bluuebunny/crossref_metadata_2025 huggingface dataset:
Vitalized yeast with high ethanol productivity
Authors: Liu Xiumei , Xu Wenjuan , Zhang Chao , Yan Peifang , Jia Songyan , Xu Zhanwei , Zhang Z. Conrad
Published: October 2014

Yeast cells exo-protected by water soluble PEGs are tolerant to higher ethanol concentrations, and offer high ethanol productivity.
Ultra-high performance liquid chromatography coupled with time-of-flight mass spectrometry screening and analysis of potential bioactive compounds from traditional chinese medicine Kai-Xin-San, using a multivariate data processing approach and the MetaboLynx tool
Authors: Liu Chang , Zhang Aihua , Han Ying , Lu Shengwen , Sun Hui , Yan Guangli , Wang Ping , Wang Xijun
Published: October 2014

Traditional Chinese Medicine (TCM) has been used in clinical practice for several thousand years, with an indispensable role in prevention and treatment of disease using multiple ingredients.
Low-temperature facile solution-processed gate dielectric for combustion derived oxide thin film transistors
Authors: Wang Han , Sun Tieyu , Xu Wangying , Xie Fangyan , Ye Lei , Xiao Yubin , Wang Yu , Chen Jian , Xu Jianbin
Published: October 2014

An improved hydrophilic aluminum nitrate solution was designed to spin coat robust dielectric layers for thin film transistors.
In situ synthesis of hierarchical mesoporous Fe3O4@C nanowires derived from coordination polymers for high-performance lithium-ion batteries
Authors: Li Huanhuan , Xu Ruyu , Wang Yaping , Qian Binbin , Wang Hongbo , Chen Long , Jiang Haobin , Yang Yulu , Xu Yiyun
Published: October 2014

Hierarchical nanostructured Fe3O4@C mesoporous nanowires from Fe-based coordination polymers show superior electrochemical performance as anode materials for lithium-ion batteries.
Three-dimensional ultrathin Sn/polypyrrole nanosheet network as high performance lithium-ion battery anode
Authors: Fan Xin , Jiang Anni , Dou Peng , Ma Daqian , Xu Xinhua
Published: October 2014

A schematic depiction of the detailed structure of 3D Sn/PPy nanosheet network as a lithium ion battery anode material.
Polymer-immobilized chiral catalysts
Authors: Itsuno Shinichi , Hassan Md. Mehadi
Published: October 2014

This review illustrates the current strategies and potential of polymer-immobilized chiral catalysts for highly enantioselective asymmetric synthesis.
Direct conversion of cellulose into C6 alditols over Ru/C combined with H+-released boron phosphate in an aqueous phase
Authors: Liu Yong , Chen Lungang , Wang Tiejun , Xu Ying , Zhang Qi , Ma Longlong , Liao Yuhe , Shi Ning
Published: October 2014

Non-edible cellulose has considerable attention to be converted into valuable platform chemicals.
Copper-catalysed reductive amination of nitriles and organic-group reductions using dimethylamine borane
Authors: van der Waals Dominic , Pettman Alan , Williams Jonathan M. J.
Published: October 2014

A mild convenient method for the aqueous reduction of a range of organic functionalities and the reductive amination of nitriles using a heterogeneous copper catalyst formed in situ.
Ultrafast nano-spherical single-crystalline LiMn0.792Fe0.198Mg0.010PO4solid-solution confined among unbundled interstices of SGCNTs
Authors: Kisu Kazuaki , Iwama Etsuro , Onishi Wataru , Nakashima Shota , Naoi Wako , Naoi Katsuhiko
Published: October 2014

Spherical LiMn0.792Fe0.198Mg0.010PO4nanocrystals, which are highly dispersed and encapsulated within the interstices of supergrowth (single-walled) carbon nanotubes (SGCNTs), were successfully synthesized byin situmaterial processing technology called “ultra-centrifuging (UC) treatment”.
Full capacitance potential of SWCNT electrode in ionic liquids at 4 V
Authors: Yu Yuntao , Cui Chaojie , Qian Weizhong , Wei Fei
Published: October 2014

SWCNT electrode exhibited a capacitance of 16 μF cm−2 and an energy density of 107 W h kg−1 in a wide power density range at 4 V.
Comprehensive study of medium-bandgap conjugated polymer merging a fluorinated quinoxaline with branched side chains for highly efficient and air-stable polymer solar cells
Authors: Tseng Wei-Hsuan , Chen Hsieh-Chih , Chien Yun-Chen , Liu Chi-Chang , Peng Yung-Kang , Wu Yu-Sin , Chang Jung-Hung , Liu Shih-Hung , Chou Shang-Wei , Liu Chien-Liang , Chen Ying-Hsiao , Wu Chih-I. , Chou Pi-Tai
Published: October 2014

A new polymer solar cell with PCE of 6.36% and long-term stability.
Highly efficient fullerene/perovskite planar heterojunction solar cells via cathode modification with an amino-functionalized polymer interlayer
Authors: Xue Qifan , Hu Zhicheng , Liu Jiang , Lin Jiahui , Sun Chen , Chen Ziming , Duan Chunhui , Wang Jing , Liao Cheng , Lau Woon Ming , Huang Fei , Yip Hin-Lap , Cao Yong
Published: October 2014

A new amino-functionalized polymer, PN4N, was developed and applied as an efficient interlayer to improve the cathode interface of fullerene/perovskite (CH3NH3PbIxCl3−x) planar heterojunction solar cells.
Chemistry of active oxygen in RuOx and its influence on the atomic layer deposition of TiO2 films
Authors: Jeon Woojin , Lee Woongkyu , Yoo Yeon Woo , An Cheol Hyun , Han Jeong Hwan , Kim Seong Keun , Hwang Cheol Seong
Published: October 2014

