bluuebunny/crossref_metadata_2025 huggingface dataset:
Rate region of unicast routing networks
Authors: Liu Yantao , Morgan Yasser
Published: September 2016

Rate region precisely measures the transmission ability of a network. Three graph processing techniques are presented: reduced graph, union reduced graph, and virtual node. Applying these techniques, an operable method to completely solve the calculation of rate regions for unicast routing networks is developed. The correctness of the method is proved theoretically and illustrated with an example. This method is helpful in both theoretical perspective and industrial implementation.
Magnitude–frequency responses of fractional order systems: properties and subsequent results
Authors: Tavazoei Mohammad Saleh
Published: September 2016

This study deals with the properties of magnitude–frequency responses in fractional order systems. Using Phragmén–Lindelöf theorem in complex analysis, it is shown that the supremum of the magnitude–frequency response of a fractional system with a commensurate order less than one cannot be greater than that of its integer order bounded‐input, bounded‐output stable counterpart. Further results are also obtained on magnitude–frequency response of stable/unstable fractional order systems. Moreover, it is found that the supremum (infimum) of the magnitude‐scaling frequency of the family of fractional order systems having a fixed structure and different orders in the range (0, 2) is a piecewise logarithmically convex (concave) function of the scaling frequency. On the basis of the properties of magnitude–frequency responses in fractional order systems, some sample consequent results which are useful in analysis of fractional order circuits and systems are derived. These results are validated by various numerical examples.
Automatic measurement method for the size of large forgings based on scattering on rough surface
Authors: Zhang Yu‐Cun , Luo Cheng , Fu Xian‐Bin , Chen Yi‐Ming
Published: September 2016

The size measurement of large hot forgings plays an important role during the process of production. In order to realise the size measurement of large forgings in thermal state, an automatic size measurement method for large forgings based on the scattering of rough surface is proposed in this study. In the method, the theory of random facets is applied to research the characteristic of laser scattering on the surface of hot forgings. The model of laser scattering on the random rough surface of cylinder is built. According to the model, the edges of forgings can be detected and the size of forgings can be got. First, the charge coupled device (CCD) camera and the green laser are driven by the motor to move on the guide rail. The real‐time images of forgings are captured by CCD camera and the positional information of laser is acquired by pulse coder. Then according to the change of the intensity of the scattered light, whether the laser line is on the edge of forgings is decided. Second, the positional information of two edges is got by pulse coder and the size of forgings is figured out by the positional information. Finally, the feasibility of the method is verified by the experiment of size measurement.
Pinched hysteresis loops and symmetry
Authors: Wang Xiao‐Meng , Hui Shu‐Yuen Ron
Published: September 2016

Pinched hysteresis loops (PHLs) can be clockwise, counter‐clockwise, self‐crossing and non‐self‐crossing. While it is difficult to differentiate these features from the measured PHLs on the oscilloscope, this study shows that PHL exhibits different forms of symmetry. Self‐crossing PHLs display reflection symmetry and non‐self‐crossing ones display point symmetry. These features are confirmed with practical measurements based on the memristor characteristics of Hewlett‐Packard (self‐crossing) and of a discharge lamp (non‐self‐crossing). It is shown that the symmetry graph is a useful tool to identify the features of PHLs.
Electron density profile measurements from hydrogen line intensity ratio method in Versatile Experiment Spherical Torus
Authors: Kim YooSung , Shi Yue-Jiang , Yang Jeong-hun , Kim SeongCheol , Kim Young-Gi , Dang Jeong-Jeung , Yang Seongmoo , Jo Jungmin , Oh Soo-Ghee , Chung Kyoung-Jae , Hwang Y. S.
Published: September 2016

Electron density profiles of versatile experiment spherical torus plasmas are measured by using a hydrogen line intensity ratio method. A fast-frame visible camera with appropriate bandpass filters is used to detect images of Balmer line intensities. The unique optical system makes it possible to take images of Hα and Hβ radiation simultaneously, with only one camera. The frame rate is 1000 fps and the spatial resolution of the system is about 0.5 cm. One-dimensional local emissivity profiles have been obtained from the toroidal line of sight with viewing dumps. An initial result for the electron density profile is presented and is in reasonable agreement with values measured by a triple Langmuir probe.
Modifications to the synthetic aperture microwave imaging diagnostic
Authors: Brunner K. J. , Chorley J. C. , Dipper N. A. , Naylor G. , Sharples R. M. , Taylor G. , Thomas D. A. , Vann R. G. L.
Published: September 2016

The synthetic aperture microwave imaging diagnostic has been operating on the MAST experiment since 2011. It has provided the first 2D images of B-X-O mode conversion windows and showed the feasibility of conducting 2D Doppler back-scattering experiments. The diagnostic heavily relies on field programmable gate arrays to conduct its work. Recent successes and newly gained experience with the diagnostic have led us to modify it. The enhancements will enable pitch angle profile measurements, O and X mode separation, and the continuous acquisition of 2D DBS data. The diagnostic has also been installed on the NSTX-U and is acquiring data since May 2016.
Hole transport in c-plane InGaN-based green laser diodes
Authors: Cheng Yang , Liu Jianping , Tian Aiqin , Zhang Feng , Feng Meixin , Hu Weiwei , Zhang Shuming , Ikeda Masao , Li Deyao , Zhang Liqun , Yang Hui
Published: September 2016

