bluuebunny/crossref_metadata_2025 huggingface dataset:
An optical measurement method for the simultaneous assessment of respiration and heart rates in preterm infants
Authors: Marchionni P. , Scalise L. , Ercoli I. , Tomasini E. P.
Published: December 2013

Many conventional medical monitoring devices, while not technically invasive, are nevertheless obtrusive insofar as they require contact with the patient. This obtrusiveness sometimes poses problems in daily clinical practice. The need for contact with electrodes or transducers is particularly relevant in the case of patients recovering in intensive care units where continuous monitoring is required, in turn requiring continuous direct transducer contact for prolonged periods. Among the many physiological parameters commonly acquired, the respiratory and the cardiac rates of the patients are of primary importance. Typically these two parameters are measured respectively using spirometry and electrocardiography (ECG), both involving obtrusive measurement systems requiring contact with the patient with an air conduit and electrodes. This paper presents an optical measurement method for the simultaneous assessment of respiration and heart rates based on the measurement of the chest wall movements, associated with inspiratory/expiratory activities of the lungs and by the mechanical pumping action of the heart. The measurement method has been adapted for use with preterm infants and it has been applied to 55 patients recovering in a Neonatal Intensive Care Unit. The method is based on the use of a laser Doppler vibrometer (LDVi) pointed at the left, ventral thoracic surface of the patient. LDVi-based measures of respiration and heart rate have been simultaneously acquired for each patient, in parallel with the same quantities acquired using conventional reference instrumentation (flow-meter and ECG) for comparison purposes. Results show that for respiration rate, differences with respect to the spirometer data are <3%, while for the cardiac rate they are <6% with respect to ECG data. The method proposed in this paper has the advantage of requiring no contact with the patient. Moreover, it supports, by means of a single instrument, the simultaneous measurement of respiration and heart rates, thus reducing the burden of the number of electrodes, transducers, and other instrumentation that must be applied to the patient—a consideration that is particularly important in the Neonatal Intensive Care Unit. In addition to the measurement of respiration rate, we also describe the sensitivity of the LDVi method in detecting key respiration events (irregular inspiration/expiration cycles, apneas, and hiccups) which are relevant to clinical monitoring.
Effect of parasitic series resistances and spurious currents on the extracted temperature of a bipolar junction transistor
Authors: Mimila-Arroyo J.
Published: December 2013

Verster's proposition to directly extract the temperature of a bipolar junction transistor using its collector current is widely used. However, the resulting temperature is low accurate even when calibrated. Here, it is demonstrated that the misuse of the emitter current instead of the collector one, because of the presence of spurious currents other than the injection-diffusion one and transistor parasitic series resistances both contribute to the observed inaccuracy. Particularly parasitic series resistances increase the inaccuracy and introduce a strong dependence of the extracted temperature on the collector currents used to extract the temperature; the higher those resistances the higher the inaccuracy. A proposition is made to reduce the effect of those resistances on the inaccuracy of this thermometric element, which allows obtaining a more accurate value on a wider range of the collector probe currents.
Controlled fabrication of Si nanocrystal delta-layers in thin SiO2 layers by plasma immersion ion implantation for nonvolatile memories
Authors: Bonafos C. , Spiegel Y. , Normand P. , Ben-Assayag G. , Groenen J. , Carrada M. , Dimitrakis P. , Kapetanakis E. , Sahu B. S. , Slaoui A. , Torregrosa F.
Published: December 2013

Plasma Immersion Ion Implantation (PIII) is a promising alternative to beam line implantation to produce a single layer of nanocrystals (NCs) in the gate insulator of metal-oxide semiconductor devices. We report herein the fabrication of two-dimensional Si-NCs arrays in thin SiO2 films using PIII and rapid thermal annealing. The effect of plasma and implantation conditions on the structural properties of the NC layers is examined by transmission electron microscopy. A fine tuning of the NCs characteristics is possible by optimizing the oxide thickness, implantation energy, and dose. Electrical characterization revealed that the PIII-produced-Si NC structures are appealing for nonvolatile memories.
A dynamic model for the Lagrangian stochastic dispersion coefficient
Authors: Pesmazoglou I. , Kempf A. M. , Navarro-Martinez S.
Published: December 2013

A stochastic sub-grid model is often used to accurately represent particle dispersion in turbulent flows using large eddy simulations. Models of this type have a free parameter, the dispersion coefficient, which is not universal and is strongly grid-dependent. In the present paper, a dynamic model for the evaluation of the coefficient is proposed and validated in decaying homogeneous isotropic turbulence. The grid dependence of the static coefficient is investigated in a turbulent mixing layer and compared to the dynamic model. The dynamic model accurately predicts dispersion statistics and resolves the grid-dependence. Dispersion statistics of the dynamically calculated constant are more accurate than any static coefficient choice for a number of grid spacings. Furthermore, the dynamic model produces less numerical artefacts than a static model and exhibits smaller sensitivity in the results predicted for different particle relaxation times.
A new prediction of wavelength selection in radial viscous fingering involving normal and tangential stresses
Authors: Nagel Mathias , Gallaire François
Published: December 2013

