bluuebunny/crossref_metadata_2025 huggingface dataset:
Estimates of effective aerodynamic roughness length over mountainous areas of the Tibetan Plateau
Authors: Han Cunbo , Ma Yaoming , Su Zhongbo , Chen Xuelong , Zhang Lang , Li Maoshan , Sun Fanglin
Published: September 2014

Wind profile data were measured by a wind profiler at QOMS (The Qomolangma Station for Atmospheric Environmental Observation and Research, Chinese Academy of Sciences) and, in separate experiments, GPS radiosondes were used at Shiquanhe Station and Litang Station on the Tibetan Plateau (TP). All three stations are located in the most rugged areas of the TP. QOMS is surrounded by the Himalaya, Shiquanhe Station by the Transhimalaya and Litang station is near the Hengduan Mountains. Using observational wind profile data, effective aerodynamic roughness length and zero‐plane displacement height d0 are determined using the neutral logarithmic wind profile law. The results show that the values of derived from the wind profiles can be considerably larger than the small‐scale aerodynamic roughness lengths of the land surface around the three stations. Subsequently, several parametrization schemes which use land surface characteristics to estimate and d0, such as roughness obstacle height and density, were assessed. The result indicates that of all the methods available, that proposed by Grant and Mason, where the drag coefficient D = 0.5, gives the best estimate of . The interim European Centre for Medium‐range Weather Forecasts (ECMWF) Re‐Analysis (ERA‐Interim) dataset underestimates effective aerodynamic roughness length in mountainous areas of the TP due to its use of a smaller drag coefficient of D = 0.4. For estimating d0, the method of Kutzbach performs well when the density of roughness obstacles (λ) is low, whereas the method of Raupach et al. gives a more reliable estimate when λ is high. Although this analysis has some limitations, it can feasibly account for form drag being exerted by an unresolved topography in the mountainous areas of the TP.
Identification of the chemical components of Saussurea involucrata by high‐resolution mass spectrometry and the mass spectral trees similarity filter technique
Authors: Jia Zhixin , Wu Caisheng , Jin Hongtao , Zhang Jinlan
Published: September 2014

RATIONALE

Saussurea involucrata is a rare traditional Chinese medicine (TCM) that displays anti‐fatigue, anti‐inflammatory and anti‐tumor effects. In this paper, the different chemical components of Saussurea involucrata were characterized and identified over a wide dynamic range by high‐performance liquid chromatography coupled with high‐resolution hybrid mass spectrometry (HPLC/HRMS/MSn) and the mass spectral trees similarity filter (MTSF) technique.

METHODS

The aerial parts of Saussurea involucrata were extracted with 75% ethanol. The partial extract was separated on a chromatography column to concentrate the low‐concentration compounds. Mass data were acquired using full‐scan mass analysis (resolving power 50 000) with data‐dependent incorporation of dynamic exclusion analysis. The identified compounds were used as templates to construct a database of mass spectral trees. Data for the unknown compounds were matched with those templates and matching candidate structures were obtained.

RESULTS

The detected compounds were characterized based on matching to candidate structures by the MTSF technique and were further identified by their accurate mass weight, multiple‐stage analysis and fragmentation patterns and through comparison with literature data. A total of 38 compounds were identified including 19 flavones, 11 phenylpropanoids and 8 sphingolipids. Among them, 7 flavonoids, 8 phenylpropanoids and 8 sphingolipids were identified for the first time in Saussurea involucrata.

CONCLUSIONS

HPLC/HRMS/MSn combined with MTSF was successfully used to discover and identify the chemical compounds in Saussurea involucrata. The results indicated that this combined technique was extremely useful for the rapid detection and identification of the chemical components in TCMs. Copyright © 2014 John Wiley & Sons, Ltd.
Mass resolution of linear quadrupole ion traps with round rods
Authors: Douglas D. J. , Konenkov N. V.
Published: September 2014

RATIONALE

Auxiliary dipole excitation is widely used to eject ions from linear radio‐frequency quadrupole ion traps for mass analysis. Linear quadrupoles are often constructed with round rod electrodes. The higher multipoles introduced to the electric potential by round rods might be expected to change the ion ejection process. We have therefore investigated the optimum ratio of rod radius, r, to field radius, r0, for excitation and ejection of ions.

METHODS

Trajectory calculations are used to determine the excitation contour, S(q), the fraction of ions ejected when trapped at q values close to the ejection (or excitation) q. Initial conditions are randomly selected from Gaussian distributions of the x and y coordinates and a thermal distribution of velocities. The N = 6 (12 pole) and N = 10 (20 pole) multipoles are added to the quadrupole potential. Peak shapes and resolution were calculated for ratios r/r0 from 1.09 to 1.20 with an excitation time of 1000 cycles of the trapping radio‐frequency.

RESULTS

Ratios r/r0 in the range 1.140 to 1.160 give the highest resolution and peaks with little tailing. Ratios outside this range give lower resolution and peaks with tails on either the low‐mass side or the high‐mass side of the peaks. This contrasts with the optimum ratio of 1.126–1.130 for a quadrupole mass filter operated conventionally at the tip of the first stability region. With the optimum geometry the resolution is 2.7 times greater than with an ideal quadrupole field. Adding only a 2.0% hexapole field to a quadrupole field increases the resolution by a factor of 1.6 compared with an ideal quadrupole field. Addition of a 2.0% octopole lowers resolution and degrades peak shape. With the optimum value of r/r0, the resolution increases with the ejection time (measured in cycles of the trapping rf, n) approximately as R0.5 = 6.64n, in contrast to a pure quadrupole field where R0.5 = 1.94n.

