The supply of energy to the internal wave field in the ocean is, in total, sufficient to support the mixing required to maintain the stratification of the ocean, but can the required rates of ...turbulent dissipation in mid-water be sustained by breaking internal waves? It is assumed that turbulence occurs in regions where the field of motion can be represented by an exact solution of the equations that describe waves propagating through a uniformly stratified fluid and becoming unstable. Two instabilities leading to wave breaking are examined, convective instability and shear-induced Kelvin–Helmholtz instability. Models are constrained by data representative of the mid-water ocean. Calculations of turbulent dissipation are first made on the assumption that all the waves representing local breaking have the same steepness,
$s$
, and frequency,
$\unicodeSTIX{x1D70E}$
. For some ranges of
$s$
and
$\unicodeSTIX{x1D70E}$
, breaking can support the required transfer of energy to turbulence. For convective instability this proves possible for sufficiently large
$s$
, typically exceeding 2.0, over a range of
$\unicodeSTIX{x1D70E}$
, while for shear-induced instability near-inertial waves are required. Relaxation of the constraint that the model waves all have the same
$s$
and
$\unicodeSTIX{x1D70E}$
requires new assumptions about the nature and consequences of wave breaking. Examples predict an overall dissipation consistent with the observed rates. Further observations are, however, required to test the validity of the assumptions made in the models and, in particular, to determine the nature and frequency of internal wave breaking in the mid-water ocean.
The aim of this study was to determine whether arthrocentesis is superior to conservative treatment in the management of painful temporomandibular joint disorders with restricted opening. A ...systematic review was undertaken of prospective randomized controlled trials (RCT) comparing arthrocentesis to conservative management, identified in the MEDLINE and PubMed databases. Inclusion criteria included a 6-month follow-up, with clinical assessment of the patients and painful restricted mouth opening. Data extracted included pain measured on a visual analogue scale and maximum mouth opening measured in millimetres. Risk of bias was assessed using the Cochrane Risk of Bias Tool 2 for RCTs, and a meta-analysis with the random-effects model was undertaken. Of 879 records retrieved, seven met the inclusion criteria; these RCTs reported the results at 6 months for 448 patients. One study had a low risk of bias, four studies had an uncertain risk, and two had a high risk of bias. In the meta-analysis, arthrocentesis was statistically superior to conservative management at 6 months for an increase in maximum mouth opening (1.12 mm, 95% confidence interval 0.45–1.78 mm; P = 0.001; I2 = 87%) and borderline superior for pain reduction (−1.09 cm, 95% confidence interval −2.19 to 0.01 cm; P = 0.05; I2 = 100%). However, these differences are unlikely to be clinically relevant.
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We previously reported a synthetic Laponite® crosslinked pNIPAM-co-DMAc (L-pNIPAM-co-DMAc) hydrogel which promotes differentiation of mesenchymal stem cells (MSCs) to nucleus pulposus ...(NP) cells without additional growth factors. The clinical success of this hydrogel is dependent on: integration with surrounding tissue; the capacity to restore mechanical function; as well as supporting the viability and differentiation of delivered MSCs. Bovine NP tissue explants were injected with media (control), human MSCs (hMSCs) alone, acellular L-pNIPAM-co-DMAc hydrogel or hMSCs incorporated within the L-pNIPAM-co-DMAc hydrogel and maintained at 5% O2 for 6weeks. Viability of native NP cells and delivered MSCs was maintained. Furthermore hMSCs delivered via the L-pNIPAM-co-DMAc hydrogel differentiated and produced NP matrix components: aggrecan, collagen type II and chondroitin sulphate, with integration of the hydrogel with native NP tissue. In addition L-pNIPAM-co-DMAc hydrogel injected into collagenase digested bovine discs filled micro and macro fissures, were maintained within the disc during loading and restored IVD stiffness. The mechanical support of the L-pNIPAM-co-DMAc hydrogel, to restore disc height, could provide immediate symptomatic pain relief, whilst the delivery of MSCs over time regenerates the NP extracellular matrix; thus the L-pNIPAM-co-DMAc hydrogel could provide a combined cellular and mechanical repair approach.
