Reply to “Comments on ‘Langmuir Turbulence and Surface Heating in the Ocean Surface Boundary Layer’”

The differences between the conclusions of Noh and Choi and of Pearson et al., which are largely a result of defining different length scales based on different quantities, are discussed. This study shows that the layer over which Langmuir turbulence mixes (nominally hTKE) under a stabilizing surface buoyancy flux should be scaled by a combination of the Langmuir stability length LL and initial/nocturnal boundary layer depth h0 rather than by the Zilitinkevich length

Strengthening approaches to respond to the social and emotional well-being needs of Aboriginal and Torres Strait Islander people: the Cultural Pathways Program

Aboriginal and Torres Strait Islander holistic health represents the interconnection of social, emotional, spiritual and cultural factors on health and well-being. Social factors (education, employment, housing, transport, food and financial security) are internationally described and recognised as the social determinants of health. The social determinants of health are estimated to contribute to 34% of the overall burden of disease experienced by Aboriginal and Torres Strait Islander people. Primary health care services currently ‘do what it takes’ to address social and emotional well-being needs, including the social determinants of health, and require culturally relevant tools and processes for implementing coordinated and holistic responses. Drawing upon a research-setting pilot program, this manuscript outlines key elements encapsulating a strengths-based approach aimed at addressing Aboriginal and Torres Strait Islander holistic social and emotional well-being. The Cultural Pathways Program is a response to community identified needs, designed and led by Aboriginal and Torres Strait Islander people and informed by holistic views of health. The program aims to identify holistic needs of Aboriginal and Torres Strait Islander people as the starting point to act on the social determinants of health. Facilitators implement strengths-based practice to identify social and cultural needs (e.g. cultural and community connection, food and financial security, housing, mental health, transport), engage in a goal setting process and broker connections with social and health services. An integrated culturally appropriate clinical supervision model enhances delivery of the program through reflective practice and shared decision making. These embedded approaches enable continuous review and improvement from a program and participant perspective. A developmental evaluation underpins program implementation and the proposed culturally relevant elements could be further tailored for delivery within primary health care services as part of routine care to strengthen systematic identification and response to social and emotional well-being needs.Tina Brodie, Odette Pearson, Luke Cantley, Peita Cooper, Seth Westhead, Alex Brown and Natasha J Howar

Anticipated climate and land-cover changes reveal refuge areas for Borneo's orang-utans

Habitat loss and climate change pose a double jeopardy for many threatened taxa, making the identification of optimal habitat for the future a conservation priority. Using a case study of the endangered Bornean orang-utan, we identify environmental refuges by integrating bioclimatic models with projected deforestation and oil-palm agriculture suitability from the 1950s to 2080s. We coupled a maximum entropy algorithm with information on habitat needs to predict suitable habitat for the present day and 1950s. We then projected to the 2020s, 2050s and 2080s in models incorporating only land-cover change, climate change or both processes combined. For future climate, we incorporated projections from four model and emission scenario combinations. For future land cover, we developed spatial deforestation predictions from 10 years of satellite data. Refuges were delineated as suitable forested habitats identified by all models that were also unsuitable for oil palm – a major threat to tropical biodiversity. Our analyses indicate that in 2010 up to 260 000 km2 of Borneo was suitable habitat within the core orang-utan range; an 18–24% reduction since the 1950s. Land-cover models predicted further decline of 15–30% by the 2080s. Although habitat extent under future climate conditions varied among projections, there was majority consensus, particularly in northeastern and western regions. Across projections habitat loss due to climate change alone averaged 63% by 2080, but 74% when also considering land-cover change. Refuge areas amounted to 2000–42 000 km2 depending on thresholds used, with 900–17 000 km2 outside the current species range. We demonstrate that efforts to halt deforestation could mediate some orang-utan habitat loss, but further decline of the most suitable areas is to be expected given projected changes to climate. Protected refuge areas could therefore become increasingly important for ongoing translocation efforts. We present an approach to help identify such areas for highly threatened species given environmental changes expected this century

Java GUI for InterProScan (JIPS): A tool to help process multiple InterProScans and perform ortholog analysis