Hole transport in c-plane InGaN-based green laser diodes (LDs) has been investigated by both simulations and experiments. It is found that holes can overflow from the green double quantum wells (DQWs) at high current density, which reduces carrier injection efficiency of c-plane InGaN-based green LDs. A heavily silicon-doped layer right below the green DQWs can effectively suppress hole overflow from the green DQWs.
Boundedness of the mixed velocity-temperature derivative skewness in homogeneous isotropic turbulence
Authors: Tang S. L. , Antonia R. A. , Djenidi L. , Danaila L. , Zhou Y.
Published: September 2016

The transport equation for the mean scalar dissipation rate ϵ¯θ is derived by applying the limit at small separations to the generalized form of Yaglom’s equation in two types of flows, those dominated mainly by a decay of energy in the streamwise direction and those which are forced, through a continuous injection of energy at large scales. In grid turbulence, the imbalance between the production of ϵ¯θ due to stretching of the temperature field and the destruction of ϵ¯θ by the thermal diffusivity is governed by the streamwise advection of ϵ¯θ by the mean velocity. This imbalance is intrinsically different from that in stationary forced periodic box turbulence (or SFPBT), which is virtually negligible. In essence, the different types of imbalance represent different constraints imposed by the large-scale motion on the relation between the so-called mixed velocity-temperature derivative skewness ST and the scalar enstrophy destruction coefficient Gθ in different flows, thus resulting in non-universal approaches of ST towards a constant value as Reλ increases. The data for ST collected in grid turbulence and in SFPBT indicate that the magnitude of ST is bounded, this limit being close to 0.5.
First neutron spectroscopy measurements with a pixelated diamond detector at JET
Authors: Muraro A. , Giacomelli L. , Nocente M. , Rebai M. , Rigamonti D. , Belli F. , Calvani P. , Figueiredo J. , Girolami M. , Gorini G. , Grosso G. , Murari A. , Popovichev S. , Trucchi D. M. , Tardocchi M. ,   JET Contributors
Published: September 2016

A prototype Single crystal Diamond Detector (SDD) was installed at the Joint European Torus (JET) in 2013 along an oblique line of sight and demonstrated the possibility to carry out neutron spectroscopy measurements with good energy resolution and detector stability in discharges heated by neutral beam injection and radio-frequency waves. Starting from these positive results, within the Vertical Neutron Spectrometer project of the Joint European Torus, we have developed a pixelated instrument consisting of a matrix of 12 independent SDDs, called the Diamond Vertical Neutron Spectrometer (DVNS), which boosts the detection efficiency of a single SDD by an order of magnitude. In this paper we describe the main features of the DVNS, including the detector design, energy resolution, and data acquisition system for on-line processing. Preliminary spectroscopy measurements of 2.5 MeV neutrons from the present deuterium plasma at JET are finally presented.
Angle-dependent strong-field molecular ionization rates with tuned range-separated time-dependent density functional theory
Authors: Sissay Adonay , Abanador Paul , Mauger François , Gaarde Mette , Schafer Kenneth J. , Lopata Kenneth
Published: September 2016

Strong-field ionization and the resulting electronic dynamics are important for a range of processes such as high harmonic generation, photodamage, charge resonance enhanced ionization, and ionization-triggered charge migration. Modeling ionization dynamics in molecular systems from first-principles can be challenging due to the large spatial extent of the wavefunction which stresses the accuracy of basis sets, and the intense fields which require non-perturbative time-dependent electronic structure methods. In this paper, we develop a time-dependent density functional theory approach which uses a Gaussian-type orbital (GTO) basis set to capture strong-field ionization rates and dynamics in atoms and small molecules. This involves propagating the electronic density matrix in time with a time-dependent laser potential and a spatial non-Hermitian complex absorbing potential which is projected onto an atom-centered basis set to remove ionized charge from the simulation. For the density functional theory (DFT) functional we use a tuned range-separated functional LC-PBE*, which has the correct asymptotic 1/r form of the potential and a reduced delocalization error compared to traditional DFT functionals. Ionization rates are computed for hydrogen, molecular nitrogen, and iodoacetylene under various field frequencies, intensities, and polarizations (angle-dependent ionization), and the results are shown to quantitatively agree with time-dependent Schrödinger equation and strong-field approximation calculations. This tuned DFT with GTO method opens the door to predictive all-electron time-dependent density functional theory simulations of ionization and ionization-triggered dynamics in molecular systems using tuned range-separated hybrid functionals.
Effect of transition metal impurities on the strength of grain boundaries in vanadium
Authors: Wu Xuebang , Kong Xiang-Shan , You Yu-Wei , Liu Wei , Liu C. S. , Chen Jun-Ling , Luo G.-N.
Published: September 2016

