bluuebunny/crossref_metadata_2025 huggingface dataset:
Modeling scalar dissipation and scalar variance in large eddy simulation: Algebraic and transport equation closures
Authors: Knudsen E. , Richardson E. S. , Doran E. M. , Pitsch H. , Chen J. H.
Published: May 2012

Scalar dissipation rates and subfilter scalar variances are important modeling parameters in large eddy simulations (LES) of reacting flows. Currently available models capture the general behavior of these parameters, but these models do not always perform with the degree of accuracy that is needed for predictive LES. Here, two direct numerical simulations (DNS) are used to analyze LES dissipation rate and variance models, and to propose a new model for the dissipation rate that is based on a transport equation. The first DNS that is considered is a non-premixed auto-igniting C2H4 jet flame simulation originally performed by Yoo et al. [Proc. Combust. Inst. 33, 1619–1627 (2011)]10.1016/j.proci.2010.06.147. A LES of this case is run using algebraic models for the dissipation rate and subfilter variance. It is shown that the algebraic models fail to adequately reproduce the DNS results. This motivates the introduction of a transport equation model for the LES dissipation rate. Closure of the equation is addressed by formulating a new adapted dynamic approach. This approach borrows dynamically computed information from LES quantities that, unlike the dissipation rate, do not reside on the smallest flow length scales. The adapted dynamic approach is analyzed by considering a second DNS of scalar mixing in homogeneous isotropic turbulence. Data from this second DNS are used to confirm that the adapted dynamic approach successfully closes the dissipation rate equation over a wide range of LES filter widths. The first reacting jet case is then returned to and used to test the LES transport equation models. The transport equation model for the dissipation rate is shown to be more accurate than its algebraic counterpoint, and the dissipation rate is eliminated as a source of error in the transported variance model.
Dynamics of localized excitons in Ga0.69In0.31N0.015As0.985/GaAs quantum well: Experimental studies and Monte-Carlo simulations
Authors: Baranowski M. , Kudrawiec R. , Latkowska M. , Syperek M. , Misiewicz J. , Gupta J. A.
Published: May 2012

Time resolved photoluminescence (PL) spectroscopy has been applied to study dynamics of localized excitons in a single Ga0.7In0.3N0.015As0.985/GaAs quantum well (QW). The decay time constant, τPL, has been determined for different PL peak energies at various temperatures. An increase in temperature produced two effects: (i) a reduction of τPL and (ii) changes in the τPL dispersion. These two experimental observations as well as the shape of PL decay curves were very well reproduced by Monte-Carlo simulations of hopping excitons with parameters derived from PL and photoreflectance measurements for this QW.
Kinetic damping of resistive wall modes in ITER
Authors: Chapman I. T. , Liu Y. Q. , Asunta O. , Graves J. P. , Johnson T. , Jucker M.
Published: May 2012

Full drift kinetic modelling including finite orbit width effects has been used to assess the passive stabilisation of the resistive wall mode (RWM) that can be expected in the ITER advanced scenario. At realistic plasma rotation frequency, the thermal ions have a stabilising effect on the RWM, but the stability limit remains below the target plasma pressure to achieve Q = 5. However, the inclusion of damping arising from the fusion-born alpha particles, the NBI ions, and ICRH fast ions extends the RWM stability limit above the target β for the advanced scenario. The fast ion damping arises primarily from finite orbit width effects and is not due to resonance between the particle frequencies and the instability.
Transport properties of graphene nanoribbon transistors on chemical-vapor-deposition grown wafer-scale graphene
Authors: Hwang Wan Sik , Tahy Kristof , Li Xuesong , Xing Huili (Grace) , Seabaugh Alan C. , Sung Chun Yung , Jena Debdeep
Published: May 2012

Graphene nanoribbon (GNR) field-effect transistors (FETs) with widths down to 12 nm have been fabricated by electron beam lithography using a wafer-scale chemical vapor deposition (CVD) process to form the graphene. The GNR FETs show drain-current modulation of approximately 10 at 300 K, increasing to nearly 106 at 4 K. The strong temperature dependence of the minimum current indicates the opening of a bandgap for CVD-grown GNR-FETs. The extracted bandgap is estimated to be around 0.1 eV by differential conductance methods. This work highlights the development of CVD-grown large-area graphene and demonstrates the opening of a bandgap in nanoribbon transistors.
Red-green-blue polymer light-emitting diode pixels printed by optimized laser-induced forward transfer
Authors: Shaw Stewart James , Lippert Thomas , Nagel Matthias , Nüesch Frank , Wokaun Alexander
Published: May 2012

An optimized laser-induced forward transfer (LIFT) technique has been used to fabricate tri-color organic light-emitting diode (OLED) pixels. At reduced pressures, and with a defined donor-receiver gap, patterned depositions of polyfluorene-based OLED pixels have been achieved. OLED pixel functionality has been demonstrated and compared with devices made using conventional deposition techniques. In addition, improved functionality has been obtained by coating the cathode with an electron-injecting layer, a process not possible using conventional OLED fabrication techniques. The OLED pixels fabricated by LIFT reach efficiencies on the range of conventionally fabricated devices and even surpass them in the case of blue pixels.
Effect of oxygen deficiency on room temperature ferromagnetism in Co doped ZnO
Authors: Gu Hao , Zhang Wen , Xu Yongbing , Yan Mi
Published: May 2012