We reconsider the radial Saffman-Taylor instability, when a fluid injected from a point source displaces another fluid of higher viscosity in a Hele-Shaw cell, where the fluids are confined between two neighboring flat plates. The advancing fluid front is unstable and forms fingers along the circumference. The so-called Brinkman equation is used to describe the flow field, which also takes into account viscous stresses in the plane of the confining plates and, unlike the Darcy equation, not only viscous stresses due to the confining plates. We show why in-plane stresses cannot always be neglected and how they appear naturally in the potential flow problem. The dispersion relation obtained with the Brinkman equation agrees better with the experimental results than the classical linear stability analysis of radial fingering in Hele-Shaw cells that uses Darcy's law as a model for the fluid motion.
Instrument for x-ray absorption spectroscopy with in situ electrical control characterizations
Authors: Huang Chun-Chao , Chang Shu-Jui , Yang Chao-Yao , Chou Hsiung , Tseng Yuan-Chieh
Published: December 2013

We report a synchrotron-based setup capable of performing x-ray absorption spectroscopy and x-ray magnetic circular dichroism with simultaneous electrical control characterizations. The setup can enable research concerning electrical transport, element- and orbital-selective magnetization with an in situ fashion. It is a unique approach to the real-time change of spin-polarized electronic state of a material/device exhibiting magneto-electric responses. The performance of the setup was tested by probing the spin-polarized states of cobalt and oxygen of Zn1-xCoxO dilute magnetic semiconductor under applied voltages, both at low (∼20 K) and room temperatures, and signal variations upon the change of applied voltage were clearly detected.
Simulation of a new grid-connected hybrid generation system with Stirling engine and wind turbine
Authors: Shariatpanah H. , Zareian Jahromi M. , Fadaeinedjad R.
Published: December 2013

A detail model including all mechanical and electrical aspects is necessary to fully study hybrid grid operation. In this paper, a new grid-connected hybrid generation system with a Stirling engine and a wind turbine, which are connected to a grid through a common dc bus, is presented. The Stirling is more efficient than photo voltaic array and its combination with the wind turbine can create an efficient hybrid system. Fatigue, Aerodynamics, Structures, and Turbulence and Simulink/MATLAB are used to model the mechanical parts of the wind turbine, Stirling engine, and electrical parts. Field oriented control method is developed on voltage source converter. Power signal feedback method is implemented to determine generators reference shaft speed in hybrid system. Permanent magnet synchronous generator is used in the wind turbine and Stirling engine. Simulation results show that a new hybrid generation system with Stirling and wind turbine can work like other hybrid system and has suitable performance.
Nonlinear and linear models for losses of plug in hybrid electric vehicle: A computation approach
Authors: Feshki Farahani H. , Khalili M. , Rabiee A. , Barati M.
Published: December 2013

This paper presents nonlinear and linear models for the losses of Plug in Hybrid Electric Vehicle (PHEV). An accurate model to calculate the PHEV losses for just one vehicle is not remarkable. However, in the case of including thousands of vehicles, even a slight error for each vehicle leads to significant total losses which decreases the vehicles' owner profit. In previous works, the losses of PHEV charging and discharging mode are equally considered as a percentage of PHEV rating power. However, the charging and discharging mode losses are neither equal nor constant. Therefore, a nonlinear model of PHEV losses is presented for different parts of PHEV structure, i.e., AC/DC inverter, DC/DC converter and battery. After that, a simplified linear model for PHEV losses is presented to decrease the computation burden in the case of participating large number of PHEVs in the energy market. In the case study, the proposed losses formulation is used to obtain optimal charging and discharging time of PHEV. The profit of the PHEV owner is also maximized considering energy price in the energy market.
Investigation of hydroelectric energy potential of the Zab River Basin using geographic information systems and remote sensing methods
Authors: Çabuk S. N. , Bakış R. , Göncü S. , Gümüşlüoğlu E. , Çabuk A.
Published: December 2013

Turkey's energy need is increasing day by day. The required energy is mostly imported from foreign countries since it cannot be met by the country's own resources. However, Turkey has rich renewable water resources to produce energy. To fulfill the aim of closing this energy gap and using the country's water resources more efficiently, the hydropower potential of the Zab River Basin is investigated in this paper. The overall objective of the study is to evaluate the hydropower potential of the Zab River Basin using Geographic Information Systems and Remote Sensing methods, and utilize this potential for the economical development of the region and the country. Within the study, appropriate locations were determined for 12 dams in the basin; estimated costs and annual electric energy generation were calculated with the Simahpp Software. According to these calculations, the total cost, installed power capacity and the annual electric energy generation of the dams were found, respectively, as 838.753 × 106 US$, 580.928 MW and 1112.327 GWh.
Continuous-wave quasi-phase-matched waveguide correlated photon pair source on a III–V chip
Authors: Sarrafi Peyman , Zhu Eric Y. , Dolgaleva Ksenia , Holmes Barry M. , Hutchings David C. , Aitchison J. Stewart , Qian Li
Published: December 2013

We report on the demonstration of correlated photon pair generation in a quasi-phase-matched superlattice GaAs/AlGaAs waveguide using a continuous-wave pump. Our photon pair source has a low noise level and achieves a high coincidence-to-accidental ratio greater than 100, which is the highest value reported in III–V chips so far. This correlated photon pair source has the potential to be monolithically integrated with on-chip pump laser sources fabricated on the same superlattice wafer structure, enabling direct correlated/entangled photon pair production from a compact electrically powered chip.
Structural tunability and switchable exciton emission in inorganic-organic hybrids with mixed halides
Authors: Ahmad Shahab , Baumberg Jeremy J. , Vijaya Prakash G.
Published: December 2013