CONCLUSIONS

Adding weak nonlinear fields to a quadrupole field can improve the resolution with mass‐selective ejection of ions by up to a factor of 2.7. The optimum ratio r/r0 is 1.14 to 1.16, which differs from the optimum ratio for a mass filter of 1.128–1.130. Copyright © 2014 John Wiley & Sons, Ltd.
Sample matrix effects on measured carbon and oxygen isotope ratios during continuous‐flow isotope‐ratio mass spectrometry
Authors: Levitt Nicholas Paul
Published: September 2014

RATIONALE

Continuous‐flow isotope‐ratio mass spectrometry (CF‐IRMS) is frequently used to analyze CO2 found in media such as air, breath, and soil pore space gas with the aid of a sample preparation and transfer device such as a Gasbench II. This study investigated the effect that matrices other than helium (He) have on the measured δ13C and δ18O isotope ratios of CO2.

METHODS

Identical CO2 was added to sample vials with matrices of pure He, pure N2, or a 21:79 mixture of O2/N2 and analyzed by a ThermoFinnigan DeltaPlus XP isotope‐ratio mass spectrometer coupled to a ThermoFinnigan Gasbench II. Variables such as CO2 concentration, sample analysis sequence, and sample matrix removal ('blanking') through manipulation of an injection and dilution open split were tested to identify systematic isotope ratio offsets between the different matrix types.

RESULTS

The process of blanking induced a δ13C and δ18O offset of ≤0.2‰ between otherwise identical populations of CO2 samples in He. The 13C/12C and 18O/16O isotope ratios of CO2 sampled from pure N2 or a mixture of O2/N2 were found to be within 0.1 to 0.2‰ of those of an identical CO2 sampled from a He matrix when N2 or O2/N2 was removed prior to transport to the mass spectrometer. The measured oxygen isotope ratios of CO2 sampled from N2 and O2/N2 varied by as much as 0.6‰ and 4‰, respectively, if matrix gas was not removed prior to ionization.

CONCLUSIONS

Sampling CO2 from matrices similar to air does not significantly affect the measured 13C/12C and 18O/16O isotope ratios of CO2 when a gas‐handling procedure that includes the removal of matrix gas is utilized. This procedure is much preferable to introducing matrix gas and potentially isobaric interference to the ion source. Copyright © 2014 John Wiley & Sons, Ltd.
Desorption atmospheric pressure photoionization and direct analysis in real time coupled with travelling wave ion mobility mass spectrometry
Authors: Räsänen Riikka‐Marjaana , Dwivedi Prabha , Fernández Facundo M. , Kauppila Tiina J.
Published: September 2014

RATIONALE

Ambient mass spectrometry (MS) is a tool for screening analytes directly from sample surfaces. However, background impurities may complicate the spectra and therefore fast separation techniques are needed. Here, we demonstrate the use of travelling wave ion mobility spectrometry in a comparative study of two ambient MS techniques.

METHODS

Desorption atmospheric pressure photoionization (DAPPI) and direct analysis in real time (DART) were coupled with travelling wave ion mobility mass spectrometry (TWIM‐MS) for highly selective surface analysis. The ionization efficiencies of DAPPI and DART were compared. Test compounds were: bisphenol A, benzo[a]pyrene, ranitidine, cortisol and α‐tocopherol. DAPPI‐MS and DART‐TWIM‐MS were also applied to the analysis of chloroquine from dried blood spots, and α‐tocopherol from almond surface, and DAPPI‐TWIM‐MS was applied to analysis of pharmaceuticals and multivitamin tablets.

RESULTS

DAPPI was approximately 100 times more sensitive than DART for bisphenol A and 10–20 times more sensitive for the other compounds. The limits of detection were between 30–290 and 330–8200 fmol for DAPPI and DART, respectively. Also, from the authentic samples, DAPPI ionized chloroquine and α‐tocopherol more efficiently than DART. The mobility separation enabled the detection of species with low signal intensities, e.g. thiamine and cholecalciferol, in the DAPPI‐TWIM‐MS analysis of multivitamin tablets.

CONCLUSIONS

DAPPI ionized the studied compounds of interest more efficiently than DART. For both DAPPI and DART, the mobility separation prior to MS analysis reduced the amount of chemical noise in the mass spectrum and significantly increased the signal‐to‐noise ratio for the analytes. Copyright © 2014 John Wiley & Sons, Ltd.
Microfluidic Platforms for the Investigation of Intercellular Signalling Mechanisms
Authors: Nahavandi Sofia , Tang Shi‐Yang , Baratchi Sara , Soffe Rebecca , Nahavandi Saeid , Kalantar‐zadeh Kourosh , Mitchell Arnan , Khoshmanesh Khashayar
Published: September 2014

Intercellular signalling has been identified as a highly complex process, responsible for orchestrating many physiological functions. While conventional methods of investigation have been useful, their limitations are impeding further development. Microfluidics offers an opportunity to overcome some of these limitations. Most notably, microfluidic systems can emulate the in‐vivo environments. Further, they enable exceptionally precise control of the microenvironment, allowing complex mechanisms to be selectively isolated and studied in detail. There has thus been a growing adoption of microfluidic platforms for investigation of cell signalling mechanisms. This review provides an overview of the different signalling mechanisms and discusses the methods used to study them, with a focus on the microfluidic devices developed for this purpose.
Functional Nanomaterials Can Optimize the Efficacy of Vaccines
Authors: Liu Ye , Xu Yingying , Tian Yue , Chen Chunying , Wang Chen , Jiang Xingyu
Published: September 2014

