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  • Molecular Diversity Preservation International  (56,267)
  • Institute of Electrical and Electronics Engineers (IEEE)  (26,651)
  • Frontiers Media
  • 2020-2022
  • 2015-2019  (98,772)
  • 1945-1949
  • 2017  (57,144)
  • 2016  (41,628)
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  • 2020-2022
  • 2015-2019  (98,772)
  • 1945-1949
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  • 1
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    Bacterial biogeography across the Amazon river-ocean continuum (2017)
    Frontiers Media
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 8 (2017): 882, doi:10.3389/fmicb.2017.00882.
    Description: Spatial and temporal patterns in microbial biodiversity across the Amazon river-ocean continuum were investigated along ∼675 km of the lower Amazon River mainstem, in the Tapajós River tributary, and in the plume and coastal ocean during low and high river discharge using amplicon sequencing of 16S rRNA genes in whole water and size-fractionated samples (0.2–2.0 μm and 〉2.0 μm). River communities varied among tributaries, but mainstem communities were spatially homogeneous and tracked seasonal changes in river discharge and co-varying factors. Co-occurrence network analysis identified strongly interconnected river assemblages during high (May) and low (December) discharge periods, and weakly interconnected transitional assemblages in September, suggesting that this system supports two seasonal microbial communities linked to river discharge. In contrast, plume communities showed little seasonal differences and instead varied spatially tracking salinity. However, salinity explained only a small fraction of community variability, and plume communities in blooms of diatom-diazotroph assemblages were strikingly different than those in other high salinity plume samples. This suggests that while salinity physically structures plumes through buoyancy and mixing, the composition of plume-specific communities is controlled by other factors including nutrients, phytoplankton community composition, and dissolved organic matter chemistry. Co-occurrence networks identified interconnected assemblages associated with the highly productive low salinity near-shore region, diatom-diazotroph blooms, and the plume edge region, and weakly interconnected assemblages in high salinity regions. This suggests that the plume supports a transitional community influenced by immigration of ocean bacteria from the plume edge, and by species sorting as these communities adapt to local environmental conditions. Few studies have explored patterns of microbial diversity in tropical rivers and coastal oceans. Comparison of Amazon continuum microbial communities to those from temperate and arctic systems suggest that river discharge and salinity are master variables structuring a range of environmental conditions that control bacterial communities across the river-ocean continuum.
    Description: This research is funded by the Gordon and Betty Moore Foundation (GBMF 2293 and 2928), the U.S. National Science Foundation (OCE-0934095, OCE-0424602, DEB-1256724), and the São Paulo Research Foundation (FAPESP 12/51187-0).
    Keywords: Amazon River ; Tropical Atlantic Ocean ; River plume ; Microbial diversity ; Freshwater bacteria ; Marine bacteria ; Diatom-diazotroph assemblage ; Columbia River
    Repository Name: Woods Hole Open Access Server
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    Seasonal succession and spatial patterns of Synechococcus microdiversity in a salt marsh estuary revealed through 16S rRNA gene oligotyping (2017)
    Frontiers Media
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 8 (2017): 1496, doi:10.3389/fmicb.2017.01496.
    Description: Synechococcus are ubiquitous and cosmopolitan cyanobacteria that play important roles in global productivity and biogeochemical cycles. This study investigated the fine scale microdiversity, seasonal patterns, and spatial distributions of Synechococcus in estuarine waters of Little Sippewissett salt marsh (LSM) on Cape Cod, MA. The proportion of Synechococcus reads was higher in the summer than winter, and higher in coastal waters than within the estuary. Variations in the V4–V6 region of the bacterial 16S rRNA gene revealed 12 unique Synechococcus oligotypes. Two distinct communities emerged in early and late summer, each comprising a different set of statistically co-occurring Synechococcus oligotypes from different clades. The early summer community included clades I and IV, which correlated with lower temperature and higher dissolved oxygen levels. The late summer community included clades CB5, I, IV, and VI, which correlated with higher temperatures and higher salinity levels. Four rare oligotypes occurred in the late summer community, and their relative abundances more strongly correlated with high salinity than did other co-occurring oligotypes. The analysis revealed that multiple, closely related oligotypes comprised certain abundant clades (e.g., clade 1 in the early summer and clade CB5 in the late summer), but the correlations between these oligotypes varied from pair to pair, suggesting they had slightly different niches despite being closely related at the clade level. Lack of tidal water exchange between sampling stations gave rise to a unique oligotype not abundant at other locations in the estuary, suggesting physical isolation plays a role in generating additional microdiversity within the community. Together, these results contribute to our understanding of the environmental and ecological factors that influence patterns of Synechococcus microbial community composition over space and time in salt marsh estuarine waters.
    Description: This work was supported through a subcontract from the Woods Hole Center for Oceans and Human Health, from the National Institutes of Health and the National Science Foundation (NIH/NIEHS 1 P50 ES012742-01 and NSF/OCE 0430724), a National Research Council Research Associateship Award and L'Oreal USA Fellowship (JH), an Alfred P. Sloan Research Fellowship in Ocean Sciences and the Clare Boothe Luce Program (KM), NASA Astrobiology Institute Cooperative Agreement NNA04CC04A (MS), the Alfred P. Sloan Foundation's ICoMM field project, and the W. M. Keck Foundation.
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    Forecasting the seasonal timing of Maine's lobster fishery (2017)
    Frontiers Media
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Marine Science 4 (2017): 337, doi:10.3389/fmars.2017.00337.
    Description: The fishery for American lobster is currently the highest-valued commercial fishery in the United States, worth over US$620 million in dockside value in 2015. During a marine heat wave in 2012, the fishery was disrupted by the early warming of spring ocean temperatures and subsequent influx of lobster landings. This situation resulted in a price collapse, as the supply chain was not prepared for the early and abundant landings of lobsters. Motivated by this series of events, we have developed a forecast of when the Maine (USA) lobster fishery will shift into its high volume summer landings period. The forecast uses a regression approach to relate spring ocean temperatures derived from four NERACOOS buoys along the coast of Maine to the start day of the high landings period of the fishery. Tested against conditions in past years, the forecast is able to predict the start day to within 1 week of the actual start, and the forecast can be issued 3–4 months prior to the onset of the high-landings period, providing valuable lead-time for the fishery and its associated supply chain to prepare for the upcoming season. Forecast results are conveyed in a probabilistic manner and are updated weekly over a 6-week forecasting period so that users can assess the certainty and consistency of the forecast and factor the uncertainty into their use of the information in a given year. By focusing on the timing of events, this type of seasonal forecast provides climate-relevant information to users at time scales that are meaningful for operational decisions. As climate change alters seasonal phenology and reduces the reliability of past experience as a guide for future expectations, this type of forecast can enable fishing industry participants to better adjust to and prepare for operating in the context of climate change.
    Description: This forecast was initiated with support from NSF Coastal SEES (OCE 1325484) and was developed with funds from NASA EPSCoR through Maine Space Grant Consortium (EP-15-03).
    Keywords: Seasonal forecast ; Temperature ; Fishery landings ; Lobster fishery ; Climate variability
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    Seasonal succession of free-living bacterial communities in coastal waters of the Western Antarctic Peninsula (2016)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 7 (2016): 1731, doi: 10.3389/fmicb.2016.01731.
    Description: The marine ecosystem along the Western Antarctic Peninsula undergoes a dramatic seasonal transition every spring, from almost total darkness to almost continuous sunlight, resulting in a cascade of environmental changes, including phytoplankton blooms that support a highly productive food web. Despite having important implications for the movement of energy and materials through this ecosystem, little is known about how these changes impact bacterial succession in this region. Using 16S rRNA gene amplicon sequencing, we measured changes in free-living bacterial community composition and richness during a 9-month period that spanned winter to the end of summer. Chlorophyll a concentrations were relatively low until summer when a major phytoplankton bloom occurred, followed 3 weeks later by a high peak in bacterial production. Richness in bacterial communities varied between ~1,200 and 1,800 observed operational taxonomic units (OTUs) before the major phytoplankton bloom (out of ~43,000 sequences per sample). During peak bacterial production, OTU richness decreased to ~700 OTUs. The significant decrease in OTU richness only lasted a few weeks, after which time OTU richness increased again as bacterial production declined toward pre-bloom levels. OTU richness was negatively correlated with bacterial production and chlorophyll a concentrations. Unlike the temporal pattern in OTU richness, community composition changed from winter to spring, prior to onset of the summer phytoplankton bloom. Community composition continued to change during the phytoplankton bloom, with increased relative abundance of several taxa associated with phytoplankton blooms, particularly Polaribacter. Bacterial community composition began to revert toward pre-bloom conditions as bacterial production declined. Overall, our findings clearly demonstrate the temporal relationship between phytoplankton blooms and seasonal succession in bacterial growth and community composition. Our study highlights the importance of high-resolution time series sampling, especially during the relatively under-sampled Antarctic winter and spring, which enabled us to discover seasonal changes in bacterial community composition that preceded the summertime phytoplankton bloom.
    Description: CL was partially funded by the Graduate School and the Department of Ecology and Evolutionary Biology at Brown University and the Brown University-Marine Biological Laboratory Joint Graduate Program. This material is based upon work supported by the National Science Foundation under Grant Nos. ANT-1142114 to LA-Z, OPP-0823101 and PLR-1440435 to HD, and ANT-1141993 to JR.
    Keywords: 16S rRNA gene ; Ecological succession ; Antarctica ; Bacterial production ; Bacterial community composition ; Polaribacter ; Pelagibacter ubique (SAR11) ; Rhodobacteraceae
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    A few Pseudomonas oligotypes dominate in the meat and dairy processing environment (2017)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 8 (2017): 264, doi:10.3389/fmicb.2017.00264.
    Description: The occurrence of bacteria in the food processing environments plays a key role in food contamination and development of spoilage. Species of the genus Pseudomonas are recognized as major food spoilers and the capability to actually determine spoilage can be species- as well as strain-dependent. In order to improve the taxonomic resolution of 16S rRNA gene amplicons, in this study we used oligotyping to investigate the diversity of Pseudomonas populations in meat and dairy processing environments. Sequences of the V1–V3 regions from previous studies were used, including environmental swabs and food samples from both meat and dairy processing plants. We showed that the most frequently found oligotypes belonged to Pseudomonas fragi and P. fluorescens, that the most abundant oligotypes co-occurred, and were shared between the meat and dairy datasets. All the oligotypes occurring in foods were also identified in the environmental samples of the corresponding plants, highlighting the important role of the environment as a source of strains for food contamination. Oligotypes of the same species showed different levels depending on food processing and type of sample, suggesting that different strains of the same species can have different adaptation efficiency, leading to resilient bacterial associations.
    Keywords: Pseudomonas fragi ; Food contamination ; Food processing environment ; Oligotyping ; 16S rRNA gene sequencing
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    Underwater ambient noise in a baleen whale migratory habitat off the Azores (2017)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Marine Science 4 (2017): 109, doi:10.3389/fmars.2017.00109.