Effects of 3d (Ti-Ni), 4d (Zr-Pd), and 5d (Hf-Pt) transition metal impurities on strength of two representative vanadium grain boundaries (GBs), symmetric Σ3(111) and asymmetric Σ5(210), were studied by first-principles calculations within the framework of the Rice-Wang thermodynamic model and within the computational tensile test. The desirable elements to increase the GB cohesion were predicted based on their segregation and strengthening behaviors across the different GB sites. It reveals that the elements Ti, Zr, Hf, Nb, and Ta are good choices for the GB cohesion enhancers. In addition, the GB strengthening by solutes is sensitive to the GB structures. The elements Cr, Mn, Fe, Co, and Ni decrease the GB strength of the Σ3(111) GB but they can increase the cohesion of the Σ5(210) GB. Furthermore, the origin of Ti-induced change of the GB strength was uncovered by analyzing the atomic bonds and electronic structures as well as the tensile strength. This work provides a theoretical guidance to screen promising alloying elements in V-based materials with improved resistance to GB decohesion and also helps us to understand the formation mechanism of Ti-rich precipitates in the V-Cr-Ti alloys under neutron or ion irradiation environments.
Role of the inversion layer on the charge injection in silicon nanocrystal multilayered light emitting devices
Authors: Tondini S. , Pucker G. , Pavesi L.
Published: September 2016

The role of the inversion layer on injection and recombination phenomena in light emitting diodes (LEDs) is here studied on a multilayer (ML) structure of silicon nanocrystals (Si-NCs) embedded in SiO2. Two Si-NC LEDs, which are similar for the active material but different in the fabrication process, elucidate the role of the non-radiative recombination rates at the ML/substrate interface. By studying current- and capacitance-voltage characteristics as well as electroluminescence spectra and time-resolved electroluminescence under pulsed and alternating bias pumping scheme in both the devices, we are able to ascribe the different experimental results to an efficient or inefficient minority carrier (electron) supply by the p-type substrate in the metal oxide semiconductor LEDs.
Temperature and field dependent low frequency noise characterization of Ge n-FETs
Authors: Ghosh Sayantan , Bhatt Piyush , Tiwari Yogesh , Joishi Chandan , Lodha Saurabh
Published: September 2016

We report temperature (RT-150 K) and field dependent low frequency noise measurements on Ge n-FETs. Specifically, we delineate the temperature, field, and interfacial layer (GeON vs. GeO2) dependence of the gate overdrive index (β) on corresponding changes in volume interface trap density (Nit) and mobility (μ). For Nit < 1 × 1020 cm−3 eV−1, the dominant noise mechanism, number or mobility fluctuation, depends on the change in μ, but for Nit > 1 × 1020 cm−3eV−1 near the conduction band edge, changes in μ as well as Nit determine the noise mechanism. Finally, we show that the β values of Ge n-FETs are significantly different from conventional Si transistors as well as Ge p-FETs at RT and 150 K due to much higher Nit and/or μ values of the Ge n-FETs.
Very thin and stable thin-film silicon alloy triple junction solar cells by hot wire chemical vapor deposition
Authors: Veldhuizen L. W. , Schropp R. E. I.
Published: September 2016

We present a silicon-based triple junction solar cell that requires a deposition time of less than 15 min for all photoactive layers. As a low-bandgap material, we used thin layers of hydrogenated amorphous silicon germanium with lower band gap than commonly used, which is possible due to the application of hot wire chemical vapor deposition. The triple junction cell shows an initial energy conversion efficiency exceeding 10%, and with a relative performance stability within 6%, the cell shows a high tolerance to light-induced degradation. With these results, we help to demonstrate that hot wire chemical vapor deposition is a viable deposition method for the fabrication of low-cost solar cells.
Size dictated thermal conductivity of GaN
Authors: Beechem Thomas E. , McDonald Anthony E. , Fuller Elliot J. , Talin A. Alec , Rost Christina M. , Maria Jon-Paul , Gaskins John T. , Hopkins Patrick E. , Allerman Andrew A.
Published: September 2016

The thermal conductivity of n- and p-type doped gallium nitride (GaN) epilayers having thicknesses of 3–4 μm was investigated using time domain thermoreflectance. Despite possessing carrier concentrations ranging across 3 decades (1015–1018 cm–3), n-type layers exhibit a nearly constant thermal conductivity of 180 W/mK. The thermal conductivity of p-type epilayers, in contrast, reduces from 160 to 110 W/mK with increased doping. These trends—and their overall reduction relative to bulk—are explained leveraging established scattering models where it is shown that, while the decrease in p-type layers is partly due to the increased impurity levels evolving from its doping, size effects play a primary role in limiting the thermal conductivity of GaN layers tens of microns thick. Device layers, even of pristine quality, will therefore exhibit thermal conductivities less than the bulk value of 240 W/mK owing to their finite thickness.
The effect of cavity tuning on oxygen beam currents of an A-ECR type 14 GHz electron cyclotron resonance ion source
Authors: Tarvainen O. , Orpana J. , Kronholm R. , Kalvas T. , Laulainen J. , Koivisto H. , Izotov I. , Skalyga V. , Toivanen V.
Published: September 2016