The catalytic decomposition of RuO2 with the help of Ru in the film played the crucial role for the increase in the active oxygen, which results that the growth per cycle of TiO2 at the initial growth stage was drastically increased on RuOx (RuO2/Ru mixture) compared to Ru and RuO2.
A resonance energy transfer approach for the selective detection of aromatic amino acids
Authors: Hazra Chanchal , Samanta Tuhin , Mahalingam Venkataramanan
Published: October 2014

In this article, we report for the first time the use of Ln3+-doped nanocrystals to detect aromatic amino acids (AAs) up to nanomolar concentration.
GPKOW is essential for pre-mRNA splicing in vitro and suppresses splicing defect caused by dominant-negative DHX16 mutation in vivo
Authors: Zang Shengbing , Lin Ting-Yu , Chen Xinji , Gencheva Marieta , Newo Alain N. S. , Yang Lixin , Rossi Daniel , Hu Jianda , Lin Shwu-Bin , Huang Aimin , Lin Ren-Jang
Published: October 2014

Human GPKOW [G-patch (glycine-rich) domain and KOW (Kyrpides, Ouzounis and Woese) domain] protein contains a G-patch domain and two KOW domains, and is a homologue of Arabidopsis MOS2 and Saccharomyces Spp2 protein. GPKOW is found in the human spliceosome, but its role in pre-mRNA splicing remains to be elucidated. In this report, we showed that GPKOW interacted directly with the DHX16/hPRP2 and with RNA. Immuno-depletion of GPKOW from HeLa nuclear extracts resulted in an inactive spliceosome that still bound DHX16. Adding back recombinant GPKOW restored splicing to the depleted extract. In vivo, overexpression of GPKOW partially suppressed the splicing defect observed in dominant-negative DHX16 mutant expressing cells. Mutations at the G-patch domain greatly diminished the GPKOW–DHX16 interaction; however, the mutant was active in splicing and was able to suppress splicing defect. Mutations at the KOW1 domain slightly altered the GPKOW–RNA interaction, but the mutant was less functional in vitro and in vivo. Our results indicated that GPKOW can functionally impact DHX16 but that interaction between the proteins is not required for this activity.
Inter-relationships between proprotein convertase subtilisin/kexin type 9, apolipoprotein C-III and plasma apolipoprotein B-48 transport in obese subjects: a stable isotope study in the postprandial state
Authors: Chan Dick C. , Wong Annette T. Y. , Pang Jing , Barrett P. Hugh R. , Watts Gerald F.
Published: October 2014

Postprandial lipaemia, due to elevated plasma apolipoprotein (apo) B-48 concentrations, contributes to increased cardiovascular (CV) risk in obesity. Proprotein convertase subtilisin/kexin type 9 (PCSK9) and apoC-III may play a role in regulating triacylglycerol-rich lipoprotein (TRL)–apoB-48 metabolism. We investigated the associations between plasma PCSK9 and apoC-III concentrations and the kinetics of apoB-48 in obese subjects. Seventeen obese subjects were given an oral fat load. ApoB-48 tracer/tracee ratios were measured after an intravenous 2H3-leucine administration using GC–MS. Kinetic parameters, including secretion and fractional catabolic rates (FCRs), were derived using a multi-compartmental model. Plasma PCSK9 and apoC-III concentrations were significantly and positively (P<0.05 in all) associated with the total area-under-curve (AUC) and incremental AUC for apoB-48 and inversely with TRL–apoB-48 FCR. Plasma PCSK9 and apoC-III concentrations were not correlated (P>0.05 in all) with basal secretion or the number of TRL–apoB-48 secreted over the postprandial period. In the stepwise regression analysis, plasma PCSK9 was the best predictor of the total and incremental AUCs for plasma apoB-48 and the FCR of TRL–apoB-48. The association between plasma PCSK9 and apoC-III and TRL–apoB-48 FCR remained significant (P<0.05 in all) after adjusting for age, homoeostasis model assessment (HOMA) score, hepatic lipase or lipoprotein lipase (LPL). In a multiple regression model, 31% of variance in TRL–apoB-48 FCR was accounted for by plasma PCSK9 and apoC-III concentrations (adjusted R2=0.306, P<0.05). However, their associations with TRL–apoB-48 FCR were not independent of each other. Our results suggest that the catabolism of TRL–apoB-48 in the postprandial state may be co-ordinated by PCSK9 and apoC-III in obese individuals.
Low‐frequency robust control for singularly perturbed system
Authors: Yuan Yuan , Sun Fuchun , Liu Huaping , Yang Hongjiu
Published: October 2014

This study is concerned with the low‐frequency (LF) integral quadratic constraints (IQC) of the linear singularly perturbed model (SPM). The conditions satisfying LF IQC are derived in terms of linear matrix inequalities by using the generalised Kalman–Yakubovich–Popov lemma. As special cases of LF IQC, LF bounded realness and LF positive realness are exploited in detail. In addition, upper bound of the small perturbation parameter, which relates to the robustness of SPM, can be estimated. Numerical simulations demonstrate that the proposed method can reduce the conservatism and characterise the SPM more specifically by ignoring the unrelated frequency range.
Distributed average consensus based on structural weight‐balanceability
Authors: Haghighi Reza , Cheah Chien Chern
Published: October 2014