BACKGROUND: Recent, rapid growth in the quantity of available genomic data has generated many protein sequences that are not yet biochemically classified. Thus, the prediction of biochemical function based on structural motifs is an important task in post-genomic analysis. The InterPro databases are a major resource for protein function information. For optimal results, these databases should be searched at regular intervals, since they are frequently updated. RESULTS: We describe here a new program JIPS (Java GUI for InterProScan), a tool for tracking and viewing results obtained from repeated InterProScan searches. JIPS stores matches (in a local database) obtained from InterProScan searches performed with multiple versions of the InterPro database and highlights hits that have been added since the last search of the InterPro database. Results are displayed in an easy-to-use tabular format. JIPS also contains tools to assist with ortholog-based comparative studies of protein signatures. CONCLUSION: JIPS is an efficient tool for performing repeated InterProScans on large batches of protein sequences, tracking and viewing search results, and mining the collected data

Fluoromycobacteriophages for rapid, specific, and sensitive antibiotic susceptibility testing of Mycobacterium tuberculosis

Rapid antibiotic susceptibility testing of Mycobacterium tuberculosis is of paramount importance as multiple- and extensively- drug resistant strains of M. tuberculosis emerge and spread. We describe here a virus-based assay in which fluoromycobacteriophages are used to deliver a GFP or ZsYellow fluorescent marker gene to M. tuberculosis, which can then be monitored by fluorescent detection approaches including fluorescent microscopy and flow cytometry. Pre-clinical evaluations show that addition of either Rifampicin or Streptomycin at the time of phage addition obliterates fluorescence in susceptible cells but not in isogenic resistant bacteria enabling drug sensitivity determination in less than 24 hours. Detection requires no substrate addition, fewer than 100 cells can be identified, and resistant bacteria can be detected within mixed populations. Fluorescence withstands fixation by paraformaldehyde providing enhanced biosafety for testing MDR-TB and XDR-TB infections. © 2009 Piuri et al

Mammalian communities as indicators of disturbance across Indonesian Borneo

Using camera traps at eight grids across Indonesian Borneo we show how mammalian species assemblages can provide reliable information about how disturbance affects a forest. This enables us to use the large mammal community structure at each site to assess the impacts of human disturbance and habitat variables. Occupancy ranged from 0.01–0.77 with pig-tailed macaques, muntjac, orang-utans, sun bears, bearded pigs and common porcupines consistently having an occupancy of >0.5. These large mammals were generally making use of the whole forest surveyed and avoided the forest edge in only a few grids. A General Linear Model with general contrasts and survey effort as a covariate was performed to assess the impact of different variables. Logging and hunting were positively associated with low species number (F=6.3, p=0.012 and F=5.4, p=0.003 respectively). Logging and hunting contributed to a low % of carnivorous species (F=1.5, p=0.021 and F=4.8, p=0.041 respectively) and a higher % of IUCN Endangered and Vulnerable species (F=5.9, p=0.044 and F=5.0, p=0.044 respectively). The presence of burnt areas within the study grids was positively associated with reduced species numbers (F=5.3, p=0.018) and reducted % of carnivorous species (F=6.8, p=0.023) but not the % of IUCN Endangered and Vulnerable species. This is likely a result of burnt areas reducing the area of suitable habitat for many mammals. The proximity of the grids to roads, villages, rivers and presence of logging camps have been proposed as suitable parameters to indicate disturbance. In our study none of these parameters significantly affected the total species numbers, % of carnivores, and % of IUCN concern (Endangered and Vulnerable), nor did the protected status of the forest. We have identified 4 species as specific indicators whose presence or absence can help determine the type and/or extent of forest disturbance and/or be a proxy indicator for the presence of other species. Leopard cat (Prionailurus bengalensis) and pig-tailed macaques (Macaca nemestrina, generalists); sambar deer (Rusa unicolour, large, wide-ranging herbivores) and clouded leopards (Neofelis diardi) as a proxy for at least 2 of the smaller felid species

Comparing ocean surface boundary vertical mixing schemes including langmuir turbulence

