Spatial contrasts in hepatic and biliary PAHs in Tilefish (Lopholatilus chamaeleonticeps) throughout the Gulf of Mexico, with comparison to the Northwest Atlantic

A multinational demersal longline survey was conducted on the Gulf of Mexico continental shelf over the years 2015 and 2016 to generate a Gulf-wide baseline of polycyclic aromatic hydrocarbon (PAH) concentrations in demersal fishes. Tilefish (Lopholatilus chamaeleonticeps) were sampled in all regions of the Gulf of Mexico for biometrics, bile, and liver. Tilefish liver was also obtained from surveys in the northwest Atlantic Ocean for comparison. Liver tissues (n ¼ 305) were analyzed for PAHs and select alkylated homologs using QuEChERS extractions and gas chromatography tandem mass spectrometry. Bile samples (n ¼ 225) were analyzed for biliary PAH metabolites using high-performance liquid chromatography with fluorescence detection. Spatial comparisons indicate the highest levels of PAH exposure and hepatic accumulation in the north central Gulf of Mexico, with decreasing concentrations moving from the north central Gulf counterclockwise, and an increase on the Yucatan Shelf. Hepatic PAH concentrations were similar between the Gulf of Mexico and the northwest Atlantic, however, Tilefish from the northwest Atlantic had higher concentrations and more frequent detection of carcinogenic high molecular weight PAHs. Overall, results demonstrate that PAH pollution was ubiquitous within the study regions, with recent exposure and hepatic accumulation observed in Tilefish from both the Gulf of Mexico and northwest Atlantic

Continental shelf seafloor mapping, benthic habitat surveys, and reef fish assessments in the eastern Gulf of Mexico

In April 2010, The Deepwater Horizon (DWH) oil spill originated in the deep sea 1,500 m below the ocean surface at the edge of the continental shelf off Louisiana. Surface and sub-surface dispersal of the oil eventually encompassed an area of over 200,000 km2. Impacts of DWH on biota of the Gulf of Mexico were severe, wide-spread, and are ongoing even a decade after the spill. Because of its offshore origin, the spill caused injury to many resources on the continental shelf, including important reef fish species (e.g., snappers and groupers, etc.) and protected species including sea turtles. Habitats which these species occupy were oiled which resulted in the loss of key supporting plant and animal species. Because so little of the offshore habitat of reef fish species and sea turtles was mapped and characterized prior to the spill, restoration efforts aimed at improving degraded habitats and strengthening species populations proved difficult. This project was specifically developed to discover additional, high conservation value, habitats of reef fishes and sea turtles on the continental shelf of the Gulf of Mexico off Florida (the West Florida Shelf, WFS). The goal of the project was to map such habitats and quantify the density and biodiversity of species occupying them, and to facilitate additional conservation management decisions to enhance their long-term sustainability. The project resulted in mapping and classifying and characterizing 2,350 km2 of heretofore unmapped habitats, the development of new methods to extrapolate habitat types from a sub-sample from video surveys, and new technologies to automate the counting and identification of fish species and habitat features using artificial intelligence. Project personnel have presented these materials to the competent management authorities responsible for fish and sea turtle management. Here we provide technical detail on the methods, procedures and findings from this project.Funded by the National Fish and Wildlife Foundation (NFWF) Gulf Environmental Benefit Fund (2015 - 2020

Polynomial-time equivalence testing for deterministic fresh-register automata

Register automata are one of the most studied automata models over infinite alphabets. The complexity of language equivalence for register automata is quite subtle. In general, the problem is undecidable but, in the deterministic case, it is known to be decidable and in NP. Here we propose a polynomial-time algorithm building upon automata- and group-theoretic techniques. The algorithm is applicable to standard register automata with a fixed number of registers as well as their variants with a variable number of registers and ability to generate fresh data values (fresh-register automata). To complement our findings, we also investigate the associated inclusion problem and show that it is PSPACE-complete

Why compare marine ecosystems?