Low back pain (LBP) is associated with degeneration of the intervertebral disc (IVD). We have previously described development of a jelly delivery system (hydrogel). This has the potential to deliver adult stem cells to the centre of the IVD, known as the nucleus pulposus (NP). Here, we have demonstrated that adult stem cells can be safely injected into the NP using small bore needles, reducing damage to the disc. Following injection the hydrogel integrates with surrounding NP tissue, promotes differentiation of stem cells towards disc cells and restores IVD mechanical function. The hydrogel could be used to restore mechanical function to the IVD and deliver cells to promote regeneration of the disc as a minimally invasive treatment for LBP.
Adolescence is an important ontogenetic period that is characterized by behaviors such as enhanced novelty-seeking, impulsivity, and reward preference, which can give rise to an increased risk for ...substance use. While substance use rates in adolescence are generally on a decline, the current rates combined with emerging trends, such as increases in e-cigarette use, remain a significant public health concern. In this review, we focus on the neurobiological divergences associated with adolescent substance use, derived from cross-sectional, retrospective, and longitudinal studies, and highlight how use of these substances during adolescence may relate to behavioral outcomes. Identifying and understanding the associations between adolescent substance use and changes in cognition, mental health, and future substance use risk may assist our understanding of the consequences of drug exposure during this critical window.
In their transition from a laminar state to turbulence, some unstable flows pass through a set of well-defined stages involving different and distinct processes. This is so, in particular, for ...Kelvin–Helmholtz instability, although details of its transition still retain many mysterious aspects. Billows develop in the primary stage of this stratified shear flow instability, separated by thin braids in which the shear is relatively high. Fluid is statically unstable within the billows and consequently potentially prone to convective instability. Numerical studies by Mashayek & Peltier (J. Fluid Mech., this issue, vol 708, 2012a,b, pp. 5–44 and 45–70) have discovered several new types of secondary instability in the braids and billow cores that may hasten the eventual transition to turbulence. The instabilities are illustrated by the authors in colour figures, remarkable for their beauty and (recalling William Blake’s ‘The Tyger’) ‘fearful symmetry’. But are they helpful in establishing the subsequent turbulence in the natural environment?
Laboratory experiments in which uniformly stratified fluids are stirred by horizontally moving vertical grids, or arrays of vertical rods, are reviewed to examine their consistency and to compare ...their findings, particularly those relating to the generation of layers. Selected experiments are of three types, those in which (a) turbulence spreads from a horizontally confined region where it is continuously generated by an oscillating grid; (b) grid stirring is maintained throughout a rectangular tank; or (c) a ‘cloud’ of turbulence decays after a short period of horizontally localized grid mixing. In all the experiments turbulence is generated over the full vertical extent of the tank. In the experiments of types (a) and (c) layers of comparable scale are observed to intrude into the ambient fluid from the turbulent region. In the type (b) experiments, layers form only when the time interval between the passage of the grid through the stratified fluid is sufficiently long, allowing turbulence to decay substantially between grid strokes. Two mechanisms are found to be dominant in the production of layers. In experiments of type (a) and (c) overturning eddies in the turbulent region of scale significantly larger than the Ozmidov length scale collapse and spread, intruding and forming layers in the adjoining laminar region. Internal shear waves propagating ahead of the intrusions have a vertical wavelength that is approximately twice the layer height. In type (b) experiments, layers are formed through a process described by Holford & Linden (Dyn. Atmos. Oceans, vol. 30, 1999a, pp. 173–198): the bending of vortices shed by the grid bars. The height of the layers is approximately half the vertical wavelength of internal shear waves that travel at the speed of the grid. It is proposed that the flow field of the shear waves bends the vortices, resulting in diapycnal mixing that forms the layers. The relationship of layers and internal shear waves in the experiments is therefore as follows: in type (a) and (c) experiments internal waves are generated by layers intruding from the turbulent region into the quiescent stratified region, but in experiments of type (b) internal waves drive and dictate the height of the layers; layers are generated as a consequence of vortex bending by internal waves. There is insufficient evidence to establish whether zigzag instability, either of vortex pairs or of vortex streets shed by a moving grid, accounts for the layers in any of the three types of grid experiments. The Phillips and Posmentier instability may reinforce layers formed by other processes. The generation of pancake vortices or vortical mode motion is left for later review.