The efficiency of the microwave-plasma coupling plays a significant role in the production of highly charged ion beams with electron cyclotron resonance ion sources (ECRISs). The coupling properties are affected by the mechanical design of the ion source plasma chamber and microwave launching system, as well as damping of the microwave electric field by the plasma. Several experiments attempting to optimize the microwave-plasma coupling characteristics by fine-tuning the frequency of the injected microwaves have been conducted with varying degrees of success. The inherent difficulty in interpretation of the frequency tuning results is that the effects of microwave coupling system and the cavity behavior of the plasma chamber cannot be separated. A preferable approach to study the effect of the cavity properties of the plasma chamber on extracted beam currents is to adjust the cavity dimensions. The results of such cavity tuning experiments conducted with the JYFL 14 GHz ECRIS are reported here. The cavity properties were adjusted by inserting a conducting tuner rod axially into the plasma chamber. The extracted beam currents of oxygen charge states O3+–O7+ were recorded at various tuner positions and frequencies in the range of 14.00–14.15 GHz. It was observed that the tuner position affects the beam currents of high charge state ions up to several tens of percent. In particular, it was found that at some tuner position / frequency combinations the plasma exhibited “mode-hopping” between two operating regimes. The results improve the understanding of the role of plasma chamber cavity properties on ECRIS performances.
Sensitivity of magnetic field-line pitch angle measurements to sawtooth events in tokamaks
Authors: Ko J.
Published: September 2016

The sensitivity of the pitch angle profiles measured by the motional Stark effect (MSE) diagnostic to the evolution of the safety factor, q, profiles during the tokamak sawtooth events has been investigated for Korea Superconducting Tokamak Advanced Research (KSTAR). An analytic relation between the tokamak pitch angle, γ, and q estimates that Δγ ∼ 0.1° is required for detecting Δq ∼ 0.05 near the magnetic axis (not at the magnetic axis, though). The pitch angle becomes less sensitive to the same Δq for the middle and outer regions of the plasma (Δγ ∼ 0.5°). At the magnetic axis, it is not straightforward to directly relate the γ sensitivity to Δq since the gradient of γ(R), where R is the major radius of the tokamak, is involved. Many of the MSE data obtained from the 2015 KSTAR campaign, when calibrated carefully, can meet these requirements with the time integration down to 10 ms. The analysis with the measured data shows that the pitch angle profiles and their gradients near the magnetic axis can resolve the change of the q profiles including the central safety factor, q0, during the sawtooth events.
First results from solid state neutral particle analyzer on experimental advanced superconducting tokamak
Authors: Zhang J. Z. , Zhu Y. B. , Zhao J. L. , Wan B. N. , Li J. G. , Heidbrink W. W.
Published: September 2016

Full function integrated, compact solid state neutral particle analyzers (ssNPA) based on absolute extreme ultraviolet silicon photodiode have been successfully implemented on the experimental advanced superconducting tokamak to measure energetic particle. The ssNPA system has been operated in advanced current mode with fast temporal and spatial resolution capabilities, with both active and passive charge exchange measurements. It is found that the ssNPA flux signals are increased substantially with neutral beam injection (NBI). The horizontal active array responds to modulated NBI beam promptly, while weaker change is presented on passive array. Compared to near-perpendicular beam, near-tangential beam brings more passive ssNPA flux and a broader profile, while no clear difference is observed on active ssNPA flux and its profile. Significantly enhanced intensities on some ssNPA channels have been observed during ion cyclotron resonant heating.
Automated analysis of hot spot X-ray images at the National Ignition Facility
Authors: Khan S. F. , Izumi N. , Glenn S. , Tommasini R. , Benedetti L. R. , Ma T. , Pak A. , Kyrala G. A. , Springer P. , Bradley D. K. , Town R. P. J.
Published: September 2016

At the National Ignition Facility, the symmetry of the hot spot of imploding capsules is diagnosed by imaging the emitted x-rays using gated cameras and image plates. The symmetry of an implosion is an important factor in the yield generated from the resulting fusion process. The x-ray images are analyzed by decomposing the image intensity contours into Fourier and Legendre modes. This paper focuses on the additional protocols for the time-integrated shape analysis from image plates. For implosions with temperatures above ∼4 keV, the hard x-ray background can be utilized to infer the temperature of the hot spot.
A streak camera based fiber optic pulsed polarimetry technique for magnetic sensing to sub-mm resolution
Authors: Smith R. J. , Weber T. E.
Published: September 2016

The technique of fiber optic pulsed polarimetry, which provides a distributed (local) measurement of the magnetic field along an optical fiber, has been improved to the point where, for the first time, photocathode based optical detection of backscatter is possible with sub-mm spatial resolutions. This has been realized through the writing of an array of deterministic fiber Bragg gratings along the fiber, a so-called backscatter-tailored optical fiber, producing a 34 000-fold increase in backscatter levels over Rayleigh. With such high backscatter levels, high repetition rate lasers are now sufficiently bright to allow near continuous field sensing in both space and time with field resolutions as low as 0.005 T and as high as 170 T over a ∼mm interval given available fiber materials.
Suppression of alloy fluctuations in GaAs-AlGaAs core-shell nanowires
Authors: Loitsch Bernhard , Jeon Nari , Döblinger Markus , Winnerl Julia , Parzinger Eric , Matich Sonja , Wurstbauer Ursula , Riedl Hubert , Abstreiter Gerhard , Finley Jonathan J. , Lauhon Lincoln J. , Koblmüller Gregor
Published: September 2016