Nanoscale materials can improve the efficacy of vaccines. Herein we review latest developments that use nanomaterials for vaccines. By highlighting the relationships between the nanoscale physicochemical characteristics and working mechanisms of nanomaterials, this paper shows the current status of the developments where researchers employ functional nanomaterials as vector and/or immunoregulators for vaccines. It also provides us some clues for improving the design and application of nanomaterials to optimize the efficacy of vaccines.
Chinese Art in the Social Context: Unfolding the Interplay of the ‘Four Enemies’
Authors: Li Jian‐Jing
Published: September 2014

Chinese art has an important status in the world. The aesthetic value of Chinese art is embedded in the social context. The meanings of art to human beings are perceived through their inner values that could limit their vision regarding the systems of interest. Unfolding the values and ‘sweeping‐in’ the social, cultural, political and economic considerations could provide systemic insights into the complex world. Based on Churchman's ‘unfolding’ concept, this study examined the implications of politics, morality and religion in regard to the aesthetic system of Chinese art. The results show that the interactions of the four ‘enemies’ have had a deep influence on Chinese art and generated artistic styles and forms that should be interpreted in their temporal and social contexts to acquire the whole meaning of the works. The implications and potential sweeping‐in of other considerations in the social context are also discussed. Copyright © 2014 John Wiley & Sons, Ltd.
The Development of Organizational Capabilities and Corporate Entrepreneurial Processes: The Case of Chinese Automobile Firms
Authors: Guo Chun , Jiang Crystal X. , Yang Qin
Published: September 2014

Corporate entrepreneurship (CE) has contributed to the rapid growth of emerging‐market firms (EMFs), yet little is known about this phenomenon from a process perspective. This article examines how EMFs develop organizational capabilities in pursuit of CE as a strategy to catch up with their global competitors. By adopting a case study method, our in‐depth analysis of two leading Chinese automobile companies identifies specific organizational capabilities that enable firms’ CE activities at different stages—initiation, development, and implementation. Our findings also reveal how different means of developing organizational capabilities lead to different catch‐up strategies, which subsequently influence firms’ entrepreneurial transformation and value creation. © 2014 Wiley Periodicals, Inc.
Correction of Beam‐Shadowing Effects Due to Partially Filled Sample Holders in Bragg–Brentano Experiments
Authors: Lührs Hanna , Birkenstock Johannes , Fischer Reinhard X.
Published: September 2014

In Bragg–Brentano powder X‐ray diffraction, incompletely filled sample holders result in a significant loss of intensity for diffraction peaks at small 2θ angles due to shadowing of the diffracted beam by the sample holder. This has to be considered in crystal structure refinements for samples with diffraction peaks in the low 2θ range when shifts of sample height cannot be avoided. Herein a geometrically derived correction algorithm to account for the intensity loss as a function of shift in sample height is presented. The algorithms were verified based on a series of zeolite A diffraction patterns from samples with deliberately induced, well defined reductions in sample height.
Morphological and Phylogenetic Analysis of Fusarium solani Species Complex in Malaysia
Authors: Chehri Khosrow , Salleh Baharuddin , Zakaria Latiffah
Published: September 2014

Members of Fusarium solani species complex (FSSC) have been known as plant, animal, and human pathogens. Nevertheless, the taxonomic status of such an important group of fungi is still very confusing and many new species as well as lineages have been elucidated recently. Unfortunately, most of the new taxa came from temperate and subtropical regions. Therefore, the objectives of the present study were to identify strains of FSSC recovered from different sources in Malaysia. In the present study, 55 strains belonging to the FSSC were examined and phylogenetically analyzed on the basis of internal transcribed spacer (ITS) regions and partial translation elongation factor-1 (TEF-1α) sequences. Based on morphological features, a total of 55 strains were selected for molecular studies. Based on morphological features, the strains were classified into four described Fusarium species, namely Fusarium keratoplasticum, Fusarium falciforme, FSSC 5, and Fusarium cf. ensiforme, and one unknown phylogenetic species was introduced. Although the data obtained from morphological and molecular studies sufficiently supported each other, the phylogenetic trees based on ITS and TEF-1α dataset clearly distinguished closely related species and distinctly separated all morphological taxa. All members of FSSC in this research were reported for the first time for Malaysian mycoflora.
An overview of inborn errors of complex lipid biosynthesis and remodelling
Authors: Lamari Foudil , Mochel Fanny , Saudubray Jean‐Marie
Published: September 2014