This study presents the concept of structural weight‐balanceability of network systems as a useful method to examine the average consensus of the systems. The authors introduce the notion of structurally unobservable node based on structural observability concept to determine the structural weight‐balanceability of a network. They propose a simple technique to identify structurally unobservable nodes, and consequently infer on structural weight‐balanceability of the network. A mathematical method based on principal minors of the associated Laplacian matrix of the network is developed to modify a structurally weight‐balanceable network into a weight‐balanced one. A distributed method is presented to compute normalised principal minors in a large‐scale network system with directed communication topology. This is the first work that provides a rigorous mathematical formulation to check the structural weight‐balanceability of network systems and make a structurally weight‐balanceable network, weight‐balanced. Finally, simulation results are presented to illustrate the performance of the proposed method in dealing with networks with a large number of nodes.
Bonding mechanism of a yttrium iron garnet film on Si without the use of an intermediate layer
Authors: Pantzas Konstantinos , Patriarche Gilles , Talneau Anne , Youssef Jamal Ben
Published: October 2014

Direct bonding of yttrium iron garnet (YIG) on silicon without the use of an intermediate bonding layer is demonstrated and characterized using scanning transmission electron microscopy and energy-dispersive x-ray spectroscopy. During the bonding experiment, the garnet is reduced in the presence of oxide-free silicon. As a result, a 5 nm thick SiO2/amorphous-YIG bilayer is formed and welds the garnet to silicon.
A source of high-power pulses of elliptically polarized ultrawideband radiation
Authors: Andreev Yu. A. , Efremov A. M. , Koshelev V. I. , Kovalchuk B. M. , Petkun A. A. , Sukhushin K. N. , Zorkaltseva M. Yu.
Published: October 2014

Here, we describe a source of high-power ultrawideband radiation with elliptical polarization. The source consisting of a monopolar pulse generator, a bipolar pulse former, and a helical antenna placed into a radioparent container may be used in tests for electromagnetic compatibility. In the source, the helical antenna with the number of turns N = 4 is excited with a high-voltage bipolar pulse. Preliminary, we examined helical antennas at a low-voltage source aiming to select an optimal N and to estimate a radiation center position and boundary of a far-field zone. Finally, characteristics of the source in the operating mode at a pulse repetition rate of 100 Hz are presented in the paper as well. Energy efficiency of the antenna is 0.75 at the axial ratio equal to 1.3. The effective potential of radiation of the source at the voltage amplitudes of the bipolar pulse generator equal to −175/+200 kV reaches 280 kV.
Note: Increasing dynamic range of digital-to-analog converter using a superconducting quantum interference device
Authors: Nakanishi Masakazu
Published: October 2014

Responses of a superconducting quantum interference device (SQUID) are periodically dependent on magnetic flux coupling to its superconducting ring and the period is a flux quantum (Φo = h/2e, where h and e, respectively, express Planck's constant and elementary charge). Using this periodicity, we had proposed a digital to analog converter using a SQUID (SQUID DAC) of first generation with linear current output, interval of which corresponded to Φo. Modification for increasing dynamic range by interpolating within each interval is reported. Linearity of the interpolation was also based on the quantum periodicity. A SQUID DAC with dynamic range of about 1.4 × 107 was created as a demonstration.
Influence of thermal environment on optimal working conditions of thermoelectric generators
Authors: Apertet Y. , Ouerdane H. , Goupil C. , Lecoeur Ph.
Published: October 2014

Optimization analysis of thermoelectric generators operation is of importance both for practical applications and theoretical considerations. Depending on the desired goal, two different strategies are possible to achieve high performance: through optimization one may seek either power output maximization or conversion efficiency maximization. Recent literature reveals the persistent flawed notion that these two optimal working conditions may be achieved simultaneously. In this article, we lift all source of confusion by correctly posing the problem and solving it. We assume and discuss two possibilities for the environment of the generator to govern its operation: constant incoming heat flux, and constant temperature difference between the heat reservoirs. We demonstrate that, while power and efficiency are maximized simultaneously if the first assumption is considered, this is not possible with the second assumption. This latter corresponds to the seminal analyses of Ioffe who put forth and stressed the importance of the thermoelectric figure of merit ZT. We also provide a simple procedure to determine the different optimal design parameters of a thermoelectric generator connected to heat reservoirs through thermal contacts with a finite and fixed thermal conductance.
Investigation of thin films of organic-based magnets grown by physical vapor deposition
Authors: Kao C. Y. , Li B. , Lu Y. , Yoo J.-W. , Epstein A. J.
Published: October 2014

Thin films of organic-based magnet, V[TCNE]x (TCNE: tetracyanoethylene), were deposited by physical vapor deposition (PVD) based reactive evaporation. The growth conditions were studied in detail. A saturated composition of V[TCNE]∼1.9 was determined by optimizing the growth condition. Two sets of films with different V to TCNE ratios were characterized. Both films were magnetic ordered up to 400 K and held coercive field of 60 Oe at room temperature. With the presence of excess vanadium within the film, the increase of defects created by PVD results in significant change in electronic property.
Preparation of Ag Schottky contacts on n-type GaN bulk crystals grown in nitrogen rich atmosphere by the hydride vapor phase epitaxy technique
Authors: Stübner R. , Kolkovsky Vl. , Leibiger Gunnar , Habel Frank , Weber J.
Published: October 2014