Probing localized alloy fluctuations and controlling them by growth kinetics have been relatively limited so far in nanoscale structures such as semiconductor nanowires (NWs). Here, we demonstrate the tuning of alloy fluctuations in molecular beam epitaxially grown GaAs-AlGaAs core-shell NWs by modifications of shell growth temperature, as investigated by correlated micro-photoluminescence, scanning transmission electron microscopy, and atom probe tomography. By reducing the shell growth temperature from T > 600 °C to below 400 °C, we find a strong reduction in alloy fluctuation mediated sharp-line luminescence, concurrent with a decrease in the non-randomness of the alloy distribution in the AlGaAs shell. This trend is further characterized by a change in the alloy compositional structure from unintentional quasi-superlattices of Ga- and Al-rich AlGaAs layers at high T to a nearly homogeneous random alloy distribution at low T.
Enhanced gamma ray sensitivity in bismuth triiodide sensors through volumetric defect control
Authors: Johns Paul M. , Baciak James E. , Nino Juan C.
Published: September 2016

Some of the more attractive semiconducting compounds for ambient temperature radiation detector applications are impacted by low charge collection efficiency due to the presence of point and volumetric defects. This has been particularly true in the case of BiI3, which features very attractive properties (density, atomic number, band gap, etc.) to serve as a gamma ray detector, but has yet to demonstrate its full potential. We show that by applying growth techniques tailored to reduce defects, the spectral performance of this promising semiconductor can be realized. Gamma ray spectra from >100 keV source emissions are now obtained from high quality Sb:BiI3 bulk crystals with limited concentrations of defects (point and extended). The spectra acquired in these high quality crystals feature photopeaks with resolution of 2.2% at 662 keV. Infrared microscopy is used to compare the local microstructure between radiation sensitive and non-responsive crystals. This work demonstrates that BiI3 can be prepared in melt-grown detector-grade samples with superior quality and can acquire the spectra from a variety of gamma ray sources.
Differences in cooperative behavior among Damaraland mole rats are consequences of an age-related polyethism
Authors: Zöttl Markus , Vullioud Philippe , Mendonça Rute , Torrents Ticó Miquel , Gaynor David , Mitchell Adam , Clutton-Brock Tim
Published: September 2016

Significance

Nonreproductive group members of naked and Damaraland mole rats are thought to be organized in permanent, distinct castes that differ in behavior and physiology, suggesting that their social organization resembles that of obligatorily eusocial insects. This study tests predictions about the distribution of cooperative behavior based on the suggestion that individual differences represent a caste system. Our data provide no evidence that helpers show fixed, divergent developmental pathways or specialize in particular tasks. Instead, variation in their behavior appears to represent an age-related polyethism. The results suggest that the behavioral organization of social mole-rat groups is similar to that of other singular cooperatively breeding vertebrates, and that similarities to obligatorily eusocial insects have been overestimated.
Academic achievement and language proficiency in early total Mandarin immersion education
Authors: Fortune Tara , Song Wei
Published: September 2016

Two types of Mandarin immersion programs for elementary age children are growing in popularity: the early total (90/10) program model and the partial (50/50) model; however, little empirical data exists on student learning in either program type. This paper reports on a multi-year research study of K–5 students who participated in the early total Mandarin immersion program. Findings show achievement in English reading and math that is commensurate with, and at times better than grade-level non-immersion peers’ achievement in the same school, district, and state. There was also evidence of a “math advantage” for the Mandarin immersion learner group both in Grades 3 and 5. Beyond academics, the majority of Grade 5 students demonstrated proficiency in Mandarin at Intermediate levels with listening and speaking skills outpacing character writing and reading. This finding suggests a need to further explore character literacy development to better understand best practice for English-proficient children in the U.S.
Can speakers’ virtual lexical richness be calculated?
Authors: Ávila Muñoz Antonio Manuel
Published: September 2016

The aim of this paper is to show an original method of calculating individual lexical richness. This method leads to a non-linear optimization. A randomized algorithm, Simulated Annealing, is used in order to carry out the optimization. This procedure has allowed us to represent a function from which we obtain a reliable pattern for lexical estimation. Furthermore, this method is compatible with other traditional procedures used for the estimation of lexical richness. Therefore, in this work we have taken an alternative and more general approach: we wish to calculate the virtual richness of the individual’s vocabulary. In order to validate the new model that calculates lexical richness, we carried out a pilot study based on the subjects’ sociolinguistic patterns that govern their lexical richness. We have explored the lexical variation of the Spanish system that occurs during the oral exchanges of 86 speakers born in Malaga.
Selected dehydrogenases in Yarrowia lipolytica JMY 861: their role in the synthesis of flavor compounds
Authors: Aziz Marya , St-Louis Richard , Husson Florence , Kermasha Selim
Published: September 2016

The presence of selected dehydrogenases, including alcohol dehydrogenase (ADH-YL) and aldehyde dehydrogenase (ALDH-YL), in Yarrowia lipolytica JMY 861, and their potential role in flavor synthesis were investigated. The experimental findings showed that using reduced form of nicotinamide adenine dinucleotide (NADH) as cofactor, the ADH-YL activity in vitro was 6-fold higher than that with reduced form of nicotinamide adenine dinucleotide phosphate (NADPH); however, under the experimental conditions used in this study, an ALDH-YL activity was not detected. The in situ hexanal reduction reaction was found to be instantaneous; however, when the yeast cells suspension was diluted 150 times, the initial relative hexanal concentration was increased by 84.1%. The chromatographic analyses indicated the conversion, in situ, of linoleic acid hydroperoxides (HPODs) into volatile C6-compounds after 60 min of HPODs addition to the yeast cells suspension.
Comparison of Phytoplankton Communities in Catfish Split-Pond Aquaculture Systems with Conventional Ponds
Authors: Schrader Kevin K , Tucker Craig S , Brown Travis W , Torrans Eugene L , Whitis Gregory N
Published: September 2016

