches for replication control of human-pathogenic viruses and of their function in fully cytoplasmic (virus) systems. For future applications, aptazymes can be customized in other viruses facilitating analyses of viral gene functions or as a safety switch in oncolytic viruses. Because of their small size and RNA-intrinsic activity, we propose aptazymes as an alternative for inducible promoters in eukaryotic gene expression control.
Essential role of poly(ADP-ribosyl)ation in cocaine action
Authors: Scobie Kimberly N. , Damez-Werno Diane , Sun HaoSheng , Shao NingYi , Gancarz Amy , Panganiban Clarisse H. , Dias Caroline , Koo JaWook , Caiafa Paola , Kaufman Lewis , Neve Rachael L. , Dietz David M. , Shen Li , Nestler Eric J.
Published: January 2014

Significance

We demonstrate that chronic cocaine, including cocaine self-administration, induces poly(ADP-ribose) polymerase-1 (PARP-1) in the nucleus accumbens (NAc). Using a combination of viral-mediated gene transfer and pharmacological tools, we show that upregulation of PARP-1 in NAc dramatically enhances behavioral responses to cocaine, whereas downregulation of PARP-1 has the opposite effect. We used chromatin immunoprecipitation sequencing to map genome-wide binding of PARP-1 in NAc. The data demonstrate upregulation of PARP-1 binding across the genome after cocaine administration and identify numerous target genes for PARP-1. Among these is sidekick-1 (SDK1), previously implicated in regulating synaptic connections during development. We confirm SDK1 induction in NAc after chronic cocaine and demonstrate its ability to promote both cocaine’s behavioral effects and induction of dendritic plasticity in NAc.
Induced multipotency in adult keratinocytes through down-regulation of
ΔNp63
or
DGCR8
Authors: Chakravarti Deepavali , Su Xiaohua , Cho Min Soon , Bui Ngoc Hoang Bao , Coarfa Cristian , Venkatanarayan Avinashnarayan , Benham Ashley L. , Flores González Ramón E. , Alana Jennifer , Xiao Weimin , Leung Marco L. , Vin Harina , Chan Io Long , Aquino Arianexys , Müller Nicole , Wang Hongran , Cooney Austin J. , Parker-Thornburg Jan , Tsai Kenneth Y. , Gunaratne Preethi H. , Flores Elsa R.
Published: January 2014

Significance

The p53 family member deltaNp63 (ΔNp63) is required for transcriptional activation of the microprocessor complex subunit DGCR8 in epidermal cells, leading to terminal differentiation of tissues such as the epidermis. We show here that loss of ΔNp63 leads to the generation of cells with self-renewing but limited differentiation capacity. When DGCR8 is reexpressed in cells deficient for ΔNp63, these cells can terminally differentiate into all three germ layers. We dubbed these cells induced multipotent stem cells because of their remarkable plasticity and ability to differentiate into multiple cell lineages. Based on our results using human keratinocytes, we predict that epidermal cells can be extracted from patient skin biopsies and reprogrammed into multipotent stem cells by knockdown of ΔNp63 or DGCR8.
Comprehensive structural model of the mechanochemical cycle of a mitotic motor highlights molecular adaptations in the kinesin family
Authors: Goulet Adeline , Major Jennifer , Jun Yonggun , Gross Steven P. , Rosenfeld Steven S. , Moores Carolyn A.
Published: January 2014

Significance

Kinesins are a superfamily of ATP-dependent motors that are important for a wide variety of microtubule-based functions in eukaryotic cells. Kinesins have evolved to allow variable tuning of their motor properties, but the link between molecular variation and motor function is largely unknown. To understand this link, we have studied an essential mitotic kinesin, kinesin-5, which is the target of anticancer drugs. We used cryo-electron microscopy to visualize directly sequential conformational changes of structural elements during the motor ATPase cycle. We have identified the contribution of kinesin-5–specific variations to motor function indicating that kinesins indeed are precisely tuned according to cellular function. This insight will be important in designing kinesin-specific inhibitors in different disease contexts.
Molecular indexing enables quantitative targeted RNA sequencing and reveals poor efficiencies in standard library preparations
Authors: Fu Glenn K. , Xu Weihong , Wilhelmy Julie , Mindrinos Michael N. , Davis Ronald W. , Xiao Wenzhong , Fodor Stephen P. A.
Published: January 2014

Significance

RNA sequencing (RNA-Seq) is a common tool for measuring relative gene expression levels. However, as an absolute quantitative tool, the data are prone to various distortions due to biases from library preparation. We improve the quantitative aspects of RNA-Seq by barcoding individual cDNA molecules to correct for amplification bias, distinguish clonal replicates, and obtain absolute measurements of gene expression. We have also developed a set of barcoded synthetic RNAs that can be spiked into samples as easy-to-use quantitative controls. Additionally, we demonstrate the combined use of capture enrichment with molecular barcoding for the sequencing of targeted genes. These results demonstrate low library preparation efficiency leading to the stochastic loss of low-abundance transcripts, which cannot be overcome by simply increasing sequencing depth.
Different modes of endothelial–smooth muscle cell interaction elicit differential β-catenin phosphorylations and endothelial functions
Authors: Chang Shun-Fu , Chen Li-Jing , Lee Pei-Ling , Lee Ding-Yu , Chien Shu , Chiu Jeng-Jiann
Published: January 2014

