Acoustic Remote-Sensing of Reef Benthos in Broward County, Florida (USA)

Benthic assemblages of variable density cover three progressively deeper ridges that parallel the Broward County, Florida, coast. An acoustic bottom classification survey using QTCView5 with a 50 kHz transducer showed different acoustic classes on the shallow reef-ridge and the two deeper reef-lines, which both showed the same acoustic signature. Ground-truthing showed that the differences in acoustic signature corresponded to different benthic assemblages: nearshore hardgrounds had low live cover and were dominated by algae covering substrate, the two deeper reef-ridges had the same acoustic signature and similar benthic assemblages (dominated by sponges and gorgonians). The QTCView5 was also able to differentiate between stable sands covered by a thin red algae turf and more mobile sand without turf cover. Acoustic remote-sensing methods can be used to differentiate benthic assemblages, as long as enough differences exist in the growth-form characteristics of the dominant species to provide for a different acoustic roughness

Development of GIS Maps for Southeast Florida Coral Reefs

The present report outlines the results of an integrated mapping project undertaken to provide a habitat map of the shallow Broward County seafloor between the 0m and 35m contour. The study area stretched from Golden Beach in northern Dade County to just north of the Palm Beach County line. To produce this map and assure its compatibility with other, in particular NOAA, mapping products, a series of data were integrated. Data types included Laser Airborne Depth Sounder (LADS) bathymetry, multi- and single-beam bathymetry, acoustic seafloor discrimination, ecological assessments, and groundtruthing. The method used for acoustic seafloor discrimination was based on the first echo and its associated tail, and on the second echo returns of a 200 kHz signal. Two survey systems were employed: QTC View and Echoplus. A series of controlled experiments and field verifications indicated that it was possible to distinguish acoustically between different scattering classes that correlated to different seafloor types. For the production of the final map, information obtained from LADS bathymetry, NOAA classification and scattering classes obtained by QTC View and Echoplus was fused. The final map showed three well-developed linear reef complexes, a series of deep and shallow ridges believed to be old shorelines, a large sand area between the middle and outer reefs, and a considerable amount of colonized pavement. Due to the lack of distinct geomorphologic zones, the maps were based solely on habitat as defined by the NOAA biogeography program; however distinctions between areas such as linear reef, spur and groove, and colonized pavement were based on benthic cover (as seen by acoustic seafloor discrimination and biological transects) and geomorphology. The outer linear reef was subdivided into four habitats: aggregated patch reef, spur and groove, linear reef and deep colonized pavement. The area east of the outer linear reef consisted of a very patchy environment with large patches of reef interspersed amongst the deep sand. These were more prevalent close to the reef and tapered off eastward, becoming sandier. The spur and groove, linear reef, and deep colonized pavement comprised the outer reef and were separated mainly based on geomorphology. The outer reef was separated from the middle linear reef by a wide sandy plane (deep sand), which was characterized overall by a different scattering class in QTC View than the shallow sand found inshore. Acoustic ground discrimination identified patches of higher scatter and lower scatter amongst the outer, middle, and inner linear reefs suggesting distinct benthic cover between these structures. The eastern boundary of the middle reef was distinct and easily mapped whereas acoustic discrimination aided in determining the western boundary. The inner reef was the least distinct reef as it is not a mature reef. Much of this reef is patchy growth atop an inshore ridge and reef zonation is absent. Acoustic ground discrimination suggested that patches of higher versus lower scatter existed between and within the linear reefs, indicating that dense fauna is patchily distributed. Shoreward of the inner reef, another sand area or a mixture of sand and colonized pavements were found. Several nearshore ridges were mapped that could be classified as linear reef habitat, but were thought to be of non-reefal origin. Therefore these structures were mapped separately even though similar habitat comprises the inshore ridges, the inner linear reef, and the shallow colonized pavements. Excluded habitats such as submerged vegetation and large rubble zones were not detected sufficiently enough to be mapped during this effort. Groundtruthing by way of underwater video drop cameras and in situ biological assessments aided in the refinement of the mapping categories. Accuracy assessment of an independent grid of target points showed the map to have a users accuracy between 83% and 97% and a producers accuracy between 81% and 95%. These are acceptable accuracies and compare similarly to NOAA published map accuracies. In conclusion, the amalgamation of several mapping approaches and data products provided a representative map of Broward County submarine habitats that was accurate to a very satisfactory level. The results of this survey are a good example of how similar mapping products can be attained through different means. The method employed to map Broward County appears to have equally and accurately illustrated the benthic community as more traditional methods like photo interpretation. Similar methodology should be used in other areas where photo interpretation is not feasible due to either absence of data or the turbidity of the water