In a review published in 2012, we delineated 14 inborn errors of metabolism (IEM) related to defects in biosynthesis of complex lipids, particularly phospholipids and sphingolipids (Lamari et al 2013). Given the numerous roles played by these molecules in membrane integrity, cell structure and function, this group of diseases is rapidly expanding as predicted. Almost 40 new diseases related to genetic defects in enzymes involved in the biosynthesis and remodelling of phospholipids, sphingolipids and complex fatty acids are now reported. While the clinical phenotype associated with these defects is currently difficult to outline, with only a few patients identified to date, it appears that all organs and systems may be affected — central and peripheral nervous system, eye, muscle, skin, bone, liver, immune system, etc. This chapter presents an introductive overview of this new group of IEM. More broadly, this special issue provides an update on other IEM involving complex lipids, namely dolichol and isoprenoids, glycolipids and congenital disorders of glycosylation, very long chain fatty acids and plasmalogens. Likewise, more than 100 IEM may actually lead to primary or secondary defects of complex lipids synthesis and remodelling. Because of the implication of several cellular compartments, this new group of disorders affecting the synthesis and remodelling of complex molecules challenges our current classification of IEM still largely based on cellular organelles—i.e. mitochondrial, lysosomal, peroxisomal disorders. While most of these new disorders have been identified by next generation sequencing, we wish to emphasize the promising role of lipidomics in deciphering their pathophysiology and identifying therapeutic targets.
In the Realms of Ethnicity, Religion and Emigration: New Communities of Memory in Israel
Authors: Feldman Anat
Published: September 2014

Ethnic-religious communities of memory have been active in Israel for the past twenty years. These are peripheral communities with their activity concentrated around sacred burial sites. They utilize and fashion their ethnic-religious memories according to their political requirements, so as to create communities. This study will introduce three such communities in Israel and describe the circumstances surrounding their establishment and operating methods. We will discuss communities of Libyan, Moroccan and Tunisian origin.
Mean flow stability analysis of oscillating jet experiments
Authors: Oberleithner Kilian , Rukes Lothar , Soria Julio
Published: September 2014

Linear stability analysis (LSA) is applied to the mean flow of an oscillating round jet with the aim of investigating the robustness and accuracy of mean flow stability wave models. The jet’s axisymmetric mode is excited at the nozzle lip through a sinusoidal modulation of the flow rate at amplitudes ranging from 0.1 % to 100 %. The instantaneous flow field is measured via particle image velocimetry (PIV) and decomposed into a mean and periodic part utilizing proper orthogonal decomposition (POD). Local LSA is applied to the measured mean flow adopting a weakly non-parallel flow approach. The resulting global perturbation field is carefully compared with the measurements in terms of spatial growth rate, phase velocity, and phase and amplitude distribution. It is shown that the stability wave model accurately predicts the excited flow oscillations during their entire growth phase and during a large part of their decay phase. The stability wave model applies over a wide range of forcing amplitudes, showing no pronounced sensitivity to the strength of nonlinear saturation. The upstream displacement of the neutral point and the successive reduction of gain with increasing forcing amplitude is very well captured by the stability wave model. At very strong forcing ($\def \xmlpi #1{}\def \mathsfbi #1{\boldsymbol {\mathsf {#1}}}\let \le =\leqslant \let \leq =\leqslant \let \ge =\geqslant \let \geq =\geqslant \def \Pr {\mathit {Pr}}\def \Fr {\mathit {Fr}}\def \Rey {\mathit {Re}}{>}40\, \%$), the flow becomes essentially stable to the axisymmetric mode. For these extreme cases, the prediction deteriorates from the measurements due to an interaction of the forced wave with the geometric confinement of the nozzle. Moreover, the model fails far downstream in a region where energy is transferred from the oscillation back to the mean flow. This study supports previously conducted mean flow stability analysis of self-excited flow oscillations in the cylinder wake and in the vortex breakdown bubble and extends the methodology to externally forced convectively unstable flows. The high accuracy of mean flow stability wave models as demonstrated here is of great importance for the analysis of coherent structures in turbulent shear flows.
Mixed convection in a horizontal duct with bottom heating and strong transverse magnetic field
Authors: Zhang Xuan , Zikanov Oleg
Published: September 2014

Mixed convection in a horizontal duct with imposed transverse horizontal magnetic field is studied using direct numerical simulations (DNS) and linear stability analysis. The duct’s walls are electrically insulated and thermally insulated with the exception of the bottom wall, at which constant-rate heating is applied. The focus of the study is on flows at high Hartmann ($\def \xmlpi #1{}\def \mathsfbi #1{\boldsymbol {\mathsf {#1}}}\let \le =\leqslant \let \leq =\leqslant \let \ge =\geqslant \let \geq =\geqslant \def \Pr {\mathit {Pr}}\def \Fr {\mathit {Fr}}\def \Rey {\mathit {Re}}\mathit{Ha}\le 800$) and Grashof ($\mathit{Gr}\le 10^9$) numbers. It is found that, while conventional turbulence is fully suppressed, the natural convection mechanism leads to the development of large-scale coherent structures. Two types of flows are found. One is the ‘low-$\mathit{Gr}$’ regime, in which the structures are rolls aligned with the magnetic field and velocity and temperature fields are nearly uniform along the magnetic field lines outside of the boundary layers. Another is the ‘high-$\mathit{Gr}$’ regime, in which the convection appears as a combination of similar rolls oriented along the magnetic field lines and streamwise-oriented rolls. In this case, velocity and temperature distributions are anisotropic, but three-dimensional.
Flow and heat transfer in convectively unstable turbulent channel flow with solid-wall heat conduction
Authors: Garai Anirban , Kleissl Jan , Sarkar Sutanu
Published: September 2014