Significance

β-Catenin is an important versatile protein in most types of cells and its activity is regulated by differential phosphorylations and, hence, affects cellular functions. In this study, we defined a unique mechanism by which different modes of heterocellular interaction between vascular endothelial cells (ECs) and smooth muscle cells (SMCs) play differential roles in regulating EC β-catenin phosphorylations and functions. Direct physical interaction of SMCs to ECs causes their β-catenin Tyr142-phosphorylation via connexin 43/Fer to induce EC inflammation. In contrast, paracrine interaction of SMCs to ECs induces Ser45/Thr41-phosphorylation of VE-cadherin–associated β-catenin in ECs to cause their barrier dysfunction, with increased permeability. Our findings suggest that different phosphorylated forms of β-catenin play important roles in modulating vascular pathophysiology through different heterocellular interactions.
Morpheus: a user-friendly modeling environment for multiscale and multicellular systems biology
Authors: Starruß Jörn , de Back Walter , Brusch Lutz , Deutsch Andreas
Published: January 2014

Summary: Morpheus is a modeling environment for the simulation and integration of cell-based models with ordinary differential equations and reaction-diffusion systems. It allows rapid development of multiscale models in biological terms and mathematical expressions rather than programming code. Its graphical user interface supports the entire workflow from model construction and simulation to visualization, archiving and batch processing.

Availability and implementation: Binary packages are available at http://imc.zih.tu-dresden.de/wiki/morpheus for Linux, Mac OSX and MS Windows.

Contact:  walter.deback@tu-dresden.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
estMOI: estimating multiplicity of infection using parasite deep sequencing data
Authors: Assefa Samuel A. , Preston Mark D. , Campino Susana , Ocholla Harold , Sutherland Colin J. , Clark Taane G.
Published: January 2014

Summary: Individuals living in endemic areas generally harbour multiple parasite strains. Multiplicity of infection (MOI) can be an indicator of immune status and transmission intensity. It has a potentially confounding effect on a number of population genetic analyses, which often assume isolates are clonal. Polymerase chain reaction-based approaches to estimate MOI can lack sensitivity. For example, in the human malaria parasite Plasmodium falciparum, genotyping of the merozoite surface protein (MSP1/2) genes is a standard method for assessing MOI, despite the apparent problem of underestimation. The availability of deep coverage data from massively parallizable sequencing technologies means that MOI can be detected genome wide by considering the abundance of heterozygous genotypes. Here, we present a method to estimate MOI, which considers unique combinations of polymorphisms from sequence reads. The method is implemented within the estMOI software. When applied to clinical P.falciparum isolates from three continents, we find that multiple infections are common, especially in regions with high transmission.

Availability and implementation:  estMOI is freely available from http://pathogenseq.lshtm.ac.uk.

Contact:  samuel.assefa@lshtm.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
ProbMetab: an R package for Bayesian probabilistic annotation of LC–MS-based metabolomics
Authors: Silva Ricardo R. , Jourdan Fabien , Salvanha Diego M. , Letisse Fabien , Jamin Emilien L. , Guidetti-Gonzalez Simone , Labate Carlos A. , Vêncio Ricardo Z. N.
Published: January 2014

Summary: We present ProbMetab, an R package that promotes substantial improvement in automatic probabilistic liquid chromatography–mass spectrometry-based metabolome annotation. The inference engine core is based on a Bayesian model implemented to (i) allow diverse source of experimental data and metadata to be systematically incorporated into the model with alternative ways to calculate the likelihood function and (ii) allow sensitive selection of biologically meaningful biochemical reaction databases as Dirichlet-categorical prior distribution. Additionally, to ensure result interpretation by system biologists, we display the annotation in a network where observed mass peaks are connected if their candidate metabolites are substrate/product of known biochemical reactions. This graph can be overlaid with other graph-based analysis, such as partial correlation networks, in a visualization scheme exported to Cytoscape, with web and stand-alone versions.

Availability and implementation: ProbMetab was implemented in a modular manner to fit together with established upstream (xcms, CAMERA, AStream, mzMatch.R, etc) and downstream R package tools (GeneNet, RCytoscape, DiffCorr, etc). ProbMetab, along with extensive documentation and case studies, is freely available under GNU license at: http://labpib.fmrp.usp.br/methods/probmetab/.

Contact:  rvencio@usp.br

Supplementary information:  Supplementary data are available at Bioinformatics online.
GR-Align: fast and flexible alignment of protein 3D structures using graphlet degree similarity
Authors: Malod-Dognin Noël , Pržulj Nataša
Published: January 2014

Motivation: Protein structure alignment is key for transferring information from well-studied proteins to less studied ones. Structural alignment identifies the most precise mapping of equivalent residues, as structures are more conserved during evolution than sequences. Among the methods for aligning protein structures, maximum Contact Map Overlap (CMO) has received sustained attention during the past decade. Yet, known algorithms exhibit modest performance and are not applicable for large-scale comparison.