Room-temperature tunable excitonic photoluminescence is demonstrated in alloy-tuned layered Inorganic-Organic (IO) hybrids, (C12H25NH3)2PbI4(1−y)Br4y (y = 0 to 1). These perovskite IO hybrids adopt structures with alternating stacks of low-dimensional inorganic and organic layers, considered to be naturally self-assembled multiple quantum wells. These systems resemble stacked monolayer 2D semiconductors since no interlayer coupling exists. Thin films of IO hybrids exhibit sharp and strong photoluminescence (PL) at room-temperature due to stable excitons formed within the low-dimensional inorganic layers. Systematic variation in the observed exciton PL from 510 nm to 350 nm as the alloy composition is changed, is attributed to the structural readjustment of crystal packing upon increase of the Br content in the Pb-I inorganic network. The energy separation between exciton absorption and PL is attributed to the modified exciton density of states and diffusion of excitons from relatively higher energy states corresponding to bromine rich sites towards the lower energy iodine sites. Apart from compositional fluctuations, these excitons show remarkable reversible flips at temperature-induced phase transitions. All the results are successfully correlated with thermal and structural studies. Such structural engineering flexibility in these hybrids allows selective tuning of desirable exciton properties within suitable operating temperature ranges. Such wide-range PL tunability and reversible exciton switching in these novel IO hybrids paves the way to potential applications in new generation of optoelectronic devices.
Charged impurity-induced scatterings in chemical vapor deposited graphene
Authors: Li Ming-Yang , Tang Chiu-Chun , Ling D. C. , Li L. J. , Chi C. C. , Chen Jeng-Chung
Published: December 2013

We investigate the effects of defect scatterings on the electric transport properties of chemical vapor deposited (CVD) graphene by measuring the carrier density dependence of the magneto-conductivity. To clarify the dominant scattering mechanism, we perform extensive measurements on large-area samples with different mobility to exclude the edge effect. We analyze our data with the major scattering mechanisms such as short-range static scatters, short-range screened Coulomb disorders, and weak-localization (WL). We establish that the charged impurities are the predominant scatters because there is a strong correlation between the mobility and the charge impurity density. Near the charge neutral point (CNP), the electron-hole puddles that are induced by the charged impurities enhance the inter-valley scattering, which is favorable for WL observations. Away from the CNP, the charged-impurity-induced scattering is weak because of the effective screening by the charge carriers. As a result, the local static structural defects govern the charge transport. Our findings provide compelling evidence for understanding the scattering mechanisms in graphene and pave the way for the improvement of fabrication techniques to achieve high-quality CVD graphene.
Photon sorting in the near field using subwavelength cavity arrays in the near-infrared
Authors: Mandel Isroel M. , Lansey Eli , Gollub Jonah N. , Sarantos Chris H. , Akhmechet Roman , Golovin Andrii B. , Crouse David T.
Published: December 2013

A frequency selective metasurface capable of sorting photons in the near-infrared spectral range is designed, fabricated, and characterized. The metasurface, a periodic array of dielectric cylindrical cavities in a gold film, localizes and transmits light of two spectral frequency bands into spatially separated cavities, resulting in near-field light splitting. The design and fabrication methodologies of the metasurface are discussed. The transmittance and photon sorting properties of the designed structure is simulated numerically and the measured transmission is presented.
High-performance self-aligned inversion-channel In0.53Ga0.47As metal-oxide-semiconductor field-effect-transistors by in-situ atomic-layer-deposited HfO2
Authors: Lin T. D. , Chang W. H. , Chu R. L. , Chang Y. C. , Chang Y. H. , Lee M. Y. , Hong P. F. , Chen Min-Cheng , Kwo J. , Hong M.
Published: December 2013

Self-aligned inversion-channel In0.53Ga0.47As metal-oxide-semiconductor field-effect-transistors (MOSFETs) have been fabricated using the gate dielectrics of in-situ directly atomic-layer-deposited (ALD) HfO2 followed by ALD-Al2O3. There were no surface pretreatments and no interfacial passivation/barrier layers prior to the ALD. TiN/Al2O3 (4 nm)/HfO2 (1 nm)/In0.53Ga0.47As/InP MOS capacitors exhibited well-behaved capacitance-voltage characteristics with true inversion behavior, low leakage current densities of ∼10−8 A/cm2 at ±1 MV/cm, and thermodynamic stability at high temperatures. Al2O3 (3 nm)/HfO2 (1 nm)/In0.53Ga0.47As MOSFETs of 1 μm gate length, with 700 °C–800 °C rapid thermal annealing in source/drain activation, have exhibited high extrinsic drain current (ID) of 1.5 mA/μm, transconductance (Gm) of 0.84 mS/μm, ION/IOFF of ∼104, low sub-threshold swing of 103 mV/decade, and field-effect electron mobility of 1100 cm2/V · s. The devices have also achieved very high intrinsic ID and Gm of 2 mA/μm and 1.2 mS/μm, respectively.
Characterization and modeling of a ZnO nanowire ultraviolet photodetector with graphene transparent contact
Authors: Zhang H. , Babichev A. V. , Jacopin G. , Lavenus P. , Julien F. H. , Yu. Egorov A. , Zhang J. , Pauporté T. , Tchernycheva M.
Published: December 2013