Most turbulent coherent structures in a convectively unstable atmospheric boundary layer are caused by or manifested in ascending warm fluid and descending cold fluids. These structures not only cause ramps in the air temperature timeseries, but also imprint on the underlying solid surface as surface temperature fluctuations. The coupled flow and heat transport mechanism was examined through direct numerical simulation (DNS) of a channel flow allowing for realistic solid–fluid thermal coupling. The thermal activity ratio (TAR; the ratio of thermal inertias of fluid and solid), and the thickness of the solid domain were found to affect the solid–fluid interfacial temperature variations. The solid–fluid interface with large (small) thermal activity ration behaves as an isoflux (isothermal) boundary. For the range of parameters considered here (Grashof number, $\def \xmlpi #1{}\def \mathsfbi #1{\boldsymbol {\mathsf {#1}}}\let \le =\leqslant \let \leq =\leqslant \let \ge =\geqslant \let \geq =\geqslant \def \Pr {\mathit {Pr}}\def \Fr {\mathit {Fr}}\def \Rey {\mathit {Re}}\mathit{Gr} = 3\times 10^5\text {--} 325\times 10^5$; $\textit {TAR} = 0.01\text {--}1$; solid thickness normalized by heat penetration $\text {depth} = 0.1\text {--}10$), the solid thermal properties and thickness influence the fluid temperature only in the viscous or conduction region while the convective forcing influences the turbulent flow. Flow structures influence the interfacial temperature more effectively with increasing TAR and solid thickness compared with a constant temperature boundary condition. The change of channel flow structures with increasing convective instability is examined and the concomitant change of thermal patterns is quantified. Despite large differences in friction Reynolds and Richardson number between the DNS and atmospheric observations, similarities in the flow features were observed.
The boundary layer instability of a gliding fish helps rather than prevents object identification
Authors: Maertens Audrey P. , Triantafyllou Michael S.
Published: September 2014

Inspired by the function of the lateral line in aquatic animals, we study the shape identification of a stationary cylinder through pressure measurements made by sensors located on the surface of a steadily moving foil, modelling a fish gliding in close proximity to an object. Comparing experimental results, potential flow predictions and viscous simulations, we first show that the pressure in the boundary layer of the foil is significantly affected by unsteady viscous effects, especially in the posterior half of the foil. Therefore, even after the effects of the boundary layer thickness are accounted for, potential flow predictions are inaccurate. Subsequently, we show that the spatial features of the unsteady patterns developing when the foil is moving near a cylinder can be predicted accurately through linear stability analysis of the average boundary layer velocity profile under open water conditions. Because these unsteady patterns result from amplification of the potential flow-like disturbance caused in the front part of the foil, they are specific to the cylinder that generated them and could be used to identify its shape. We develop and demonstrate a methodology to calculate the unsteady pressure based on combining potential flow predictions with results from linear stability analysis of the boundary layer. The findings can be useful for object identification in underwater vehicles, and support the intriguing possibility that the significant viscous effects caused by nearby bodies on the fish boundary layer, far from preventing detection, could actually be used by animals to identify objects.
Laboratory experiments and simulations for solitary internal waves with trapped cores
Authors: Luzzatto-Fegiz Paolo , Helfrich Karl R.
Published: September 2014

We perform simultaneous coplanar measurements of velocity and density in solitary internal waves with trapped cores, as well as viscous numerical simulations. Our set-up comprises a thin stratified layer (approximately 15 % of the overall fluid depth) overlaying a deep homogeneous layer. We consider waves propagating near a free surface, as well as near a rigid no-slip lid. In the free-surface case, all trapped-core waves exhibit a strong shear instability. We propose that Marangoni effects are responsible for this instability, and use our velocity measurements to perform quantitative calculations supporting this hypothesis. These surface-tension effects appear to be difficult to avoid at the experimental scale. By contrast, our experiments with a no-slip lid yield robust waves with large cores. In order to consider larger-amplitude waves, we complement our experiments with viscous numerical simulations, employing a longer virtual tank. Where overlap exists, our experiments and simulations are in good agreement. In order to provide a robust definition of the trapped core, we propose bounding it as a Lagrangian coherent structure (instead of using a closed streamline, as has been done traditionally). This construction is less sensitive to small errors in the velocity field, and to small three-dimensional effects. In order to retain only flows near equilibrium, we introduce a steadiness criterion, based on the rate of change of the density in the core. We use this criterion to successfully select within our experiments and simulations a family of quasi-steady robust flows that exhibit good collapse in their properties. The core circulation is small (at most, around 10 % of the baroclinic wave circulation). The core density is essentially uniform; the standard deviation of the density, in the core region, is less than 4 % of the full density range. We also calculate the circulation, kinetic energy and available potential energy of these waves. We find that these results are consistent with predictions from Dubreil-Jacotin–Long theory for waves with a uniform-density irrotational core, except for an offset, which we suggest is associated with viscous effects. Finally, by computing Richardson-number fields, and performing a temporal stability analysis based on the Taylor–Goldstein equation, we show that our results are consistent with empirical stability criteria in the literature.
Asymmetric flux models for particle-size segregation in granular avalanches
Authors: Gajjar P. , Gray J. M. N. T.
Published: September 2014