Electrical properties of Schottky contacts on n-type GaN grown in nitrogen rich atmosphere with different N/Ga ratios by hydride vapor phase epitaxy were investigated. We show that tunneling of electrons from the conduction band of GaN to the metal is dominant in our samples. The quality of Schottky contacts does not only depend on surface preparation but also on the growth conditions of the crystals. Schottky contacts on these crystals show an increasing deterioration when higher N/Ga growth ratios are used. We correlate our results with the presence of negatively charged gallium vacancies in the samples. These charges compensate the positively charged donors and lead to a significant increase in series resistance.
Mid-infrared light emission from a Fe2+:ZnSe polycrystal using quantum cascade laser pumping
Authors: Song Yu , Sonntag Jens , Mirov Sergey B. , Gmachl Claire F. , Khurgin Jacob B.
Published: October 2014

We report the realization of light emission from a Fe2+ doped ZnSe polycrystal with efficient pumping from a quantum cascade (QC) laser. The QC laser photon energy is near the absorption edge of the Fe2+:ZnSe with less than ∼60 meV Stokes' shift. The Fe2+:ZnSe polycrystal shows an absorption band of ∼2.2 – 5 μm in the mid-infrared (mid-IR) at room temperature, which narrows down to ∼2.4–4.2 μm at 80 K. Clear photoluminescence (PL) from 4.5 μm to 6 μm are observed throughout the temperature range of 300 K to 80 K. At room temperature, the luminescence lifetime is about 0.38 ± 0.1 μs which increases up to 101 ± 2 μs at 118 K. This system transfers energy stored in the upper state of a QC laser with ∼ps lifetime to the Fe2+:ZnSe with 105 to 108 times longer lifetime, at the cost of minute photon energy losses.
Efficient enhancement of solar-water-splitting by modified “Z-scheme” structural WO3-W-Si photoelectrodes
Authors: Xing Zhuo , Shen Shaohua , Wang Meng , Ren Feng , Liu Ying , Zheng Xudong , Liu Yichao , Xiao Xiangheng , Wu Wei , Jiang Changzhong
Published: October 2014

N-type WO3 and p-type Si can be assembled into a composite structure called “Z-scheme,” which is a high efficiency model for overall water splitting. However, due to the existence of Schottky barrier, its relatively low photocurrent density is still a great challenge for application. Here, a modified “Z-scheme” structure by inserting a W interlayer is presented. A great enhancement of photocurrent density over 10 times is achieved, which can be ascribed to the introduction of the ohmic contacts between W interlayer with both WO3 and Si layers and the elimination of Si-O bands at the interface.
Reversed boiling curve phenomenon on surfaces with interlaced wettability
Authors: Hsu C. C. , Chiu W. C. , Kuo L. S. , Chen P. H.
Published: October 2014

We experimentally investigated the effects of contact angle difference of heterogeneous wettability surfaces on pool boiling. For surfaces exhibiting heterogeneous wettability, this study determined that the pool boiling curve experiences a superheat decrease in some regions before the system achieves the critical heat flux. In addition, oscillation of the vapor column and bubble transverse motions on the heterogeneous wettability coated surface were observed.
Impact of artificial lateral quantum confinement on exciton-spin relaxation in a two-dimensional GaAs electronic system
Authors: Kiba Takayuki , Tanaka Toru , Tamura Yosuke , Higo Akio , Thomas Cedric , Samukawa Seiji , Murayama Akihiro
Published: October 2014

We demonstrate the effect of artificial lateral quantum confinement on exciton-spin relaxation in a GaAs electronic system. GaAs nanodisks (NDs) were fabricated from a quantum well (QW) by top-down nanotechnology using neutral-beam etching aided by protein-engineered bio-nano-templates. The exciton-spin relaxation time was 1.4 ns due to ND formation, significantly extended compared to 0.44 ns for the original QW, which is attributed to weakening of the hole-state mixing in addition to freezing of the carrier momentum. The temperature dependence of the spin-relaxation time depends on the ND thickness, reflecting the degree of quantum confinement.
Anisotropic-strain-relaxation-induced crosshatch morphology in epitaxial SrTiO3/NdGaO3 thin films
Authors: Tan X. L. , Chen F. , Chen P. F. , Xu H. R. , Chen B. B. , Jin F. , Gao G. Y. , Wu W. B.
Published: October 2014

We investigate the strain relaxation and surface morphology of epitaxial SrTiO3 (STO) films grown on (001)O and (110)O planes of orthorhombic NdGaO3 (NGO), and (001) plane of cubic (LaAlO3)0.3(Sr2AlTaO6)0.7 (LSAT) substrates. Although the average lattice mismatches are similar, strikingly regular crosshatched surface patterns can be found on STO/NGO(001)O[(110)O] films, contrary to the uniform surface of STO/LSAT(001). Based on the orientation and thickness dependent patterns and high-resolution x-ray diffractions, we ascribe the crosshatch morphology to the anisotropic strain relaxation with possibly the 60° misfit dislocation formation and lateral surface step flow in STO/NGO films, while an isotropic strain relaxation in STO/LSAT. Further, we show that the crosshatched STO/NGO(110)O surface could be utilized as a template to modify the magnetotransport properties of epitaxial La0.6Ca0.4MnO3 films. This study highlights the crucial role of symmetry mismatch in determining the surface morphology of the perovskite oxide films, in addition to their epitaxial strain states, and offers a different route for designing and fabricating functional perovskite-oxide devices.
Magnetic anisotropies in epitaxial Fe3O4/GaAs(100) patterned structures
Authors: Zhang W. , Wong P. K. J. , Zhang D. , Yuan S. J. , Huang Z. C. , Zhai Y. , Wu J. , Xu Y. B.
Published: October 2014