    Description: Assessment of underwater noise is of particular interest given the increase in noise-generating human activities and the potential negative effects on marine mammals which depend on sound for many vital processes. The Azores archipelago is an important migratory and feeding habitat for blue (Balaenoptera musculus), fin (Balaenoptera physalus) and sei whales (Balaenoptera borealis) en route to summering grounds in northern Atlantic waters. High levels of low frequency noise in this area could displace whales or interfere with foraging behavior, impacting energy intake during a critical stage of their annual cycle. In this study, bottom-mounted Ecological Acoustic Recorders were deployed at three Azorean seamounts (Condor, Açores, and Gigante) to measure temporal variations in background noise levels and ship noise in the 18–1,000 Hz frequency band, used by baleen whales to emit and receive sounds. Monthly average noise levels ranged from 90.3 dB re 1 μPa (Açores seamount) to 103.1 dB re 1 μPa (Condor seamount) and local ship noise was present up to 13% of the recording time in Condor. At this location, average contribution of local boat noise to background noise levels is almost 10 dB higher than wind contribution, which might temporally affect detection ranges for baleen whale calls and difficult communication at long ranges. Given the low time percentatge with noise levels above 120 dB re 1 μPa found here (3.3% at Condor), we woud expect limited behavioral responses to ships from baleen whales. Sound pressure levels measured in the Azores are lower than those reported for the Mediterranean basin and the Strait of Gibraltar. However, the currently unknown effects of baleen whale vocalization masking and the increasing presence of boats at the monitored sites underline the need for continuous monitoring to understand any long-term impacts on whales.
    Description: Fundação para a Ciência e a Tecnologia (FCT) and Fundo Regional da Ciência e Tecnologia (FRCT), through research projects TRACE (PTDC/MAR/74071/2006), MAPCET (M2.1.2/F/012/2011), and FCT Exploratory project (IF/00943/2013/CP1199/CT0001), supported by funds from FEDER, the Competitiveness Factors Operational (COMPETE), QREN, POPH, European Social Fund, Portuguese Ministry for Science and Education, and Proconvergencia Açores/EU Program. We also acknowledge funds provided by FCT to MARE, through the strategic project UID/MAR/04292/2013, that also supported fees for this open access publication. MR is supported by a DRCT doctoral grant (M3.1.a/F/028/2015), IC was supported by a FCT doctoral grant (SFRH/BD/41192/2007) and MAS is supported by an FCT-Investigator contract (IF/00943/2013).
    Keywords: Underwater noise ; Ship noise ; Baleen whales ; MSFD ; Open ocean environment
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    Comparative genomic analysis of the class Epsilonproteobacteria and proposed reclassification to Epsilonbacteraeota (phyl. nov.) (2017)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 8 (2017): 682, doi:10.3389/fmicb.2017.00682.
    Description: The Epsilonproteobacteria is the fifth validly described class of the phylum Proteobacteria, known primarily for clinical relevance and for chemolithotrophy in various terrestrial and marine environments, including deep-sea hydrothermal vents. As 16S rRNA gene repositories have expanded and protein marker analysis become more common, the phylogenetic placement of this class has become less certain. A number of recent analyses of the bacterial tree of life using both 16S rRNA and concatenated marker gene analyses have failed to recover the Epsilonproteobacteria as monophyletic with all other classes of Proteobacteria. In order to address this issue, we investigated the phylogenetic placement of this class in the bacterial domain using 16S and 23S rRNA genes, as well as 120 single-copy marker proteins. Single- and concatenated-marker trees were created using a data set of 4,170 bacterial representatives, including 98 Epsilonproteobacteria. Phylogenies were inferred under a variety of tree building methods, with sequential jackknifing of outgroup phyla to ensure robustness of phylogenetic affiliations under differing combinations of bacterial genomes. Based on the assessment of nearly 300 phylogenetic tree topologies, we conclude that the continued inclusion of Epsilonproteobacteria within the Proteobacteria is not warranted, and that this group should be reassigned to a novel phylum for which we propose the name Epsilonbacteraeota (phyl. nov.). We further recommend the reclassification of the order Desulfurellales (Deltaproteobacteria) to a novel class within this phylum and a number of subordinate changes to ensure consistency with the genome-based phylogeny. Phylogenomic analysis of 658 genomes belonging to the newly proposed Epsilonbacteraeota suggests that the ancestor of this phylum was an autotrophic, motile, thermophilic chemolithotroph that likely assimilated nitrogen from ammonium taken up from the environment or generated from environmental nitrate and nitrite by employing a variety of functional redox modules. The emergence of chemoorganoheterotrophic lifestyles in several Epsilonbacteraeota families is the result of multiple independent losses of various ancestral chemolithoautotrophic pathways. Our proposed reclassification of this group resolves an important anomaly in bacterial systematics and ensures that the taxonomy of Proteobacteria remains robust, specifically as genome-based taxonomies become more common.
    Description: The study was supported by a Discovery Outstanding Researcher Award (DP120103498) and an Australian Laureate Fellowship (FL150100038) from the Australian Research Council.
    Keywords: Epsilonproteobacteria ; Taxonomy ; Classification ; Genome ; Phylogenomics ; Epsilonbacteraeota ; Evolution
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    High Latitude epipelagic and mesopelagic scattering layers—a reference for future Arctic ecosystem change (2017)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Marine Science 4 (2017): 334, doi:10.3389/fmars.2017.00334.
    Description: Scattering structures, including deep (〉200 m) scattering layers are common in most oceans, but have not previously been properly documented in the Arctic Ocean. In this work, we combine acoustic data for distribution and abundance estimation of zooplankton and fish with biological sampling from the region west and north of Svalbard, to examine high latitude meso- and epipelagic scattering layers and their biological constituents. Our results show that typically, there was strong patchy scattering in the upper part of the epipelagic zone (〈50 m) throughout the area. It was mainly dominated by copepods, krill, and amphipods in addition to 0-group fish that were particularly abundant west of the Spitsbergen Archipelago. Off-shelf there was a distinct deep scattering layer (DSL) between 250 and 600 m containing a range of larger longer lived organisms (mesopelagic fish and macrozooplankton). In eastern Fram Strait, the DSL also included and was in fact dominated by larger fish close to the shelf/slope break that were associated with Warm Atlantic Water moving north toward the Arctic Ocean, but switched to dominance by species having weaker scattering signatures further offshore. The Weighted Mean Depths of the DSL were deeper (WMD 〉 440 m) in the Arctic habitat north of Svalbard compared to those south in the Fram Strait west of Svalbard (WMD ~400 m). The surface integrated backscatter [Nautical Area-Scattering Coefficient, NASC, sA (m2 nmi−2)] was considerably lower in the waters around Svalbard compared to the more southern regions (62–69°N). Also, the integrated DSL nautical area scattering coefficient was a factor of ~6–10 lower around Svalbard compared to the areas in the south-eastern part of the Norwegian Sea ~62°30′N. The documented patterns and structures, particularly the DSL and its constituents, will be key reference points for understanding and quantifying future changes in the pelagic ecosystem at the entrance to the Arctic Ocean.
    Description: The Research Council of Norway is thanked for the financial support through the projects “The Arctic Ocean Ecosystem”—(SI_ARCTIC, RCN 228896), the “Effects of climate change on the Calanus complex”—(ECCO, RCN 200508), “Harvesting marine cold water plankton species—abundance estimation and stock assessment”—(Harvest II, RCN 203871) as well as the Institute of Marine Research, Bergen.
    Keywords: Arctic ; Bioacoustics ; Scattering layers ; Fish ; Micronekton ; Zooplankton ; Svalbard
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    Species-level variability in extracellular production rates of reactive oxygen species by diatoms (2016)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Chemistry 4 (2016): 5, doi:10.3389/fchem.2016.00005.
    Description: Biological production and decay of the reactive oxygen species (ROS) hydrogen peroxide (H2O2) and superoxide (O−2) likely have significant effects on the cycling of trace metals and carbon in marine systems. In this study, extracellular production rates of H2O2 and O−2 were determined for five species of marine diatoms in the presence and absence of light. Production of both ROS was measured in parallel by suspending cells on filters and measuring the ROS downstream using chemiluminescence probes. In addition, the ability of these organisms to break down O−2 and H2O2 was examined by measuring recovery of O−2 and H2O2 added to the influent medium. O−2 production rates ranged from undetectable to 7.3 × 10−16 mol cell−1 h−1, while H2O2 production rates ranged from undetectable to 3.4 × 10−16 mol cell−1 h−1. Results suggest that extracellular ROS production occurs through a variety of pathways even amongst organisms of the same genus. Thalassiosira spp. produced more O−2 in light than dark, even when the organisms were killed, indicating that O−2 is produced via a passive photochemical process on the cell surface. The ratio of H2O2 to O−2 production rates was consistent with production of H2O2 solely through dismutation of O−2 for T. oceanica, while T. pseudonana made much more H2O2 than O−2. T. weissflogii only produced H2O2 when stressed or killed. P. tricornutum cells did not make cell-associated ROS, but did secrete H2O2-producing substances into the growth medium. In all organisms, recovery rates for killed cultures (94–100% H2O2; 10–80% O−2) were consistently higher than those for live cultures (65–95% H2O2; 10–50% O−2). While recovery rates for killed cultures in H2O2 indicate that nearly all H2O2 was degraded by active cell processes, O−2 decay appeared to occur via a combination of active and passive processes. Overall, this study shows that the rates and pathways for ROS production and decay vary greatly among diatom species, even between those that are closely related, and as a function of light conditions.
    Description: This research was supported by NSF grant OCE-1131734/1246174 to BV and CH.
    Keywords: Reactive oxygen species ; Superoxide ; Hydrogen peroxide ; Diatoms ; Culture
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    New insights into microbial ecology through subtle nucleotide variation (2016)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 7 (2016): 1318, doi:10.3389/fmicb.2016.01318.
    Description: Characterizing the community structure of naturally occurring microbes through marker gene amplicons has gained widespread acceptance for profiling microbial populations. The 16S ribosomal RNA (rRNA) gene provides a suitable target for most studies since (1) it meets the criteria for robust markers of evolution, e.g., both conserved and rapidly evolving regions that do not undergo horizontal gene transfer, (2) microbial ecologists have identified widely adopted primers and protocols for generating amplicons for sequencing, (3) analyses of both cultivars and environmental DNA have generated well-curated databases for taxonomic profiling, and (4) bioinformaticians and computational biologists have published comprehensive software tools for interpreting the data and generating publication-ready figures. Since the initial descriptions of high-throughput sequencing of 16S rRNA gene amplicons to survey microbial diversity, we have witnessed an explosion of association-based inferences of interactions between microbes and their environment.
    Description: AME was supported by the University of Chicago and the Marine Biological Laboratory collaboration award.
