The gradient of potential vorticity, quaternions and an orthonormal frame for fluid particles

The gradient of potential vorticity (PV) is an important quantity because of the way PV (denoted as $q$) tends to accumulate locally in the oceans and atmospheres. Recent analysis by the authors has shown that the vector quantity \bdB = \bnabla q\times \bnabla\theta for the three-dimensional incompressible rotating Euler equations evolves according to the same stretching equation as for \bom the vorticity and \bB, the magnetic field in magnetohydrodynamics (MHD). The \bdB-vector therefore acts like the vorticity \bom in Euler's equations and the \bB-field in MHD. For example, it allows various analogies, such as stretching dynamics, helicity, superhelicity and cross helicity. In addition, using quaternionic analysis, the dynamics of the \bdB-vector naturally allow the construction of an orthonormal frame attached to fluid particles\,; this is designated as a quaternion frame. The alignment dynamics of this frame are particularly relevant to the three-axis rotations that particles undergo as they traverse regions of a flow when the PV gradient \bnabla q is large.Comment: Dedicated to Raymond Hide on the occasion of his 80th birthda

On the Deformation of a Hyperelastic Tube Due to Steady Viscous Flow Within

In this chapter, we analyze the steady-state microscale fluid--structure interaction (FSI) between a generalized Newtonian fluid and a hyperelastic tube. Physiological flows, especially in hemodynamics, serve as primary examples of such FSI phenomena. The small scale of the physical system renders the flow field, under the power-law rheological model, amenable to a closed-form solution using the lubrication approximation. On the other hand, negligible shear stresses on the walls of a long vessel allow the structure to be treated as a pressure vessel. The constitutive equation for the microtube is prescribed via the strain energy functional for an incompressible, isotropic Mooney--Rivlin material. We employ both the thin- and thick-walled formulations of the pressure vessel theory, and derive the static relation between the pressure load and the deformation of the structure. We harness the latter to determine the flow rate--pressure drop relationship for non-Newtonian flow in thin- and thick-walled soft hyperelastic microtubes. Through illustrative examples, we discuss how a hyperelastic tube supports the same pressure load as a linearly elastic tube with smaller deformation, thus requiring a higher pressure drop across itself to maintain a fixed flow rate.Comment: 19 pages, 3 figures, Springer book class; v2: minor revisions, final form of invited contribution to the Springer volume entitled "Dynamical Processes in Generalized Continua and Structures" (in honour of Academician D.I. Indeitsev), eds. H. Altenbach, A. Belyaev, V. A. Eremeyev, A. Krivtsov and A. V. Porubo

Platypus globin genes and flanking loci suggest a new insertional model for beta-globin evolution in birds and mammals

Background: Vertebrate alpha (α)- and beta (β)-globin gene families exemplify the way in which genomes evolve to produce functional complexity. From tandem duplication of a single globin locus, the α- and β-globin clusters expanded, and then were separated onto different chromosomes. The previous finding of a fossil β-globin gene (ω) in the marsupial α-cluster, however, suggested that duplication of the α-β cluster onto two chromosomes, followed by lineage-specific gene loss and duplication, produced paralogous α- and β-globin clusters in birds and mammals. Here we analyse genomic data from an egg-laying monotreme mammal, the platypus (Ornithorhynchus anatinus), to explore haemoglobin evolution at the stem of the mammalian radiation. Results: The platypus α-globin cluster (chromosome 21) contains embryonic and adult α- globin genes, a β-like ω-globin gene, and the GBY globin gene with homology to cytoglobin, arranged as 5'-ζ-ζ'-αD-α3-α2-α1-ω-GBY-3'. The platypus β-globin cluster (chromosome 2) contains single embryonic and adult globin genes arranged as 5'-ε-β-3'. Surprisingly, all of these globin genes were expressed in some adult tissues. Comparison of flanking sequences revealed that all jawed vertebrate α-globin clusters are flanked by MPG-C16orf35 and LUC7L, whereas all bird and mammal β-globin clusters are embedded in olfactory genes. Thus, the mammalian α- and β-globin clusters are orthologous to the bird α- and β-globin clusters respectively. Conclusion: We propose that α- and β-globin clusters evolved from an ancient MPG-C16orf35-α-β-GBY-LUC7L arrangement 410 million years ago. A copy of the original β (represented by ω in marsupials and monotremes) was inserted into an array of olfactory genes before the amniote radiation (>315 million years ago), then duplicated and diverged to form orthologous clusters of β-globin genes with different expression profiles in different lineages.Vidushi S. Patel, Steven J.B. Cooper, Janine E. Deakin, Bob Fulton, Tina Graves, Wesley C. Warren, Richard K. Wilson and Jennifer A.M. Grave