This paper is not subject to U.S. copyright. The definitive version was published in ICES Journal of Marine Science: Journal du Conseil 67 (2010): 1-9, doi:10.1093/icesjms/fsp221.Effective marine ecosystem-based management (EBM) requires understanding the key processes and relationships controlling the aspects of biodiversity, productivity, and resilience to perturbations. Unfortunately, the scales, complexity, and non-linear dynamics that characterize marine ecosystems often confound managing for these properties. Nevertheless, scientifically derived decision-support tools (DSTs) are needed to account for impacts resulting from a variety of simultaneous human activities. Three possible methodologies for revealing mechanisms necessary to develop DSTs for EBM are: (i) controlled experimentation, (ii) iterative programmes of observation and modelling ("learning by doing"), and (iii) comparative ecosystem analysis. We have seen that controlled experiments are limited in capturing the complexity necessary to develop models of marine ecosystem dynamics with sufficient realism at appropriate scales. Iterative programmes of observation, model building, and assessment are useful for specific ecosystem issues but rarely lead to generally transferable products. Comparative ecosystem analyses may be the most effective, building on the first two by inferring ecosystem processes based on comparisons and contrasts of ecosystem response to human-induced factors. We propose a hierarchical system of ecosystem comparisons to include within-ecosystem comparisons (utilizing temporal and spatial changes in relation to human activities), within-ecosystem-type comparisons (e.g. coral reefs, temperate continental shelves, upwelling areas), and cross-ecosystem-type comparisons (e.g. coral reefs vs. boreal, terrestrial vs. marine ecosystems). Such a hierarchical comparative approach should lead to better understanding of the processes controlling biodiversity, productivity, and the resilience of marine ecosystems. In turn, better understanding of these processes will lead to the development of increasingly general laws, hypotheses, functional forms, governing equations, and broad interpretations of ecosystem responses to human activities, ultimately improving DSTs in support of EBM

MultiscaleDTM : an open‐source R package for multiscale geomorphometric analysis

Digital terrain models (DTMs) are datasets containing altitude values above or below a reference level, such as a reference ellipsoid or a tidal datum over geographic space, often in the form of a regularly gridded raster. They can be used to calculate terrain attributes that describe the shape and characteristics of topographic surfaces. Calculating these terrain attributes often requires multiple software packages that can be expensive and specialized. We have created a free, open‐source R package, MultiscaleDTM , that allows for the calculation of members from each of the five major thematic groups of terrain attributes: slope, aspect, curvature, relative position, and roughness, from a regularly gridded DTM. Furthermore, these attributes can be calculated at multiple spatial scales of analysis, a key feature that is missing from many other packages. Here, we demonstrate the functionality of the package and provide a simulation exploring the relationship between slope and roughness. When roughness measures do not account for slope, these attributes exhibit a strong positive correlation. To minimize this correlation, we propose a new roughness measure called adjusted standard deviation. In most scenarios tested, this measure produced the lowest rank correlation with slope out of all the roughness measures tested. Lastly, the simulation shows that some existing roughness measures from the literature that are supposed to be independent of slope can actually exhibit a strong inverse relationship with the slope in some cases

Female rats display higher methamphetamine-primed reinstatement and c-Fos immunoreactivity than male rats

Methamphetamine (meth) dependence is often characterized by persistent and chronic relapse (i.e., return to drug use). Previous work suggests females may be at greater risk to relapse. In this study, we extended this limited evidence and identified sex-dependent neural substrates related to meth-triggered reinstatement. Male and female Sprague-Dawley rats were implanted with indwelling jugular catheters. Half of the rats were then trained to self-administer meth (0.05 mg/kg/inf); the other half self-administered saline during 21 daily sessions (2 h). Rats were then given 12 extinction sessions. Twenty-four hours after the last extinction session, rats received reinstatement testing. Half of the rats received a meth-prime (0.3 mg/kg, IP) injection and the remaining rats received a saline injection. This design resulted in 4 separate groups for each sex, allowing for careful investigation of brain regions related to meth-triggered reinstatement. Brains were harvested following the reinstatement session and c-Fos immunoreactivity was measured in multiple brain regions. Meth triggered reinstatement in both sexes and this effect was more robust in females compared to males. Significant sex differences were detected. Females showed greater c-Fos immunoreactivity in the cingulate cortex area 1, lateral orbitofrontal cortex, prelimbic cortex, caudate-putamen, nucleus accumbens core and shell, and central nucleus of the amygdala following meth-primed reinstatement

Solutions for Recovering and Sustaining the Bounty of the Ocean Combining Fishery Reforms, Rights-Based Fisheries Management, and Marine Reserves