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    Isolation and characterization of bacteria that degrade phosphonates in marine dissolved organic matter (2017)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 8 (2017): 1786, doi:10.3389/fmicb.2017.01786.
    Description: Semi-labile dissolved organic matter (DOM) accumulates in surface waters of the oligotrophic ocean gyres and turns over on seasonal to annual timescales. This reservoir of DOM represents an important source of carbon, energy, and nutrients to marine microbial communities but the identity of the microorganisms and the biochemical pathways underlying the cycling of DOM remain largely uncharacterized. In this study we describe bacteria isolated from the North Pacific Subtropical Gyre (NPSG) near Hawaii that are able to degrade phosphonates associated with high molecular weight dissolved organic matter (HMWDOM), which represents a large fraction of semi-labile DOM. We amended dilution-to-extinction cultures with HMWDOM collected from NPSG surface waters and with purified HMWDOM enriched with polysaccharides bearing alkylphosphonate esters. The HMWDOM-amended cultures were enriched in Roseobacter isolates closely related to Sulfitobacter and close relatives of hydrocarbon-degrading bacteria of the Oceanospirillaceae family, many of which encoded phosphonate degradation pathways. Sulfitobacter cultures encoding C-P lyase were able to catabolize methylphosphonate and 2-hydroxyethylphosphonate, as well as the esters of these phosphonates found in native HMWDOM polysaccharides to acquire phosphorus while producing methane and ethylene, respectively. Conversely, growth of these isolates on HMWDOM polysaccharides as carbon source did not support robust increases in cell yields, suggesting that the constituent carbohydrates in HMWDOM were not readily available to these individual isolates. We postulate that the complete remineralization of HMWDOM polysaccharides requires more complex microbial inter-species interactions. The degradation of phosphonate esters and other common substitutions in marine polysaccharides may be key steps in the turnover of marine DOM.
    Description: Financial support for this work was provided by the National Science Foundation Center for Microbial Oceanography: Research and Education (award #EF0424599 to DK and ED), the National Science Foundation HOT program (OCE-1260164 to M. J. Church and DK), the Gordon and Betty Moore Foundation (grants #492.01 and #3777 to ED, #3298 to DR, and #3794 to DK), and the Simons Foundation (award ID 329108 to DK, DR, and ED). Additional support was provided by the Agouron Institute through a fellowship to OS.
    Keywords: Bacterial degradation ; Dissolved organic matter (DOM) ; Phosphonate metabolism ; C-P lyase ; Methane ; Ethylene ; Oligotrophic conditions
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    A bacterial quorum-sensing precursor induces mortality in the marine coccolithophore, Emiliania huxleyi (2016)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 7 (2016): 59, doi:10.3389/fmicb.2016.00059.
    Description: Interactions between phytoplankton and bacteria play a central role in mediating biogeochemical cycling and food web structure in the ocean. However, deciphering the chemical drivers of these interspecies interactions remains challenging. Here, we report the isolation of 2-heptyl-4-quinolone (HHQ), released by Pseudoalteromonas piscicida, a marine gamma-proteobacteria previously reported to induce phytoplankton mortality through a hitherto unknown algicidal mechanism. HHQ functions as both an antibiotic and a bacterial signaling molecule in cell–cell communication in clinical infection models. Co-culture of the bloom-forming coccolithophore, Emiliania huxleyi with both live P. piscicida and cell-free filtrates caused a significant decrease in algal growth. Investigations of the P. piscicida exometabolome revealed HHQ, at nanomolar concentrations, induced mortality in three strains of E. huxleyi. Mortality of E. huxleyi in response to HHQ occurred slowly, implying static growth rather than a singular loss event (e.g., rapid cell lysis). In contrast, the marine chlorophyte, Dunaliella tertiolecta and diatom, Phaeodactylum tricornutum were unaffected by HHQ exposures. These results suggest that HHQ mediates the type of inter-domain interactions that cause shifts in phytoplankton population dynamics. These chemically mediated interactions, and other like it, ultimately influence large-scale oceanographic processes.
    Description: This research was support through funding from the Gordon and Betty Moore Foundation through Grant GBMF3301 to MJ and TM; NIH grant from the National Institute of Allergy and Infectious Disease (NIAID – 1R21Al119311-01) to TM and KW; the National Science Foundation (OCE – 1313747) and US National Institute of Environmental Health Science (P01-ES021921) through the Oceans and Human Health Program to BM. Additional financial support was provided to TM from the Flatley Discovery Lab.
    Keywords: Infochemicals ; Algicidal compound ; Bacteria–phytoplankton interaction ; HHQ ; Pseudoalteromonas ; Emiliania huxleyi ; IC50 ; Mortality
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    Relative importance of chemoautotrophy for primary production in a light exposed marine shallow hydrothermal system (2017)
    Frontiers Media
    Details
    Publication Date: 2022-05-25
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 8 (2017): 702, doi:10.3389/fmicb.2017.00702.
    Description: The unique geochemistry of marine shallow-water hydrothermal systems promotes the establishment of diverse microbial communities with a range of metabolic pathways. In contrast to deep-sea vents, shallow-water vents not only support chemosynthesis, but also phototrophic primary production due to the availability of light. However, comprehensive studies targeting the predominant biogeochemical processes are rare, and consequently a holistic understanding of the functioning of these ecosystems is currently lacking. To this end, we combined stable isotope probing of lipid biomarkers with an analysis of the bacterial communities to investigate if chemoautotrophy, in parallel to photoautotrophy, plays an important role in autotrophic carbon fixation and to identify the key players. The study was carried out at a marine shallow-water hydrothermal system located at 5 m water depth off Dominica Island (Lesser Antilles), characterized by up to 55°C warm hydrothermal fluids that contain high amounts of dissolved Fe2+. Analysis of the bacterial diversity revealed Anaerolineae of the Chloroflexi as the most abundant bacterial class. Furthermore, the presence of key players involved in iron cycling generally known from deep-sea hydrothermal vents (e.g., Zetaproteobacteria and Geothermobacter), supported the importance of iron-driven redox processes in this hydrothermal system. Uptake of 13C-bicarbonate into bacterial fatty acids under light and dark conditions revealed active photo- and chemoautotrophic communities, with chemoautotrophy accounting for up to 65% of the observed autotrophic carbon fixation. Relatively increased 13C-incorporation in the dark allowed the classification of aiC15:0, C15:0, and iC16:0 as potential lipid biomarkers for bacterial chemoautotrophy in this ecosystem. Highest total 13C-incorporation into fatty acids took place at the sediment surface, but chemosynthesis was found to be active down to 8 cm sediment depth. In conclusion, this study highlights the relative importance of chemoautotrophy compared to photoautotrophy in a shallow-water hydrothermal system, emphasizing chemosynthesis as a prominent process for biomass production in marine coastal environments influenced by hydrothermalism.
    Description: SS was supported by NSF grant OCE-1124272. This work was financed through the DFG Emmy Noether Grant BU 2606/1-1 to SB.
    Keywords: Chemoautotrophy ; Marine shallow-water hydrothermal systems ; Lipid biomarker ; Stable isotope probing (SIP) ; Fatty acids ; Dominica (Lesser Antilles) ; Zetaproteobacteria ; Geothermobacter
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    Quantifying Effusion Rates at Active Volcanoes through Integrated Time-Lapse Laser Scanning and Photography (2016)
    Molecular Diversity Preservation International
    Details
    Publication Date: 2017-04-04
    Description: During volcanic eruptions, measurements of the rate at which magma is erupted underpin hazard assessments. For eruptions dominated by the effusion of lava, estimates are often made using satellite data; here, in a case study at Mount Etna (Sicily), we make the first measurements based on terrestrial laser scanning (TLS), and we also include explosive products. During the study period (17–21 July 2012), regular Strombolian explosions were occurring within the Bocca Nuova crater, producing a ~50 m-high scoria cone and a small lava flow field. TLS surveys over multi-day intervals determined a mean cone growth rate (effusive and explosive products) of ~0.24 m3·s−1. Differences between 0.3-m resolution DEMs acquired at 10-minute intervals captured the evolution of a breakout lava flow lobe advancing at 0.01–0.03 m3·s−1. Partial occlusion within the crater prevented similar measurement of the main flow, but integrating TLS data with time-lapse imagery enabled lava viscosity (7.4 × 105 Pa·s) to be derived from surface velocities and, hence, a flux of 0.11 m3·s−1 to be calculated. Total dense rock equivalent magma discharge estimates are ~0.1–0.2 m3·s−1 over the measurement period and suggest that simultaneous estimates from satellite data are somewhat overestimated. Our results support the use of integrated TLS and time-lapse photography for ground-truthing space-based measurements and highlight the value of interactive image analysis when automated approaches, such as particle image velocimetry (PIV), fail.
    Description: Published
    Description: 14967 - 14987
    Description: 3V. Dinamiche e scenari eruttivi
    Description: JCR Journal
    Description: open
    Keywords: lava flow; scoria cone; effusion rate; terrestrial laser scanning; time-lapse photography; Mt. Etna ; 04. Solid Earth::04.08. Volcanology::04.08.06. Volcano monitoring ; 04. Solid Earth::04.08. Volcanology::04.08.07. Instruments and techniques ; 05. General::05.02. Data dissemination::05.02.03. Volcanic eruptions
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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    The Use of Surveillance Cameras for the Rapid Mapping of Lava Flows: An Application to Mount Etna Volcano (2017)
    Molecular Diversity Preservation International
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    Publication Date: 2017-04-04
    Description: In order to improve the observation capability in one of the most active volcanic areas in the world, Mt. Etna, we developed a processing method to use the surveillance cameras for a quasi real-time mapping of syn-eruptive processes. Following an evaluation of the current performance of the Etna permanent ground NEtwork of Thermal and Visible Sensors (Etna_NETVIS), its possible implementation and optimization was investigated to determine the locations of additional observation sites to be rapidly set up during emergencies. A tool was then devised to process time series of ground-acquired images and extract a coherent multi-temporal dataset of georeferenced map. The processed datasets can be used to extract 2D features such as evolution maps of active lava flows. The tool was validated on ad-hoc test fields and then adopted to map the evolution of two recent lava flows. The achievable accuracy (about three times the original pixel size) and the short processing time makes the tool suitable for rapidly assessing lava flow evolutions, especially in the case of recurrent eruptions, such as those of the 2011–2015 Etna activity. The tool can be used both in standard monitoring activities and during emergency phases (eventually improving the present network with additional mobile stations) when it is mandatory to carry out a quasi-real-time mapping to support civil protection actions. The developed tool could be integrated in the control room of the Osservatorio Etneo, thus enabling the Etna_NETVIS for mapping purposes and not only for video surveillance.
