A scaling theory of 3D spinodal turbulence

A new scaling theory for spinodal decomposition in the inertial hydrodynamic regime is presented. The scaling involves three relevant length scales, the domain size, the Taylor microscale and the Kolmogorov dissipation scale. This allows for the presence of an inertial "energy cascade", familiar from theories of turbulence, and improves on earlier scaling treatments based on a single length: these, it is shown, cannot be reconciled with energy conservation. The new theory reconciles the t^{2/3} scaling of the domain size, predicted by simple scaling, with the physical expectation of a saturating Reynolds number at late times.Comment: 5 pages, no figures, revised version submitted to Phys Rev E Rapp Comm. Minor changes and clarification

Signatures of two-dimensionalisation of 3D turbulence in presence of rotation

A reason has been given for the inverse energy cascade in the two-dimensionalised rapidly rotating 3D incompressible turbulence. For such system, literature shows a possibility of the exponent of wavenumber in the energy spectrum's relation to lie between -2 and -3. We argue the existence of a more strict range of -2 to -7/3 for the exponent in the case of rapidly rotating turbulence which is in accordance with the recent experiments. Also, a rigorous derivation for the two point third order structure function has been provided helping one to argue that even with slow rotation one gets, though dominated, a spectrum with the exponent -2.87, thereby hinting at the initiation of the two-dimensionalisation effect with rotation.Comment: An extended and typos-corrected version of the earlier submissio

Trials

BACKGROUND: An international workshop on population health intervention research (PHIR) was organized to foster exchanges between experts from different disciplines and different fields. This paper aims to summarize the discussions around some of the issues addressed: (1) the place of theories in PHIR, (2) why theories can be useful, and (3) how to choose and use the most relevant of them in evaluating PHIR. METHODS: The workshop included formal presentations by participants and moderated discussions. An oral synthesis was produced by a rapporteur to validate, through an expert consensus, the key points of the discussion and the recommendations. All discussions were recorded and have been fully transcribed. RESULTS: The following recommendations were generated through a consensus in the workshop discussions: (i) The evaluation of interventions, like their development, could be improved through better use of theory. (ii) The referenced theory and framework must be clarified. (iii) An intervention theory should be developed by a partnership of researchers and practitioners. (iv) More use of social theory is recommended. (v) Frameworks and a common language are helpful in selecting and communicating a theory. (vi) Better reporting of interventions and theories is needed. CONCLUSION: Theory-driven interventions and evaluations are key in PHIR as they facilitate the understanding of mechanisms of change. There are many challenges in developing the most appropriate theories for interventions and evaluations. With the wealth of information now being generated, this subject is of increasing importance at many levels, including for public health policy. It is, therefore, timely to consider how to build on the experiences of many different disciplines to enable the development of better theories and facilitate evidence-based decisions

Normalized Affymetrix expression data are biased by G-quadruplex formation

Probes with runs of four or more guanines (G-stacks) in their sequences can exhibit a level of hybridization that is unrelated to the expression levels of the mRNA that they are intended to measure. This is most likely caused by the formation of G-quadruplexes, where inter-probe guanines form Hoogsteen hydrogen bonds, which probes with G-stacks are capable of forming. We demonstrate that for a specific microarray data set using the Human HG-U133A Affymetrix GeneChip and RMA normalization there is significant bias in the expression levels, the fold change and the correlations between expression levels. These effects grow more pronounced as the number of G-stack probes in a probe set increases. Approximately 14 of the probe sets are directly affected. The analysis was repeated for a number of other normalization pipelines and two, FARMS and PLIER, minimized the bias to some extent. We estimate that ∼15 of the data sets deposited in the GEO database are susceptible to the effect. The inclusion of G-stack probes in the affected data sets can bias key parameters used in the selection and clustering of genes. The elimination of these probes from any analysis in such affected data sets outweighs the increase of noise in the signal. © 2011 The Author(s)

Nitrogen transfers off Walvis Bay: a 3-D coupled physical/biogeochemical modeling approach in the Namibian upwelling system