Localized anthropogenic sources of atmospheric CH4 are highly uncertain and temporally variable. Airborne remote measurement is an effective method to detect and quantify these emissions. In a ...campaign context, the science yield can be dramatically increased by real-time retrievals that allow operators to coordinate multiple measurements of the most active areas. This can improve science outcomes for both single- and multiple-platform missions. We describe a case study of the NASA/ESA CO2 and MEthane eXperiment (COMEX) campaign in California during June and August/September 2014. COMEX was a multi-platform campaign to measure CH4 plumes released from anthropogenic sources including oil and gas infrastructure. We discuss principles for real-time spectral signature detection and measurement, and report performance on the NASA Next Generation Airborne Visible Infrared Spectrometer (AVIRIS-NG). AVIRIS-NG successfully detected CH4 plumes in real-time at Gb s−1 data rates, characterizing fugitive releases in concert with other in situ and remote instruments. The teams used these real-time CH4 detections to coordinate measurements across multiple platforms, including airborne in situ, airborne non-imaging remote sensing, and ground-based in situ instruments. To our knowledge this is the first reported use of real-time trace-gas signature detection in an airborne science campaign, and presages many future applications. Post-analysis demonstrates matched filter methods providing noise-equivalent (1σ) detection sensitivity for 1.0 % CH4 column enhancements equal to 141 ppm m.
Abstract
Background
Cataloguing the distribution of genes within natural bacterial populations is essential for understanding evolutionary processes and the genetic basis of adaptation. Advances in ...whole genome sequencing technologies have led to a vast expansion in the amount of bacterial genomes deposited in public databases. There is a pressing need for software solutions which are able to cluster, catalogue and characterise genes, or other features, in increasingly large genomic datasets.
Results
Here we present a pangenomics toolbox, PIRATE (Pangenome Iterative Refinement and Threshold Evaluation), which identifies and classifies orthologous gene families in bacterial pangenomes over a wide range of sequence similarity thresholds. PIRATE builds upon recent scalable software developments to allow for the rapid interrogation of thousands of isolates. PIRATE clusters genes (or other annotated features) over a wide range of amino acid or nucleotide identity thresholds and uses the clustering information to rapidly identify paralogous gene families and putative fission/fusion events. Furthermore, PIRATE orders the pangenome using a directed graph, provides a measure of allelic variation, and estimates sequence divergence for each gene family.
Conclusions
We demonstrate that PIRATE scales linearly with both number of samples and computation resources, allowing for analysis of large genomic datasets, and compares favorably to other popular tools. PIRATE provides a robust framework for analysing bacterial pangenomes, from largely clonal to panmictic species.