    Description: Published
    Description: 192
    Description: 5V. Sorveglianza vulcanica ed emergenze
    Description: JCR Journal
    Description: open
    Keywords: volcano monitoring ; lava flow mapping ; surveillance camera ; hazard assessment ; geo spatial dataset ; 04. Solid Earth::04.08. Volcanology::04.08.07. Instruments and techniques
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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    Joint Terrestrial and Aerial Measurements to Study Ground Deformation: Application to the Sciara Del Fuoco at the Stromboli Volcano (Sicily) (2017)
    Molecular Diversity Preservation International
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    Publication Date: 2017-04-04
    Description: The 2002-2003 Stromboli eruption triggered the failure of part of the Sciara del Fuoco slope, which generated a tsunami that struck the island and the northern coastline of Sicily. The Sciara del Fuoco is a very steep slope where all lava flows from the craters' emplacement; most lateral eruptions usually take place from fissures propagating in this sector of the volcano. The eruption went on to produce a lava field that filled the area affected by the landslide. This in turn led to further instability, renewing the threat of another slope failure and a potentially related tsunami. This work describes a new joint approach, combining surveying data and aerial image correlometry methods, to study the motion of this unstable slope. The combination has the advantage of very precise surveying measurements, which can be considered the ground truth to constrain the very-high-resolution aerial photogrammetric data, thereby obtaining highly detailed and accurate ground deformation maps. The joint use of the two methods can be very useful to obtain a more complete image of the deformation field for monitoring dangerous and/or rather inaccessible places. The proposed combined methodology improves our ability to study and assess hazardous processes associated with significant ground deformation.
    Description: This Research has been supported by the Spanish Ministry of Economy and Competitiveness research projects AYA2010-17448 and ESP2013-47780-557 C2-1-R, and the EU 7th FP MED-SUV project (contract 308665). It is a contribution to the Moncloa Campus of International Excellence
    Description: Published
    Description: 463
    Description: 1V. Storia e struttura dei sistemi vulcanici
    Description: JCR Journal
    Description: open
    Keywords: surveying ; data integration ; aerial photogrammetry ; monitoring ; flank instability ; sector collapse ; landslide ; tsunami ; volcanoes ; 04. Solid Earth::04.08. Volcanology::04.08.07. Instruments and techniques
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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    Individuality, stability, and variability of the plaque microbiome (2016)
    Frontiers Media
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 7 (2016): 564, doi:10.3389/fmicb.2016.00564.
    Description: Dental plaque is a bacterial biofilm composed of a characteristic set of organisms. Relatively little information from cultivation-independent, high-throughput analyses has been published on the temporal dynamics of the dental plaque microbiome. We used Minimum Entropy Decomposition, an information theory-based approach similar to oligotyping that provides single-nucleotide resolution, to analyze a previously published time series data set and investigate the dynamics of the plaque microbiome at various analytic and taxonomic levels. At both the genus and 97% Operational Taxonomic Unit (OTU) levels of resolution, the range of variation within each individual overlapped that of other individuals in the data set. When analyzed at the oligotype level, however, the overlap largely disappeared, showing that single-nucleotide resolution enables differentiation of individuals from one another without ambiguity. The overwhelming majority of the plaque community in all samples was made up of bacteria from a moderate number of plaque-typical genera, indicating that the overall community framework is shared among individuals. Each of these genera fluctuated in abundance around a stable mean that varied between individuals, with some genera having higher inter-individual variability than others. Thus, at the genus level, differences between individuals lay not in the identity of the major genera but in consistently differing proportions of these genera from mouth to mouth. However, at the oligotype level, we detected oligotype “fingerprints,” a highly individual-specific set of persistently abundant oligotypes fluctuating around a stable mean over time. For example, within the genus Corynebacterium, more than a dozen oligotypes were detectable in each individual, of which a different subset reached high abundance in any given person. This pattern suggests that each mouth contains a subtly different community of organisms. We also compared the Chinese plaque community characterized here to previously characterized Western plaque communities, as represented by analyses of data emerging from the Human Microbiome Project, and found no major differences between Chinese and Western supragingival plaque. In conclusion, we found the plaque microbiome to be highly individualized at the oligotype level and characterized by stability of community membership, with variability in the relative abundance of community members between individuals and over time.
    Description: Our work was supported by National Institutes of Health (NIH) National Institute of Dental and Craniofacial Research Grant DE022586 (to GGB). Additional support was provided by Harvard University's Department of Organismic and Evolutionary Biology graduate program (to DRU).
    Keywords: Human microbiome ; 16S rRNA ; Community dynamics ; Oral microbiota ; Community ecology
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    The Guaymas Basin hiking guide to hydrothermal mounds, chimneys, and microbial mats : complex seafloor expressions of subsurface hydrothermal circulation (2016)
    Frontiers Media
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 7 (2016): 75, doi:10.3389/fmicb.2016.00075.
    Description: The hydrothermal mats, mounds, and chimneys of the southern Guaymas Basin are the surface expression of complex subsurface hydrothermal circulation patterns. In this overview, we document the most frequently visited features of this hydrothermal area with photographs, temperature measurements, and selected geochemical data; many of these distinct habitats await characterization of their microbial communities and activities. Microprofiler deployments on microbial mats and hydrothermal sediments show their steep geochemical and thermal gradients at millimeter-scale vertical resolution. Mapping these hydrothermal features and sampling locations within the southern Guaymas Basin suggest linkages to underlying shallow sills and heat flow gradients. Recognizing the inherent spatial limitations of much current Guaymas Basin sampling calls for comprehensive surveys of the wider spreading region.
    Description: AT acknowledges a W. Reynolds research leave from UNC, Guaymas-relevant support from the Center for Dark Energy Biosphere Investigations (C-DEBI) at the University of Southern California
    Keywords: Guaymas basin ; Hydrothermal circulation ; Hydrothermal sediment ; Beggiatoa mat ; In situ profiles ; Heatflow ; Porewater chemistry
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    Intracellular isotope localization in Ammonia sp. (Foraminifera) of oxygen-depleted environments : results of nitrate and sulfate labeling experiments (2016)
    Frontiers Media
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 7 (2016): 163, doi:10.3389/fmicb.2016.00163.
    Description: Some benthic foraminiferal species are reportedly capable of nitrate storage and denitrification, however, little is known about nitrate incorporation and subsequent utilization of nitrate within their cell. In this study, we investigated where and how much 15N or 34S were assimilated into foraminiferal cells or possible endobionts after incubation with isotopically labeled nitrate and sulfate in dysoxic or anoxic conditions. After 2 weeks of incubation, foraminiferal specimens were fixed and prepared for Transmission Electron Microscopy (TEM) and correlative nanometer-scale secondary ion mass spectrometry (NanoSIMS) analyses. TEM observations revealed that there were characteristic ultrastructural features typically near the cell periphery in the youngest two or three chambers of the foraminifera exposed to anoxic conditions. These structures, which are electron dense and ~200–500 nm in diameter and co-occurred with possible endobionts, were labeled with 15N originated from 15N-labeled nitrate under anoxia and were labeled with both 15N and 34S under dysoxia. The labeling with 15N was more apparent in specimens from the dysoxic incubation, suggesting higher foraminiferal activity or increased availability of the label during exposure to oxygen depletion than to anoxia. Our results suggest that the electron dense bodies in Ammonia sp. play a significant role in nitrate incorporation and/or subsequent nitrogen assimilation during exposure to dysoxic to anoxic conditions.
    Description: This work was supported by a Grant-in-Aid for Scientific Research from the Ministry of Education, Culture, Sports, Science and Technology, Japan (Young Scientists B No. 22740340 and Scientific Research C No. 24540504 to HN), an Invitation Fellowship for Research in Japan to JB by Japan Society for the Promotion of Science (JSPS), the Robert W. Morse Chair for Excellence in Oceanography at WHOI to JB, and The Investment in Science Fund at WHOI to JB.
    Keywords: Foraminifer ; Nitrate ; NanoSIMS ; Electron dense body ; Endobionts ; Ultrastructure ; Denitrification
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    Diversity and distribution of prokaryotes within a shallow-water pockmark field (2016)
    Frontiers Media
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 7 (2016): 941, doi:10.3389/fmicb.2016.00941.
    Description: Pockmarks are crater-like depression on the seafloor associated with hydrocarbon ascent through muddy sediments in continental shelves around the world. In this study, we examine the diversity and distribution of benthic microbial communities at shallow-water pockmarks adjacent to the Middle Adriatic Ridge. We integrate microbial diversity data with characterization of local hydrocarbons concentrations and sediment geochemistry. Our results suggest these pockmarks are enriched in sedimentary hydrocarbons, and host a microbial community dominated by Bacteria, even in deeper sediment layers. Pockmark sediments showed higher prokaryotic abundance and biomass than surrounding sediments, potentially due to the increased availability of organic matter and higher concentrations of hydrocarbons linked to pockmark activity. Prokaryotic diversity analyses showed that the microbial communities of these shallow-water pockmarks are unique, and comprised phylotypes associated with the cycling of sulfur and nitrate compounds, as well as numerous know hydrocarbon degraders. Altogether, this study suggests that shallow-water pockmark habitats enhance the diversity of the benthic prokaryotic biosphere by providing specialized environmental niches.
    Description: This work was partially supported by a Postdoctoral Fellowship from the Center for Dark Energy Biosphere Investigations [C-DEBI, grant OCE-0939564] awarded to DG, by National Science Foundation grant OCE 11-24141 to CV, and European Science Foundation EuroDeep BIOFUN grant CTM2007-28739-E to EM. This article commits to EU HERMIONE [contract no. 226354] and CoCoNet [contract no. 287844] programs, and the Italian MIUR flag Ritmare within the National Research Program 2011–2013.
    Keywords: Pockmarks ; Cold seeps ; Hydrocarbons ; Prokaryotic diversity ; Bacteria ; Archaea ; Hydrocarbon degradation ; Microbial diversity
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    Hydrogen limitation and syntrophic growth among natural assemblages of thermophilic methanogens at deep-sea hydrothermal vents (2016)
    Frontiers Media
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 7 (2016): 1240, doi:10.3389/fmicb.2016.01240.
    Description: Thermophilic methanogens are common autotrophs at hydrothermal vents, but their growth constraints and dependence on H2 syntrophy in situ are poorly understood. Between 2012 and 2015, methanogens and H2-producing heterotrophs were detected by growth at 80∘C and 55∘C at most diffuse (7–40∘C) hydrothermal vent sites at Axial Seamount. Microcosm incubations of diffuse hydrothermal fluids at 80∘C and 55∘C demonstrated that growth of thermophilic and hyperthermophilic methanogens is primarily limited by H2 availability. Amendment of microcosms with NH4+ generally had no effect on CH4 production. However, annual variations in abundance and CH4 production were observed in relation to the eruption cycle of the seamount. Microcosm incubations of hydrothermal fluids at 80∘C and 55∘C supplemented with tryptone and no added H2 showed CH4 production indicating the capacity in situ for methanogenic H2 syntrophy. 16S rRNA genes were found in 80∘C microcosms from H2-producing archaea and H2-consuming methanogens, but not for any bacteria. In 55∘C microcosms, sequences were found from H2-producing bacteria and H2-consuming methanogens and sulfate-reducing bacteria. A co-culture of representative organisms showed that Thermococcus paralvinellae supported the syntrophic growth of Methanocaldococcus bathoardescens at 82∘C and Methanothermococcus sp. strain BW11 at 60∘C. The results demonstrate that modeling of subseafloor methanogenesis should focus primarily on H2 availability and temperature, and that thermophilic H2 syntrophy can support methanogenesis within natural microbial assemblages and may be an important energy source for thermophilic autotrophs in marine geothermal environments.
