Investigating the role of larval dispersal models in the development of an 'ecologically coherent' network of deep sea marine protected areas

Parts of Chapter 1 (predominantly section 1.2) are published within the article: Hilário, A., Metaxas, A., Gaudron, S.M., Howell, K.L., Mercier, A., Mestre, N.C., Ross, R.E., Thurnherr, A.M., Young, C., 2015. Estimating dispersal distance in the deep sea: challenges and applications to marine reserves. Frontiers in Marine Science, 2: 00006. doi: 10.3389/fmars.2015.0000 Chapter 2 was also published in full (pre-corrections) as follows: Ross, R.E., Nimmo-Smith, W.A.M., Howell, K.L., 2016. Increasing the Depth of Current Understanding: Sensitivity Testing of Deep-Sea Larval Dispersal Mode. PLoS ONE, 11, e0161220 . doi:10.1371/journal.pone.0140061There is currently worldwide pressure to establish Marine Protected Area (MPA) networks which are self-sustaining and will persistently protect habitats and species. In order for MPA networks to be effective, the species targeted for conservation must be able to disperse between protected areas and maintain a gene-flow necessary for population sustainability and persistence. This warrants new research on how to quantify and map faunal dispersal to ensure that protection will be effective and sustainable. Population genetic methods have merit, with the ability to track parentage and gene flow between areas directly. However the costs, quantity of samples, and time required to genetically quantify dispersal for multiple species make these approaches prohibitive as the only method of assessment, especially in relatively inaccessible offshore waters. Dispersal modelling is now becoming more accessible and may fulfil immediate needs in this field (although ground truthing will be necessary in the future). There have been very few dispersal modelling studies focussed on deep sea or offshore areas, predominantly due to the lack of high resolution hydrodynamic models with sufficient geographic extent away from shore. Current conclusions have been drawn based on shallow water coastal studies, informing offshore MPA network size and spacing. However the differences between these two environments may mean that dispersal abilities are not comparable. Deep water receives less influence from wind and weather, and the scales are vastly different in terms of a) the depth ranges covered, b) the planktonic larval durations (PLDs) of animals, and c) the geographic areas concerned as a consequence. Global hydrodynamic models with reasonable resolution are now becoming more accessible. With the outputs from these models, and freely available particle simulators, it is becoming more practical to undertake offshore deep water dispersal studies. This thesis aims to undertake an analysis of these accessible modelling tools within a deep sea context. The guidelines which are currently available to dispersal modellers are yet to encompass the needs of deep water modellers which may require some additional considerations given the extended depth range covered and the different hydrodynamic drivers away from the air/sea interface. Chapter 1 reviews the larval dispersal process, the factors which may affect dispersal success, and those which should be incorporated into future predictions of dispersal. The current methods for assessing larval dispersal are explored covering genetics, elemental tagging and modelling approaches with an extended look at modelling considerations. Existing marine conservation policy is also touched on in the context of connectivity and larval dispersal. Chapter 2 is designed to inform future deep sea modellers on how to parameterise and understand a dispersal model. As models appear as a ‘black box’ to the majority of users, sensitivity tests can offer a way of scaling model inputs and tempering expectations from model outputs. A commonly used model pairing (the HYCOM hydrodynamic model and the Connectivity Modeling System) is assessed, using parameters which link to the temporal and spatial scales of mixing in the modelled system: timestep of particle tracer, horizontal and vertical positioning of release points, release frequency of larvae, and temporal range of simulation. All parameters were shown to have a decreased sensitivity with depth, with patterns reflecting local watermass structure. Future studies observing similar hydrodynamic conditions seeking to optimise their model set up would be advised to stratify their model release locations with depth. A means to incorporate all sensitivity test results into optimal input parameters for future studies is demonstrated. Chapter 3 investigates whether dispersal models provide any advantage over a “sphere of influence” estimate based on average current speeds and PLDs: there is no use pursuing dispersal modelling if the outputs are too erroneous to provide any advantage over a back-of-the-envelope calculation. This chapter examines the outputs of two dispersal models driven by two different hydrodynamic models in order to observe the variability in prediction between models. This model comparison revealed a greater disparity between hydrodynamic model predictions than has been previously understood by ecologists. The two models compared (POLCOMS and HYCOM) may equally be considered as suitable to promote realism in the study region, but slight differences in resolution and numerical error handling resulted in dispersal predictions from which opposing conclusions can be drawn. This chapter therefore emphasises the necessity for model ground truthing before predictions can be trusted. Chapter 4 assimilates the findings of the previous chapters and applies their advice to a study of MPA network dispersal connectivity. Using the hydrodynamic model which performed best in chapter 3 (HYCOM), a simulation was undertaken for cold water coral (Lophelia pertusa (Linnaeus 1758)) larval dispersal between already established MPAs in the NE Atlantic. As larval characters have only been observed ex situ, dispersal was simulated using two null models (passive and active vertical migration) and averaged to provide an intermediate prediction. A method for assessing dispersal within MPAs and MPA networks is offered based on the intermediate prediction, as well as a network wide assessment of the difference in dispersal patterns for passive and active larvae. It was found that the existing network performs well at supplying larvae to non-networked sites, but performs poorly at supplying other MPAs. The ‘best’ MPAs were central to the network and facilitated the traverse of regional gaps in suitable habitat. The ‘worst’ MPAs were peripheral to the network and small in size. Network-wide passive and active dispersal matrices had no significant difference between them. However site specific variability in the effect of vertical migration was detected subject to variability in local topographic barriers to dispersal, only some of which could be surmounted with vertical migration. All chapters aim to inform future deep sea dispersal modellers, and encourage exploration of this tool in other contexts, as well as marine conservation. The thesis cautions against the transplantation of shallow water assumptions to deep water environments, and advocates region specific studies and mandatory ground truthing of predictions. An upcoming study will ground truth the findings of this thesis with both genetic and oceanographic data, allowing the accuracy of study results to be quantified