A Tale of Germs, Storms, and Bombs: Geomorphology and Coral Assemblage Structure at Vieques (Puerto Rico) Compared to St. Croix (U.S. Virgin Islands)

The former U.S. Navy range at Vieques Island (Puerto Rico, United States) is now the largest national wildlife refuge in the Caribbean. We investigated the geomorphology and benthic assemblage structure to understand the status of the coral reefs. Coral assemblages were quantified at 24 sites at Vieques and at 6 sites at St. Croix, U.S. Virgin Islands. These sites were chosen to represent the major zones of reef geomorphology. Sites consisted of two or three 21-m-long photo-quadrate belt transects. The results revealed surprisingly little differentiation in the coral assemblages within and between reefs of comparable geomorphological and oceanographic setting at Vieques and St. Croix. At Vieques, the Acropora palmata zone was almost completely lost, and it was severely reduced at St. Croix, presumably primarily due to diseases and hurricane impacts since the 1970s. Subtle, but nonsignificant, differences with respect to the nature of the shelf margin (north adjacent to the bank, south adjacent to the open sea) and depth zone were observed at Vieques. At St. Croix, benthic assemblages differed more between depth zones but not between north and south. Effects of natural disturbances were severe at Vieques, outweighing impacts of past military activity— which were present but not quantitatively discernible at our scale of sampling. Germs and storms, rather than bombs (and associated naval activities), primarily seem to have taken the worst toll on corals at both Vieques and St. Croix

Testing the Utility of Geochemical Proxies to Reconstruct Holocene Coastal Environments and Relative Sea Level: A Case Study from Hungry Bay, Bermuda

On low-lying, tropical and sub-tropical coastlines freshwater marshes may be replaced by salt-tolerant mangroves in response to relative sea-level rise. Pollen analysis of radiocarbon-dated sediment cores showed that such a change occurred in Hungry Bay, Bermuda during the late Holocene. This well-established paleoenvironmental trajectory provides an opportunity to explore if geochemical proxies (bulk-sediment δ13C and Rock-Eval pyrolysis) can reconstruct known environmental changes and relative sea level. We characterized surface sediment from depositional environments in Bermuda (freshwater wetlands, saline mangroves, and wrack composed of Sargassum natans macroalgae) using geochemical measurements and demonstrate that a multi-proxy approach can objectively distinguish among these environments. However, application of these techniques to the transgressive sediment succession beneath Hungry Bay suggests that freshwater peat and mangrove peat cannot be reliably distinguished in the sedimentary record, possibly because of post-depositional convergence of geochemical characteristics on decadal to multi-century timescales and/or the relatively small number of modern samples analyzed. Sediment that includes substantial contributions from Sargassum is readily identified by geochemistry, but has a limited spatial extent. Radiocarbon dating indicates that beginning at –700 CE, episodic marine incursions into Hungry Bay (e.g., during storms) carried Sargassum that accumulated as wrack and thickened through repeated depositional events until ~300 CE. It took a further ~550 years for a peat-forming mangrove community to colonize Hungry Bay, which then accumulated sediment rapidly, but likely out of equilibrium with regional relative sea-level rise

A pilot feasibility trial of alcohol screening and brief intervention in the police custody setting (ACCEPT): study protocol for a cluster randomised controlled trial

BACKGROUND: There is evidence of an association between alcohol use and offending behaviour and around a quarter of police time is spent on alcohol-related incidents. Police custody, therefore, provides an important opportunity to intervene. This pilot trial aims to investigate whether a definitive evaluation of screening and brief interventions aimed at reducing risky drinking in arrestees is acceptable and feasible in the custody suite setting. METHODS: Screening will be carried out by trained detention officers or drug and alcohol workers in four police forces across two geographical areas (North East and South West England). Detention officers (or drug and alcohol workers) will be cluster randomised to one of three conditions: screening only (control group), screening followed immediately by 10 min of manualised brief structured advice delivered by the individual responsible for screening (intervention 1) or screening followed by 10 min of manualised brief structured advice delivered by the individual responsible for screening plus the offer of a subsequent 20-min session of behaviour change counselling delivered by a trained alcohol health worker (intervention 2). Participants will be arrestees aged 18+ who screen positive on the Alcohol Use Disorders Identification Test. Participants will be followed up at 6 and 12 months post-intervention. An embedded qualitative process evaluation will explore acceptability of alcohol screening and brief intervention to staff and arrestees as well as facilitators and barriers to the delivery of such approaches in this setting. RESULTS: Recruitment is currently underway and due to end May 2015. CONCLUSION: Results from this pilot trial will determine if a definitive evaluation is possible in the future and will provide stakeholder input to its design. TRIAL REGISTRATION: Reference number: ISRCTN89291046