Previous studies on epitaxial Fe3O4 rings in the context of spin-transfer torque effect have revealed complicated and undesirable domain structures, attributed to the intrinsic fourfold magnetocrystalline anisotropy in the ferrite. In this Letter, we report a viable solution to this problem, utilizing a 6-nm-thick epitaxial Fe3O4 thin film on GaAs(100), where the fourfold magnetocrystalline anisotropy is negligible. We demonstrate that in the Fe3O4 planar wires patterned from our thin film, such a unique magnetic anisotropy system has been preserved, and relatively simple magnetic domain configurations compared to those previous reports can be obtained.
Reproductive biology of the pelagic stingray, Pteroplatytrygon violacea (Bonaparte, 1832), in the equatorial and south-western Atlantic Ocean
Authors: Veras D. P. , Hazin F. H. V. , Branco I. S. L. , Tolotti M. T. , Burgess G. H.
Published: October 2014

From October 2005 to March 2010, a total of 480 pelagic stingray, Pteroplatytrygon violacea, specimens, 188 females and 292 males (0.64 female : 1 male), were taken in the equatorial and south-western Atlantic by the commercial tuna longline fishery and their reproductive biology was studied. Disc widths (DW) ranged from 28.0 to 66.0 cm for females and from 34.0 to 59.6 cm for males. Size at first sexual maturity was estimated at ~48.0 cm DW (first pregnant female) for females and ~41.0 cm DW for males. Ovarian fecundity, considering only follicles larger than 0.5 cm in diameter, ranged from 1 to 17 follicles per female, while the uterine fecundity of embryos in pregnant females in Stages 2 and 3 ranged from 1 to 5 embryos per female. The sex ratio between the embryos was almost equal (1.08 female : 1 male) and the size at birth was 19.0 cm DW.
Video-surveillance system for remote long-term in situ observations: recording diel cavity use and behaviour of wild European lobsters (Homarus gammarus)
Authors: Steen Ronny , Ski Sondre
Published: October 2014

Long-term studies of subtidal marine animals in the wild are a demanding enterprise. Traditionally, data collection has been limited to direct observations during SCUBA diving. In the past decade, video technology has improved rapidly and behavioural monitoring of marine organisms has successfully been conducted by using modern video-recording equipment. Here, we describe a video-monitoring system that employs video motion detection (VMD) and describe its use with the European lobster (Homarus gammarus). There is a shortage of detailed information on lobster behaviour in the wild, with virtually no published data on the fine-scale behaviour of the European lobster under natural conditions. This dearth of information reflects the difficulties in observing behaviour in nocturnal marine animals. Here, we explore whether a remote video-surveillance system is suitable for long-term monitoring of European lobsters inhabiting an artificial cavity in a natural habitat. From the video recordings, we were able to register diel cavity use and categorise behavioural elements such as resting, feeding, burrowing and substrate moving, self-cleaning, burrow occupancy and interactions among individuals. We propose that this novel system will contribute to more efficient data sampling of lobsters and facilitate non-invasive, long-term behavioural studies of other marine and freshwater animals.
Ecological response of Eucalyptus camaldulensis (river red gum) to extended drought and flooding along the River Murray, South Australia (1997–2011) and implications for environmental flow management
Authors: Doody Tanya M. , Benger Simon N. , Pritchard Jodie L. , Overton Ian C.
Published: October 2014

Riparian forest and woodlands of the lower River Murray floodplain are exhibiting deteriorating health as a result of anthropogenic alterations to flow regimes and south-eastern Australia’s long-term ‘Millennium Drought’ from 1997 to 2009. Extensive flooding in 2010/2011 brought the drought to an end, providing an opportunity to monitor ecological floodplain recovery. The relationship between flooding and lateral recharge and condition of the dominant riparian tree species, Eucalyptus camaldulensis, was determined between 2007 and 2011 using the Landsat (LTM5) Normalised Difference Vegetation Index (NDVI). Linking the river hydrograph with the River Murray Floodplain Inundation Model (RiM-FIM) allowed exploration of the relationship between inundation duration and E. camaldulensis water requirements. Results indicate lateral bank recharge is an important mechanism in the maintenance of vegetation condition along the River Murray channel. Higher in-channel irrigation water delivery during summer months was identified as critical to survival of trees adjacent to the channel during the drought. The research suggests that weir pool manipulation to create in-channel flood pulses will aid E. camaldulensis maintenance. Furthermore, release of environmental flows once every 3 to 5 years to create bank-full flow or preferably overbank flows, will increase hydrological connectivity between river banks, wetlands and riparian zones, providing positive ecological benefits to E. camaldulensis and other floodplain and aquatic ecological assets.
Long term-cultured and cryopreserved primordial germ cells from various chicken breeds retain high proliferative potential and gonadal colonisation competency
Authors: Tonus Céline , Cloquette Karine , Ectors Fabien , Piret Joëlle , Gillet Laurent , Antoine Nadine , Desmecht Daniel , Vanderplasschen Alain , Waroux Olivier , Grobet Luc
Published: October 2014

When derived from chicken embryos, avian primordial germ cells (PGCs) have been reported to keep their germline-specific properties and proliferative potential even after long-term culture and genetic modifications. Few teams to date have reported such long-term expansion and engineering without differentiation of primary avian PGCs’ cultures. We have developed original and robust methods that allow more than 1 year culture, expansion and cryobanking of primary cultures of PGCs without obvious effects on their biological properties, including their ability to colonise the genital ridges. Overall, 38% of embryonic samples gave rise to PGCs lines derived from three commercial layers and two Belgian endangered breeds. The lines kept their proliferative potential and their characteristic PGCs phenotype after 20 months in culture, whether or not interrupted by a cryopreservation step. All the resulting lines appeared devoid of female cells, although initially pooled from male and female embryos. Labelled PGCs from 12 long-term cultured lines colonised the genital ridges of recipient embryos. Thus, this procedure allows derivation, long-term expansion and cryobanking of primary cultures of PGCs without obvious changes to their original characteristics, providing an alternative access to applications in avian biotechnology and preservation of genetic resources.
Unnecessary Angels: Jewish Angelology in theŠkand Gumānīg Wizār
Authors: Thrope Samuel
Published: October 2014