Giant sacral schwannoma: A report of six cases

Sacral and presacral schwannomas are often found incidentally, because they present with vague symptoms or symptomless. Schwannoma occurring in this area occasionally presents with enormous dimensions, known as a giant schwannoma. The tumor removal is a surgical challenge due to the difficult approach and abundant vascularity. The aim of this study is to review cases of giant sacral schwannomas focusing the surgical management and outcome. Six patients with sacral and presacral schwannoma were treated surgically. The patients included two males and four females, and the mean age was 47.8 years. All patients experienced pain at the time of presentation. The tumors were classified as intraosseous type in one case, dumb-bell type in four cases, and retroperitoneal type in one case. The tumors were removed with a piecemeal subtotal excision in three patients, a partial excision in two patients, and enucleation in one patient. The surgeries were performed by the combination of an anterior and posterior approach in three patients, a posterior approach in two patients, and an anterior approach in one patient. The mean surgical time was 7.8 hrs, and the mean blood loss was 2572 g. The tumor recurred in one patient after the partial excision and was removed completely in a second surgery. No patient, including the patient who underwent the second surgery, presented with pain and obvious neurological deficit at the final follow-up. The surgical treatment of the giant sacral schwannoma with a piecemeal subtotal excision can achieve a good outcome, avoiding unnecessary neurological deficit

The changing landscape of disaster volunteering: opportunities, responses and gaps in Australia

There is a growing expectation that volunteers will have a greater role in disaster management in the future compared to the past. This is driven largely by a growing focus on building resilience to disasters. At the same time, the wider landscape of volunteering is fundamentally changing in the twenty-first century. This paper considers implications of this changing landscape for the resilience agenda in disaster management, with a focus on Australia. It first reviews major forces and trends impacting on disaster volunteering, highlighting four key developments: the growth of more diverse and episodic volunteering styles, the impact of new communications technology, greater private sector involvement and growing government expectations of and intervention in the voluntary sector. It then examines opportunities in this changing landscape for the Australian emergency management sector across five key strategic areas and provides examples of Australian responses to these opportunities to date. The five areas of focus are: developing more flexible volunteering strategies, harnessing spontaneous volunteering, building capacity to engage digital (and digitally enabled) volunteers, tapping into the growth of employee and skills-based volunteering and co-producing community-based disaster risk reduction. Although there have been considerable steps taken in Australia in some of these areas, overall there is still a long way to go before the sector can take full advantage of emerging opportunities. The paper thus concludes by identifying important research and practice gaps in this area

Conserved community structure and simultaneous divergence events in the fig wasps associated with Ficus benjamina in Australia and China

Localised patterns of species diversity can be influenced by many factors, including regional species pools, biogeographic features and interspecific interactions. Despite recognition of these issues, we still know surprisingly little about how invertebrate biodiversity is structured across geographic scales. In particular, there have been few studies of how insect communities vary geographically while using the same plant host. We compared the composition (species, genera) and functional structure (guilds) of the chalcid wasp communities associated with the widespread fig tree, Ficus benjamina, towards the northern (Hainan province, China) and southern (Queensland, Australia) edges of its natural range. Sequence data were generated for nuclear and mtDNA markers and used to delimit species, and Bayesian divergence analyses were used to test patterns of community cohesion through evolutionary time. Both communities host at least 14 fig wasp species, but no species are shared across continents. Community composition is similar at the genus level, with six genera shared although some differ in species diversity between China and Australia; a further three genera occur in only China or Australia. Community functional structure remains very similar in terms of numbers of species in each ecological guild despite community composition differing a little (genera) or a lot (species), depending on taxonomic level. Bayesian clustering analyses favour a single community divergence event across continents over multiple events for different ecological guilds. Molecular dating estimates of lineage splits between nearest inter-continental species pairs are broadly consistent with a scenario of synchronous community divergence from a shared "ancestral community". Fig wasp community structure and genus-level composition are largely conserved in a wide geographic comparison between China and Australia. Moreover, dating analyses suggest that the functional community structure has remained stable for long periods during historic range expansions. This suggests that ecological interactions between species may play a persistent role in shaping these communities, in contrast to findings in some comparable temperate systems

Application of site and haplotype-frequency based approaches for detecting selection signatures in cattle