Eastern boundary upwelling systems (EBUS) are regions of high primary production often associated with oxygen minimum zones (OMZs). They represent key regions for the oceanic nitrogen (N) cycle. By exporting organic matter (OM) and nutrients produced in the coastal region to the open ocean, EBUS can play an important role in sustaining primary production in subtropical gyres. However, losses of fixed inorganic N through denitrification and anammox processes take place in oxygen depleted environments such as EBUS, and can potentially mitigate the role of these regions as a source of N to the open ocean. EBUS can also represent a considerable source of nitrous oxide (N2O) to the atmosphere, affecting the atmospheric budget of N2O. In this paper a 3-D coupled physical/biogeochemical model (ROMS/BioEBUS) is used to investigate the N budget in the Namibian upwelling system. The main processes linked to EBUS and associated OMZs are taken into account. The study focuses on the northern part of the Benguela upwelling system (BUS), especially the Walvis Bay area (between 22° S and 24° S) where the OMZ is well developed. Fluxes of N off the Walvis Bay area are estimated in order to understand and quantify (1) the total N offshore export from the upwelling area, representing a possible N source that sustains primary production in the South Atlantic subtropical gyre; (2) export production and subsequent losses of fixed N via denitrification and anammox under suboxic conditions (O2 < 25 mmol O2 m−3); and (3) the N2O emission to the atmosphere in the upwelling area. In the mixed layer, the total N offshore export is estimated as 8.5 ± 3.9 × 1010 mol N yr−1 at 10° E off the Walvis Bay area, with a mesoscale contribution of 20%. Extrapolated to the whole BUS, the coastal N source for the subtropical gyre corresponds to 0.1 ± 0.04 mol N m−2 yr−1. This N flux represents a major source of N for the gyre compared with other N sources, and contributes 28% of the new primary production estimated for the South Atlantic subtropical gyre. Export production (16.9 ± 1.3 × 1010 mol N yr−1) helps to maintain an OMZ off Namibia in which coupled nitrification, denitrification and anammox processes lead to losses of fixed N and N2O production. However, neither N losses (0.04 ± 0.025 × 1010 mol N yr−1) nor N2O emissions (0.03 ± 0.002 × 1010 mol N yr−1) significantly impact the main N exports of the Walvis Bay area. The studied area does not significantly contribute to N2O emissions (0.5 to 2.7%) compared to the global coastal upwelling emissions. Locally produced N2O is mostly advected southward by the poleward undercurrent

Preclinical Evaluation of a Lentiviral Vector for Huntingtin Silencing.

Huntington's disease (HD) is an autosomal dominant neurodegenerative disorder resulting from a polyglutamine expansion in the huntingtin (HTT) protein. There is currently no cure for this disease, but recent studies suggest that RNAi to downregulate the expression of both normal and mutant HTT is a promising therapeutic approach. We previously developed a small hairpin RNA (shRNA), vectorized in an HIV-1-derived lentiviral vector (LV), that reduced pathology in an HD rodent model. Here, we modified this vector for preclinical development by using a tat-independent third-generation LV (pCCL) backbone and removing the original reporter genes. We demonstrate that this novel vector efficiently downregulated HTT expression in vitro in striatal neurons derived from induced pluripotent stem cells (iPSCs) of HD patients. It reduced two major pathological HD hallmarks while triggering a minimal inflammatory response, up to 6 weeks after injection, when administered by stereotaxic surgery in the striatum of an in vivo rodent HD model. Further assessment of this shRNA vector in vitro showed proper processing by the endogenous silencing machinery, and we analyzed gene expression changes to identify potential off-targets. These preclinical data suggest that this new shRNA vector fulfills primary biosafety and efficiency requirements for further development in the clinic as a cure for HD

On the relevance of subcritical hydrodynamic turbulence to accretion disk transport

Hydrodynamic unstratified keplerian flows are known to be linearly stable at all Reynolds numbers, but may nevertheless become turbulent through nonlinear mechanisms. However, in the last ten years, conflicting points of view have appeared on this issue. We have revisited the problem through numerical simulations in the shearing sheet limit. It turns out that the effect of the Coriolis force in stabilizing the flow depends on whether the flow is cyclonic (cooperating shear and rotation vorticities) or anticyclonic (competing shear and rotation vorticities); keplerian flows are anticyclonic. We have obtained the following results: i/ The Coriolis force does not quench turbulence in subcritical flows; ii/ The resolution demand, when moving away from the marginal stability boundary, is much more severe for anticyclonic flows than for cyclonic ones. Presently available computer resources do not allow numerical codes to reach the keplerian regime. iii/ The efficiency of turbulent transport is directly correlated to the Reynolds number of transition to turbulence $Rg$, in such a way that the Shakura-Sunyaev parameter $\alpha\sim 1/Rg$. iv/ Even the most optimistic extrapolations of our numerical data show that subcritical turbulent transport would be too inefficient in keplerian flows by several orders of magnitude for astrophysical purposes. v/ Our results suggest that the data obtained for keplerian-like flows in a Taylor-Couette settings are largely affected by secondary flows, such as Ekman circulation.Comment: 21 pages, 17 figures, accepted in Astronomy and Astrophysic