We report the demonstration of a ZnO nanowire ultraviolet photodetector with a top transparent electrode made of a few-layered graphene sheet. The nanowires have been synthesized using a low-cost electrodeposition method. The detector is shown to be visible-blind and to present a responsivity larger than 104 A/W in the near ultraviolet range thanks to a high photoconductive gain in ZnO nanowires. The device exhibits a peak responsivity at 370 nm wavelength and shows a sub bandgap response down to 415 nm explained by an Urbach tail with a characteristic energy of 83 meV. The temporal response of the detector and the power dependence are discussed. A model of the photoconductive mechanism is proposed showing that the main process responsible for the photoconductive gain is the modulation of the conducting surface due to the variation of the surface depletion layer and not the reduction of recombination efficiency stemming from the electron-hole spatial separation. The gain is predicted to decrease at high incident power due to the flattening of the lateral band bending in agreement with experimental data.
Evaluation of renewable energy development in power generation in Finland
Authors: Aslani Alireza , Helo Petri , Naaranoja Marja
Published: December 2013

Renewable energy resources have historically played an important role for heat/electricity generation in Finland. Although diffusion costs of renewable energy utilization are higher than fossil fuels and nuclear power plants, other policy aspects and operation costs of renewables cover this gap particularly in high dependent countries to fossil fuels. The current paper discusses the role of renewable portfolio in the Finland's energy action plan during 2011–2020. A system dynamics model is constructed to evaluate different costs of renewable energy utilization by 2020. Results show that total costs of new capacities of renewable energy systems as well as operation and maintenance costs of current systems bring 7% saving compared to total costs of new natural gas power plants (as a sample for second scenario) in Finland.
Bottom-up graphene nanoribbon field-effect transistors
Authors: Bennett Patrick B. , Pedramrazi Zahra , Madani Ali , Chen Yen-Chia , de Oteyza Dimas G. , Chen Chen , Fischer Felix R. , Crommie Michael F. , Bokor Jeffrey
Published: December 2013

Recently developed processes have enabled bottom-up chemical synthesis of graphene nanoribbons (GNRs) with precise atomic structure. These GNRs are ideal candidates for electronic devices because of their uniformity, extremely narrow width below 1 nm, atomically perfect edge structure, and desirable electronic properties. Here, we demonstrate nano-scale chemically synthesized GNR field-effect transistors, made possible by development of a reliable layer transfer process. We observe strong environmental sensitivity and unique transport behavior characteristic of sub-1 nm width GNRs.
Intensive two-photon absorption induced decay pathway in a ZnO crystal: Impact of light-induced defect state
Authors: Li Zhong-guo , Yang Jun-yi , Wei Tai-Huei , Song Ying-lin
Published: December 2013

Using the pump-probe with phase object technique with 20 ps laser pulses at 532 nm, we investigated the carrier relaxation process subsequent to two-photon absorption (TPA) in ZnO. As a result, we found that an additional subnanosecond decay pathway is activated when the pump beam intensity surpasses 0.4 GW/cm2. We attributed this intensity-dependent pathway to a TPA induced bulk defect state and our results demonstrate that this photo induced defect state has potential applications in ZnO based optoelectronic and spintronic devices.
Deciphering mechanisms of enhanced-retarded oxygen diffusion in doped Si
Authors: Timerkaeva Dilyara , Caliste Damien , Pochet Pascal
Published: December 2013

We study enhanced/retarded diffusion of oxygen in doped silicon by means of first principle calculations. We evidence that the migration energy of oxygen dimers cannot be significantly affected by strain, doping type, or concentration. We attribute the enhanced oxygen diffusion in p-doped silicon to reduced monomer migration energy and the retarded oxygen diffusion in Sb-doped to monomer trapping close to a dopant site. These two mechanisms can appear simultaneously for a given dopant leading to contradictory experimental results. More generally, our findings cast a new light on phenomena involving oxygen diffusion: precipitation, thermal donors formation, and light induced degradation.
Terahertz generation and detection with InGaAs-based large-area photoconductive devices excited at 1.55 μm
Authors: Xu Ming , Mittendorff Martin , Dietz Roman J. B. , Künzel Harald , Sartorius Bernd , Göbel Thorsten , Schneider Harald , Helm Manfred , Winnerl Stephan
Published: December 2013

We report on scalable large-area terahertz emitters and detectors based on In0.53Ga0.47As/In0.52Al0.48As heterostructures for excitation with 1.55 μm radiation. Different geometries involving three different electrode gap sizes are compared with respect to terahertz (THz) emission, bias field distribution, and Joule heating. The field distribution becomes more favorable for THz emission as gap size increases, while Joule heating exhibits the opposite dependence. Devices with three different gap sizes, namely 3 μm, 5 μm, and 7.5 μm, have been investigated experimentally, the emitter with a gap size of 7.5 μm showed the best performance. The scalable devices are furthermore employed as detectors. The scalable electrode geometry enables spatially integrated detection, which is attractive for specific applications, e.g., where an unfocused THz beam has to be used.
In situ tuning the single photon emission from single quantum dots through hydrostatic pressure
Authors: Wu Xuefei , Dou Xiuming , Ding Kun , Zhou Pengyu , Ni Haiqiao , Niu Zhichuan , Jiang Desheng , Sun Baoquan
Published: December 2013