There has been a growing interest and use of variations of partitioned aquaculture systems (PAS) in recent years by the southeastern U.S. catfish farming industry. Split-pond systems, one type of PAS, are designed to better manage fish waste byproducts (e.g., ammonia) and dissolved oxygen levels than the conventional earthen ponds that have been used by farmers for many decades. Recent studies have focused on design, water flow rates, and other management areas of catfish split-ponds, but so far there has not been a focused examination of phytoplankton community composition and biomass in these split-ponds. In the current study, pond water samples were collected from split-ponds at a research facility in western Mississippi and at a commercial fish farm in western Alabama approximately every 3 weeks during the fish grow-out period (May to November). Water samples were analyzed for chlorophyll a concentration (phytoplankton biomass) of several major phytoplankton divisions and for types of phytoplankton and their abundance. Overall, chlorophyll a concentrations in the split-ponds were maintained within the typical range (0–800 µg/L) found in non-PAS (conventional) catfish ponds. The phytoplankton communities in split-ponds were dominated by cyanobacteria or blue-green algae (Cyanophyta) and by the same common species of cyanobacteria (e.g., Planktothrix agardhii, P. perornata, Microcystis aeruginosa, Raphidiopsis brookii) reported in previous studies for conventional catfish ponds. In addition, many types of phytoplankton in the other major divisions—Chlorophyta (green algae), Bacillariophyta (diatoms), Chrysophyta (golden brown algae), Cryptophyta (cryptomonads), Euglenophyta (euglenophytes), and Pyrrhophyta (dinoflagellates)—present in the split-ponds were the same as those reported previously in conventional catfish ponds. Therefore, issues related to management practices for pond water quality (e.g., dissolved oxygen) and undesirable cyanobacteria are expected to be similar to those used for conventional ponds.
Optimization of a mirror-based neutron source using differential evolution algorithm
Authors: Yurov D.V. , Prikhodko V.V.
Published: September 2016

This study is dedicated to the assessment of capabilities of gas-dynamic trap (GDT) and gas-dynamic multiple-mirror trap (GDMT) as potential neutron sources for subcritical hybrids. In mathematical terms the problem of the study has been formulated as determining the global maximum of fusion gain (Q
pl), the latter represented as a function of trap parameters. A differential evolution method has been applied to perform the search. Considered in all calculations has been a configuration of the neutron source with 20 m long distance between the mirrors and 100 MW heating power. It is important to mention that the numerical study has also taken into account a number of constraints on plasma characteristics so as to provide physical credibility of searched-for trap configurations. According to the results obtained the traps considered have demonstrated fusion gain up to 0.2, depending on the constraints applied. This enables them to be used either as neutron sources within subcritical reactors for minor actinides incineration or as material-testing facilities.
Cooperative DNA binding by a splice variant of the transcription factor ETS1 that lacks autoinhibition
Authors: Samorodnitsky Daniel , Szyjka Courtney , Koudelka Gerald B.
Published: September 2016

ETS1 is the archetypal member of the metazoan ETS transcription factor family. All the members of this family bind to the conserved GGA(A/T) core ETS binding sequence (EBS). Several ETS family members exhibit autoinhibition, wherein one domain of ETS blocks its own DNA-binding activity until certain conditions are met. Relief of autoinhibition in these proteins is coupled to homo- or hetero-dimer formation. Relief of autoinhibition in full-length ETS1 is catalyzed by non-specific interaction with DNA, which facilitates the formation of protein dimers.The ETS1 splice variant, ETS1-p42, lacks an exon that encodes a crucial part of the autoinhibitory module. Thus,ETS1-p42 does not autoinhibit. We showed that the absence of autoinhibition allows ETS1Δ335, an N-terminal deletion that recapitulates the DNA-binding of ETS1-p42, to form homodimers in the absence of DNA. However, ETS1-p42 is thought to bind its DNA sites only as monomers. Here, we explore this paradox and show that ETS1Δ335 binds cooperatively to DNA containing two EBSs. We also show that residues in ETS1’s DNA recognition helix mediate this DNA-binding cooperativity. Furthermore we also find that a single EBS can bind two ETS1Δ335 subunits. Finally, we show that DNA acts catalytically to separate unbound ETS1Δ335 dimers into monomers. Together,these results suggest a model of ETS1-p42 DNA-binding, where ETS1-p42 can bind to a single EBS with 2:1 stoichiometry.
The impacts of drift and selection on genomic evolution in holometabolous insects
Authors: Tong K. Jun , Duchêne Sebastián , Lo Nathan , Ho Simon Y. W.
Published: September 2016