    Description: This work was funded by the Gordon and Betty Moore Foundation grant GBMF 3297, the NASA Earth and Space Science Fellowship Program grant NNX11AP78H, the National Science Foundation grant OCE-1547004, with funding from NOAA/PMEL, contribution #4493, and JISAO under NOAA Cooperative Agreement NA15OAR4320063, contribution #2706.
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    Optical dignatures of dissolved organic matter transformation in the global ocean (2017)
    Frontiers Media
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Marine Science 2 (2016): 118, doi:10.3389/fmars.2015.00118.
    Description: Characterization of dissolved organic matter (DOM) in terms of its composition and optical properties, with an eye toward ultimately understanding its deep ocean dynamics, is the currently active frontier in DOM research. We used UV-visible absorption spectroscopy and fluorescence excitation-emission matrix (EEM) spectroscopy to characterize DOM in the open ocean along sections of the U.S. CO2/CLIVAR Repeat Hydrography Project located in all the major ocean basins outside the Arctic. Despite large differences in fluorescence intensity between ocean basins, some variability patterns were similar throughout the global ocean, suggesting similar processes controlling the composition of the DOM. We find that commercially available single channel CDOM sensors are sensitive to the fluorescence of humic materials in the deep ocean and thermocline but not to the UVA-fluorescing and absorbing materials that characterize freshly produced CDOM in surface waters, revealing fundamental diversity in the DOM profile. In surface waters, UVA fluorescence and absorption signatures indicate the presence of freshly produced material and the process of bleaching removal, but in the upper mesopelagic and in the main thermocline these optical signatures are replaced by those of humic materials, with distribution patterns correlated to apparent oxygen utilization (AOU) and other signatures of remineralization. Empirical orthogonal function analysis (EOF) of the EEM data suggests the presence of two (unidentified) processes which convert “fresh” DOM to humic materials: one located in the surface ocean (shallower than 500 m) and one located in the main thermocline. These inferred humification processes represent less than 5% of the overall variability in oceanic humic DOM fluorescence, which appears to be dominated by terrestrial input and solar bleaching of humic materials.
    Description: This research was supported by grants from NASA (grants NAG5-13277 and NNX14AG24G) and NSF (OCE-0241614 and OCE-0648541) to NN and D. A. Siegel.
    Keywords: CDOM ; FDOM ; Humic material ; Oceanic CDOM cycling ; Fluorescence analysis
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    Iron-binding ligands in the Southern California Current System : mechanistic studies (2017)
    Frontiers Media
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Marine Science 3 (2016): 27, doi:10.3389/fmars.2016.00027.
    Description: The distributions of dissolved iron and organic iron-binding ligands were examined in water column profiles and deckboard incubation experiments in the southern California Current System (sCCS) along a transition from coastal to semi-oligotrophic waters. Analysis of the iron-binding ligand pool by competitive ligand exchange-adsorptive cathodic stripping voltammetry (CLE-ACSV) using multiple analytical windows (MAWs) revealed three classes of iron-binding ligands present throughout the water column (L1−L3), whose distributions closely matched those of dissolved iron and nitrate. Despite significant biogeochemical gradients, ligand profiles were similar between stations, with surface minima in strong ligands (L1 and L2), and relatively constant concentrations of weaker ligands (L3) down to 500 m. A phytoplankton grow-out incubation, initiated from an iron-limited water mass, showed dynamic temporal cycling of iron-binding ligands. A biological iron model was able to capture the patterns of the strong ligands in the grow-out incubation relatively well with only the microbial community as a biological source. An experiment focused on remineralization of particulate organic matter showed production of both strong and weak iron-binding ligands by the heterotrophic community, supporting a mechanism for in-situ production of both strong and weak iron-binding ligands in the subsurface water column. Photochemical experiments showed a variable influence of sunlight on the degradation of natural iron-binding ligands, providing some evidence to explain differences in surface ligand concentrations between stations. Patterns in ligand distributions between profiles and in the incubation experiments were primarily related to macronutrient concentrations, suggesting microbial remineralization processes might dominate on longer time-scales over short-term changes associated with photochemistry or phytoplankton growth.
    Description: RB, KB, and MC were supported by NSF OCE #10-2667 for the CCE-LTER program. MJ was funded by NSF ANT grant 0948378 and Harbor Branch Oceanographic Institute Foundation.
    Keywords: California Current Ecosystem ; Long term ecological research ; Iron limitation ; Dissolved iron-binding ligands ; Multiple analytical windows ; Electrochemistry
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    Arctic deltaic lake sediments as recorders of fluvial organic matter deposition (2017)
    Frontiers Media
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Earth Science 4 (2016): 77, doi:10.3389/feart.2016.00077.
    Description: Arctic deltas are dynamic and vulnerable regions that play a key role in land-ocean interactions and the global carbon cycle. Delta lakes may provide valuable historical records of the quality and quantity of fluvial fluxes, parameters that are challenging to investigate in these remote regions. Here we study lakes from across the Mackenzie Delta, Arctic Canada, that receive fluvial sediments from the Mackenzie River when spring flood water levels rise above natural levees. We compare downcore lake sediments with suspended sediments collected during the spring flood, using bulk (% organic carbon, % total nitrogen, δ13C, Δ14C) and molecular organic geochemistry (lignin, leaf waxes). High-resolution age models (137Cs, 210Pb) of downcore lake sediment records (n = 11) along with lamina counting on high-resolution radiographs show sediment deposition frequencies ranging between annually to every 15 years. Down-core geochemical variability in a representative delta lake sediment core is consistent with historical variability in spring flood hydrology (variability in peak discharge, ice jamming, peak water levels). Comparison with earlier published Mackenzie River depth profiles shows that (i) lake sediments reflect the riverine surface suspended load, and (ii) hydrodynamic sorting patterns related to spring flood characteristics are reflected in the lake sediments. Bulk and molecular geochemistry of suspended particulate matter from the spring flood peak and lake sediments are relatively similar showing a mixture of modern higher-plant derived material, older terrestrial permafrost material, and old rock-derived material. This suggests that deltaic lake sedimentary records hold great promise as recorders of past (century-scale) riverine fluxes and may prove instrumental in shedding light on past behavior of arctic rivers, as well as how they respond to a changing climate.
    Description: Funding was provided by the US National Science Foundation as part of the Arctic Great Rivers Observatory (NSF-0732522 and NSF-1107774), as well as the Netherlands Organization for Scientific Research (Rubicon #825.10.022, and Veni #863.12.004). Additional funding for the lake coring was provided from WHOI through its Ocean and Climate Change Institute.
    Keywords: Lignin ; Biomarkers ; Mackenzie River ; Carbon isotopes ; Lake sediments
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    Prediction of the export and fate of global ocean net primary production : the EXPORTS Science Plan (2017)
    Frontiers Media
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Marine Science 3 (2016): 22, doi:10.3389/fmars.2016.00022.
    Description: Ocean ecosystems play a critical role in the Earth's carbon cycle and the quantification of their impacts for both present conditions and for predictions into the future remains one of the greatest challenges in oceanography. The goal of the EXport Processes in the Ocean from Remote Sensing (EXPORTS) Science Plan is to develop a predictive understanding of the export and fate of global ocean net primary production (NPP) and its implications for present and future climates. The achievement of this goal requires a quantification of the mechanisms that control the export of carbon from the euphotic zone as well as its fate in the underlying “twilight zone” where some fraction of exported carbon will be sequestered in the ocean's interior on time scales of months to millennia. Here we present a measurement/synthesis/modeling framework aimed at quantifying the fates of upper ocean NPP and its impacts on the global carbon cycle based upon the EXPORTS Science Plan. The proposed approach will diagnose relationships among the ecological, biogeochemical, and physical oceanographic processes that control carbon cycling across a range of ecosystem and carbon cycling states leading to advances in satellite diagnostic and numerical prognostic models. To collect these data, a combination of ship and robotic field sampling, satellite remote sensing, and numerical modeling is proposed which enables the sampling of the many pathways of NPP export and fates. This coordinated, process-oriented approach has the potential to foster new insights on ocean carbon cycling that maximizes its societal relevance through the achievement of research goals of many international research agencies and will be a key step toward our understanding of the Earth as an integrated system.
    Description: The development of the EXPORTS Science Plan was supported by NASA Ocean Biology and Biogeochemistry program (award NNX13AC35G).
    Keywords: Satellite remote sensing ; Field campain ; Science plan ; Ocean carbon cycling ; Biological pump
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    Seasonal shifts in bacterial community responses to phytoplankton-derived dissolved organic matter in the Western Antarctic Peninsula (2017)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 8 (2017): 2117, doi:10.3389/fmicb.2017.02117.
    Description: Bacterial consumption of dissolved organic matter (DOM) drives much of the movement of carbon through the oceanic food web and the global carbon cycle. Understanding complex interactions between bacteria and marine DOM remains an important challenge. We tested the hypothesis that bacterial growth and community succession would respond differently to DOM additions due to seasonal changes in phytoplankton abundance in the environment. Four mesocosm experiments were conducted that spanned the spring transitional period (August–December 2013) in surface waters of the Western Antarctic Peninsula (WAP). Each mesocosm consisted of nearshore surface seawater (50 L) incubated in the laboratory for 10 days. The addition of DOM, in the form of cell-free exudates extracted from Thalassiosira weissflogii diatom cultures led to changes in bacterial abundance, production, and community composition. The timing of each mesocosm experiment (i.e., late winter vs. late spring) influenced the magnitude and direction of bacterial changes. For example, the same DOM treatment applied at different times during the season resulted in different levels of bacterial production and different bacterial community composition. There was a mid-season shift from Collwelliaceae to Polaribacter having the greatest relative abundance after incubation. This shift corresponded to a modest but significant increase in the initial relative abundance of Polaribacter in the nearshore seawater used to set up experiments. This finding supports a new hypothesis that starting community composition, through priority effects, influenced the trajectory of community succession in response to DOM addition. As strong inter-annual variability and long-term climate change may shift the timing of WAP phytoplankton blooms, and the corresponding production of DOM exudates, this study suggests a mechanism by which different seasonal successional patterns in bacterial communities could occur.