Diagnostic and decision-support tools for effective faecal sludge management (FSM) services

Achieving effective faecal sludge management (FSM) from on-site sanitation systems is critical to improving sanitation in urban settlements. Research conducted in 2014-16 by OPM Ltd and WEDC, on behalf of and with the World Bank WSP, used extensive primary data from five cities in the global South to develop a comprehensive suite of FSM diagnostic and decision-support tools. This paper describes the development and use of the tools, while illustrating two key tools. The resulting suite of tools, together with associated resources, provides a comprehensive and usable basis to help guide FSM intervention options, informed by an understanding of existing FSM services, within the context of the enabling environment and political economy realities of the city

Major Depression among methamphetamine users entering drug treatment programs

Objective: To determine the prevalence of major depression among people entering treatment for methamphetamine use. Design, setting and participants: The study was a cross-sectional survey involving 41 specialised drug and alcohol treatment agencies in Brisbane and Sydney. Services provided by these agencies included residential rehabilitation, detoxification and counselling. Participants were 400 people entering treatment for methamphetamine use who were recruited from participating treatment agencies between January 2006 and November 2007. Participants underwent a structured, face-to-face, 1.5-hour interview. Assessment instruments included the Composite International Diagnostic Interview and the Short Form 12. Main outcome measure: Diagnosis of a major depressive episode in the year prior to the study. Results: The prevalence of major depression in the year prior to the study was 40% (95% CI, 35%-44%). A noteworthy post-hoc observation was that a further 44% of participants met the symptom criteria for major depression but were excluded from a diagnosis because their symptoms were better accounted for by psychoactive substance use. Both major depression and these latter cases of "substance-induced depression" were associated with severe symptoms of depression, high levels of disability and suicidal ideation. Conclusion: Most people entering treatment programs for methamphetamine use have levels of depression that require clinical management. Making a diagnosis of major depression in the context of heavy methamphetamine use is problematic because of substance-induced symptoms of depression

Viscous Torque and Dissipation in the Inner Region of a Thin Accretion Disk: Implications for Measuring Black Hole Spin