Genomes evolve through a medley of mutation, drift, and selection, all of which act heterogeneously across genes and lineages. The pacemaker models of genomic evolution describe the resulting patterns of evolutionary rate variation: genes that are governed by the same pacemaker exhibit the same pattern of rate heterogeneity across lineages. However, the relative importance of drift and selection in determining the structure of these pacemakers is unknown. Here, we propose a novel phylogenetic approach to explain the formation of pacemakers. We apply this method to a genomic dataset from holometabolous insects, an ancient and diverse group of organisms. We show that when drift is the dominant evolutionary process, each pacemaker tends to govern a large number of fast-evolving genes. In contrast, strong negative selection leads to many distinct pacemakers, each of which governs a few slow-evolving genes. Our results provide new insights into the interplay between drift and selection in driving genomic evolution.
Cost Effective Acoustic Monitoring of Biodiversity and Bird Populations in Kenya
Authors: wa Maina Ciira , Muchiri David , Njoroge Peter
Published: September 2016

With the increasing need to effectively monitor a growing number of ecosystems of interest due to risks posed to these ecosystems by human activity and climate change, novel approaches to biodiversity monitoring are needed. In this work we demonstrate the application of low cost acoustic recorders based on the Raspberry Pi microprocessor to biodiversity monitoring. The recorders are capable of capturing audio recordings from which we can compute acoustic indices of biodiversity and identify bird species of interest. We compare the acoustic indices of biodiversity and results of point counts aimed at determining bird species presence and find that the acoustic complexity index has a significant positive correlation to point count results. In addition, we show that the presence of the Hartlaub’s Turaco, a ubiquitous species in montane forests in Kenya with a distinct call, can be automatically determined using recordings obtained using our setup. Montane species are of interest for long-term automatic monitoring since they are particularly vulnerable to the effects of climate change. Our system is able to deal with the large amounts of data generated by the acoustic recorders. The automatic screening of approximately five hours of recordings for presence of the Hartlaub’s Turaco call is achieved in approximately three minutes representing a large time saving that makes use of audio recordings for species identification feasible.
dms2dfe: Comprehensive Workflow for Analysis of Deep Mutational Scanning Data
Authors: Dandage Rohan , Chakraborty Kausik
Published: September 2016

High throughput genotype to phenotype (G2P) data is increasingly being generated by widely applicable Deep Mutational Scanning (DMS) method. dms2dfe is a comprehensive end-to-end workflow that addresses critical issue with noise reduction and offers variety of crucial downstream analyses. Noise reduction is carried out by normalizing counts of mutants by depth of sequencing and subsequent dispersion shrinkage at the level of calculation of preferential enrichments. In downstream analyses, dms2dfe workflow provides identification of relative selection pressures, potential molecular constraints and generation of data-rich visualizations.

Availability

dms2dfe is implemented as a python package and it is available athttps://kc-lab.github.io/dms2dfe.

Contact

kausik@igib.in,rohan@igib.in

Supplementary information

Supplementary data are available at Bioinformatics online.
Targeted reconstruction of T cell receptor sequence from single cell RNA-sequencing links CDR3 length to T cell differentiation state
Authors: Afik Shaked , Yates Kathleen B. , Bi Kevin , Darko Samuel , Godec Jernej , Gerdemann Ulrike , Swadling Leo , Douek Daniel C. , Klenerman Paul , Barnes Eleanor J. , Sharpe Arlene H. , Haining W. Nicholas , Yosef Nir
Published: September 2016

The T cell compartment must contain diversity in both TCR repertoire and cell state to provide effective immunity against pathogens1,2. However, it remains unclear how differences in the TCR contribute to heterogeneity in T cell state at the single cell level because most analysis of the TCR repertoire has, to date, aggregated information from populations of cells. Single cell RNA-sequencing (scRNA-seq) can allow simultaneous measurement of TCR sequence and global transcriptional profile from single cells. However, current protocols to directly sequence the TCR require the use of long sequencing reads, increasing the cost and decreasing the number of cells that can be feasibly analyzed. Here we present a tool that can efficiently extract TCR sequence information from standard, short-read scRNA-seq libraries of T cells: TCR Reconstruction Algorithm for Paired-End Single cell (TRAPeS). We apply it to investigate heterogeneity in the CD8+T cell response in humans and mice, and show that it is accurate and more sensitive than previous approaches3,4. We applied TRAPeS to single cell RNA-seq of CD8+T cells specific for a single epitope from Yellow Fever Virus5. We show that the recently-described "naive-like" memory population of YFV-specific CD8+T cells have significantly longer CDR3 regions and greater divergence from germline sequence than do effector-memory phenotype CD8+T cells specific for YFV. This suggests that TCR usage contributes to heterogeneity in the differentiation state of the CD8+T cell response to YFV. TRAPeS is publicly available, and can be readily used to investigate the relationship between the TCR repertoire and cellular phenotype.
Schizophrenia and human self-domestication: an evolutionary linguistics approach
Authors: Benítez-Burraco Antonio , Pietro Lorena Di , Barba Marta , Lattanzi Wanda
Published: September 2016