We demonstrate that exciton emission wavelength in InAs/GaAs quantum dots (QDs) can be shifted up to 160 nm using hydrostatic pressure (0.4–4 GPa) in situ in an optical cryostat through an improved diamond anvil cell driven by piezoelectric actuator. It is confirmed that the high pressure does not destroy the photon anti-bunching properties of single QD emitter. Exciton emission intensity is not obviously weakened under the pressure range of 0–4 GPa. Such a tunable QD single photon emitter enables a flexibly tuned source for quantum optical experiments.
Distinct local structure of nanoparticles and nanowires of V2O5 probed by x-ray absorption spectroscopy
Authors: Joseph B. , Iadecola A. , Maugeri L. , Bendele M. , Okubo M. , Li H. , Zhou H. , Mizokawa T. , Saini N. L.
Published: December 2013

We have used V K-edge x-ray absorption spectroscopy to study local structures of bulk, nanoparticles and nanowires of V2O5. The extended x-ray absorption fine structure measurements show different local displacements in the three morphologically different V2O5 samples. It is found that the nanowires have a significantly ordered chain structure in comparison to the V2O5 bulk. In contrast, nanoparticles have larger interlayer disorder. The x-ray absorption near-edge structure spectra show different electronic structure that appears to be related with the local atomic disorder in the three V2O5 samples.
Hierarchy of graphene wrinkles induced by thermal strain engineering
Authors: Meng Lan , Su Ying , Geng Dechao , Yu Gui , Liu Yunqi , Dou Rui-Fen , Nie Jia-Cai , He Lin
Published: December 2013

Here, we study hierarchy of graphene wrinkles induced by thermal strain engineering and demonstrate that the wrinkling hierarchy can be accounted for by the wrinklon theory. We derive an equation λ = (ky)0.5, explaining evolution of wrinkling wavelength λ with the distance to the edge y observed in our experiment by considering both bending energy and stretching energy of the graphene flakes. The prefactor k in the equation is determined to be about 55 nm. Our experimental result indicates that the classical membrane behavior of graphene persists down to about 100 nm of the wrinkling wavelength.
Diamagnetic to ferromagnetic switching in VO2 epitaxial thin films by nanosecond excimer laser treatment
Authors: Molaei R. , Bayati R. , Nori S. , Kumar D. , Prater J. T. , Narayan J.
Published: December 2013

VO2(010)/NiO(111) epitaxial heterostructures were integrated with Si(100) substrates using a cubic yttria-stabilized zirconia (c-YSZ) buffer. The epitaxial alignment across the interfaces was determined to be VO2(010)‖NiO(111)‖c-YSZ(001)‖Si(001) and VO2[100]‖NiO⟨110⟩‖c-YSZ⟨100⟩‖Si⟨100⟩. The samples were subsequently treated by a single shot of a nanosecond KrF excimer laser. Pristine as-deposited film showed diamagnetic behavior, while laser annealed sample exhibited ferromagnetic behavior. The population of majority charge carriers (e−) and electrical conductivity increased by about two orders of magnitude following laser annealing. These observations are attributed to the introduction of oxygen vacancies into the VO2 thin films and the formation of V3+ defects.
Enhanced stability of Mcl1, a prosurvival Bcl2 relative, blunts stress-induced apoptosis, causes male sterility, and promotes tumorigenesis
Authors: Okamoto Toru , Coultas Leigh , Metcalf Donald , van Delft Mark F. , Glaser Stefan P. , Takiguchi Megumi , Strasser Andreas , Bouillet Philippe , Adams Jerry M. , Huang David C. S.
Published: December 2013

Significance

We obtained evidence that the rapid turnover of Mcl1 has physiological significance by analyzing mice bearing a modified allele of
Mcl1
that proved to encode a stabilized form of Mcl1. In cells under stresses such as protein synthesis inhibition or UV radiation, its life span was much longer than WT Mcl1. Male mice bearing only the modified allele were sterile due to excess early spermatogenesis, and the modified allele ameliorated the polycystic kidney disease arising in mice lacking prosurvival Bcl2. Notably, the
Mcl1
allele accelerated Myc-induced acute myeloid leukemia. Thus, under certain circumstances, the Mcl1 N terminus regulates its degradation, certain cell types require Mcl1 degradation to induce apoptosis, and Mcl1 turnover serves as a tumor-suppressive mechanism.
SplicePlot: a utility for visualizing splicing quantitative trait loci
Authors: Wu Eric , Nance Tracy , Montgomery Stephen B.
Published: December 2013

Summary: RNA sequencing has provided unprecedented resolution of alternative splicing and splicing quantitative trait loci (sQTL). However, there are few tools available for visualizing the genotype-dependent effects of splicing at a population level. SplicePlot is a simple command line utility that produces intuitive visualization of sQTLs and their effects. SplicePlot takes mapped RNA sequencing reads in BAM format and genotype data in VCF format as input and outputs publication-quality Sashimi plots, hive plots and structure plots, enabling better investigation and understanding of the role of genetics on alternative splicing and transcript structure.

Availability and implementation: Source code and detailed documentation are available at http://montgomerylab.stanford.edu/spliceplot/index.html under Resources and at Github. SplicePlot is implemented in Python and is supported on Linux and Mac OS. A VirtualBox virtual machine running Ubuntu with SplicePlot already installed is also available.