We consider a simple Newtonian model of a steady accretion disk around a black hole. The model is based on height-integrated hydrodynamic equations, alpha-viscosity, and a pseudo-Newtonian potential that results in an innermost stable circular orbit (ISCO) that closely approximates the one predicted by GR. We find that the hydrodynamic models exhibit increasing deviations from the standard disk model of Shakura & Sunyaev as disk thickness H/R or the value of alpha increases. The latter is an analytical model in which the viscous torque is assumed to vanish at the ISCO. We consider the implications of the results for attempts to estimate black hole spin by using the standard disk model to fit continuum spectra of black hole accretion disks. We find that the error in the spin estimate is quite modest so long as H/R < 0.1 and alpha < 0.2. At worst the error in the estimated value of the spin parameter is 0.1 for a non-spinning black hole; the error is much less for a rapidly spinning hole. We also consider the density and disk thickness contrast between the gas in the disk and that inside the ISCO. The contrast needs to be large if black hole spin is to be successfully estimated by fitting the relativistically-broadened X-ray line profile of fluorescent iron emission from reflection off an accretion disk. In our hydrodynamic models, the contrast in density and thickness is low when H/R>0.1, sugesting that the iron line technique may be most reliable in extemely thin disks. We caution that these results have been obtained with a viscous hydrodynamic model and need to be confirmed with MHD simulations of radiatively cooled thin disks.Comment: 32 pages, 10 figures; accepted by Ap

Influence of GABA and GABA-producing Lactobacillus brevis DPC 6108 on the development of diabetes in a streptozotocin rat model

peer-reviewedThe aim of this study was to investigate if dietary administration of γ-aminobutyric acid (GABA)-producing Lactobacillus brevis DPC 6108 and pure GABA exert protective effects against the development of diabetes in streptozotocin (STZ)-induced diabetic Sprague Dawley rats. In a first experiment, healthy rats were divided in 3 groups (n=10/group) receiving placebo, 2.6 mg/kg body weight (bw) pure GABA or L. brevis DPC 6108 (~109microorganisms). In a second experiment, rats (n=15/group) were randomised to five groups and four of these received an injection of STZ to induce type 1 diabetes. Diabetic and non-diabetic controls received placebo [4% (w/v) yeast extract in dH2O], while the other three diabetic groups received one of the following dietary supplements: 2.6 mg/kg bw GABA (low GABA), 200 mg/kg bw GABA (high GABA) or ~109 L. brevis DPC 6108. L. brevis DPC 6108 supplementation was associated with increased serum insulin levels (P0.05), compared with non-diabetic controls while all other diabetic groups displayed reduced diversity (P<0.05). L. brevis DPC 6108 attenuated hyperglycaemia induced by diabetes but additional studies are needed to understand the mechanisms involved in this reduction.The authors and their work were supported by the APC Microbiome Institute. The APC Microbiome Institute is funded by Science Foundation Ireland (SFI). This publication has emanated from research supported by a research grant from Science Foundation Ireland (SFI) under Grant Number SFI/12/RC/2273

Induced earthquake families reveal distinctive evolutionary patterns near disposal wells

The timing of events in seismic sequences can provide insights into the physical processes controlling fault slip. In southern Kansas, the rate of earthquakes rose rapidly starting in 2013 following expansion of energy production into the area, demanding the disposal of large volumes of wastewater into deep wells. Seismicity catalogs that are complete to low magnitudes can provide insights into the physical processes that induce seismicity near wastewater disposal. We develop a catalog of over 130,000 earthquakes recorded in southern Kansas from mid‐March 2014 through December 2017 by applying a matched filter algorithm to an original catalog of 5,831 template earthquakes. Detections have nearly identical waveforms to their associated template event and represent slip on nearly co‐located sections of a fault. We select template events with at least 100 associated detections and examine the characteristics of these prolific families of earthquakes. We find that families located close (<10 km) to areas with significant volumes of injected fluids have near‐Poissonian interevent times and the families remain active over longer durations. Families farther from high‐volume injection wells show strong clustering of interevent times and shorter sequence durations. We conclude that increasing pore fluid pressures from nearby disposal of large volumes of wastewater is the primary driver of these long duration episodes, with earthquake‐earthquake interactions driving sequences at greater distance from the wells

Proteomic risk markers for coronary heart disease and stroke: validation and mediation of randomized trial hormone therapy effects on these diseases