The Škand Gumānīg Wizār (ŠGW) contains Middle Persian Zoroastrian literature's most extensive polemic against Judaism. This article explores the ŠGW's polemic in light of recent scholarship demonstrating the connection between Babylonian rabbinic Judaism and Zoroastrianism in late antique Iran. Taking this connection as a starting point, the article considers the ŠGW's critique of three angelic citations that are all closely paralleled by passages in the Babylonian Talmud. After demonstrating that the ŠGW citations depict angels as weaker and more oppressed than the rabbinic parallels, the article sets these portrayals of weakened angels in the context of the widespread belief among Jews in this period in Metatron, an angelic coequal to the divine. The article argues that the ŠGW's depictions of downtrodden angels are not borrowed from rabbinic polemics, found in the Talmud, against this theology, but is an independent reaction to the same belief in Metatron's co-regency, a belief that sources testify was still common in the early Islamic period. The ŠGW's motivating theological imperative to portray Judaism as radically monotheistic, and thus the binary opposite of Zoroastrianism, underlies the text's descriptions of angelic suffering and degradation.
Managing for Coexistence of Kokanee and Trophy Lake Trout in a Montane Reservoir
Authors: Pate William M. , Johnson Brett M. , Lepak Jesse M. , Brauch Daniel
Published: October 2014

Kokanee Oncorhynchus nerka and Lake Trout Salvelinus namaycush are stocked for sportfishing in lakes and reservoirs throughout the western United States and Canada. However, where the two species co-occur, unsustainable levels of predation by Lake Trout can lead to declines in kokanee abundance and declines in Lake Trout growth and body condition. Such declines occurred in Blue Mesa Reservoir, Colorado. In 2009, managers began removing Lake Trout (<740 mm TL) in an attempt to sustain the hatchery-dependent kokanee population while still providing a trophy Lake Trout fishery. To evaluate this and other strategies for achieving the dual management goals, we developed age-structured kokanee and Lake Trout population models and linked them to a bioenergetics model of Lake Trout predation. We found that the existing level of Lake Trout removal (0.23; ages 4–9) is insufficient to prevent further decline and ultimately the extirpation of the kokanee population. If removal of age-4–9 Lake Trout is intensified to 0.38, the kokanee population would persist; however, removal would have to be increased to 0.63 to allow a return to historic kokanee abundance. Focusing removal on age-4 Lake Trout (0.78) would allow for persistence of kokanee and would leave more trophy Lake Trout for anglers, suggesting that the two goals are compatible under some circumstances. However, management costs of balancing kokanee with trophy Lake Trout are high and put both fisheries at risk unless Lake Trout abundance is controlled.

Received October 31, 2013; accepted May 5, 2014
A probabilistic model for analysing the effect of performance levels on visual behaviour patterns of young sailors in simulated navigation
Authors: Manzanares Aarón , Menayo Ruperto , Segado Francisco , Salmerón Diego , Cano Juan Antonio
Published: October 2014

The visual behaviour is a determining factor in sailing due to the influence of the environmental conditions. The aim of this research was to determine the visual behaviour pattern in sailors with different practice time in one star race, applying a probabilistic model based on Markov chains. The sample of this study consisted of 20 sailors, distributed in two groups, top ranking (n = 10) and bottom ranking (n = 10), all of them competed in the Optimist Class. An automated system of measurement, which integrates the VSail‐Trainer® sail simulator and the Eye Tracking SystemTM was used. The variables under consideration were the sequence of fixations and the fixation recurrence time performed on each location by the sailors. The event consisted of one of simulated regatta start, with stable conditions of wind, competitor and sea. Results show that top ranking sailors perform a low recurrence time on relevant locations and higher on irrelevant locations while bottom ranking sailors make a low recurrence time in most of the locations. The visual pattern performed by bottom ranking sailors is focused around two visual pivots, which does not happen in the top ranking sailor's pattern. In conclusion, the Markov chains analysis has allowed knowing the visual behaviour pattern of the top and bottom ranking sailors and its comparison.
Rethinking volitional control over task choice in multitask environments: Use of a stimulus set selection strategy in voluntary task switching
Authors: Arrington Catherine M. , Weaver Starla M.
Published: October 2014

Under conditions of volitional control in multitask environments, subjects may engage in a variety of strategies to guide task selection. The current research examines whether subjects may sometimes use a top-down control strategy of selecting a task-irrelevant stimulus dimension, such as location, to guide task selection. We term this approach a stimulus set selection strategy. Using a voluntary task switching procedure, subjects voluntarily switched between categorizing letter and number stimuli that appeared in two, four, or eight possible target locations. Effects of stimulus availability, manipulated by varying the stimulus onset asynchrony between the two target stimuli, and location repetition were analysed to assess the use of a stimulus set selection strategy. Considered across position condition, Experiment 1 showed effects of both stimulus availability and location repetition on task choice suggesting that only in the 2-position condition, where selection based on location always results in a target at the selected location, subjects may have been using a stimulus set selection strategy on some trials. Experiment 2 replicated and extended these findings in a visually more cluttered environment. These results indicate that, contrary to current models of task selection in voluntary task switching, the top-down control of task selection may occur in the absence of the formation of an intention to perform a particular task.
Industrializing the Arab world: a speculative case study
Authors: Zahlan A.B.
Published: October 2014