    Description: CL was partially funded by the Graduate School and the Department of Ecology and Evolutionary Biology at Brown University and the Brown University-Marine Biological Laboratory Joint Graduate Program. This material is based upon work supported by the National Science Foundation under Grant Nos. ANT-1142114 to LA-Z, OPP-0823101 and PLR-1440435 to HD, and ANT-1141993 to JR. The Gordon and Betty Moore Foundation grant 1711 supported work by DR.
    Keywords: 16S rRNA ; Amplicon sequencing ; Community assembly ; Bacterial succession ; Mesocosms ; Collwelliaceae ; Polaribacter ; Phytoplankton exudates
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    Evidence of diel vertical migration of mesopelagic sound-scattering organisms in the Arctic (2017)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Marine Science 4 (2017): 332, doi:10.3389/fmars.2017.00332.
    Description: While sound scattering layers (SSLs) have been described previously from ice-covered waters in the Arctic, the existence of a viable mesopelagic community that also includes mesopelagic fishes in the Arctic has been questioned. In addition, it has been hypothesized that vertical migration would hardly exist in these areas. We wanted to check if deep scattering layers (DSLs) was found to the west and north of Svalbard (79°30′N−82°10′N) during autumn 2015, and if present; whether organisms in such DSLs undertook vertical migrations. Our null hypothesis was that there would be no evidence of diel vertical migration. Multi-frequency acoustic observations by hull mounted echo sounder (18, 38, and 120 kHz) revealed a DSL at depths ~210–510 m in areas with bottom depths exceeding ~600 m. Investigating eight geographical locations that differed with respect to time periods, light cycle and sea ice conditions, we show that the deeper layer of DSL displayed a clear ascending movement during night time and a descending movement during daytime. The high-light weighted mean depth (WMD) (343–514 m) with respect to backscattered energy was statistically deeper than the low-light WMD (179–437 m) for the locations studied. This behavior of the DSL was found to be consistent both when the sun was continuously above the horizon and after it started to set on 1 September, and both in open water and sea ice covered waters. The WMD showed an increasing trend, while the nautical area backscattering strength from the DSL showed a decreasing trend from south to north among the studied locations. Hydrographic observations revealed that the diel migration was found in the lower part of the north-flowing Atlantic Water, and was disconnected from the surface water masses above the Atlantic Water during day and night. The organisms conducting vertical migrations were studied by vertical and oblique hauls with zooplankton nets and pelagic trawls. These data suggest that these organisms were mainly various mesopelagic fishes, some few larger fishes, large zooplankton like krill and amphipods, and various gelatinous forms.
    Description: The Research Council of Norway is thanked for the financial support through the projects “The Arctic Ocean Ecosystem” — (SI_ARCTIC, RCN 228896), the “Effects of climate change on the Calanus complex”—(ECCO, RCN 200508), “Harvesting marine cold water plankton species—abundance estimation and stock assessment”—(Harvest II, RCN 203871).
    Keywords: Arctic Ocean ; Deep scattering layer ; Diel vertical migration ; Mesopelagic organisms ; Acoustics
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    Evidence for strain-specific exometabolomic responses of the coccolithophore Emiliania huxleyi to grazing by the dinoflagellate oxyrrhis marina (2017)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Marine Science 3 (2016): 1, doi:10.3389/fmars.2016.00001.
    Description: The coccolithophore Emiliania huxleyi forms massive blooms and plays a critical role in global elemental cycles, sequestering significant amounts of atmospheric carbon dioxide on geological time scales via production of calcium carbonate coccoliths and emitting dimethyl sulfoniopropionate (DMSP), which has the potential for increasing atmosph-eric albedo. Because grazing in pelagic systems is a major top-down force structuring microbial communities, the influence of grazers on E. huxleyi populations has been of interest to researchers. Roles of DMSP (and related metabolites) in interactions between E. huxleyi and protist grazers have been investigated, however, little is known about the release of other metabolites that may influence, or be influenced by, such grazing interactions. We used high-resolution mass spectrometry in an untargeted approach to survey the suite of low molecular weight compounds released by four different E. huxleyi strains in response to grazing by the dinoflagellate Oxyrrhis marina. Overall, a strikingly small number of metabolites were detected from E. huxleyi and O. marina cells, but these were distinctly informative to construct metabolic footprints. At most, E. huxleyi strains shared 25% of released metabolites. Furthermore, there appeared to be no unified metabolic response in E. huxleyi strains to grazing; rather, these responses were strain specific. Concentrations of several metabolites also positively correlated with grazer activities, including grazing, ingestion, and growth rates; however, no single metabolite responded uniformly across all strains of E. huxleyi tested. Regardless, grazing clearly transformed the constituents of dissolved organic matter produced by these marine microbes. This study addresses several technical challenges, and presents a platform to further study the influence of chemical cues in aquatic systems and demonstrates the impact of strain diversity and grazing on the complexity of dissolved organic matter in marine systems.
    Description: Funding for this work was provided by the Gordon and Betty Moore Foundation, Grant #3301 awarded to A Vardi, BAS. Van Mooy, K Bidle, MJ, and TM. Additional funding for this work was provided by an award from the Flatley Discovery Lab to TM.
    Keywords: Dissolved organic matter ; Environmental metabolomics ; Grazing ; Metabolic footprinting ; Phytoplankton
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    Modeling the potential distribution and richness of cetaceans in the Azores from Fisheries Observer Program data (2017)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Marine Science 2 (2016): 202, doi:10.3389/fmars.2016.00202.
    Description: Marine spatial planning and ecological research call for high-resolution species distribution data. However, those data are still not available for most marine large vertebrates. The dynamic nature of oceanographic processes and the wide-ranging behavior of many marine vertebrates create further difficulties, as distribution data must incorporate both the spatial and temporal dimensions. Cetaceans play an essential role in structuring and maintaining marine ecosystems and face increasing threats from human activities. The Azores holds a high diversity of cetaceans but the information about spatial and temporal patterns of distribution for this marine megafauna group in the region is still very limited. To tackle this issue, we created monthly predictive cetacean distribution maps for spring and summer months, using data collected by the Azores Fisheries Observer Programme between 2004 and 2009. We then combined the individual predictive maps to obtain species richness maps for the same period. Our results reflect a great heterogeneity in distribution among species and within species among different months. This heterogeneity reflects a contrasting influence of oceanographic processes on the distribution of cetacean species. However, some persistent areas of increased species richness could also be identified from our results. We argue that policies aimed at effectively protecting cetaceans and their habitats must include the principle of dynamic ocean management coupled with other area-based management such as marine spatial planning.
    Description: This work was supported by FEDER funds, through the Competitiveness Factors Operational Programme - COMPETE, by national funds, through FCT - Foundation for Science and Technology, under project TRACE (PTDC/ MAR/74071/2006), and by regional funds, through DRCT/SRCTE, under projects MAPCET (M2.1.2/F/012/2011) and 2020 (M2.1.2/I/026/2011). We acknowledge funds provided by FCT to MARE, through the strategic project UID/MAR/04292/2013. RP is supported by an FCT postdoctoral grant (SFRH/BPD/108007/2015); MAS is supported by Program Investigator FCT (IF/00943/2013) and MT was supported by a research fellowship under the Exploratory project (IF/00943/2013/CP1199/CT0001) that also paid the fees for this open-access publication. IF/00943/2013 and IF/00943/2013/CP1199/CT0001 are funded by FSE and MCTES, through POPH and QREN.
    Keywords: Cetacean ; Spatio-temporal distribution ; Azores ; Species distribution models (SDMs) ; Richness ; MaxEnt
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    Lateralization of eye use in cuttlefish : opposite direction for anti-predatory and predatory behaviors (2017)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Physiology 7 (2016): 620, doi:10.3389/fphys.2016.00620.
    Description: Vertebrates with laterally placed eyes typically exhibit preferential eye use for ecological activities such as scanning for predators or prey. Processing visual information predominately through the left or right visual field has been associated with specialized function of the left and right brain. Lateralized vertebrates often share a general pattern of lateralized brain function at the population level, whereby the left hemisphere controls routine behaviors and the right hemisphere controls emergency responses. Recent studies have shown evidence of preferential eye use in some invertebrates, but whether the visual fields are predominately associated with specific ecological activities remains untested. We used the European common cuttlefish, Sepia officinalis, to investigate whether the visual field they use is the same, or different, during anti-predatory, and predatory behavior. To test for lateralization of anti-predatory behavior, individual cuttlefish were placed in a new environment with opaque walls, thereby obliging them to choose which eye to orient away from the opaque wall to scan for potential predators (i.e., vigilant scanning). To test for lateralization of predatory behavior, individual cuttlefish were placed in the apex of an isosceles triangular arena and presented with two shrimp in opposite vertexes, thus requiring the cuttlefish to choose between attacking a prey item to the left or to the right of them. Cuttlefish were significantly more likely to favor the left visual field to scan for potential predators and the right visual field for prey attack. Moreover, individual cuttlefish that were leftward directed for vigilant scanning were predominately rightward directed for prey attack. Lateralized individuals also showed faster decision-making when presented with prey simultaneously. Cuttlefish appear to have opposite directions of lateralization for anti-predatory and predatory behavior, suggesting that there is functional specialization of each optic lobe (i.e., brain structures implicated in visual processing). These results are discussed in relation to the role of lateralized brain function and the evolution of population level lateralization.
    Description: This work was supported by a post-doctoral study grant from the Fyssen Foundation to AS, and by a research grant “Sélavie” from the Fyssen Foundation to CJ-A. The Sholley Foundation provided partial support for the research in Woods Hole.
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    Recent scientific publications cast doubt on North Atlantic right whale future (2017)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Marine Science 3 (2016): 137, doi:10.3389/fmars.2016.00137.
    Keywords: Right whales ; Conservation ; Mortalities ; Entanglements ; Population recovery
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    A review of protist grazing below the photic zone emphasizing studies of oxygen-depleted water columns and recent applications of in situ approaches (2017)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Marine Science 4 (2017): 105, doi:10.3389/fmars.2017.00105.
    Description: Little is still known of the impacts of protist grazing on bacterioplankton communities in the dark ocean. Furthermore, the accuracy of assessments of in situ microbial activities, including protist grazing, can be affected by sampling artifacts introduced during sample retrieval and downstream manipulations. Potential artifacts may be increased when working with deep-sea samples or samples from chemically unique water columns such as oxygen minimum zones (OMZs). OMZs are oxygen-depleted regions in the ocean, where oxygen concentrations can drop to 〈20 μM. These regions are typically located near eastern boundary upwelling systems and currently occur in waters occupying below about 8% of total ocean surface area, representing ~1% of the ocean's volume. OMZs have a profound impact not only on the distribution of marine Metazoa, but also on the composition and activities of microbial communities at the base of marine food webs. Here we present an overview of current knowledge of protist phagotrophy below the photic zone, emphasizing studies of oxygen-depleted waters and presenting results of the first attempt to implement new technology for conducting these incubation studies completely in situ (the Microbial Sampling- Submersible Incubation Device, MS-SID). We performed 24-h incubation experiments in the Eastern Tropical South Pacific (ETSP) OMZ. This preliminary study shows that up to 28% of bacterial biomass may be consumed by protists in waters where oxygen concentrations were down to ~4.8 μM and up to 13% at a station with nitrite accumulation where oxygen concentrations were undetectable. Results also show that shipboard measurements of grazing rates were lower than rates measured from the same water using the MS-SID, suggesting that in situ experiments help to minimize artifacts that may be introduced when conducting incubation studies using waters collected from below the photic zone, particularly from oxygen-depleted regions of the water column.