Particle-size segregation commonly occurs in both wet and dry granular free-surface flows through the combined processes of kinetic sieving and squeeze expulsion. As the granular material is sheared downslope, the particle matrix dilates slightly and small grains tend to percolate down through the gaps, because they are more likely than the large grains to fit into the available space. Larger particles are then levered upwards in order to maintain an almost uniform solids volume fraction through the depth. Recent experimental observations suggest that a single small particle can percolate downwards through a matrix of large particles faster than a large particle can be levered upwards through a matrix of fines. In this paper, this effect is modelled by using a flux function that is asymmetric about its maximum point, differing from the symmetric quadratic form used in recent models of particle-size segregation. For illustration, a cubic flux function is examined in this paper, which can be either a convex or a non-convex function of the small-particle concentration. The method of characteristics is used to derive exact steady-state solutions for non-diffuse segregation in two dimensions, with an inflow concentration that is (i) homogeneous and (ii) normally graded, with small particles above the large. As well as generating shocks and expansion fans, the new asymmetric flux function generates semi-shocks, which have characteristics intersecting with the shock just from one side. In the absence of diffusive remixing, these can significantly enhance the distance over which complete segregation occurs.
Similar worldwide patterns in the sex pheromone signal and response in the oriental fruit moth, Grapholita molesta (Lepidoptera: Tortricidae)
Authors: Knight A.L. , Barros-Parada W. , Bosch D. , Escudero-Colomar L.A. , Fuentes-Contreras E. , Hernández-Sánchez J. , Yung C. , Kim Y. , Kovanci O.B. , Levi A. , Lo P. , Molinari F. , Valls J. , Gemeno C.
Published: September 2014

The response of Grapholita molesta (Busck) males to three-component sex pheromone blends containing a 100% ratio of the major sex pheromone component, (Z)-8-dodecenyl acetate and a 10% ratio of (Z)-8-dodecenol, but with varying ratios of (E)-8-dodecenyl acetate (0.4, 5.4, 10.4, 30.4, and 100.1% E-blends) was tested with populations in eight stone and pome fruit orchards in Europe, Asia, and North and South America. Traps baited with the 5.4% E-blend caught significantly more males than traps with any other blend with all populations. Significantly more males were caught in traps baited with the 10.4% E-blend than in traps with the remaining blends, except with the 0.4% E-blend in Turkey. Significant differences in male moth catches occurred between the other blends with the 0.4>30.4% E-blend, and the 30.4>100.1% E-blend. Male moth catches with the 100.1% E-blend only differed from the hexane control in Chile. No apparent differences were noted to these blends in populations collected from pome or stone fruits. Flight tunnel assays to synthetic blends with a subset of populations were similar to the field results, but the breadth of the most attractive E-blends was wider. Flight tunnel assays also demonstrated a high level of male–female cross-attraction among field-collected populations. Female gland extracts from field-collected populations did not show any significant variation in their three-component blends. The only exceptions in these assays were that long-term laboratory populations were less responsive and attractive, and produced different blend ratios of the two minor components than recently collected field populations.
Effect of changes in milking routine on milking related behaviour and milk removal in Tunisian dairy dromedary camels
Authors: Atigui Moufida , Marnet Pierre-Guy , Ayeb Naziha , Khorchani Touhami , Hammadi Mohamed
Published: September 2014

We studied the effects of changes in the milking routine (lack or presence of 30-s prestimulation, 0 or 1, 2 or 4-min delay between preparation and cluster attachment) and environmental perturbation (unusual loud sounds capable of frightening animals just after stall entry or during the course of milking) on milk removal and milking-related behaviour in dairy dromedary camels. A 30-s prestimulation decreased incidence of bimodal milk flow curves and increased occurrence of the best milk ejection patterns with higher milk flow but had limited effect on milk production in our well-trained animals within a good machine milking setting. However, unusual sounds heard from the beginning of milking or even after milk ejection caused inhibition or disruption of milk removal and modification of camels’ behaviour. Milk ejection was significantly delayed (1·58±0·17 min), residual milk increased over 40% of total milk yield and average and peak milk flow rates were significantly lowered when unusual noises were heard from the beginning of milking. These environmental perturbations increased signs of vigilance and the number of attempts to escape the milking parlour. Delaying cluster attachment for over 1 min after the end of udder preparation caused serious milk losses. Up to 62% of total milk was withheld in the udder when the delay reached 4 min. Average and peak milk flow rates also decreased significantly with delayed milking. Signs of vigilance and attempts to escape from the milking parlour appeared when camels waited for over 2 min. After a 4-min delay, camels showed signs of acute stress. Defaecation prior to milk ejection (solid faeces) and rumination during milking can be used to assess camels’ milk ejection during milking. Animal welfare and milking efficiency can be ensured when camels are pre-stimulated, milked in calm conditions and with cluster attachment within a maximum of a 1-min delay after stimulation
The Euthyphro, Divine Command Theory and Moral Realism
Authors: Harrison Gerald K.
Published: September 2014

Divine command theories of metaethics are commonly rejected on the basis of the Euthyphro problem. In this paper, I argue that the Euthyphro can be raised for all forms of moral realism. I go on to argue that this does not matter as the Euthyphro is not really a problem after all. I then briefly outline some of the attractions of a divine command theory of metaethics. I suggest that given one of the major reasons for rejecting such an analysis has been found to be unsound divine command theories deserve to be taken more seriously in contemporary metaethics.
Revisiting Styblo's law: could mathematical models aid in estimating incidence from prevalence data?
Authors: BEGUN M. , NEWALL A. T. , MARKS G. B. , WOOD J. G.
Published: September 2014