Schizophrenia (SZ) is a pervasive neurodevelopmental disorder entailing social and cognitive deficits, including marked problems with language. Its complex multifactorial etiopathogenesis, including genetic and environmental factors, is still widely uncertain. SZ incidence has always been high and quite stable in human populations, across time and regardless of cultural implications, due to unclear reasons. It has been hypothesised that SZ pathophysiology may involve the biological components that changed during the recent human evolutionary history and led to our distinctive mode of cognition, which includes language skills. In this paper we explore this possibility, focusing on the self-domestication of the human species. This has been claimed to account for many human-specific distinctive traits, including aspects of our behaviour and cognition, and to favour the emergence of complex languages through cultural evolution. The “domestication syndrome” in mammals comprises the constellation of traits exhibited by domesticated strains, seemingly resulting from the hypofunction of the neural crest. It is our intention to show that people with SZ exhibit more marked domesticated traits at the morphological, physiological, and behavioural levels. We also show that genes involved in domestication and neural crest development and function comprise nearly 20% SZ candidates, most of which exhibit altered expression profiles in the brain of SZ patients, specifically in areas involved in language processing. Based on these observations, we conclude that SZ may represent an abnormal ontogenetic itinerary for the human faculty of language, resulting, at least in part, from changes in genes important for the “domestication syndrome” and, primarily involving the neural crest.
Contig annotation tool CAT robustly classifies assembled metagenomic contigs and long sequences
Authors: Cambuy Diego D. , Coutinho Felipe H. , Dutilh Bas E.
Published: September 2016

In modern-day metagenomics, there is an increasing need for robust taxonomic annotation of long DNA sequences from unknown micro-organisms. Long metagenomic sequences may be derived from assembly of short-read metagenomes, or from long-read single molecule sequencing. Here we introduce CAT, a pipeline for robust taxonomic classification of long DNA sequences. We show that CAT correctly classifies contigs at different taxonomic levels, even in simulated metagenomic datasets that are very distantly related from the sequences in the database. CAT is implemented in Python and the required scripts can be freely downloaded from Github.
Dissecting the genetics of complex traits using summary association statistics
Authors: Pasaniuc Bogdan , Price Alkes L.
Published: September 2016

During the past decade, genome-wide association studies (GWAS) have successfully identified tens of thousands of genetic variants associated with complex traits and diseases. These studies have produced vast repositories of genetic variation and trait measurements across millions of individuals, providing tremendous opportunities for further analyses. However, privacy concerns and other logistical considerations often limit access to individual-level genetic data, motivating the development of methods that analyze summary association statistics. Here we review recent progress on statistical methods that leverage summary association data to gain insights into the genetic basis of complex traits and diseases.
Selective constraints on coding sequences of nervous system genes are a major determinant of duplicate gene retention in vertebrates
Authors: Roux Julien , Liu Jialin , Robinson-Rechavi Marc
Published: September 2016

The evolutionary history of vertebrates is marked by three ancient whole-genome duplications: two successive rounds in the ancestor of vertebrates, and a third one specific to teleost fishes. Biased loss of most duplicates enriched the genome for specific genes, such as slow evolving genes, but this selective retention process is not well understood. To understand what drives the long-term preservation of duplicate genes, we characterized duplicated genes in terms of their expression patterns. We used a new method of expression enrichment analysis, TopAnat, applied toin situhybridization data from thousands of genes from zebrafish and mouse. We showed that the presence of expression in the nervous system is a good predictor of a higher rate of retention of duplicate genes after whole-genome duplication. Further analyses suggest that purifying selection against the toxic effects of misfolded or misinteracting proteins, which is particularly strong in non-renewing neural tissues, likely constrains the evolution of coding sequences of nervous system genes, leading indirectly to the preservation of duplicate genes after whole-genome duplication. Whole-genome duplications thus greatly contributed to the expansion of the toolkit of genes available for the evolution of profound novelties of the nervous system at the base of the vertebrate radiation.
Two new two-dimensional coordination polymers based on isophthalate and a flexibleN-donor ligand containing benzimidazole and pyridine rings: synthesis, crystal structures and a solid-state UV–Vis study
Authors: Hasi Qi-Meige , Fan Yan , Hou Chen , Yao Xiao-Qiang , Liu Jia-Cheng
Published: September 2016

In coordination chemistry and crystal engineering, many factors influence the construction of coordination polymers and the final frameworks depend greatly on the organic ligands used.N-Donor ligands with diverse coordination modes and conformations have been employed to assemble metal–organic frameworks. Carboxylic acid ligands can deprotonate completely or partially when bonding to metal ions and can also act as donors or acceptors of hydrogen bonds and are thus good candidates for the construction of supramolecular architectures. Two new transition metal complexes, namely poly[diaqua(μ4-1,4-bis{[1-(pyridin-3-ylmethyl)-1H-benz[d]imidazol-2-yl]methoxy}benzene)bis(μ2-isophthalato)dicobalt(II)], [Co(C8H4O4)(C34H28N6O2)0.5(H2O)]n, (1), and poly[diaqua(μ4-1,4-bis{[1-(pyridin-3-ylmethyl)-1H-benz[d]imidazol-2-yl]methoxy}benzene)bis(μ2-isophthalato)dicadmium(II)], [Cd(C8H4O4)(C34H28N6O2)0.5(H2O)]n, have been constructed using a symmetricN-donor ligand and a carboxylate ligand under hydrothermal conditions. X-ray crystallographic studies reveal that complexes (1) and (2) are isostructural, both of them exhibiting three-dimensional supramolecular architectures built by hydrogen bonds in which the coordinated water molecules serve as donors, while the O atoms of the carboxylate groups act as acceptors. Furthermore, (1) and (2) have been characterized by elemental, IR spectroscopic, powder X-ray diffraction (PXRD) and thermogravimetric analyses. The UV–Vis absorption spectrum of complex (1) has also been investigated.