Results: Graphlets are small induced subgraphs that are used to design sensitive topological similarity measures between nodes and networks. By generalizing graphlets to ordered graphs, we introduce GR-Align, a CMO heuristic that is suited for database searches. On the Proteus_300 set (44 850 protein domain pairs), GR-Align is several orders of magnitude faster than the state-of-the-art CMO solvers Apurva, MSVNS and AlEigen7, and its similarity score is in better agreement with the structural classification of proteins. On a large-scale experiment on the Gold-standard benchmark dataset (3 207 270 protein domain pairs), GR-Align is several orders of magnitude faster than the state-of-the-art protein structure comparison tools TM-Align, DaliLite, MATT and Yakusa, while achieving similar classification performances. Finally, we illustrate the difference between GR-Align’s flexible alignments and the traditional ones by querying a flexible protein in the Astral-40 database (11 154 protein domains). In this experiment, GR-Align’s top scoring alignments are not only in better agreement with structural classification of proteins, but also that they allow transferring more information across proteins.

Availability and implementation: GR-Align is coded in C++. software and supplementary material are available at: http://bio-nets.doc.ic.ac.uk/home/software/gralign/.

Contact:  n.malod-dognin@imperial.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
Automatic identification of mixed bacterial species fingerprints in a MALDI-TOF mass-spectrum
Authors: Mahé Pierre , Arsac Maud , Chatellier Sonia , Monnin Valérie , Perrot Nadine , Mailler Sandrine , Girard Victoria , Ramjeet Mahendrasingh , Surre Jérémy , Lacroix Bruno , van Belkum Alex , Veyrieras Jean-Baptiste
Published: January 2014

Motivation: Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry has been broadly adopted by routine clinical microbiology laboratories for bacterial species identification. An isolated colony of the targeted microorganism is the single prerequisite. Currently, MS-based microbial identification directly from clinical specimens can not be routinely performed, as it raises two main challenges: (i) the nature of the sample itself may increase the level of technical variability and bring heterogeneity with respect to the reference database and (ii) the possibility of encountering polymicrobial samples that will yield a ‘mixed’ MS fingerprint. In this article, we introduce a new method to infer the composition of polymicrobial samples on the basis of a single mass spectrum. Our approach relies on a penalized non-negative linear regression framework making use of species-specific prototypes, which can be derived directly from the routine reference database of pure spectra.

Results: A large spectral dataset obtained from in vitro mono- and bi-microbial samples allowed us to evaluate the performance of the method in a comprehensive way. Provided that the reference matrix-assisted laser desorption/ionization time-of-flight mass spectrometry fingerprints were sufficiently distinct for the individual species, the method automatically predicted which bacterial species were present in the sample. Only few samples (5.3%) were misidentified, and bi-microbial samples were correctly identified in up to 61.2% of the cases. This method could be used in routine clinical microbiology practice.

Availability and implementation: The complete dataset including both the reference database and the mock-up mixture spectra is available at http://archive.ics.uci.edu/ml/datasets/MicroMass.

Contact:  pierre.mahe@biomerieux.com

Supplementary information:  Supplementary data are available at Bioinformatics online.
Exploring genome characteristics and sequence quality without a reference
Authors: Simpson Jared T.
Published: January 2014

Motivation: The de novo assembly of large, complex genomes is a significant challenge with currently available DNA sequencing technology. While many de novo assembly software packages are available, comparatively little attention has been paid to assisting the user with the assembly.

Results: This article addresses the practical aspects of de novo assembly by introducing new ways to perform quality assessment on a collection of sequence reads. The software implementation calculates per-base error rates, paired-end fragment-size distributions and coverage metrics in the absence of a reference genome. Additionally, the software will estimate characteristics of the sequenced genome, such as repeat content and heterozygosity that are key determinants of assembly difficulty.

Availability: The software described is freely available online (https://github.com/jts/sga) and open source under the GNU Public License.

Contact:  jared.simpson@oicr.on.ca

Supplementary Information:  Supplementary data are available at Bioinformatics online.
PhyloJIVE: Integrating biodiversity data with the Tree of Life
Authors: Jolley-Rogers Garry , Varghese Temi , Harvey Paul , dos Remedios Nick , Miller Joseph T.
Published: January 2014

Motivation: Rich collections of biodiversity information such as spatial distributions, species descriptions and trait data are now synthesized in publicly available online sources such as GBIF. Also phylogenetic knowledge now provides a sound understanding of the origin of organisms and their place in the tree of life. We demonstrate with PhyloJIVE that any phylogenetic tree can be linked to online biodiversity data in the browser. This evolutionary view of biodiversity data is demonstrated in a case study that suggests that this approach may be useful to scientists and non-experts users.

Contact:  joe@acaciamulga.net

Supplementary information:  Supplementary data are available at Bioinformatics online.