Agronomic Management of Indigenous Mycorrhizas

Many of the advantages conferred to plants by arbuscular mycorrhiza (AM) are associated to the ability of AM plants to explore a greater volume of soil through the extraradical mycelium. Sieverding (1991) estimates that for each centimetre of colonized root there is an increase of 15 cm3 on the volume of soil explored, this value can increase to 200 cm3 depending on the circumstances. Due to the enhancement of the volume of soil explored and the ability of the extraradical mycelium to absorb and translocate nutrients to the plant, one of the most obvious and important advantages resulting from mycorrhization is the uptake of nutrients. Among of which the ones that have immobilized forms in soil, such as P, assume particular significance. Besides this, many other benefits are recognized for AM plants (Gupta et al, 2000): water stress alleviation (Augé, 2004; Cho et al, 2006), protection from root pathogens (Graham, 2001), tolerance to toxic heavy metals and phytoremediation (Audet and Charest, 2006; Göhre and Paszkowski, 2006), tolerance to adverse conditions such as very high or low temperature, high salinity (Sannazzaro et al, 2006), high or low pH (Yano and Takaki, 2005) or better performance during transplantation shock (Subhan et al, 1998). The extraradical hyphae also stabilize soil aggregates by both enmeshing soil particles (Miller e Jastrow, 1992) and producing a glycoprotein, golmalin, which may act as a glue-like substance to adhere soil particles together (Wright and Upadhyaya, 1998). Despite the ubiquous distribution of mycorrhizal fungi (Smith and Read, 2000) and only a relative specificity between host plants and fungal isolates (McGonigle and Fitter, 1990), the obligate nature of the symbiosis implies the establishment of a plant propagation system, either under greenhouse conditions or in vitro laboratory propagation. These techniques result in high inoculum production costs, which still remains a serious problem since they are not competitive with production costs of phosphorus fertilizer. Even if farmers understand the significance of sustainable agricultural systems, the reduction of phosphorus inputs by using AM fungal inocula alone cannot be justified except, perhaps, in the case of high value crops (Saioto and Marumoto, 2002). Nurseries, high income horticulture farmers and no-agricultural application such as rehabilitation of degraded or devegetated landscapes are examples of areas where the use of commercial inoculum is current. Another serious problem is quality of commercial available products concerning guarantee of phatogene free content, storage conditions, most effective application methods and what types to use. Besides the information provided by suppliers about its inoculum can be deceiving, as from the usually referred total counts, only a fraction may be effective for a particular plant or in specific soil conditions. Gianinazzi and Vosátka (2004) assume that progress should be made towards registration procedures that stimulate the development of the mycorrhizal industry. Some on-farm inoculum production and application methods have been studied, allowing farmers to produce locally adapted isolates and generate a taxonomically diverse inoculum (Mohandas et al, 2004; Douds et al, 2005). However the inocula produced this way are not readily processed for mechanical application to the fields, being an obstacle to the utilization in large scale agriculture, especially row crops, moreover it would represent an additional mechanical operation with the corresponding economic and soil compaction costs. It is well recognized that inoculation of AM fungi has a potential significance in not only sustainable crop production, but also environmental conservation. However, the status quo of inoculation is far from practical technology that can be widely used in the field. Together a further basic understanding of the biology and diversity of AM fungi is needed (Abbott at al, 1995; Saito and Marumoto, 2002). Advances in ecology during the past decade have led to a much more detailed understanding of the potential negative consequences of species introductions and the potential for negative ecological consequences of invasions by mycorrhizal fungi is poorly understood. Schwartz et al, (2006) recommend that a careful assessment documenting the need for inoculation, and the likelihood of success, should be conducted prior to inoculation because inoculations are not universally beneficial. Agricultural practices such as crop rotation, tillage, weed control and fertilizer apllication all produce changes in the chemical, physical and biological soil variables and affect the ecological niches available for occupancy by the soil biota, influencing in different ways the symbiosis performance and consequently the inoculum development, shaping changes and upset balance of native populations. The molecular biology tools developed in the latest years have been very important for our perception of these changes, ensuing awareness of management choice implications in AM development. In this context, for extensive farming systems and regarding environmental and economic costs, the identification of agronomic management practices that allow controlled manipulation of the fungal community and capitalization of AM mutualistic effect making use of local inoculum, seem to be a wise option for mycorrhiza promotion and development of sustainable crop production

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts