Seafloor Segmentation Based on Bathymetric Measurements from Multibeam Echosounders Data

Bathymetric data depicts the geomorphology of the seabottom and allows characterization of spatial distributions of apparent benthic habitats. The variability of seafloor topography can be defined as a texture. This prompts for the application of well developed image processing techniques for automatic delineation of regions with clucially different physiographic characteristics. In the present paper histograms of biologically motivated invariant image attributes are used for characterization of local geomorphological feahires. This technique can be naturally applied in a range of spatial scales. Local feature vectors are then submitted to a procedure which divides the set into a number of clusters each representing a distinct type of the seafloor. Prior knowledge about benthic habitat locations allows the use of supervised classification, by training a Suppolt Vector Machine on a chosen data set, and then applying the developed model to a full set. The classification method is shown to perform well on the multibeam echosounder (MBES) data from Piscataqua River, New Hampshire, USA

Sensor-assisted Video Mapping of the Seafloor

In recent years video surveys have become an increasingly important ground-truthing of acousticseafloor characterization and benthic habitat mapping studies. However, the ground-truthing and detailed characterization provided by video are still typically done using sparse sample imagery supplemented by physical samples. Combining single video frames in a seamless mosaic can provide a tool by which imagery has significant areal coverage, while at the same time showing small fauna and biological features at mm resolution. The generation of such a mosaic is a challenging task due to height variations of the imaged terrain and decimeter scale knowledge of camera position. This paper discusses the current role of underwater video survey, and the potential for generating consistent, quantitative image maps using video data, accompanied by data that can be measured by auxiliary sensors with sufficient accuracy, such as camera tilt and heading, and their use in automated mosaicking techniques. The camera attitude data also provide the necessary information to support the development of a video collage. The collage provides a quick look at the large spatial scale features in a scene and can be used to pinpoint regions that are likely to yield useful information when rendered into high-resolution mosaics. It is proposed that high quality mosaics can be produced using consumer-grade cameras and low-cost sensors, thereby allowing for the economical scientific video surveys. A case study is presented with the results from benthic habitat mapping and the ground-truthing ofseafloor acoustic data using both real underwater imagery and simulations. A computer modeling of the process of video data acquisition (in particular on a non-flat terrain) allows for a better understanding of the main sources of error in mosaic generation and for the choice of near-optimal processing strategies. Various spatial patterns of video survey coverage are compared and it is shown that some patterns have certain advantages in the sense of accumulated error and overall mosaic accuracy

Divergent responses of Atlantic coastal and oceanic Synechococcus to iron limitation

Author Posting. © The Author(s), 2015. This is the author's version of the work. It is posted here by permission of National Academy of Sciences for personal use, not for redistribution. The definitive version was published in Proceedings of the National Academy of Sciences of the United States of America 112 (2015): 9944-9949, doi:10.1073/pnas.1509448112.Marine Synechococcus are some of the most diverse and ubiquitous phytoplankton, and iron (Fe) is an essential micronutrient that limits productivity in many parts of the ocean. To investigate how coastal and oceanic Atlantic Synechococcus strains acclimate to Fe availability, we compared the growth, photophysiology, and quantitative proteomics of two Synechococcus strains from different Fe regimes. Synechococcus strain WH8102, from a region in the southern Sargasso Sea that receives substantial dust deposition, showed impaired growth and photophysiology as Fe declined, yet utilized few acclimation responses. Coastal WH8020, from the dynamic, seasonally variable New England shelf, displayed a multi-tiered, hierarchical cascade of acclimation responses with different Fe thresholds. The multi-tiered response included changes in Fe acquisition, storage, and photosynthetic proteins, substitution of flavodoxin for ferredoxin, and modified photophysiology, all while maintaining remarkably stable growth rates over a range of Fe concentrations. Modulation of two distinct ferric uptake regulator (Fur) proteins that coincided with the multi-tiered proteome response was found, implying the coastal strain has different regulatory threshold responses to low Fe availability. Low nitrogen (N) and phosphorus (P) availability in the open ocean may favor the loss of Fe response genes when Fe availability is consistent over time, whereas these genes are retained in dynamic environments where Fe availability fluctuates and N and P are more abundant.This work was supported by a National Science Foundation Postdoctoral Research Fellowship in Biology to K.R.M.M. (NSF 1103575), National Science Foundation Oceanography grants OCE-1220484, OCE-0928414, OCE-1233261, OCE- 1155566, OCE-1131387, and OCE-0926092, as well as Gordon and Betty Moore Foundation grants 3782 and 3934

Divergent Responses of Atlantic Coastal and Oceanic Synechococcus to Iron Limitation

Marine Synechococcus are some of the most diverse and ubiquitous phytoplankton, and iron (Fe) is an essential micronutrient that limits productivity in many parts of the ocean. To investigate how coastal and oceanic Atlantic Synechococcus strains acclimate to Fe availability, we compared the growth, photophysiology, and quantitative proteomics of two Synechococcus strains from different Fe regimes. Synechococcus strain WH8102, from a region in the southern Sargasso Sea that receives substantial dust deposition, showed impaired growth and photophysiology as Fe declined, yet used few acclimation responses. Coastal WH8020, from the dynamic, seasonally variable New England shelf, displayed a multitiered, hierarchical cascade of acclimation responses with different Fe thresholds. The multitiered response included changes in Fe acquisition, storage, and photosynthetic proteins, substitution of flavodoxin for ferredoxin, and modified photophysiology, all while maintaining remarkably stable growth rates over a range of Fe concentrations. Modulation of two distinct ferric uptake regulator (Fur) proteins that coincided with the multitiered proteome response was found, implying the coastal strain has different regulatory threshold responses to low Fe availability. Low nitrogen (N) and phosphorus (P) availability in the open ocean may favor the loss of Fe response genes when Fe availability is consistent over time, whereas these genes are retained in dynamic environments where Fe availability fluctuates and N and P are more abundant

Trust, morality and altruism in the donation of biological material : the case of Portugal

This paper examines a number of social, ethical and cultural issues related to the application of biotechnology. The focus of the paper relies on two different cases of governing biotechnology in Portugal, referring to donation of biological material: the act of donation of eggs and sperm; and volunteers for donation of DNA material for the forensic national DNA database. We analyze the discourses on donation of biological material framing them in rhetorical devices of gift, altruism, informed consent and social responsibility. This comes blended with still unclear and emergent regulation and policies of access, retention, preservation and governing of biological material and of donors’ identification. The risks are mitigated by narratives of science and technology as social progress and providers of public good and health benefits, as well as by underlining the individual responsibility in this domain and by reinforcing the rhetoric of gene quality, based on socio-cultural and bio-genetic criteria

Hydrographic Observations During the 2002 IOC Contaminant Baseline Survey in the Western Pacific Ocean

The 2002 IOC Contaminant Baseline Survey in the western Pacific Ocean was the fourth in a series of cruises intended to establish the contemporary concentrations of trace elements and other materials in the major water masses of the ocean and to illuminate the pathways by which materials delivered to the surface ocean are incorporated in the subsurface waters. The expedition occupied 9 vertical profile stations encompassing the subtropical and subarctic gyre of the western North Pacific. In addition, underway surface water samples were collected during transits between the stations. This paper uses the temperature, salinity, nutrient, oxygen, and chlorophyll data to set the hydrographic and biological background for the other papers in this theme

Study protocol: improving cognition in people with progressive multiple sclerosis: a multi-arm, randomized, blinded, sham-controlled trial of cognitive rehabilitation and aerobic exercise (COGEx)

Background: Cognitive dysfunction affects up to 70% of people with progressive MS (PMS). It can exert a deleterious effect on activities of daily living, employment and relationships. Preliminary evidence suggests that performance can improve with cognitive rehabilitation (CR) and aerobic exercise (EX), but existing data are predominantly from people with relapsing-remitting MS without cognitive impairment. There is therefore a need to investigate whether this is also the case in people with progressive forms of the disease who have objectively identified cognitive impairment. It is hypothesized that CR and EX are effective treatments for people with PMS who have cognitive impairment, in particular processing speed (PS) deficits, and that a combination of these two treatments is more effective than each individual treatment given alone. We further hypothesize that improvements in PS will be associated with modifications of functional and/or structural plasticity within specific brain networks/regions involved in PS measured with advanced MRI techniques. Methods: This study is a multisite, randomized, double-blinded, sham controlled clinical trial of CR and aerobic exercise. Three hundred and sixty subjects from 11 sites will be randomly assigned into one of four groups: CR plus aerobic exercise; CR plus sham exercise; CR sham plus aerobic exercise and CR sham plus sham exercise. Subjects will participate in the assigned treatments for 12 weeks, twice a week. All subjects will have a cognitive and physical assessment at baseline, 12 weeks and 24 weeks. In an embedded sub-study, approximately 30% of subjects will undergo structural and functional MRI to investigate the neural mechanisms underlying the behavioral response. The primary outcome is the Symbol Digit Modalities Test (SDMT) measuring PS. Secondary outcome measures include: indices of verbal and non-verbal memory, depression, walking speed and a dual cognitive-motor task and MRI. Discussion: The study is being undertaken in 6 countries (11 centres) in multiple languages (English, Italian, Danish, Dutch); with testing material validated and standardized in these languages. The rationale for this approach is to obtain a robustly powered sample size and to demonstrate that these two interventions can be given effectively in multiple countries and in different languages. Trial registration: The trial was registered on September 20th 2018 at www.clinicaltrials.gov having identifier NCT03679468. Registration was performed before recruitment was initiated

Mammography Facility Characteristics Associated With Interpretive Accuracy of Screening Mammography

BackgroundAlthough interpretive performance varies substantially among radiologists, such variation has not been examined among mammography facilities. Understanding sources of facility variation could become a foundation for improving interpretive performance.MethodsIn this cross-sectional study conducted between 1996 and 2002, we surveyed 53 facilities to evaluate associations between facility structure, interpretive process characteristics, and interpretive performance of screening mammography (ie, sensitivity, specificity, positive predictive value [PPV1], and the likelihood of cancer among women who were referred for biopsy [PPV2]). Measures of interpretive performance were ascertained prospectively from mammography interpretations and cancer data collected by the Breast Cancer Surveillance Consortium. Logistic regression and receiver operating characteristic (ROC) curve analyses estimated the association between facility characteristics and mammography interpretive performance or accuracy (area under the ROC curve [AUC]). All P values were two-sided.ResultsOf the 53 eligible facilities, data on 44 could be analyzed. These 44 facilities accounted for 484 463 screening mammograms performed on 237 669 women, of whom 2686 were diagnosed with breast cancer during follow-up. Among the 44 facilities, mean sensitivity was 79.6% (95% confidence interval [CI] = 74.3% to 84.9%), mean specificity was 90.2% (95% CI = 88.3% to 92.0%), mean PPV1 was 4.1% (95% CI = 3.5% to 4.7%), and mean PPV2 was 38.8% (95% CI = 32.6% to 45.0%). The facilities varied statistically significantly in specificity (P < .001), PPV1 (P < .001), and PPV2 (P = .002) but not in sensitivity (P = .99). AUC was higher among facilities that offered screening mammograms alone vs those that offered screening and diagnostic mammograms (0.943 vs 0.911, P = .006), had a breast imaging specialist interpreting mammograms vs not (0.932 vs 0.905, P = .004), did not perform double reading vs independent double reading vs consensus double reading (0.925 vs 0.915 vs 0.887, P = .034), or conducted audit reviews two or more times per year vs annually vs at an unknown frequency (0.929 vs 0.904 vs 0.900, P = .018).ConclusionMammography interpretive performance varies statistically significantly by facility