Estimation of the true incidence of tuberculosis (TB) is challenging. The approach proposed by Styblo in 1985 is known to be inaccurate in the modern era where there is widespread availability of treatment for TB. This study re-examines the relationship of incidence to prevalence and other disease indicators that can be derived from surveys. We adapt a simple, previously published model that describes the epidemiology of TB in the presence of treatment to investigate a revised ratio-based approach to estimating incidence. We show that, following changes to treatment programmes for TB, the ratio of incidence to prevalence reaches an equilibrium value rapidly; long before other model indicators have stabilized. We also show that this ratio relies on few parameters but is strongly dependent on, and requires knowledge of, the efficacy and timeliness of treatment.
ARTHUR HALLAM’S SPIRIT PHOTOGRAPH AND TENNYSON’S ELEGIAC TRACE
Authors: Hoffman Jesse
Published: September 2014

Blanche Warre Cornish's 1921–22tripartite memoir, “Memories of Tennyson,” begins in 1869 when she meets the poet by way of her parents’ friendship with Tennyson's neighbor, the photographer Julia Margaret Cameron (145) (Figure 1). The photograph that Cornish recalls as “psychophotography” is one instance of a trend in Victorian England of spirit photography that was first practiced around 1872 after it was imported from America, where William Mumler had developed it (Tucker 68; Doyle 2: 128). Reactions to these spirit photographs took various forms: while some viewers regarded them as a credible medium for communication with the dead, their detractors saw them as deliberate acts of deception. Others employed photography's spectral qualities for entertainment, such as the London Stereoscopic Company that had marketed photographs of angels, fairies, and ghosts for their customers’ amusement in the 1860s (Chéroux 45–53). By the time the “shadowy figure of a man” appears beside Arthur Hallam's erstwhile fiancé, Mrs. Jesse, Tennyson's sister, the practice had been subject to public intrigue and scandal as a part of broader and contentious Victorian debates about the status of photography as art or document. The already surreal qualities of Cornish's anecdote are amplified by Tennyson's question, “Is that Arthur?,” which entertains the possibility of Hallam being present in a visible, spectral form while unrecognized by his beloved friend.
THE MISGUIDED CONCEPT OF PARTIAL JUSTIFICATION
Authors: Eldar Shachar , Laist Elkana
Published: September 2014

Despite the fundamentally binary character of justification (an act is either right or not, permissible or impermissible), an upsurge in recent Anglo-American scholarship offers some highly sophisticated and widely diverging conceptions of “partial justification” in criminal law. In the present article we identify eight distinct conceptions of partial justification. We find, however, that each of them is predicated on a different conceptual fallacy. Any sound concept of partial justification in criminal law ought to meet the dual challenge of utility and consistency: it should usefully convey a message that advances the conduct-guiding function of criminal law and retain some consistency with the key attributes of complete justification, particularly its allowing function and the implications of its typically universal nature. We maintain that none of the conceptions offered to date meets this challenge. The different meanings attached to partial justification do not further the guiding function of criminal law beyond what is achieved by the scalar concept of wrongfulness; indeed, they undermine the guiding utility of criminal law by obscuring the distinction between the permissible and the impermissible, thereby also diminishing the expressivity of the criminal conviction. Furthermore, extending partial universality to the proposed notions of partial justification implausibly marks retaliating victims and intervening third parties, who react to allegedly partially justified conduct, as partly blameworthy, whereas present legal doctrine rightly affords them a full defense.
Seasonal dynamics of active SAR11 ecotypes in the oligotrophic Northwest Mediterranean Sea
Authors: Salter Ian , Galand Pierre E , Fagervold Sonja K , Lebaron Philippe , Obernosterer Ingrid , Oliver Matthew J , Suzuki Marcelino T , Tricoire Cyrielle
Published: September 2014

A seven-year oceanographic time series in NW Mediterranean surface waters was combined with pyrosequencing of ribosomal RNA (16S rRNA) and ribosomal RNA gene copies (16S rDNA) to examine the environmental controls on SAR11 ecotype dynamics and potential activity. SAR11 diversity exhibited pronounced seasonal cycles remarkably similar to total bacterial diversity. The timing of diversity maxima was similar across narrow and broad phylogenetic clades and strongly associated with deep winter mixing. Diversity minima were associated with periods of stratification that were low in nutrients and phytoplankton biomass and characterised by intense phosphate limitation (turnover time<5 h). We propose a conceptual framework in which physical mixing of the water column periodically resets SAR11 communities to a high diversity state and the seasonal evolution of phosphate limitation competitively excludes deeper-dwelling ecotypes to promote low diversity states dominated (>80%) by SAR11 Ia. A partial least squares (PLS) regression model was developed that could reliably predict sequence abundances of SAR11 ecotypes (Q2=0.70) from measured environmental variables, of which mixed layer depth was quantitatively the most important. Comparison of clade-level SAR11 rRNA:rDNA signals with leucine incorporation enabled us to partially validate the use of these ratios as an in-situ activity measure. However, temporal trends in the activity of SAR11 ecotypes and their relationship to environmental variables were unclear. The strong and predictable temporal patterns observed in SAR11 sequence abundance was not linked to metabolic activity of different ecotypes at the phylogenetic and temporal resolution of our study.
Warped linear mixed models for the genetic analysis of transformed phenotypes
Authors: Fusi Nicolo , Lippert Christoph , Lawrence Neil D. , Stegle Oliver
Published: September 2014