<p>Abstract</p> <p>Background</p> <p>'Selection signatures' delimit regions of the genome that are, or have been, functionally important and have therefore been under either natural or artificial selection. In this study, two different and complementary methods--integrated Haplotype Homozygosity Score (|iHS|) and population differentiation index (F_ST)--were applied to identify traces of decades of intensive artificial selection for traits of economic importance in modern cattle.</p> <p>Results</p> <p>We scanned the genome of a diverse set of dairy and beef breeds from Germany, Canada and Australia genotyped with a 50 K SNP panel. Across breeds, a total of 109 extreme |iHS| values exceeded the empirical threshold level of 5% with 19, 27, 9, 10 and 17 outliers in Holstein, Brown Swiss, Australian Angus, Hereford and Simmental, respectively. Annotating the regions harboring clustered |iHS| signals revealed a panel of interesting candidate genes like SPATA17, MGAT1, PGRMC2 and ACTC1, COL23A1, MATN2, respectively, in the context of reproduction and muscle formation. In a further step, a new Bayesian F_ST-based approach was applied with a set of geographically separated populations including Holstein, Brown Swiss, Simmental, North American Angus and Piedmontese for detecting differentiated loci. In total, 127 regions exceeding the 2.5 per cent threshold of the empirical posterior distribution were identified as extremely differentiated. In a substantial number (56 out of 127 cases) the extreme F_STvalues were found to be positioned in poor gene content regions which deviated significantly (p < 0.05) from the expectation assuming a random distribution. However, significant F_STvalues were found in regions of some relevant genes such as SMCP and FGF1.</p> <p>Conclusions</p> <p>Overall, 236 regions putatively subject to recent positive selection in the cattle genome were detected. Both |iHS| and F_STsuggested selection in the vicinity of the Sialic acid binding Ig-like lectin 5 gene on BTA18. This region was recently reported to be a major QTL with strong effects on productive life and fertility traits in Holstein cattle. We conclude that high-resolution genome scans of selection signatures can be used to identify genomic regions contributing to within- and inter-breed phenotypic variation.</p

Dynamic and Polarized Muscle Cell Behaviors Accompany Tail Morphogenesis in the Ascidian Ciona intestinalis

BACKGROUND: Axial elongation is a key morphogenetic process that serves to shape developing organisms. Tail extension in the ascidian larva represents a striking example of this process, wherein paraxially positioned muscle cells undergo elongation and differentiation independent of the segmentation process that characterizes the formation of paraxial mesoderm in vertebrates. Investigating the cell behaviors underlying the morphogenesis of muscle in ascidians may therefore reveal the evolutionarily conserved mechanisms operating during this process. METHODOLOGY/PRINCIPLE FINDINGS: A live cell imaging approach utilizing subcellularly-localized fluorescent proteins was employed to investigate muscle cell behaviors during tail extension in the ascidian Ciona intestinalis. Changes in the position and morphology of individual muscle cells were analyzed in vivo in wild type embryos undergoing tail extension and in embryos in which muscle development was perturbed. Muscle cells were observed to undergo elongation in the absence of positional reorganization. Furthermore, high-speed high-resolution live imaging revealed that the onset and progression of tail extension were characterized by the presence of dynamic and polarized actin-based protrusive activity at the plasma membrane of individual muscle cells. CONCLUSIONS/SIGNIFICANCE: Our results demonstrate that in the Ciona muscle, tissue elongation resulted from gradual and coordinated changes in cell geometry and not from changes in cell topology. Proper formation of muscle cells was found to be necessary not only for muscle tissue elongation, but also more generally for completion of tail extension. Based upon the characterized dynamic changes in cell morphology and plasma membrane protrusive activity, a three-phase model is proposed to describe the cell behavior operating during muscle morphogenesis in the ascidian embryo

Simple large wood structures promote hydromorphological heterogeneity and benthic macroinvertebrate diversity in low-gradient rivers

This work has been carried out within the SMART Joint Doctorate Programme ‘Science for the MAnagement of Rivers and their Tidal systems’ funded by the Erasmus Mundus programme of the European Union

Linking like with like: optimising connectivity between environmentally-similar habitats

Habitat fragmentation is one of the greatest threats to biodiversity. To minimise the effect of fragmentation on biodiversity, connectivity between otherwise isolated habitats should be promoted. However, the identification of linkages favouring connectivity is not trivial. Firstly, they compete with other land uses, so they need to be cost-efficient. Secondly, linkages for one species might be barriers for others, so they should effectively account for distinct mobility requirements. Thirdly, detailed information on the auto-ecology of most of the species is lacking, so linkages need being defined based on surrogates. In order to address these challenges we develop a framework that (a) identifies environmentally-similar habitats; (b) identifies environmental barriers (i.e., regions with a very distinct environment from the areas to be linked), and; (c) determines cost-efficient linkages between environmentally-similar habitats, free from environmental barriers. The assumption is that species with similar ecological requirements occupy the same environments, so environmental similarity provides a rationale for the identification of the areas that need to be linked. A variant of the classical minimum Steiner tree problem in graphs is used to address c). We present a heuristic for this problem that is capable of handling large datasets. To illustrate the framework we identify linkages between environmentally-similar protected areas in the Iberian Peninsula. The Natura 2000 network is used as a positive ‘attractor’ of links while the human footprint is used as ‘repellent’ of links.Wecompare the outcomes of our approach with cost-efficient networks linking protected areas that disregard the effect of environmental barriers. As expected, the latter achieved a smaller area covered with linkages, but with barriers that can significantly reduce the permeability of the landscape for the dispersal of some species