We investigated the correlation between magnetization and oxygen vacancies in Zn0.95Co0.05O nanoparticles. Enhanced magnetizations were found in SiO2 nanopowders and carbon nanotubes (CNTS) treated Zn0.95Co0.05O, which are attributed to minimizing nanoparticle size and increasing oxygen vacancy concentration. After oxygen annealing, the magnetization of both non-treated Zn0.95Co0.05O and CNTS treated Zn0.95Co0.05O decreased sharply with the filling of the oxygen vacancies, while the SiO2 treated Zn0.95Co0.05O was influenced little as the amorphous SiO2 shell prevents the diffusion of oxygen into magnetic particles. It demonstrated that the ferromagnetism comes from the interfacial oxygen deficiency and is tunable by changing the oxygen vacancies.
Mapping return currents in laser-generated Z-pinch plasmas using proton deflectometry
Authors: Manuel M. J.-E. , Sinenian N. , Séguin F. H. , Li C. K. , Frenje J. A. , Rinderknecht H. G. , Casey D. T. , Zylstra A. B. , Petrasso R. D. , Beg F. N.
Published: May 2012

Dynamic return currents and electromagnetic field structure in laser-generated Z-pinch plasmas have been measured using proton deflectometry. Experiments were modeled to accurately interpret deflections observed in proton radiographs. Current flow is shown to begin on axis and migrate outwards with the expanding coronal plasma. Magnetic field strengths of ∼1 T are generated by currents that increase from ∼2 kA to ∼7 kA over the course of the laser pulse. Proton deflectometry has been demonstrated to be a practical alternative to other magnetic field diagnostics for these types of plasmas.
Multiple-trapping in pentacene field-effect transistors with a nanoparticles self-assembled monolayer
Authors: Lee Keanchuan , Weis Martin , Manaka Takaaki , Iwamoto Mitsumasa
Published: May 2012

A silver nanoparticles self-assembled monolayer (SAM) was incorporated in pentacene field-effect transistor and its effects on the carrier injection and transport were investigated using the current-voltage (I − V) and impedance spectroscopy (IS) measurements. The I − V results showed that there was a significant negative shift of the threshold voltage, indicating the hole trapping inside the devices with about two orders higher in the contact resistance and an order lower in the effective mobility when a SAM was introduced. The IS measurements with the simulation using a Maxwell-Wagner equivalent circuit model revealed the existence of multiple trapping states for the devices with NPs, while the devices without NPs exhibited only a single trap state.
Closed-form density-based framework for automatic detection of cellular morphology changes
Authors: Duong Tarn , Goud Bruno , Schauer Kristine
Published: May 2012

A primary method for studying cellular function is to examine cell morphology after a given manipulation. Fluorescent markers attached to proteins/intracellular structures of interest in conjunction with 3D fluorescent microscopy are frequently exploited for functional analysis. Despite the central role of morphology comparisons in cell biological approaches, few statistical tools are available that allow biological scientists without a high level of statistical training to quantify the similarity or difference of fluorescent images containing multifactorial information. We transform intracellular structures into kernels and develop a multivariate two-sample test that is nonparametric and asymptotically normal to directly and quantitatively compare cellular morphologies. The asymptotic normality bypasses the computationally intensive calculations used by the usual resampling techniques to compute the
P
-value. Because all parameters required for the statistical test are estimated directly from the data, it does not require any subjective decisions. Thus, we provide a black-box method for unbiased, automated comparison of cell morphology. We validate the performance of our test statistic for finite synthetic samples and experimental data. Employing our test for the comparison of the morphology of intracellular multivesicular bodies, we detect changes in their distribution after disruption of the cellular microtubule cytoskeleton with high statistical significance in fixed samples and live cell analysis. These results demonstrate that density-based comparison of multivariate image information is a powerful tool for automated detection of cell morphology changes. Moreover, the underlying mathematics of our test statistic is a general technique, which can be applied in situations where two data samples are compared.
Omega-3 fatty acids cause dramatic changes in TLR4 and purinergic eicosanoid signaling
Authors: Norris Paul C. , Dennis Edward A.
Published: May 2012

Dietary fish oil containing ω3 fatty acids, eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), elicit cardioprotective and anti-inflammatory effects through unresolved mechanisms that may involve competition and inhibition at multiple levels. Here, we report the effects of arachidonic acid (AA), EPA, and DHA supplementation on membrane incorporation, phospholipase A
2
catalyzed release, and eicosanoid production in RAW264.7 macrophages. Using a targeted lipidomics approach, we observed that Toll-like receptor 4 and purinergic receptor activation of supplemented cells leads to the release of 22-carbon fatty acids that potently inhibit cyclooxygenase pathways. This inhibition was able to shunt metabolism of AA to lipoxygenase pathways, augmenting leukotriene and other lipoxygenase mediator synthesis. In resident peritoneal macrophages, docosapentaenoic acid (DPA) was responsible for cyclooxygenase inhibition after EPA supplementation, offering fresh insights into how EPA exerts anti-inflammatory effects indirectly through elongation to 22-carbon DPA.
Reactive oxygen species are second messengers of neurokinin signaling in peripheral sensory neurons
Authors: Linley John E. , Ooi Lezanne , Pettinger Louisa , Kirton Hannah , Boyle John P. , Peers Chris , Gamper Nikita
Published: May 2012