Linear mixed models (LMMs) are a powerful and established tool for studying genotype–phenotype relationships. A limitation of the LMM is that the model assumes Gaussian distributed residuals, a requirement that rarely holds in practice. Violations of this assumption can lead to false conclusions and loss in power. To mitigate this problem, it is common practice to pre-process the phenotypic values to make them as Gaussian as possible, for instance by applying logarithmic or other nonlinear transformations. Unfortunately, different phenotypes require different transformations, and choosing an appropriate transformation is challenging and subjective. Here we present an extension of the LMM that estimates an optimal transformation from the observed data. In simulations and applications to real data from human, mouse and yeast, we show that using transformations inferred by our model increases power in genome-wide association studies and increases the accuracy of heritability estimation and phenotype prediction.
Kainate receptor activation induces glycine receptor endocytosis through PKC deSUMOylation
Authors: Sun Hao , Lu Li , Zuo Yong , Wang Yan , Jiao Yingfu , Zeng Wei-Zheng , Huang Chao , Zhu Michael X. , Zamponi Gerald W. , Zhou Tong , Xu Tian-Le , Cheng Jinke , Li Yong
Published: September 2014

Surface expression and regulated endocytosis of glycine receptors (GlyRs) play a critical function in balancing neuronal excitability. SUMOylation (SUMO modification) is of critical importance for maintaining neuronal function in the central nervous system. Here we show that activation of kainate receptors (KARs) causes GlyR endocytosis in a calcium- and protein kinase C (PKC)-dependent manner, leading to reduced GlyR-mediated synaptic activity in cultured spinal cord neurons and the superficial dorsal horn of rat spinal cord slices. This effect requires SUMO1/sentrin-specific peptidase 1 (SENP1)-mediated deSUMOylation of PKC, indicating that the crosstalk between KARs and GlyRs relies on the SUMOylation status of PKC. SENP1-mediated deSUMOylation of PKC is involved in the kainate-induced GlyR endocytosis and thus plays an important role in the anti-homeostatic regulation between excitatory and inhibitory ligand-gated ion channels. Altogether, we have identified a SUMOylation-dependent regulatory pathway for GlyR endocytosis, which may have important physiological implications for proper neuronal excitability.
Genomic analyses of gynaecologic carcinosarcomas reveal frequent mutations in chromatin remodelling genes
Authors: Jones Siân , Stransky Nicolas , McCord Christine L. , Cerami Ethan , Lagowski James , Kelly Devon , Angiuoli Samuel V. , Sausen Mark , Kann Lisa , Shukla Manish , Makar Rosemary , Wood Laura D. , Diaz Luis A. , Lengauer Christoph , Velculescu Victor E.
Published: September 2014

Malignant mixed Müllerian tumours, also known as carcinosarcomas, are rare tumours of gynaecological origin. Here we perform whole-exome analyses of 22 tumours using massively parallel sequencing to determine the mutational landscape of this tumour type. On average, we identify 43 mutations per tumour, excluding four cases with a mutator phenotype that harboured inactivating mutations in mismatch repair genes. In addition to mutations in TP53 and KRAS, we identify genetic alterations in chromatin remodelling genes, ARID1A and ARID1B, in histone methyltransferase MLL3, in histone deacetylase modifier SPOP and in chromatin assembly factor BAZ1A, in nearly two thirds of cases. Alterations in genes with potential clinical utility are observed in more than three quarters of the cases and included members of the PI3-kinase and homologous DNA repair pathways. These findings highlight the importance of the dysregulation of chromatin remodelling in carcinosarcoma tumorigenesis and suggest new avenues for personalized therapy.
An Efficient Genotyping Method for Genome-modified Animals and Human Cells Generated with CRISPR/Cas9 System
Authors: Zhu Xiaoxiao , Xu Yajie , Yu Shanshan , Lu Lu , Ding Mingqin , Cheng Jing , Song Guoxu , Gao Xing , Yao Liangming , Fan Dongdong , Meng Shu , Zhang Xuewen , Hu Shengdi , Tian Yong
Published: September 2014

The rapid generation of various species and strains of laboratory animals using CRISPR/Cas9 technology has dramatically accelerated the interrogation of gene function in vivo. So far, the dominant approach for genotyping of genome-modified animals has been the T7E1 endonuclease cleavage assay. Here, we present a polyacrylamide gel electrophoresis-based (PAGE) method to genotype mice harboring different types of indel mutations. We developed 6 strains of genome-modified mice using CRISPR/Cas9 system and utilized this approach to genotype mice from F0 to F2 generation, which included single and multiplexed genome-modified mice. We also determined the maximal detection sensitivity for detecting mosaic DNA using PAGE-based assay as 0.5%. We further applied PAGE-based genotyping approach to detect CRISPR/Cas9-mediated on- and off-target effect in human 293T and induced pluripotent stem cells (iPSCs). Thus, PAGE-based genotyping approach meets the rapidly increasing demand for genotyping of the fast-growing number of genome-modified animals and human cell lines created using CRISPR/Cas9 system or other nuclease systems such as TALEN or ZFN.
MOFs synthesized by the ionothermal method addressing the leaching problem of IL–polymer composite membranes
Authors: Liu Cong , Zhang Gang , Zhao Chengji , Li Xuefeng , Li Mingyu , Na Hui
Published: September 2014

We designed a new strategy to immobilize an ionic liquid by incorporating it within ZIF-8 by the ionothermal method, and demonstrated a facile and novel method to fabricate IL–polymer composite membranes with ZIF-8 fillers for alkaline anion electrolytes.