Six recent Langmuir turbulence parameterization schemes and five traditional schemes are implemented in a common single‐column modeling framework and consistently compared. These schemes are tested in scenarios versus matched large eddy simulations, across the globe with realistic forcing (JRA55‐do, WAVEWATCH‐III simulated waves) and initial conditions (Argo), and under realistic conditions as observed at ocean moorings. Traditional non‐Langmuir schemes systematically underpredict large eddy simulation vertical mixing under weak convective forcing, while Langmuir schemes vary in accuracy. Under global, realistic forcing Langmuir schemes produce 6% (−1% to 14% for 90% confidence) or 5.2 m (−0.2 m to 17.4 m for 90% confidence) deeper monthly mean mixed layer depths than their non‐Langmuir counterparts, with the greatest differences in extratropical regions, especially the Southern Ocean in austral summer. Discrepancies among Langmuir schemes are large (15% in mixed layer depth standard deviation over the mean): largest under wave‐driven turbulence with stabilizing buoyancy forcing, next largest under strongly wave‐driven conditions with weak buoyancy forcing, and agreeing during strong convective forcing. Non‐Langmuir schemes disagree with each other to a lesser extent, with a similar ordering. Langmuir discrepancies obscure a cross‐scheme estimate of the Langmuir effect magnitude under realistic forcing, highlighting limited understanding and numerical deficiencies. Maps of the regions and seasons where the greatest discrepancies occur are provided to guide further studies and observations

Langmuir turbulence and surface heating in the ocean surface boundary layer

This study uses large-eddy simulation to investigate the structure of the ocean surface boundary layer (OSBL) in the presence of Langmuir turbulence and stabilizing surface heat fluxes. The OSBL consists of a weakly stratified layer, despite a surface heat flux, above a stratified thermocline. The weakly stratified (mixed) layer is maintained by a combination of a turbulent heat flux produced by the wave-driven Stokes drift and downgradient turbulent diffusion. The scaling of turbulence statistics, such as dissipation and vertical velocity variance, is only affected by the surface heat flux through changes in the mixed layer depth. Diagnostic models are proposed for the equilibrium boundary layer and mixed layer depths in the presence of surface heating. The models are a function of the initial mixed layer depth before heating is imposed and the Langmuir stability length. In the presence of radiative heating, the models are extended to account for the depth profile of the heating

Earthquakes: from chemical alteration to mechanical rupture

In the standard rebound theory of earthquakes, elastic deformation energy is progressively stored in the crust until a threshold is reached at which it is suddenly released in an earthquake. We review three important paradoxes, the strain paradox, the stress paradox and the heat flow paradox, that are difficult to account for in this picture, either individually or when taken together. Resolutions of these paradoxes usually call for additional assumptions on the nature of the rupture process (such as novel modes of deformations and ruptures) prior to and/or during an earthquake, on the nature of the fault and on the effect of trapped fluids within the crust at seismogenic depths. We review the evidence for the essential importance of water and its interaction with the modes of deformations. Water is usually seen to have mainly the mechanical effect of decreasing the normal lithostatic stress in the fault core on one hand and to weaken rock materials via hydrolytic weakening and stress corrosion on the other hand. We also review the evidences that water plays a major role in the alteration of minerals subjected to finite strains into other structures in out-of-equilibrium conditions. This suggests novel exciting routes to understand what is an earthquake, that requires to develop a truly multidisciplinary approach involving mineral chemistry, geology, rupture mechanics and statistical physics.Comment: 44 pages, 1 figures, submitted to Physics Report

The future of the northeast Atlantic benthic flora in a high CO₂ world

Seaweed and seagrass communities in the northeast Atlantic have been profoundly impacted by humans, and the rate of change is accelerating rapidly due to runaway CO2 emissions and mounting pressures on coastlines associated with human population growth and increased consumption of finite resources. Here, we predict how rapid warming and acidification are likely to affect benthic flora and coastal ecosystems of the northeast Atlantic in this century, based on global evidence from the literature as interpreted by the collective knowledge of the authorship. We predict that warming will kill off kelp forests in the south and that ocean acidification will remove maerl habitat in the north. Seagrasses will proliferate, and associated epiphytes switch from calcified algae to diatoms and filamentous species. Invasive species will thrive in niches liberated by loss of native species and spread via exponential development of artificial marine structures. Combined impacts of seawater warming, ocean acidification, and increased storminess may replace structurally diverse seaweed canopies, with associated calcified and noncalcified flora, with simple habitats dominated by noncalcified, turf-forming seaweeds.</p