Substance P (SP) is a prominent neuromodulator, which is produced and released by peripheral damage-sensing (nociceptive) neurons; these neurons also express SP receptors. However, the mechanisms of peripheral SP signaling are poorly understood. We report a signaling pathway of SP in nociceptive neurons: Acting predominantly through NK1 receptors and G
i/o
proteins, SP stimulates increased release of reactive oxygen species from the mitochondrial electron transport chain. Reactive oxygen species, functioning as second messengers, induce oxidative modification and augment M-type potassium channels, thereby suppressing excitability. This signaling cascade requires activation of phospholipase C but is largely uncoupled from the inositol 1,4,5-trisphosphate sensitive Ca
2+
stores. In rats SP causes sensitization of TRPV1 and produces thermal hyperalgesia. However, the lack of coupling between SP signaling and inositol 1,4,5-trisphosphate sensitive Ca
2+
stores, together with the augmenting effect on M channels, renders the SP pathway ineffective to excite nociceptors acutely and produce spontaneous pain. Our study describes a mechanism for neurokinin signaling in sensory neurons and provides evidence that spontaneous pain and hyperalgesia can have distinct underlying mechanisms within a single nociceptive neuron.
Engineering bone tissue from human embryonic stem cells
Authors: Marolt Darja , Campos Iván Marcos , Bhumiratana Sarindr , Koren Ana , Petridis Petros , Zhang Geping , Spitalnik Patrice F. , Grayson Warren L. , Vunjak-Novakovic Gordana
Published: May 2012

In extensive bone defects, tissue damage and hypoxia lead to cell death, resulting in slow and incomplete healing. Human embryonic stem cells (hESC) can give rise to all specialized lineages found in healthy bone and are therefore uniquely suited to aid regeneration of damaged bone. We show that the cultivation of hESC-derived mesenchymal progenitors on 3D osteoconductive scaffolds in bioreactors with medium perfusion leads to the formation of large and compact bone constructs. Notably, the implantation of engineered bone in immunodeficient mice for 8 wk resulted in the maintenance and maturation of bone matrix, without the formation of teratomas that is consistently observed when undifferentiated hESCs are implanted, alone or in bone scaffolds. Our study provides a proof of principle that tissue-engineering protocols can be successfully applied to hESC progenitors to grow bone grafts for use in basic and translational studies.
The polymorphism rs944289 predisposes to papillary thyroid carcinoma through a large intergenic noncoding RNA gene of tumor suppressor type
Authors: Jendrzejewski Jaroslaw , He Huiling , Radomska Hanna S. , Li Wei , Tomsic Jerneja , Liyanarachchi Sandya , Davuluri Ramana V. , Nagy Rebecca , de la Chapelle Albert
Published: May 2012

A genome-wide association study of papillary thyroid carcinoma (PTC) pinpointed two independent SNPs (rs944289 and rs965513) located in regions containing no annotated genes (14q13.3 and 9q22.33, respectively). Here, we describe a unique, long, intergenic, noncoding RNA gene (lincRNA) named
Papillary Thyroid Carcinoma Susceptibility Candidate 3
(
PTCSC3
) located 3.2 kb downstream of rs944289 at 14q.13.3 and the expression of which is strictly thyroid specific. By quantitative PCR,
PTCSC3
expression was strongly down-regulated (
P
= 2.84 × 10
−14
) in thyroid tumor tissue of 46 PTC patients and the risk allele (T) was associated with the strongest suppression (genotype [TT] (
n
= 21) vs. [CT] (
n
= 19),
P
= 0.004). In adjacent unaffected thyroid tissue, the genotype [TT] was associated with up-regulation of
PTCSC3
([TT] (
n
= 21) vs. [CT] (
n
= 19),
P
= 0.034). The SNP rs944289 was located in a binding site for the CCAAT/enhancer binding proteins (C/EBP) α and β. The risk allele destroyed the binding site in silico. Both C/EBPα and C/EBPβ activated the
PTCSC3
promoter in reporter assays (
P
= 0.0009 and
P
= 0.0014, respectively) and the risk allele reduced the activation compared with the nonrisk allele (C) (
P
= 0.026 and
P
= 0.048, respectively). Restoration of
PTCSC3
expression in PTC cell line cells (TPC-1 and BCPAP) inhibited cell growth (
P
= 0.002 and
P
= 0.019, respectively) and affected the expression of genes involved in DNA replication, recombination and repair, cellular movement, tumor morphology, and cell death. Our data suggest that SNP rs944289 predisposes to PTC through a previously uncharacterized, long intergenic noncoding RNA gene (
PTCSC3
) that has the characteristics of a tumor suppressor.
Polarization-analyzed small-angle neutron scattering. II. Mathematical angular analysis
Authors: Krycka Kathryn , Borchers Julie , Ijiri Yumi , Booth Ryan , Majetich Sara
Published: May 2012

Polarization-analyzed small-angle neutron scattering (SANS) is a powerful tool for the study of magnetic morphology with directional sensitivity. Building upon polarized scattering theory, this article presents simplified procedures for the reduction of longitudinally polarized SANS into terms of the three mutually orthogonal magnetic scattering contributions plus a structural contribution. Special emphasis is given to the treatment of anisotropic systems. The meaning and significance of scattering interferences between nuclear and magnetic scattering and between the scattering from magnetic moments projected onto distinct orthogonal axes are discussed in detail. Concise tables summarize the algorithms derived for the most commonly encountered conditions. These tables are designed to be used as a reference in the challenging task of extracting the full wealth of information available from polarization-analyzed SANS.
nxs: a program library for neutron cross section calculations
Authors: Boin Mirko
Published: May 2012