Contact:  wu.eric.g@gmail.com or smontgom@stanford.edu
Efficient clustering of identity-by-descent between multiple individuals
Authors: Qian Yu , Browning Brian L. , Browning Sharon R.
Published: December 2013

Motivation: Most existing identity-by-descent (IBD) detection methods only consider haplotype pairs; less attention has been paid to considering multiple haplotypes simultaneously, even though IBD is an equivalence relation on haplotypes that partitions a set of haplotypes into IBD clusters. Multiple-haplotype IBD clusters may have advantages over pairwise IBD in some applications, such as IBD mapping. Existing methods for detecting multiple-haplotype IBD clusters are often computationally expensive and unable to handle large samples with thousands of haplotypes.

Results: We present a clustering method, efficient multiple-IBD, which uses pairwise IBD segments to infer multiple-haplotype IBD clusters. It expands clusters from seed haplotypes by adding qualified neighbors and extends clusters across sliding windows in the genome. Our method is an order of magnitude faster than existing methods and has comparable performance with respect to the quality of clusters it uncovers. We further investigate the potential application of multiple-haplotype IBD clusters in association studies by testing for association between multiple-haplotype IBD clusters and low-density lipoprotein cholesterol in the Northern Finland Birth Cohort. Using our multiple-haplotype IBD cluster approach, we found an association with a genomic interval covering the PCSK9 gene in these data that is missed by standard single-marker association tests. Previously published studies confirm association of PCSK9 with low-density lipoprotein.

Availability and implementation: Source code is available under the GNU Public License http://cs.au.dk/~qianyuxx/EMI/.

Contact:  qianyuxx@gmail.com

Supplementary information:  Supplementary data are available at Bioinformatics online.
GPU-Meta-Storms: computing the structure similarities among massive amount of microbial community samples using GPU
Authors: Su Xiaoquan , Wang Xuetao , Jing Gongchao , Ning Kang
Published: December 2013

Motivation: The number of microbial community samples is increasing with exponential speed. Data-mining among microbial community samples could facilitate the discovery of valuable biological information that is still hidden in the massive data. However, current methods for the comparison among microbial communities are limited by their ability to process large amount of samples each with complex community structure.

Summary: We have developed an optimized GPU-based software, GPU-Meta-Storms, to efficiently measure the quantitative phylogenetic similarity among massive amount of microbial community samples. Our results have shown that GPU-Meta-Storms would be able to compute the pair-wise similarity scores for 10 240 samples within 20 min, which gained a speed-up of >17 000 times compared with single-core CPU, and >2600 times compared with 16-core CPU. Therefore, the high-performance of GPU-Meta-Storms could facilitate in-depth data mining among massive microbial community samples, and make the real-time analysis and monitoring of temporal or conditional changes for microbial communities possible.

Availability and implementation: GPU-Meta-Storms is implemented by CUDA (Compute Unified Device Architecture) and C++. Source code is available at http://www.computationalbioenergy.org/meta-storms.html.

Contact:  ningkang@qibebt.ac.cn
Ondex Web: web-based visualization and exploration of heterogeneous biological networks
Authors: Taubert Jan , Hassani-Pak Keywan , Castells-Brooke Nathalie , Rawlings Christopher J.
Published: December 2013

Summary: Ondex Web is a new web-based implementation of the network visualization and exploration tools from the Ondex data integration platform. New features such as context-sensitive menus and annotation tools provide users with intuitive ways to explore and manipulate the appearance of heterogeneous biological networks. Ondex Web is open source, written in Java and can be easily embedded into Web sites as an applet. Ondex Web supports loading data from a variety of network formats, such as XGMML, NWB, Pajek and OXL.

Availability and implementation:  http://ondex.rothamsted.ac.uk/OndexWeb.

Contact:  keywan.hassani-pak@rothamsted.ac.uk
Fast determination of displacement by PPP velocity estimation
Authors: Tu Rui
Published: December 2013

Global Positioning System (GPS) has been proven to be an effective tool to retrieve high-precision displacement for the natural hazard monitoring. The network positioning and Precise Point Positioning (PPP) are the two basic approaches for its data solution, but the former one can only get a relative displacement within the local reference frame and requires a complex and continuously linked infrastructure, and the latter one with a long convergence time to obtain the absolute displacements within the global reference frame. To overcome these drawbacks, this paper proposed a method of fast determining the displacement by PPP velocity estimation (PPPVE). The key of the approach is that the velocity vector parameters are not correlated with other unknown parameters, such as ambiguities and atmosphere, so they can be fast and accurately estimated and integrated into displacements. The validation shows that the displacement can be provided with a precision of 1–2 cm in 1 min by PPPVE. In additional, the Kalman smoothing estimation can be used to improve the PPP solution.
Found: the progenitors of AM CVn and supernovae .Ia
Authors: Kilic Mukremin , Hermes J. J. , Gianninas A. , Brown Warren R. , Heinke Craig O. , Agüeros M. A. , Chote Paul , Sullivan Denis J. , Bell Keaton J. , Harrold Samuel T.
Published: December 2013