Some of the challenges facing Arab countries could be solved if their economies were industrialized. They have made much progress in some fields, but have failed so far to industrialize. While this is obviously a complicated issue, there are, at the same time, many countries that have been very successful in doing so. Speculating about such complex issues is nothing new. A reader of Western literature is daily confronted with speculative articles on the rise or fall of American power. A number of writers appear to be concerned that China will soon displace the United States as the number 1 superpower. (For a review of three books by Edward Luce on this subject, see Financial Times February 2, 2014.) Some thoughtful writers propose various possibilities on some countries’ readiness to assume roles that may lead to a new political world order. Other writers frequently speculate on China possibly lacking sufficient creativity to displace the United States from its privileged position. There are no simple answers to such complex issues. Concern for the rise and fall of nations is of constant interest in Western literature, but by contrast concern in the Arab world is limited in scope and depth to the ultimate development of their own region. What is surprising in the Arab world is that despite the prevailing conditions the Arabs enjoy through their enormous assets, they seem oblivious to the rich possibilities that these resources provide. Arab countries are confronted with expanding populations, education, emigration and unemployment. It seems that unless they adopt a more serious interest in the challenges they face, they will be unable to escape from a state of permanent crisis. The purpose of this article is to speculate on the feasibility of utilizing the Gulf Cooperation Council’s (GCC) railway system – estimated at approximately US$200 billion – as a tool for achieving industrialization. The railway system will be 1940 km long and include all GCC countries.
Reflections on Arabs and sociology: insights into sociological schools of thought in the Arab World – challenges and issues
Authors: Abdul-Jabar Faleh
Published: October 2014

This article has two sections. The first elaborates on a new Arab proposal that is gaining prominence in the realm of sociological research, which calls for a new sociological classification based on the concept of balance/conflict. The second section explores the work of the Iraqi scholar and sociologist Ali Al-Wardi and describes how he adapted the sociological concepts useful in analysing Western societies and combined them with the work of the forerunner of Arab sociology, Ibn Khaldoun, in applying them to the Arab world. The article explores the problems that have arisen for sociology in the region, and it attempts to classify the schools of sociological thought in the areas of epistemology and ideology, characteristics and seclusion, synthesis and openness. It describes the process of how these schools of sociological thought have evolved, and how they can be simplified and rendered useful for Arab sociologists to study their societies.
Laws of the iterated logarithm for self-normalised Lévy processes at zero
Authors: Buchmann Boris , Maller Ross , Mason David
Published: October 2014

We develop tools and methodology to establish laws of the iterated logarithm (LILs) for small times (as

t
↓
0

t\downarrow 0

) for the “self-normalised” process

(

X

t

−
a
t
)

/

V

t

(X_{t}-at)/\sqrt {V_{t}}

,

t
>
0

t>0

, constructed from a Lévy process

(

X

t

)

t
≥
0

(X_{t})_{t\geq 0}

having quadratic variation process

(

V

t

)

t
≥
0

(V_{t})_{t\geq 0}

, and an appropriate choice of the constant

a
a

. We apply them to obtain LILs when

X

t

X_{t}

is in the domain of attraction of the normal distribution as

t
↓
0

t\downarrow 0

, when

X

t

X_{t}

is symmetric and in the Feller class at 0, and when

X

t

X_{t}

is a strictly

α
−

\alpha -

stable process. When

X

t

X_{t}

is attracted to the normal distribution, an important ingredient in the proof is a Cramér-type theorem which bounds above the distance of the distribution of the self-normalised process from the standard normal distribution.
HDAC6–ubiquitin interaction controls the duration of HSF1 activation after heat shock
Authors: Pernet Lydia , Faure Virginie , Gilquin Benoit , Dufour-Guérin Solenne , Khochbin Saadi , Vourc’h Claire
Published: October 2014

After heat shock, HSF1 controls a major cellular transcriptional response involving the activation of early (HSP70) and late (HSP25) heat shock gene expression. Here we show that a full response to heat shock (activation of both HSP70 and HSP25) depends on the duration of HSF1 activation, which is itself controlled by HDAC6, a unique deacetylase known to bind monoubiquitin and polyubiquitin with high affinity. On the basis of a comparative analysis of the heat shock response in cells knocked out for HDAC6 or expressing HDAC6 mutants, we show that HDAC6 binding to ubiquitinated proteins controls the duration of HSF1 activation after heat shock. In cells expressing HDAC6 mutated in the ubiquitin-binding domain, the AAA ATPase factor p97/VCP mediates rapid inactivation of HSF1, precluding late activation of the HSP25 gene. In these cells, knockdown of p97/VCP rescues HSF1 from this rapid inactivation and restores HSP25 expression. We present here a new regulatory circuit that adjusts the duration of the heat shock response to the extent of protein ubiquitination after heat shock.
Spatiotemporal dynamics of triglyceride storage in unilocular adipocytes
Authors: Chu Michael , Sampath Harini , Cahana David Y. , Kahl Christoph A. , Somwar Romel , Cornea Anda , Roberts Charles T. , Varlamov Oleg
Published: October 2014