A collection of routines for calculating neutron scattering and absorption cross sections on the basis of crystal structure descriptions is presented and implemented in the new and reusablenxsprogram library. An example program providing a graphical user interface to thenxsfunctions is created to demonstrate their usage. The flexibility of the library and the possibilities for multiple areas of application are shown by further examples involving Monte Carlo neutron simulations concerned with imaging experiment validation and neutron instrument development.
In situstudies into the formation kinetics of potassium jarosite
Authors: Brand Helen E. A. , Scarlett Nicola V. Y. , Grey Ian E.
Published: May 2012

This paper reports the results of time-resolved synchrotron powder diffraction and small-angle scattering experiments designed to investigate the kinetics of formation of potassium jarosite by co-precipitation at 353, 368 and 393 K. Only jarosite was produced in these syntheses, and the particles that formed nucleated on the walls of the capillary reaction vessels with a disc-like shape. Relative Rietveld scale factors indicating jarosite abundance have been used as the basis for kinetic modelling of the nucleation and growth stages using a modified form of the Avrami kinetic equation. The results show that jarosite forms by a single nucleation event followed by two distinct stages of growth, each characterized by a different Avrami exponent. The value of this exponent is initially between 1 and 2, and then reduces to around 1. This suggests that jarosite growth after nucleation is controlled by effects at the solution–boundary interface, with the first stage best described by two-dimensional growth which transitions to one-dimensional growth later in the reaction. An activation energy of 89 kJ mol−1was estimated for the first stage of growth, in good agreement with previous work.
Graphical tools for macromolecular crystallography inPHENIX
Authors: Echols Nathaniel , Grosse-Kunstleve Ralf W. , Afonine Pavel V. , Bunkóczi Gábor , Chen Vincent B. , Headd Jeffrey J. , McCoy Airlie J. , Moriarty Nigel W. , Read Randy J. , Richardson David C. , Richardson Jane S. , Terwilliger Thomas C. , Adams Paul D.
Published: May 2012

A new Python-based graphical user interface for thePHENIXsuite of crystallography software is described. This interface unifies the command-line programs and their graphical displays, simplifying the development of new interfaces and avoiding duplication of function. With careful design, graphical interfaces can be displayed automatically, instead of being manually constructed. The resulting package is easily maintained and extended as new programs are added or modified.
Dihydrocryptopine
Authors: Sun Wenwen , Cao Lei , Zhang Cen , Zhu Lifei , Zhou Le
Published: May 2012

In the crystal structure of the title compound [systematic name: 6,7-dimethoxy-12-methyl-16,18-dioxa-12-azatetracyclo[12.7.0.04,9.015,19]henicosa-1(21),4,6,8,14,19-hexaen-3-ol], C21H25NO5, the benzene rings exhibits a dihedral angle of 14.95 (4)°. In the crystal, molecules are linked by pairs of O—H...O hydrogen bonding into inversion dimers. These dimers are further connected by C—H...O interactions.
Methyl N-{4-[(4-methoxyphenoxy)methyl]-2-oxo-2H-chromen-7-yl}carbamate
Authors: Kumar K. Mahesh , Mahabaleshwaraiah N. M. , Kotresh O. , Jeyaseelan S , Devarajegowda H. C.
Published: May 2012

In the title compound, C19H17NO6, the dihedral angle between the 2H-chromene ring system and benzene ring is 5.34 (6)°. A short intramolecular C—H...O contact occurs. In the crystal, molecules are linked by N—H...O hydrogen bonds, generating C(8) chains propagating in [010]. The chains are linked by C—H...O interactions and the packing also exhibits π–π stacking interactions between benzene and pyran rings, with a centroid–centroid distance of 3.676 (9) Å.
Poly[[(methanol)(μ4-2,4,5,6-tetrafluorobenzene-1,3-dicarboxylato)copper(II)] methanol monosolvate]
Authors: Yan Dan , Duan Qian
Published: May 2012

In the title compound, {[Cu(C8F4O4)(CH3OH)]·CH3OH}
n
, two CuII atoms are bridged by four carboxylate groups, forming the well known paddle-wheel secondary building unit (SBU) with axial methanol ligands. In each ligand, the dihedral angles between the benzene ring and the two carboxylate groups are 80.43 (17) and 62.5 (4)°. Within each SBU, the four carboxylate groups come from four symmetry-equivalent tetrafluoroisophthalate ligands. Each tetrafluoroisophthalate group connects two SBUs, forming a layered structure . In the crystal, O—H...O hydrogen bonds involving the free and ligated methanol molecules link the molecules into a three-dimensional supramolecular network.
3-Nitro-2-phenylchroman
Authors: Zhao Pei-Hua , Hao Er-Jun , Liu Ya-Qing , Zhao Gui-Zhe
Published: May 2012

In the title compound, C15H13NO3, the dihedral angle between the two aromatic rings is 79.25 (16)°.
Bis(2-aminomethyl-1H-benzimidazole-κ2
N
2,N
3)bis(nitrato-κO)copper(II)
Authors: Zhao Jing , Zhang Heng , Zhai Xueliang , Zhu Guoyi
Published: May 2012

In the title compound, [Cu(NO3)2(C8H9N3)2], the CuII atom, lying on an inversion center, has a distorted octahedral coordination environment defined by four N atoms from two chelating 2-aminomethyl-1H-benzimidazole ligands and two O atoms from two monodentate nitrate anions. In the crystal, N—H...O hydrogen bonds link the complex molecules into a three-dimensional network. An intramolecular N—H...O hydrogen bond is also observed.
Methyl (E)-2-[(2-nitrophenoxy)methyl]-3-phenylacrylate
Authors: Anuradha T. , Devaraj A. , Seshadri P. R. , Bakthadoss M.
Published: May 2012