We present optical and X-ray observations of two tidally distorted, extremely low-mass white dwarfs (WDs) with massive companions. There is no evidence of neutron stars in our Chandra and XMM observations of these objects. SDSS J075141.18−014120.9 (J0751) is an eclipsing double WD binary containing a 0.19 M⊙ WD with a 0.97 M⊙ companion in a 1.9 h orbit. J0751 becomes the fifth eclipsing double WD system currently known. SDSS J174140.49+652638.7 (J1741) is another binary containing a 0.17 M⊙ WD with an unseen M ≥ 1.11 M⊙ WD companion in a 1.5-h orbit. With a mass ratio of ≈0.1, J1741 will have stable mass transfer through an accretion disc and turn into an interacting AM Canum Venaticorum (AM CVn) system in the next ≈160 Myr. With a mass ratio of 0.2, J0751 is likely to follow a similar evolutionary path. These are the first known AM CVn progenitor binary systems and they provide important constraints on the initial conditions for AM CVn. Theoretical studies suggest that both J0751 and J1741 may create thermonuclear supernovae in ∼108 yr, either .Ia or Ia. Such explosions can account for ∼1 per cent of the Type Ia supernova rate.
The first month of evolution of the slow-rising Type IIP SN 2013ej in M74
Authors: Valenti S. , Sand D. , Pastorello A. , Graham M. L. , Howell D. A. , Parrent J. T. , Tomasella L. , Ochner P. , Fraser M. , Benetti S. , Yuan F. , Smartt S. J. , Maund J. R. , Arcavi I. , Gal-Yam A. , Inserra C. , Young D.
Published: December 2013

We present early photometric and spectroscopic observations of SN 2013ej, a bright Type IIP supernova (SN) in M74. SN 2013ej is one of the closest SNe ever discovered. The available archive images and the early discovery help to constrain the nature of its progenitor. The earliest detection of this explosion was on 2013 July 24.125 ut and our spectroscopic monitoring with the FLOYDS spectrographs began on July 27.7 ut, continuing almost daily for two weeks. Daily optical photometric monitoring was achieved with the 1 m telescopes of the Las Cumbres Observatory Global Telescope (LCOGT) network, and was complemented by UV data from Swift and near-infrared spectra from Public ESO Spectroscopic Survey of Transient Objects and Infrared Telescope Facility. The data from our monitoring campaign show that SN 2013ej experienced a 10 d rise before entering into a well-defined plateau phase. This unusually long rise time for a Type IIP has been seen previously in SN 2006bp and SN 2009bw. A relatively rare strong absorption blueward of Hα is present since our earliest spectrum. We identify this feature as Si ii, rather than high-velocity Hα as sometimes reported in the literature.
A Common Left-Right Scale for Voters and Parties in Europe
Authors: Lo James , Proksch Sven-Oliver , Gschwend Thomas
Published: December 2013

This article presents a scaling approach to jointly estimate the locations of voters, parties, and European political groups on a common left-right scale. Although most comparative research assumes that cross-national comparisons of voters and parties are possible, few correct for systematic biases commonly known to exist in surveys or examine whether survey data are comparable across countries. Our scaling method addresses scale perception in surveys and links cross-national surveys through new bridging observations. We apply our approach to the 2009 European Election Survey and demonstrate that the improvement in party estimates that one gains from fixing various survey bias issues is significant. Our scaling strategy provides left-right positions of voters and of 162 political parties, and we demonstrate that variables based on rescaled voter and party positions on the left-right dimension significantly improve the fit of a cross-national vote choice model.
Burkholderia eburnea sp. nov., isolated from peat soil
Authors: Kang Sang Rim , Srinivasan Sathiyaraj , Lee Sang Seob
Published: December 2013

A novel aerobic bacterium, designated strain RR11T, was isolated from peat soil and was characterized by using a polyphasic taxonomic approach and identified in order to determine its taxonomic position. Strain RR11T is a Gram-negative, non-sporulating, motile, short-rod-shaped bacterium. 16S rRNA gene sequence analysis identified this strain as a member of the genus

Burkholderia

of the class

Betaproteobacteria

. The highest degrees of gene sequence similarity were found with

Burkholderia tropica

Ppe8T (98.0 %),

B. bannensis

E25T (97.3 %),

B. ferrariae

FeGI01T (97.1 %),

B. unamae

MTI-641T (97.1 %) and

B. heleia

SA41T (97.1 %). Strain RR11T had the following chemotaxonomic characteristics: the major ubiquinone was Q-8, the DNA G+C content was 60.8 mol%, the major fatty acids were C16 : 0, C19 : 0 cyclo ω8c and C17 : 0 cyclo and the polar lipid profile contained phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and an unknown aminophospholipid. Based on its morphological, physiological and chemotaxonomic characteristics, together with 16S rRNA gene sequence comparison results, strain RR11T represents a novel species, for which the name Burkholderia eburnea sp. nov. is proposed. The type strain is strain RR11T ( = KEMC 7302-065T = JCM 18070T).
Sphingomonas yantingensis sp. nov., a mineral-weathering bacterium isolated from purplish paddy soil
Authors: Huang Jing , Huang Zhi , Zhang Zhen-Dong , He Lin-Yan , Sheng Xia-Fang
Published: December 2013

A novel type of mineral-weathering bacterium was isolated from purplish soils collected from Yanting (Sichuan, south-western China). Cells of strain 1007T were Gram-stain-negative and rod-shaped, motile and yellow-pigmented. The isolate was strictly aerobic, catalase- and oxidase-positive, and grew optimally at 28-30 °C and pH 6.0-7.0. The genomic DNA G+C content of strain 1007T was 67±0.7 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 1007T belonged to the genus

Sphingomonas

and was most closely related to

Sphingomonas pruni

IFO 15498T (97.3 %),

Sphingomonas mali

IFO 15500T (97.2 %),

Sphingomonas japonica

KC7T (97.2 %) and

Sphingomonas koreensis

JSS26T (97.0 %). This affiliation of strain 1007T to the genus

Sphingomonas

was confirmed by the presence of Q-10 as the major ubiquinone, sphingoglycolipid, C14 : 0 2-OH and by the absence of 3-hydroxy fatty acids. The major polyamine was homospermidine. The main cellular fatty acids included summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c) and C16 : 0. Based on the low level of DNA–DNA relatedness (ranging from 26.1 % to 58.7 %) to these type strains of species of the genus