    Description: This work was funded by the Agouron Institute, grant AI-M010.16.1 WHO to OU, M. Sullivan, and VE, and the Millenium Science Initiative, grant IC 120019. Ship time was provided the Chilean National Commission for Scientific and Technological Research (CONICYT) grant AUB 150006/12806.
    Keywords: OMZ ; Phagotrophy ; In situ technology ; Incubation studies ; ETSP ; Eastern Tropical South Pacific OMZ
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    α-Synuclein dimers impair vesicle fission during clathrin-mediated synaptic vesicle recycling (2017)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Cellular Neuroscience 11 (2017): 388, doi:10.3389/fncel.2017.00388.
    Description: α-Synuclein is a presynaptic protein that regulates synaptic vesicle (SV) trafficking. In Parkinson’s disease (PD) and several other neurodegenerative disorders, aberrant oligomerization and aggregation of α-synuclein lead to synaptic dysfunction and neurotoxicity. Despite evidence that α-synuclein oligomers are generated within neurons under physiological conditions, and that altering the balance of monomers and oligomers contributes to disease pathogenesis, how each molecular species of α-synuclein impacts SV trafficking is currently unknown. To address this, we have taken advantage of lamprey giant reticulospinal (RS) synapses, which are accessible to acute perturbations via axonal microinjection of recombinant proteins. We previously reported that acute introduction of monomeric α-synuclein inhibited SV recycling, including effects on the clathrin pathway. Here, we report the effects of α-synuclein dimers at synapses. Similar to monomeric α-synuclein, both recombinant α-synuclein dimers that were evaluated bound to small liposomes containing anionic lipids in vitro, but with reduced efficacy. When introduced to synapses, the α-synuclein dimers also induced SV recycling defects, which included a build up of clathrin-coated pits (CCPs) with constricted necks that were still attached to the plasma membrane, a phenotype indicative of a vesicle fission defect. Interestingly, both α-synuclein dimers induced longer necks on CCPs as well as complex, branching membrane tubules, which were distinct from the CCPs induced by a dynamin inhibitor, Dynasore. In contrast, monomeric α-synuclein induced a buildup of free clathrin-coated vesicles (CCVs), indicating an inhibition of clathrin-mediated endocytosis at a later stage during the clathrin uncoating process. Taken together, these data further support the conclusion that excess α-synuclein impairs SV recycling. The data additionally reveal that monomeric and dimeric α-synuclein produce distinct effects on clathrin-mediated endocytosis, predicting different molecular mechanisms. Understanding what these mechanisms are could help to further elucidate the normal functions of this protein, as well as the mechanisms underlying PD pathologies.
    Description: This study was supported by a research grant from the National Institutes of Health (NINDS/NIA R01NS078165 to JRM), research funds from the Marine Biological Laboratory (to JRM) and a research grant from Horizon 2020 Grant no. InCure EU Joint Programme—JPND (to LB).
    Keywords: Dynamin ; Dynasore ; Endocytosis ; Lamprey ; Reticulospinal synapse
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    Dark production of extracellular superoxide by the coral Porites astreoides and representative symbionts (2017)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Marine Science 3 (2016): 232, doi:10.3389/fmars.2016.00232.
    Description: The reactive oxygen species (ROS) superoxide has been implicated in both beneficial and detrimental processes in coral biology, ranging from pathogenic disease resistance to coral bleaching. Despite the critical role of ROS in coral health, there is a distinct lack of ROS measurements and thus an incomplete understanding of underpinning ROS sources and production mechanisms within coral systems. Here, we quantified in situ extracellular superoxide concentrations at the surfaces of aquaria-hosted Porites astreoides during a diel cycle. High concentrations of superoxide (~10's of nM) were present at coral surfaces, and these levels did not change significantly as a function of time of day. These results indicate that the coral holobiont produces extracellular superoxide in the dark, independent of photosynthesis. As a short-lived anion at physiological pH, superoxide has a limited ability to cross intact biological membranes. Further, removing surface mucus layers from the P. astreoides colonies did not impact external superoxide concentrations. We therefore attribute external superoxide derived from the coral holobiont under these conditions to the activity of the coral host epithelium, rather than mucus-derived epibionts or internal sources such as endosymbionts (e.g., Symbiodinium). However, endosymbionts likely contribute to internal ROS levels via extracellular superoxide production. Indeed, common coral symbionts, including multiple strains of Symbiodinium (clades A to D) and the bacterium Endozoicomonas montiporae LMG 24815, produced extracellular superoxide in the dark and at low light levels. Further, representative P. astreoides symbionts, Symbiodinium CCMP2456 (clade A) and E. montiporae, produced similar concentrations of superoxide alone and in combination with each other, in the dark and low light, and regardless of time of day. Overall, these results indicate that healthy, non-stressed P. astreoides and representative symbionts produce superoxide externally, which is decoupled from photosynthetic activity and circadian control. Corals may therefore produce extracellular superoxide constitutively, highlighting an unclear yet potentially beneficial role for superoxide in coral physiology and health.
    Description: This work was supported by a Postdoctoral Fellowship from the Ford Foundation (JD), the National Science Foundation under grants OCE 1225801 (JD) and OCE 1233612 (AA), the Ocean and Climate Change Institute of the Woods Hole Oceanographic Institution (CH), a BIOS Grant in aid award (SM), the Sidney Stern Memorial Trust (CH and AA), as well as an anonymous donor.
    Keywords: Coral ; Superoxide ; Reactive oxygen species ; Photosynthesis ; Symbiodinium ; Stress
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    Structural characterization of natural nickel and copper binding ligands along the US GEOTRACES Eastern Pacific Zonal Transect (2017)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Marine Science 3 (2016): 243, doi:10.3389/fmars.2016.00243.
    Description: Organic ligands form strong complexes with many trace elements in seawater. Various metals can compete for the same ligand chelation sites, and the final speciation of bound metals is determined by relative binding affinities, concentrations of binding sites, uncomplexed metal concentrations, and association/dissociation kinetics. Different ligands have a wide range of metal affinities and specificities. However, the chemical composition of these ligands in the marine environment remains poorly constrained, which has hindered progress in modeling marine metal speciation. In this study, we detected and characterized natural ligands that bind copper (Cu) and nickel (Ni) in the eastern South Pacific Ocean with liquid chromatography tandem inductively coupled plasma mass spectrometry (LC-ICPMS), and high-resolution electrospray ionization mass spectrometry (ESIMS). Dissolved Cu, Ni, and ligand concentrations were highest near the coast. Chromatographically unresolved polar compounds dominated ligands isolated near the coast by solid phase extraction. Offshore, metal and ligand concentrations decreased, but several new ligands appeared. One major ligand was detected that bound both Cu2+ and Ni2+. Based on accurate mass and fragmentation measurements, this compound has a molecular formula of [C20H21N4O8S2+M]+ (M = metal isotope) and contains several azole-like metal binding groups. Additional lipophilic Ni complexes were also present only in oligotrophic waters, with masses of 649, 698, and 712 m/z (corresponding to the 58Ni metal complex). Molecular formulae of [C32H54N3O6S2Ni]+ and [C33H56N3O6S2Ni]+ were determined for two of these compounds. Addition of Cu and Ni to the samples also revealed the presence of additional compounds that can bind both Ni and Cu. Although these specific compounds represent a small fraction of the total dissolved Cu and Ni pool, they highlight the compositional diversity and spatial heterogeneity of marine Ni and Cu ligands, as well as variability in the extent to which different metals in the same environment compete for ligand binding.
    Description: Support was provided by the National Science Foundation (NSF) program in Chemical Oceanography (OCE-1356747, OCE-1233261, OCE-1233733, OCE-1233502, and OCE-1237034), the NSF Science and Technology Center for Microbial Oceanography Research and Education (C-MORE; DBI-0424599), the Gordon and Betty Moore Foundation (#3298 and 3934), and the Simons Foundation (#329108, DR).
    Keywords: Copper ; Nickel ; Marine ligands ; Metal competition ; GEOTRACES ; Eastern Pacific
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    The genetic diversity of Mesodinium and associated cryptophytes (2017)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 7 (2016): 2017, doi:10.3389/fmicb.2016.02017.
    Description: Ciliates from the genus Mesodinium are globally distributed in marine and freshwater ecosystems and may possess either heterotrophic or mixotrophic nutritional modes. Members of the Mesodinium major/rubrum species complex photosynthesize by sequestering and maintaining organelles from cryptophyte prey, and under certain conditions form periodic or recurrent blooms (= red tides). Here, we present an analysis of the genetic diversity of Mesodinium and cryptophyte populations from 10 environmental samples (eight globally dispersed habitats including five Mesodinium blooms), using group-specific primers for Mesodinium partial 18S, ITS, and partial 28S rRNA genes as well as cryptophyte large subunit RuBisCO genes (rbcL). In addition, 22 new cryptophyte and four new M. rubrum cultures were used to extract DNA and sequence rbcL and 18S-ITS-28S genes, respectively, in order to provide a stronger phylogenetic context for our environmental sequences. Bloom samples were analyzed from coastal Brazil, Chile, two Northeastern locations in the United States, and the Pribilof Islands within the Bering Sea. Additionally, samples were also analyzed from the Baltic and Barents Seas and coastal California under non-bloom conditions. Most blooms were dominated by a single Mesodinium genotype, with coastal Brazil and Chile blooms composed of M. major and the Eastern USA blooms dominated by M. rubrum variant B. Sequences from all four blooms were dominated by Teleaulax amphioxeia-like cryptophytes. Non-bloom communities revealed more diverse assemblages of Mesodinium spp., including heterotrophic species and the mixotrophic Mesodinium chamaeleon. Similarly, cryptophyte diversity was also higher in non-bloom samples. Our results confirm that Mesodinium blooms may be caused by M. major, as well as multiple variants of M. rubrum, and further implicate T. amphioxeia as the key cryptophyte species linked to these phenomena in temperate and subtropical regions.
    Description: MJ thanks the funding support of the National Science Foundations Grants NSF-OCE 1031718 and NSF-IOS 1326228.