The title compound, C17H15NO5, adopts an E conformation with respect to the C=C double bond of the phenylacrylate unit. The phenyl ring and methyl acrylate group of the phenylacrylate unit are disordered over two sets of sites with site-occupancy ratios of 0.705 (5):0.295 (5) and 0.683 (3):0.317 (3), respectively. The mean plane through the benzene ring of the phenyl acrylate makes dihedral angles of 88.4 (8) (major component) and 86.7 (8)° (minor component) with the nitrophenoxy ring; the dihedral angle between the two components is 3.64 (6)°. Intramolecular C—H...O interactions stabilise the molecular structure. In the crystal, C—H...O interactions result in a chain of molecules running along the b axis.
2,3-Dihydropyrrolo[2,1-b]quinazoline-9(1H)-thione
Authors: Nasrullayev Azizbek O. , Elmuradov Burkhon Zh. , Turgunov Kambarali K. , Tashkhodjaev Bakhodir , Shakhidoyatov Khusnutdin M.
Published: May 2012

In the crystal, molecules of the title compound, C11H10N2S, are connected by C—H...N interactions around threefold axes. Furthermore, they form stacks along the c axis showing π–π interactions between pyrimidine rings [centroid–centroid distance = 3.721 (1) Å]. The central ring is essentially planar with an r.m.s. deviation of 0.007 Å. The five-membered ring adopts an envelope conformation with the flap atom deviating by 0.241 (4) Å from the mean plane (r.m.s. deviation = 0.002 Å) through the other four ring atoms.
Bis(4′-chloro-2,2′:6′,2′′-terpyridine-κ3
N,N′,N′′)ruthenium(II) dichloride dihydrate
Authors: Wang Ying , Jiao Rui , Qiu Xiang-Lei , Wang Jian , Huang Wei
Published: May 2012

In the cation of the title compound, [Ru(C15H10ClN3)2]Cl2·2H2O, the metal atom exhibits a distorted octahedral coordination geometry provided by the N atoms of two tridentate terpyridine ligands. The ligands are approximately planar [maximum deviation = 0.156 (5) Å] and form a dihedral angle of 87.0 (3)°. In the crystal, the cations, anions and water molecules are linked into a three-dimensional network by C—H...Cl, C—H...O and O—H...Cl hydrogen bonds.
Effects of gradual salinity increase on osmoregulation in Caspian roach Rutilus caspicus
Authors: Malakpour Kolbadinezhad S. , Hajimoradloo A. , Ghorbani R. , Joshaghani H. , Wilson J. M.
Published: May 2012

This study was carried out to determine the effects of gradual salinity increase on osmoregulatory ability of the Caspian roach Rutilus caspicus, under conditions which mimic stocking conditions of hatchery‐raised fish. Initially, 30 juvenile fish (mean ±s.d. 3·20 ± 0·34 g) were transferred to 20 l circular tanks, in which salinities were changed in a stepwise fashion, from 0 to 5, 10 or 15 at 48 h intervals. The fish at salinity 15 were held for an additional 48 h at this salinity. Forty‐eight hours after salinity transfer, survival rate, haematocrit, plasma Cl−, Na+ and K+ concentrations, osmolality and gill Na+/K+‐ATPase (NKA) activity were measured. The only effect of exposure to 5 was a significant reduction in haematocrit compared to the freshwater control group. Exposure to salinity 10 raised haematocrit, Cl− and Na+ concentrations and osmolality. At 48 h exposure to salinity 15, haematocrit, Cl− and Na+ concentrations and osmolality were significantly higher than freshwater controls, and gill NKA activity was significantly lower, but the effect on NKA was no longer evident at 96 h exposure. There were no effects on survival. These results indicate that R. caspicus juveniles experience an initial non‐lethal iono‐osmotic perturbation following salinity increase but can adapt to brackish water at salinity 15.
Use of the pre‐operative shuttle walk test to predict morbidity and mortality after elective major colorectal surgery
Authors: Nutt C. L. , Russell J. C.
Published: May 2012

High‐risk surgery is performed in every acute hospital. These patients often have increased peri‐operative risk related to their poor cardiorespiratory reserve. Formal risk assessment is recommended for such patients; cardiopulmonary exercise testing is a well established triage tool, but is unavailable in many hospitals. We investigated whether a simple exercise test could predict postoperative outcome using a prospective trial of 121 patients undergoing elective major abdominal surgery. Each patient completed a shuttle walk test and was followed up for 30 days after surgery. There was one postoperative death (0.8%), with 53 patients (44%) developing complications. The mean (SD) shuttle walk test distance was significantly different between patients who suffered complications and those who did not (276.6 (134.5) vs 389.6 (138.9) m, respectively; p < 0.001). A cut‐off distance of 250 m had a specificity of 0.88 and a sensitivity of 0.58 to predict postoperative complications. Patients unable to complete a shuttle walk test above this cut‐off distance were three times more likely to have a postoperative morbidity. We conclude that the shuttle walk test can help identify patients who are at increased peri‐operative risk.
Juvenile Chinook salmon,Oncorhynchus tshawytscha,growth and diet in riverine habitat engineered to improve conditions for spawning
Authors: Utz R. M. , Zeug S. C. , Cardinale B. J.
Published: May 2012