Conditions are found in which stationary turbulent hydraulic jumps can occur in a shallow stably stratified shear flow of depth
$\def \xmlpi #1{}\def \mathsfbi #1{\boldsymbol {\mathsf {#1}}}\let \le ...=\leqslant \let \leq =\leqslant \let \ge =\geqslant \let \geq =\geqslant \def \Pr {\mathit {Pr}}\def \Fr {\mathit {Fr}}\def \Rey {\mathit {Re}}h_{1}$
moving over a rigid horizontal boundary at
$z =0$
and below a deep static layer of uniform density. The flow approaching a jump has uniform density and speed to a height
$z = h_{1}\eta _{1}\ (\eta _{1} \le 1)$
. Above this, in an interfacial layer
$h_{1}\eta _{1}<z<h_{1}$
, the density and speed decrease linearly to their values in a deep uniform and static layer above
$z = h_{1}$
. The flow downstream of a jump is supposed to be similarly stratified to a height
$ h_{2}$
, but with a lower layer of height
$h_{2}\eta _{2}$
. The flow approaching the jump is specified by
$\eta _{1}$
and by a Froude number, Fr. Stationary jumps occur in the flow only if Fr is large enough to ensure that no internal waves can propagate upstream from the transition region. The flow downstream of the jump satisfies conditions of conservation of mass, volume and momentum fluxes, and closure is obtained by the selection of its gradient Richardson number,
${\mathit{Ri}}_{F}$
. It is necessary that
$\eta _{1} \ge \eta _{2}$
for the entrainment of fluid into the moving layer from the overlying deep layer to be non-negative. The jump height,
$q = h_{2}/h_{1}$
, always exceeds unity (i.e. jumps are, overall, of elevation) and the mean thickness of the flowing layer,
$h_{i}(1+ \eta _{i})/2\ (i = 1, 2)$
, increases through the jump. There are two types of jumps, one in which the thickness of the lower layer,
$h_{i}\eta _{i}$
, increases (and all isopycnals are raised by the transition) and a second in which
$h_{i}\eta _{i}$
decreases even though
$q$
and the mean thickness ratio,
$h_{2}(1+ \eta _{2})/ h_{1}(1 + \eta _{1})$
, are greater than one. Two possible solutions for the downstream flow (i.e. two jumps of different heights,
$q$
, and different shape parameters,
$\eta _{2}$
) are possible in limited ranges of Fr depending on
$\eta _{1}$
when
$\eta _{1} > \eta _{2}$
,
$= \eta _{2max}$
, where
$\eta _{2max} =0.744$
when
${\mathit{Ri}}_{F} = 1/3$
. Only single solutions are possible for upstream flows with
$\eta _{1}< \eta _{2max}$
. The two branches of the double solutions are distinguishable. For the ‘upper’ solutions,
$\eta _{2}$
increases as Fr increases, and all isopycnals are raised in the jump. The ‘lower’ of the double solutions are continuous with the single solutions (with
$\eta _{1}<\eta _{2max}$
),
$\eta _{2}$
decreases as Fr increases, and for most of the jumps the lower uniform layer decreases in thickness through the jump. For all solutions there is a reduction in the energy flux as fluid passes through a transition, and hence a loss of energy in the turbulent mixing of a jump, as required on physical grounds. The Osborn efficiency factor,
$\varGamma $
, is generally less than the canonical value of 0.2 for upper branch solutions but greater than 0.2 for the single and lower branch solutions. A loss in vorticity flux occurs in a turbulent jump. For a hydraulic jump to be possible when
$\eta _{2}$
is less than approximately 0.3, it is not generally necessary that the flow approaching a jump is unstable to Kelvin–Helmholtz (K–H) instability, but it is more common that upstream flows in which jumps can occur are dynamically unstable.
Marginal Instability? THORPE, S. A; ZHIYU LIU
Journal of physical oceanography,
09/2009, Letnik:
39, Številka:
9
Journal Article
Recenzirano
Odprti dostop
Abstract
Some naturally occurring, continually forced, turbulent, stably stratified, mean shear flows are in a state close to that in which their stability changes, usually from being dynamically ...unstable to being stable: the time-averaged flows that are observed are in a state of marginal instability. By “marginal instability” the authors mean that a small fractional increase in the gradient Richardson number Ri of the mean flow produced by reducing the velocity and, hence, shear is sufficient to stabilize the flow: the increase makes Rimin, the minimum Ri in the flow, equal to Ric, the critical value of this minimum Richardson number. The value of Ric is determined by solving the Taylor–Goldstein equation using the observed buoyancy frequency and the modified velocity. Stability is quantified in terms of a factor, Φ, such that multiplying the flow speed by (1 + Φ) is just sufficient to stabilize it, or that Ric = Rimin/(1 + Φ)2.
The hypothesis that stably stratified boundary layer flows are in a marginal state with Φ < 0 and with |Φ| small compared to unity is examined. Some dense water cascades are marginally unstable with small and negative Φ and with Ric substantially less than ¼. The mean flow in a mixed layer driven by wind stress on the water surface is, however, found to be relatively unstable, providing a counterexample that refutes the hypothesis. In several naturally occurring flows, the time for exponential growth of disturbances (the inverse of the maximum growth rate) is approximately equal to the average buoyancy period observed in the turbulent region.
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