Background: We previously reported mass spectrometry-based proteomic discovery research to identify novel plasma proteins related to the risk of coronary heart disease (CHD) and stroke, and to identify proteins with concentrations affected by the use of postmenopausal hormone therapy. Here we report CHD and stroke risk validation studies for highly ranked proteins, and consider the extent to which protein concentration changes relate to disease risk or provide an explanation for hormone therapy effects on these outcomes. Methods: Five proteins potentially associated with CHD (beta-2 microglobulin (B2M), alpha-1-acid glycoprotein 1 (ORM1), thrombospondin-1(THBS1), complement factor D pre-protein (CFD), and insulin-like growth factor binding protein 1 (IGFBP1)) and five potentially associated with stroke (B2M, IGFBP2, IGFBP4, IGFBP6, and hemopexin (HPX)) had high discovery phase significance level ranking and an available ELISA assay, and were included in case-control validation studies within the Women’s Health Initiative (WHI) hormone therapy trials. Protein concentrations, at baseline and 1 year following randomization, were assessed for 358 CHD cases and 362 stroke cases, along with corresponding disease-free controls. Disease association, and mediation of estrogen-alone and estrogen plus progestin effects on CHD and stroke risk, were assessed using logistic regression. Results: B2M, THBS1, and CFD were confirmed (P <0.05) as novel CHD risk markers, and B2M, IGFBP2, and IGFBP4 were confirmed as novel stroke disease risk markers, while the assay for HPX proved to be unreliable. The change from baseline to 1 year in B2M was associated (P <0.05) with subsequent stroke risk, and trended similarly with subsequent CHD risk. Change from baseline to 1 year in IGFBP1 was also associated with CHD risk, and this change provided evidence of hormone therapy effect mediation. Conclusions: Plasma B2M is confirmed to be an informative risk marker for both CHD and stroke. The B2M increase experienced by women during the first year of hormone therapy trial participation conveys cardiovascular disease risk. The increase in IGFBP1 similarly conveys CHD risk, and the magnitude of the IGFBP1 increase following hormone therapy may be a mediator of hormone therapy effects. Plasma THBS1 and CFD are confirmed as CHD risk markers, and plasma IGFBP4 and IGFBP2 are confirmed as stroke risk markers. Clinical trials registration ClinicalTrials.gov identifier: NCT0000061

Galaxy Zoo: constraining the origin of spiral arms

Since the discovery that the majority of low-redshift galaxies exhibit some level of spiral structure, a number of theories have been proposed as to why these patterns exist. A popular explanation is a process known as swing amplification, yet there is no observational evidence to prove that such a mechanism is at play. By using a number of measured properties of galaxies, and scaling relations where there are no direct measurements, we model samples of SDSS and S4G spiral galaxies in terms of their relative halo, bulge and disc mass and size. Using these models, we test predictions of swing amplification theory with respect to directly measured spiral arm numbers from Galaxy Zoo 2. We find that neither a universal cored or cuspy inner dark matter profile can correctly predict observed numbers of arms in galaxies. However, by invoking a halo contraction/expansion model, a clear bimodality in the spiral galaxy population emerges. Approximately 40 per cent of unbarred spiral galaxies at z 10^10 Msolar have spiral arms that can be modelled by swing amplification. This population display a significant correlation between predicted and observed spiral arm numbers, evidence that they are swing amplified modes. The remainder are dominated by two-arm systems for which the model predicts significantly higher arm numbers. These are likely driven by tidal interactions or other mechanisms

New Constraints on Cosmic Reionization from the 2012 Hubble Ultra Deep Field Campaign

Understanding cosmic reionization requires the identification and characterization of early sources of hydrogen-ionizing photons. The 2012 Hubble Ultra Deep Field (UDF12) campaign has acquired the deepest infrared images with the Wide Field Camera 3 aboard Hubble Space Telescope and, for the first time, systematically explored the galaxy population deep into the era when cosmic microwave background (CMB) data indicates reionization was underway. The UDF12 campaign thus provides the best constraints to date on the abundance, luminosity distribution, and spectral properties of early star-forming galaxies. We synthesize the new UDF12 results with the most recent constraints from CMB observations to infer redshift-dependent ultraviolet (UV) luminosity densities, reionization histories, and electron scattering optical depth evolution consistent with the available data. Under reasonable assumptions about the escape fraction of hydrogen ionizing photons and the intergalactic medium clumping factor, we find that to fully reionize the universe by redshift z~6 the population of star-forming galaxies at redshifts z~7-9 likely must extend in luminosity below the UDF12 limits to absolute UV magnitudes of M_UV\sim -13 or fainter. Moreover, low levels of star formation extending to redshifts z~15-25, as suggested by the normal UV colors of z\simeq7-8 galaxies and the smooth decline in abundance with redshift observed by UDF12 to z\simeq10, are additionally likely required to reproduce the optical depth to electron scattering inferred from CMB observations.Comment: Version accepted by ApJ (originally submitted Jan 5, 2013). The UDF12 website can be found at http://udf12.arizona.ed