Abstract Many habitat enhancement techniques aimed at restoring salmonid populations have not been comprehensively assessed. The growth and diet of juvenile Chinook salmon,Oncorhynchus tshawytscha(Walbaum), rearing in a reach designed to enhance spawning were evaluated to determine how a non‐target life stage fared in the engineered habitat. Prior work demonstrated differences in food web structure between restored and unenhanced reaches of the Merced River, thus juvenile salmon feeding dynamics were also hypothesised to vary. Dependent variables were compared among fish collected from within and near the upper boundary of the restored reach and in an unenhanced habitat upstream. Diets, otolith‐derived growth and stable isotope‐inferred trophic positions were compared. Baetidae mayflies were particularly important prey in the restored reach, while elsewhere individuals exhibited heterogeneous diets. Salmon residing at the bottom of the restored reach exhibited slightly faster growth rates relative to fish collected elsewhere, although stable isotope and diet analyses suggested that they fed at a relatively low trophic position. SpecialisedBaetispredation and/or abundant interstitial refugia potentially improved rearing conditions in the restored reach. Data suggest that gravel enhancement and channel realignment designed to augment adult spawning habitat may simultaneously support juvenile Chinook salmon despite low invertebrate food resources.
Comparison of three standardised fish sampling methods in 14 alpine lakes in Austria
Authors: ACHLEITNER D. , GASSNER H. , LUGER M.
Published: May 2012

Abstract  Standardised fishing methods using gillnets (EN 14575), electric fishing (EN 14011) and hydroacoustics (WI 00230244 CEN enquiry) to estimate species composition, abundance, biomass and size distribution were compared in 14 alpine lakes >50 ha. More fish species were detected using benthic gillnets (mean = 72.7%) than electric fishing (mean = 59.5%) and pelagic gillnets (mean = 29.6%). For all but two lakes, additional information from a local fisheries manager was required to obtain a complete list of species. Biomass data generated by standardised gillnetting and hydroacoustic surveys were not fully comparable, but a positive correlation was found. Gill netting and hydroacoustics both indicated a nearly fishless habitat below 75 m, which confirmed the maximum required fishing depth according to the European Standard EN 14757. Size distributions obtained from gillnet and hydroacoustic surveys differed statistically for large fish (>40 cm). Each standardised method reflected typical shortcomings. The European standard (EN 14757) should be amended for pelagic fish habitat in deep alpine lakes to include sampling effort corresponding to water volume, and additional gillnets with larger mesh sizes (e.g. 70 mm). Furthermore, the electric fishing standard (EN 14011) should be extended to incorporate requirements of lake fish sampling.
Linking aquatic and terrestrial food webs – Odonata in boreal systems
Authors: SEIFERT LINDA I. , SCHEU STEFAN
Published: May 2012

1. It is increasingly realised that aquatic and terrestrial systems are closely linked. We investigated stable isotope variations in Odonata species, putative prey and basal resources of aquatic and terrestrial systems of northern Mongolia during summer.

2. In permanent ponds, δ13C values of Odonata larvae were distinctly lower than those of putative prey, suggesting that body tissue comprised largely of carbon originating from isotopically light carbon sources. Presumably, prey consumed during autumn and winter when carbon is internally recycled and/or methanotrophic bacteria form an important basal resource of the food web. In contrast, in a temporary pond, δ13C values of Odonata larvae were similar to those of putative prey, indicating that their body carbon originated mainly from prey species present.

3. Changes in δ15N and δ13C values between larvae and adults were species specific and reflected differential replacement of the larval isotopic signature by the terrestrial diet of adult Odonata. The replacement was more pronounced in Odonata species of permanent ponds than in those of the temporary pond, where larvae hatched later in the year. Replacement of larval carbon varied between tissues, with wings representing the larval isotopic signature whereas thoracic muscles and eggs reflected the δ15N and δ13C values of the terrestrial diet of adults.

4. The results suggest that because of their long larval development, Odonata species of permanent ponds carry the larval signature, which is partly replaced during their terrestrial life. Terrestrial prey forms the basis for egg production and thus the next generation of aquatic larvae. In temporary ponds, in contrast, Odonata species rely on prey from a single season, engage in a prolonged aquatic phase and hatch later, leaving less time to acquire terrestrial prey resources for offspring production. Stable isotope analysis provided important insights into the food webs of the waterbodies and their relationship to the terrestrial system.
Long‐term fitness consequences of high yolk androgen levels: sons pay the costs
Authors: Ruuskanen Suvi , Doligez Blandine , Pitala Natalia , Gustafsson Lars , Laaksonen Toni
Published: May 2012

1. Early growth conditions, for example hormonal environment during embryonic development, may have long‐lasting effects on behaviour and phenotype, with subsequent fitness consequences. Yolk androgens have been shown to affect various offspring traits in the short‐term, but fitness consequences for either offspring or parents, a prerequisite for studying the adaptiveness of this maternal effect, are poorly known in the wild.

2. We experimentally elevated yolk androgen levels of whole clutches in a wild population of collared flycatchers (Ficedula albicollis) and investigated the long‐term effects of yolk androgens on offspring local recruitment, parental return rate, and timing and success of breeding in both parents and offspring in the breeding season(s) following the manipulation.

3. Yolk androgen elevation lowered the local recruitment rate of male, but not female offspring, but had no effect on any breeding parameters of offspring of either sex. Furthermore, yolk androgen elevation of the clutch had no effect on the return rate or any breeding parameters of the parents.