Sphingomonas

and unique phenotypic characteristics, strain 1007T represents a novel species of the genus

Sphingomonas

, for which the name Sphingomonas yantingensis sp. nov. is proposed. The type strain is 1007T ( = DSM 27244T = JCM 19201T = CCTCC AB 2013146T).
Acetobacter lambici sp. nov., isolated from fermenting lambic beer
Authors: Spitaels Freek , Li Leilei , Wieme Anneleen , Balzarini Tom , Cleenwerck Ilse , Van Landschoot Anita , De Vuyst Luc , Vandamme Peter
Published: December 2013

An acetic acid bacterium, strain LMG 27439T, was isolated from fermenting lambic beer. The cells were Gram-stain-negative, motile rods, catalase-positive and oxidase-negative. Analysis of the 16S rRNA gene sequence revealed the strain was closely related to

Acetobacter okinawensis

(99.7 % 16S rRNA gene sequence similarity with the type strain of this species),

A. ghanensis

(99.6 %),

A. syzygii

(99.6 %),

A. fabarum

(99.4 %) and

A. lovaniensis

(99.2 %). DNA–DNA hybridization with the type strains of these species revealed moderate DNA–DNA hybridization values (31–45 %). Strain LMG 27439T was unable to grow on glycerol or methanol as the sole carbon source, on yeast extract with 10 % ethanol or on glucose-yeast extract medium at 37 °C. It did not produce acid from l-arabinose, d-galactose or d-mannose, nor did it produce 2-keto-d-gluconic acid, 5-keto-d-gluconic acid or 2,5-diketo-d-gluconic acid from d-glucose. It did not grow on ammonium as the sole nitrogen source and ethanol as the sole carbon source. These genotypic and phenotypic data distinguished strain LMG 27439T from established species of the genus

Acetobacter

, and therefore we propose this strain represents a novel species of the genus

Acetobacter

. The name Acetobacter lambici sp. nov. is proposed, with LMG 27439T ( = DSM 27328T) as the type strain.
Mariniluteicoccus flavus gen. nov., sp. nov., a new member of the family Propionibacteriaceae, isolated from a deep-sea sediment
Authors: Zhang Dao-Feng , Wang Hong-Fei , Xiong Zi-Jun , Tian Xin-Peng , Liu Lan , Zhang Xiao-Mei , Jiang Zhao , Zhang Si , Li Wen-Jun
Published: December 2013

A Gram-staining-positive, aerobic, non-motile, irregular coccus, designated strain YIM M13146T, was isolated from a sediment sample collected from the South China Sea at a depth of 2439 m, and its taxonomic position was determined by a polyphasic approach. Optimal growth of the strain was observed at 30 °C (range 5–40 °C), pH 7.0 (pH 6.0–9.0) and 0–1 % NaCl (0–6 %, w/v) on/in tryptic soy agar/broth. Strain YIM M13146T had the major cellular fatty acid anteiso-C15 : 0, the predominant respiratory menaquinone MK-9(H4), peptidoglycan type A3γ (ll-DAP–Gly) containing alanine, glycine, glutamic acid and ll-diaminopimelic acid (ll-DAP) and the polar lipids phosphatidylcholine, diphosphatidylglycerol, one unknown phospholipid and several glycolipids. The G+C content of the DNA was 67.2 mol%. Phenotypic and chemotaxonomic characteristics together with 16S rRNA gene sequence analyses showed that strain YIM M13146T was distinct from its close phylogenetic relatives in the genera

Propioniferax

and

Granulicoccus

of the family

Propionibacteriaceae

. Hence, a new genus and species, Mariniluteicoccus flavus gen. nov., sp. nov., is proposed. The type strain of Mariniluteicoccus flavus is YIM M13146T ( = DSM 25892T = CCTCC AB 2012055T).
Morphological reports on two species of Dexiotricha (Ciliophora, Scuticociliatia), with a note on the phylogenetic position of the genus
Authors: Fan Xinpeng , Al-Farraj Saleh A. , Gao Feng , Gu Fukang
Published: December 2013

TwoDexiotrichaspecies (Dexiotrichaellipticanov. comb. andDexiotrichacf.granulosa), respectively isolated from soil north-west of Riyadh, Saudi Arabia, and freshwater in Shanghai, eastern China, were investigated using standard methods. The speciesLoxocephalus ellipticusKahl, 1931 is reclassified here in the genusDexiotrichaand was characterized mainly by constantly showing 16 somatic kineties, three post-oral kineties with the middle one shortened, a contractile vacuole located subcaudally with an excretory pore near the posterior end of somatic kinety 2 and single caudal cilia. ADexiotricha granulosa-like organism having a subcaudally located contractile vacuole and fewer somatic kineties was designatedD.cf.granulosa.The small-subunit rRNA gene (SSU rDNA) sequences of these two species were characterized and their phylogenetic positions based on SSU rDNA sequences were revealed by means of Bayesian inference and maximum-likelihood analysis. Phylogenetic analyses confirmedDexiotrichaas a monophyletic genus and supported its assignment to the order Loxocephalida. However, its family assignment remains unsupported.