The spatiotemporal dynamics of triglyceride (TG) storage in unilocular adipocytes are not well understood. Here we applied ex vivo technology to study trafficking and metabolism of fluorescent fatty acids in adipose tissue explants. Live imaging revealed multiple cytoplasmic nodules surrounding the large central lipid droplet (cLD) of unilocular adipocytes. Each cytoplasmic nodule harbors a series of closely associated cellular organelles, including micro–lipid droplets (mLDs), mitochondria, and the endoplasmic reticulum. Exogenously added free fatty acids are rapidly adsorbed by mLDs and concurrently get esterified to TG. This process is greatly accelerated by insulin. mLDs transfer their content to the cLD, serving as intermediates that mediate packaging of newly synthesized TG in the large interior of a unilocular adipocyte. This study reveals novel cell biological features that may contribute to the mechanism of adipocyte hypertrophy.
Olfactomedin 2, a novel regulator for transforming growth factor-β–induced smooth muscle differentiation of human embryonic stem cell–derived mesenchymal cells
Authors: Shi Ning , Guo Xia , Chen Shi-You
Published: October 2014

Transforming growth factor-β (TGF-β) plays an important role in smooth muscle (SM) differentiation, but the downstream target genes regulating the differentiation process remain largely unknown. In this study, we identified olfactomedin 2 (Olfm2) as a novel regulator mediating SM differentiation. Olfm2 was induced during TGF-β–induced SM differentiation of human embryonic stem cell–derived mesenchymal cells. Olfm2 knockdown suppressed TGF-β–induced expression of SM markers, including SM α-actin, SM22α, and SM myosin heavy chain, whereas Olfm2 overexpression promoted the SM marker expression. TGF-β induced Olfm2 nuclear accumulation, suggesting that Olfm2 may be involved in transcriptional activation of SM markers. Indeed, Olfm2 regulated SM marker expression and promoter activity in a serum response factor (SRF)/CArG box–dependent manner. Olfm2 physically interacted with SRF without affecting SRF-myocardin interaction. Olfm2-SRF interaction promoted the dissociation of SRF from HERP1, a transcriptional repressor. Olfm2 also inhibited HERP1 expression. Moreover, blockade of Olfm2 expression inhibited TGF-β–induced SRF binding to SM gene promoters in a chromatin setting, whereas overexpression of Olfm2 dose dependently enhanced SRF binding. These results demonstrate that Olfm2 mediates TGF-β–induced SM gene transcription by empowering SRF binding to CArG box in SM gene promoters.
Making Time for Agricultural and Life Science Research: Technical Change and Productivity Gains
Authors: Prager Daniel L. , Foltz Jeremy D. , Barham Bradford L.
Published: October 2014

This work analyzes the research productivity of agricultural and life science faculty in U.S. Land Grant research universities from 1975 to 2005. Production function estimations that control for inputs and demographic characteristics reveal significant improvements after 1980 in faculty research productivity per unit time, especially in the non‐top ten universities. Because, however, time available to faculty for research has decreased substantially in the past three decades, overall journal article output per faculty did not increase after the 1980s. Our findings demonstrate large productivity increases but raise concerns about the optimal allocation of faculty time.
Visual workflows for
13
C-metabolic flux analysis
Authors: Nöh Katharina , Droste Peter , Wiechert Wolfgang
Published: October 2014

Motivation: The precise quantification of intracellular metabolic flow rates is of fundamental importance in bio(techno)logy and medical research. The gold standard in the field is metabolic flux analysis (MFA) with 13 C-labeling experiments. 13 C-MFA workflows orchestrate several, mainly human-in-the-loop, software applications, integrating them with plenty of heterogeneous information. In practice, this had posed a major practical barrier for evaluating, interpreting and understanding isotopic data from carbon labeling experiments.

Results: Graphical modeling, interactive model exploration and visual data analysis are the key to overcome this limitation. We have developed a first-of-its-kind graphical tool suite providing scientists with an integrated software framework for all aspects of 13 C-MFA. Almost 30 modules (plug-ins) have been implemented for the Omix visualization software. Several advanced graphical workflows and ergonomic user interfaces support major domain-specific modeling and proofreading tasks. With that, the graphical suite is a productivity enhancing tool and an original educational training instrument supporting the adoption of 13 C-MFA applications in all life science fields.

Availability: The Omix Light Edition is freely available at http://www.omix-visualization.com

Contact:  k.noeh@fz-juelich.de , p.droste@omix-visualization.com

Supplementary information:  Supplementary data are available at Bioinformatics online.
Quantifying tumor heterogeneity in whole-genome and whole-exome sequencing data
Authors: Oesper Layla , Satas Gryte , Raphael Benjamin J.
Published: October 2014

Motivation: Most tumor samples are a heterogeneous mixture of cells, including admixture by normal (non-cancerous) cells and subpopulations of cancerous cells with different complements of somatic aberrations. This intra-tumor heterogeneity complicates the analysis of somatic aberrations in DNA sequencing data from tumor samples.

Results: We describe an algorithm called THetA2 that infers the composition of a tumor sample—including not only tumor purity but also the number and content of tumor subpopulations—directly from both whole-genome (WGS) and whole-exome (WXS) high-throughput DNA sequencing data. This algorithm builds on our earlier Tumor Heterogeneity Analysis (THetA) algorithm in several important directions. These include improved ability to analyze highly rearranged genomes using a variety of data types: both WGS sequencing (including low ∼7× coverage) and WXS sequencing. We apply our improved THetA2 algorithm to WGS (including low-pass) and WXS sequence data from 18 samples from The Cancer Genome Atlas (TCGA). We find that the improved algorithm is substantially faster and identifies numerous tumor samples containing subclonal populations in the TCGA data, including in one highly rearranged sample for which other tumor purity estimation algorithms were unable to estimate tumor purity.

Availability and implementation: An implementation of THetA2 is available at http://compbio.cs.brown.edu/software

Contact:  layla@cs.brown.edu or braphael@brown.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.