4. Our results indicate that high yolk androgen levels may impose a potential direct fitness cost for male offspring, but no long‐lasting additional indirect fitness costs for parents (direct costs of transferring androgens to eggs not considered). Such a sex‐specific cost on offspring could constrain yolk androgen deposition and select for sex‐specific deposition mechanisms.

5. As yolk androgen levels in this population are heritable, our results on long‐term fitness effect of yolk androgens support the idea that hormone‐mediated maternal effects may evolve under selection and thereby affect evolutionary processes.
Managed relocation as an adaptation strategy for mitigating climate change threats to the persistence of an endangered lizard
Authors: Fordham Damien A. , Watts Michael J. , Delean Steven , Brook Brook W. , Heard Lee M.B. , Bull C.M.
Published: May 2012

The distributional ranges of many species are contracting with habitat conversion and climate change. For vertebrates, informed strategies for translocations are an essential option for decisions about their conservation management. The pygmy bluetongue lizard, Tiliqua adelaidensis, is an endangered reptile with a highly restricted distribution, known from only a small number of natural grassland fragments in South Australia. Land‐use changes over the last century have converted perennial native grasslands into croplands, pastures and urban areas, causing substantial contraction of the species' range due to loss of essential habitat. Indeed, the species was thought to be extinct until its rediscovery in 1992. We develop coupled‐models that link habitat suitability with stochastic demographic processes to estimate extinction risk and to explore the efficacy of potential climate adaptation options. These coupled‐models offer improvements over simple bioclimatic envelope models for estimating the impacts of climate change on persistence probability. Applying this coupled‐model approach to T. adelaidensis, we show that: (i) climate‐driven changes will adversely impact the expected minimum abundance of populations and could cause extinction without management intervention, (ii) adding artificial burrows might enhance local population density, however, without targeted translocations this measure has a limited effect on extinction risk, (iii) managed relocations are critical for safeguarding lizard population persistence, as a sole or joint action and (iv) where to source and where to relocate animals in a program of translocations depends on the velocity, extent and nonlinearities in rates of climate‐induced habitat change. These results underscore the need to consider managed relocations as part of any multifaceted plan to compensate the effects of habitat loss or shifting environmental conditions on species with low dispersal capacity. More broadly, we provide the first step towards a more comprehensive framework for integrating extinction risk, managed relocations and climate change information into range‐wide conservation management.
Distribution and speciation in marine intertidal tardigrades: testing the roles of climatic and geographical isolation
Authors: Faurby Søren , Jørgensen Aslak , Kristensen Reinhardt M. , Funch Peter
Published: May 2012

Aim  To analyse the importance of climatic and geographical isolation in determining the patterns of speciation and distribution of species within the tardigrade genus Echiniscoides.

Location  Marine intertidal zone, globally.

Methods  DNA was extracted from 465 individual tardigrades from 48 localities world‐wide. The tardigrades were divided into clusters using several distance‐based criteria. The phylogeny of these clusters was estimated with Bayesian analyses. The relationships between genetic distance and substrate, climate, and geographical distance were tested with a new improved Mantel test which incorporates phylogenetic uncertainties by analysing the raw tree data instead of the averaged tree.

Results  Approximately 40 clusters, each probably corresponding to species, were recovered from the genetic analysis; the number of clusters fluctuated depending on the criterion used for cluster delimitation. Each cluster had a limited temperature range and all clusters were confined to single oceans under all realistic criteria for cluster delimitation. Apart from a tropical cluster, each cluster occurred only in one hemisphere. Occurrence on different substrata was not correlated with genetic distance between clusters. Both geographical distance and climate were correlated with genetic distance; however, the correlation between geographical and genetic distance disappeared when the non‐independence of climatic and geographical distance were controlled for.

Main conclusions  The distribution of individual species of Echiniscoides is limited by climate and geographical distance. Distance does not appear to be a major factor influencing phylogeny in this genus, but ecological speciation along a temperature gradient appears to be important.
Alternative interactions define gyrase specificity in the CcdB family
Authors: De Jonge Natalie , Simic Mario , Buts Lieven , Haesaerts Sarah , Roelants Kim , Garcia‐Pino Abel , Sterckx Yann , De Greve Henri , Lah Jurij , Loris Remy
Published: May 2012

Toxin–antitoxin (TA) modules are small operons associated with stress response of bacteria. F‐plasmid CcdBF was the first TA toxin for which its target, gyrase, was identified. Plasmidic and chromosomal CcdBs belong to distinct families. Conserved residues crucial for gyrase poisoning activity of plasmidic CcdBs are not conserved among these families. Here we show that the chromosomal CcdBVfi from Vibrio fischeri is an active gyrase poison that interacts with its target via an alternative energetic mechanism. Changes in the GyrA14‐binding surface of the Vibrio and F‐plasmid CcdB family members illustrate neutral drift where alternative interactions can be used to achieve the same functionality. Differences in affinity between V. fischeri and F‐plasmid CcdB for gyrase and their corresponding CcdA antitoxin possibly reflect distinct roles for TA modules located on plasmids and chromosomes.
Diagnostic evaluation of patients with nonimmediate cutaneous hypersensitivity reactions to iodinated contrast media
Authors: Torres M. J. , Gomez F. , Doña I. , Rosado A. , Mayorga C. , Garcia I. , Blanca‐Lopez N. , Canto G. , Blanca M.
Published: May 2012

Background

Nonimmediate hypersensitivity reactions to iodinated contrast media (CM) are common. Allergological evaluation is necessary to confirm the diagnosis and to find a tolerated alternative. The aim of this study was to establish the role of skin testing and the drug provocation test (DPT) in the diagnosis of nonimmediate reactions to CM.