Food security, economic opportunities, and other benefits provided by a healthy ocean are in jeopardy because of years of overexploitation of many fisheries, and the challenges will intensify in many locales as climate and the environment continue to change. The good news is that solutions are gaining traction. Mandates to end overfishing that use scientifically determined catch limits and rights-based approaches to fishery management have produced impressive results in ending overfishing and recovering depleted stocks. Similarly, spatial protections, such as fully protected marine reserves, are increasing the diversity, size, and abundance of species within reserves; some of that bounty reaches fished areas outside of them. We review the effects of combining catch limits, rights-based fisheries approaches, and establishment of marine reserves and discuss additional advantages of these combined solutions in securing sustainable and profitable fisheries, community goals, and healthy ecosystems. This paper highlights the contribution of emerging science-based solutions and the steps needed to replicate and scale these successes. Triple-wins for the environment, the economy, and society can be achieved through integrated fisheries management and protection as conscious steps toward reversing the current degradation of our ocean’s living resources.This manuscript is based on a keynote lecture given by Jane Lubchenco at One Planet, One Ocean: The 2nd International Ocean Research Conference, Barcelona, Spain, November 17–21, 2014. This is the publisher’s final pdf. The published article is copyrighted by the Oceanography Society and can be found at: http://www.tos.org/oceanography/archive/28-2_barner.htm

Vulnerability and resilience of living marine resources to the Deepwater Horizon oil spill : an overview

Funding for the project was primarily provided by the Gulf of Mexico Research Initiative through several of its research centers.The 2010 Deepwater Horizon (DWH) oil well blowout in the Gulf of Mexico (GoM) was the largest and perhaps most consequential accidental marine oil spill in global history. This paper provides an overview of a Research Topic consisting of four additional papers that: (1) assemble time series data for ecosystem components in regions impacted by the spill, and (2) interpret temporal changes related to the vulnerability of species and ecosystems to DWH and the ensuing resilience to perturbation. Time series abundance data for many taxa pre-date DWH, often by decades, thus allowing an assessment of population- and community-level impacts. We divided the north central GoM into four interconnected “eco-types”: the coastal/nearshore, continental shelf, open-ocean pelagic and deep benthic. Key taxa in each eco-type were evaluated for their vulnerability to the circumstances of the DWH spill based on population overlap with oil, susceptibility to oil contamination, and other factors, as well their imputed resilience to population-level impacts, based on life history metrics, ecology and post-spill trajectories. Each taxon was scored as low, medium, or high for 13 vulnerability attributes and 11 resilience attributes to produce overall vulnerability and resilience scores, which themselves were also categorical (i.e., low, medium, or high). The resulting taxon-specific V-R scores provide important guidance on key species to consider and monitor in the event of future spills similar to DWH. Similar analyses may also guide resource allocation to collect baseline data on highly vulnerable taxa or those with low resilience potential in other ecosystems. For some species, even a decade of observation has been insufficient to document recovery given chronic, long-term exposure to DWH oil remaining in all eco-types and because of impacts to the reproductive output of long-lived species. Due to the ongoing threats of deep-water blowouts, continued surveillance of populations affected by DWH is warranted to document long-term recovery or change in system state. The level of population monitoring in the open-ocean and deep benthic eco-types has historically been low and is inconsistent with the continued migration of the oil industry to the ultra-deep (≥1,500 m) where the majority of leasing, exploration, and production now occurs.Publisher PDFPeer reviewe

Marine Fisheries Stock Assessment Improvement Plan: report of the National Marine Fisheries Service National Task Force for Improving Fish Stock Assessments

This report argues for greatly increased resources in terms of data collection facilities and staff to collect, process, and analyze the data, and to communicate the results, in order for NMFS to fulfill its mandate to conserve and manage marine resources. In fact, the authors of this report had great difficulty defining the "ideal" situation to which fisheries stock assessments and management should aspire. One of the primary objectives of fisheries management is to develop sustainable harvest policies that minimize the risks of overfishing both target species and associated species. This can be achieved in a wide spectrum of ways, ranging between the following two extremes. The first is to implement only simple management measures with correspondingly simple assessment demands, which will usually mean setting fishing mortality targets at relatively low levels in order to reduce the risk of unknowingly overfishing or driving ecosystems towards undesirable system states. The second is to expand existing data collection and analysis programs to provide an adequate knowledge base that can support higher fishing mortality targets while still ensuring low risk to target and associated species and ecosystems. However, defining "adequate" is difficult, especially when scientists have not even identified all marine species, and information on catches, abundances, and life histories of many target species, and most associated species, is sparse. Increasing calls from the public, stakeholders, and the scientific community to implement ecosystem-based stock assessment and management make it even more difficult to define "adequate," especially when "ecosystem-based management" is itself not well-defined. In attempting to describe the data collection and assessment needs for the latter, the authors took a pragmatic approach, rather than trying to estimate the resources required to develop a knowledge base about the fine-scale detailed distributions, abundances, and associations of all marine species. Thus, the specified resource requirements will not meet the expectations of some stakeholders. In addition, the Stock Assessment Improvement Plan is designed to be complementary to other related plans, and therefore does not duplicate the resource requirements detailed in those plans, except as otherwise noted