Methods

Skin intradermal testing and patch testing with delayed readings were carried out with different CM (iobitridol, iomeprol, iodixanol, iohexol, ioversol, iopramide and ioxaglate). Single‐blind placebo‐controlled DPT was carried out in those cases with a negative skin test. In seven cases, a skin biopsy was obtained from positive skin tests and positive DPT.

Results

Of the 161 subjects evaluated, 34 (21.1%) were skin‐test positive, 21 (50%) to Iomeprol, 7 (16.7%) to Iodixanol, 5 (11.9%) to Iobitridol, 4 (9.5%) to Ioxaglate, 3 (7.1%) to Iohexol and 1 (2.4%) to Iopramide. DPT was positive in 44 cases (34.6%) that were skin‐test negative, 38 (76%) to Iodixanol, 8 (16%) to Iomeprol and 4 (8%) to Iohexol. Of 78 cases (48.4%) with confirmed hypersensitivity, 34 (43.6%) were identified by skin testing and 44 (56.4%) by DPT. Skin biopsies showed a perivascular mononuclear cell infiltrate, mainly in the dermis, with higher levels of CD4 than CD8 T lymphocytes, with expression of activation markers and skin homing receptors.

Conclusion

Patients with nonimmediate reactions to CM were identified by skin testing in 43.6% and by DPT in 56.4%. The method to confirm the diagnosis differed depending on the CM involved.
Australian emergency doctors' and nurses' acceptance and knowledge regarding brain death: a national survey
Authors: Marck Claudia H. , Weiland Tracey J. , Neate Sandra L. , Hickey Bernadette B. , Jelinek George A.
Published: May 2012

Healthcare staff's acceptance of brain death (BD) being a valid determination of death is essential for optimized organ and tissue donation (OTD) rates. Recently, resources to increase Australian OTD rates have been aimed at emergency departments (ED) as a significant missed donor potential was discovered.

A cross‐sectional survey was conducted to assess Australian ED clinicians' acceptance and knowledge regarding BD. Most (86%) of the 599 medical and 212 nursing staff accepted BD, but only 60% passed a 5‐item‐validated BD knowledge tool. BD knowledge was related to the acceptance of BD. Accepting BD influenced attitudes toward OTD, including willingness to donate. BD acceptance and knowledge were related to education/training regarding OTD, years of experience in EDs, experience with OTD‐related tasks, and increased perceived competence and comfort with OTD‐related tasks. Of concern, more than half of respondents who did not pass the BD test reported feeling competent and comfortable explaining BD to next of kin; of respondents who had recent experience with this, more than a third failed the BD test.

Despite being generally positive toward OTD, Australian ED clinicians do not have a sound knowledge of BD. This may be hampering efforts to increase donation rates from the ED.
Covariance among premating, post‐copulatory and viability fitness components in Drosophila melanogaster and their influence on paternity measurement
Authors: DROGE‐YOUNG E. M. , MANIER M. K. , LÜPOLD S. , BELOTE J. M. , PITNICK S.
Published: May 2012

In polyandrous mating systems, male fitness depends on success in premating, post‐copulatory and offspring viability episodes of selection. We tracked male success across all of these episodes simultaneously, using transgenic Drosophila melanogaster with ubiquitously expressed green fluorescent protein (i.e. GFP) in a series of competitive and noncompetitive matings. This approach permitted us to track paternity‐specific viability over all life stages and to distinguish true competitive fertilization success from differential early offspring viability. Relationships between episodes of selection were generally not present when paternity was measured in eggs; however, positive correlations between sperm competitive success and offspring viability became significant when paternity was measured in adult offspring. Additionally, we found a significant male × female interaction on hatching success and a lack of repeatability of offspring viability across a focal male’s matings, which may underlay the limited number of correlations found between episodes of selection.
Genetic parameters for claw health and feet and leg conformation traits in Finnish Ayrshire cows
Authors: Häggman J. , Juga J. , Sillanpää M.J. , Thompson R.
Published: May 2012

Genetic parameters for different claw disorders, overall claw health and feet and leg conformation traits were estimated for Finnish Ayrshire cows. The merged data set with records of claw health and feet and leg conformation traits consisted of 105 000 observations from 52 598 Finnish Ayrshire cows between 2000 and 2010. The binary claw health data and the linearly scored conformation data were analysed using an animal model and restricted maximum likelihood method by applying the statistical package ASReml. Binomial logistic models with mixed effects were used to estimate genetic parameters for sole haemorrhages, chronic laminitis, white‐line separation, sole ulcer, interdigital dermatitis, heel horn erosion, digital dermatitis, corkscrew claw and overall claw health. Estimated heritabilities for different claw disorders using a binomial logistic model ranged from 0.01 to 0.20. Estimated heritability for overall claw health using a binomial logistic model was 0.08. Estimated heritabilities for feet and leg conformation traits ranged from 0.07 to 0.39. The genetic correlations between claw health and feet and leg conformation traits ranged from −0.40 to 0.42. All phenotypic correlations were close to zero. The moderate genetic correlation, together with higher heritability of feet and leg conformation traits, showed that RLSV (rear leg side view) is a useful indicator trait to be used together with claw trimming information to increase the accuracy of breeding values for claw health in genetic evaluation.