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    Santa Maria di Leuca province (Mediterranean Sea) : identification of suitable mounds for cold-water coral settlement using geomorphometric proxies and Maxent methods (2017)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Marine Science 4 (2017): 338, doi:10.3389/fmars.2017.00338.
    Description: The Santa Maria di Leuca (SML) cold-water coral province (northern Ionian Sea) has the largest occurrence of a living white coral community currently known in the Mediterranean Sea. Madrepora oculata and Lophelia pertusa, identified as marking sensitive habitats of relevance by the General Fisheries Commission for the Mediterranean, have been observed heterogeneously distributed on the summits of several mounds. This particularly patchy and uneven distribution in addition to their importance for regional biodiversity highlights the need to better understand their environmental preferences and predict their distribution. Bathymetric data (40 m resolution) was used to derive seafloor characteristics. A fine scale index quantifying the landscape elevation (Bathymetric Position Index at 120 m resolution) was used to select all the elevated features considered as candidate morphologies for potential coral mounds. Statistics on 22 known coral topped mounds were computed. Two statistical methods were then used to identify other potential coral mounds based on predictive variables. The first method, the Geomorphometric proxies method, consists in computing basic statistics of terrain variables, using them for a step-by-step classification in a quantitative approach to select a subset of candidate morphologies. The second method consists in using a predictive Habitat Suitability Model (Maxent model). The Geomorphometric proxies method identified 736 potential coral mounds while the Maxent method predicted 1,252 potential coral mounds. A subset of 517 potential coral mounds was common to both methods. The analysis of the contribution of each variable with the Maxent method showed that the variable “Vector Ruggedness Measure” at a resolution of 5 pixels (200 m) contributed to 53% of the final Maxent model, followed by the “Terrain Texture” index (31%) at a resolution of 11 pixels (440 m). The common potential coral mounds are mainly located in an area characterized by a mass transport deposit, also called the mounds area because of the roughness of the seafloor, in accordance with the high proportional contribution of the noticeable first roughness index to the Maxent model. The results highlight the importance of the global conservation of the entire Province, with white coral probably widespread over the entire 600 km2 SML area.
    Description: The Habitat Suitability model study was part of a post-doctoral grant funded by the “Agence de l'Eau Rhône Méditerranée & Corse” under Convention Number 2015 0348, Ifremer and ISMAR Bologna. We are grateful to all the participants and the P.I. of the Aplabes 2004; Aplabes 2005, HERMES M70-1, MEDECO 2007 (http://dx.doi.org/10.17600/7030090) and magic CoralFISH 2010 cruises. The authors also benefited from EU FP7 project CoralFish (Grant agreement number: 213144—http://www.eu-fp7-coralfish.net), the Flag Project Ritmare (Ricerca Italiana per il Mare), funded by the Italian Ministry of Universities and Research (MIUR) and the ESF COCARDE Network. FM was funded through a Ph. D. fellowship in Earth Sciences at the University of Milano-Bicocca.
    Keywords: Predictive habitat mapping ; Maxent ; Cold-water coral ; Ecological proxies ; Santa Maria di Leuca ; Mediterranean Sea
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    Metatranscriptional response of chemoautotrophic Ifremeria nautilei endosymbionts to differing sulfur regimes (2016)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 7 (2016): 1074, doi:10.3389/fmicb.2016.01074.
    Description: Endosymbioses between animals and chemoautotrophic bacteria are ubiquitous at hydrothermal vents. These environments are distinguished by high physico-chemical variability, yet we know little about how these symbioses respond to environmental fluctuations. We therefore examined how the γ-proteobacterial symbionts of the vent snail Ifremeria nautilei respond to changes in sulfur geochemistry. Via shipboard high-pressure incubations, we subjected snails to 105 μM hydrogen sulfide (LS), 350 μM hydrogen sulfide (HS), 300 μM thiosulfate (TS) and seawater without any added inorganic electron donor (ND). While transcript levels of sulfur oxidation genes were largely consistent across treatments, HS and TS treatments stimulated genes for denitrification, nitrogen assimilation, and CO2 fixation, coincident with previously reported enhanced rates of inorganic carbon incorporation and sulfur oxidation in these treatments. Transcripts for genes mediating oxidative damage were enriched in the ND and LS treatments, potentially due to a reduction in O2 scavenging when electron donors were scarce. Oxidative TCA cycle gene transcripts were also more abundant in ND and LS treatments, suggesting that I. nautilei symbionts may be mixotrophic when inorganic electron donors are limiting. These data reveal the extent to which I. nautilei symbionts respond to changes in sulfur concentration and species, and, interpreted alongside coupled biochemical metabolic rates, identify gene targets whose expression patterns may be predictive of holobiont physiology in environmental samples.
    Description: This work was supported by National Science Foundation Grants OCE-0732369 (to PG), DGE-1144152 (to RB), and (1151698 to FS) and the Alfred P. Sloan Foundation (grant RC944 to FS).
    Keywords: Ifremeria nautilei ; Chemoautotroph ; Endosymbiont ; Methanotrophic bacteria ; Sulfur oxidizers ; Metatranscriptomics ; Deep sea vents
    Repository Name: Woods Hole Open Access Server
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    IEEE Transactions on Magnetics Institutional Listings (2016)
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    Publication Date: 2016-07-19
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    Published by Institute of Electrical and Electronics Engineers (IEEE) on behalf of The IEEE Magnetics Society.
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    Technical areas and editors: AESS IEEE Aerospace & Electronic Systems Society (2016)
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    Publication Date: 2016-07-19
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    Topics: Electrical Engineering, Measurement and Control Technology , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
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    IEEE Engineering in Medicine and Biology Society (2016)
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    Publication Date: 2016-07-19
    Print ISSN: 0018-9294
    Electronic ISSN: 1558-2531
    Topics: Medicine , Technology
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    A Continuous Hand Gestures Recognition Technique for Human-Machine Interaction Using Accelerometer and Gyroscope Sensors (2016)
    Institute of Electrical and Electronics Engineers (IEEE)
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    Publication Date: 2016-07-19
    Description: Recent advances in smart devices have sustained them as a better alternative for the design of human–machine interaction (HMI), because they are equipped with accelerometer sensor, gyroscope sensor, and an advanced operating system. This paper presents a continuous hand gestures recognition technique that is capable of continuous recognition of hand gestures using three-axis accelerometer and gyroscope sensors in a smart device. To reduce the influence of unstableness of a hand making the gesture and compress the data, a gesture coding algorithm is developed. An automatic gesture spotting algorithm is developed to detect the start and end points of meaningful gesture segments. Finally, a gesture is recognized by comparing the gesture code with gesture database using dynamic time warping algorithm. In addition, a prototype system is developed to recognize the continuous hand gestures-based HMI. With the smartphone, the user is able to perform the predefined gestures and control smart appliances using the Samsung AllShare protocol.
    Print ISSN: 1530-437X
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    Topics: Electrical Engineering, Measurement and Control Technology
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    Fast Lithographic Mask Optimization Considering Process Variation (2016)
    Institute of Electrical and Electronics Engineers (IEEE)
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    Publication Date: 2016-07-19
    Description: As nanometer technology advances, conventional optical proximity correction (OPC) that minimizes the edge placement error (EPE) at the nominal process condition alone often leads to poor process windows. To improve the mask printability across various process corners, process-window OPC optimizes EPE for multiple process corners, but often suffers long runtime, due to repeated lithographic simulations. This paper presents an efficient process variation (PV)-aware mask optimization framework, namely PVOPC, to simultaneously minimize EPE and PV band with fast convergence. The PVOPC framework includes EPE-sensitivity-driven dynamic fragmentation, PV-aware EPE modeling, and correction with three new EPE-converging techniques and a systematic subresolution-assisted feature insertion algorithm. Experimental results show that our approach efficiently achieves high-quality EPE and PV band results.
    Print ISSN: 0278-0070
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    Introducing IEEE Collabratec (2016)
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    Publication Date: 2016-07-19
    Description: Advertisement, IEEE.
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    Design and Management of Sustainable and Resilient Supply Chains (2016)
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    Publication Date: 2016-07-19
    Description: Prospective authors are requested to submit new, unpublished manuscripts for inclusion in the upcoming event described in this call for papers.
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    Efficient Production Binning Using Octree Tessellation in the Alternate Measurements Space (2016)
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    Publication Date: 2016-07-19
    Description: Binning after volume production is a widely accepted technique to classify fabricated integrated circuits (ICs) into different clusters depending on different degrees of specification compliance. This allows the manufacturer to sell nonoptimal devices at lower rates, so adapting to customer’s quality-price requirements. The binning procedure can be carried out by measuring every single circuit performances, but this approach is costly and time-consuming. On the contrary, if alternate measurements are used to characterize the bins, the procedure is considerably enhanced. In such a case, the specification bin boundaries become arbitrary shape regions due to the highly nonlinear mappings between the specifications space and the alternate measurements space. The binning strategy proposed in this paper functions with the same efficiency regardless of these shapes. The digital encoding of the bins in the alternate measurements space using octrees is the key idea of the proposal. The strategy has two phases: 1) the training phase and 2) the binning phase. In the training phase, the specification bins are encoded using octrees. This first phase requires sufficient samples of each class to generate the octree under realistic variations, but it only needs to be performed once. The binning phase corresponds to the actual production binning of the fabricated ICs. This is achieved by evaluating the alternate measurements in the previously generated octree. The binning phase is fast due to the inherent sparsity of the octree data structure. In order to illustrate the proposal, the method has been applied to a band-pass Butterworth filter considering three specification bins as a proof of concept. Successful simulation results are reported showing considerable advantages as compared to a support vector machine (SVM)-based classifier. Similar bin misclassifications are obtained with both methods, 1.68% using octrees and 1.83% using SVM, while binning time is $5times $ times faster using octrees than using the SVM-based classifier.
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    Forthcoming Engineering Management Related Conferences (2016)
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    Publication Date: 2016-07-19
    Description: Presents information on forthcoming Engineering Management society conferences.
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    IEEE Technology and Engineering Management Society (2016)
    Institute of Electrical and Electronics Engineers (IEEE)
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    Publication Date: 2016-07-19
    Description: Provides a listing of the editors, board members, and current staff for this issue of the publication.
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    Dynamic Magnetomechanical Behavior of Tb x Dy 1– x Fe y Alloy Under Small-Signal AC Drive Fields Superposed With Various Bias Fields (2016)
    Institute of Electrical and Electronics Engineers (IEEE)
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    Publication Date: 2016-07-19
    Description: The small-signal vibration model of Tb x Dy 1– x Fe y plate was developed by mechanical-electrical analogy method. Based on the model, we demonstrated the reasonableness of measuring the small-signal magnetomechanical behaviors by a laser Doppler vibrometer. The strain coefficient of the Tb x Dy 1– x Fe y plates was measured as a function of frequency and bias field ( $H_{mathrm{ dc}})$ , and Young’s modulus, mechanical quality factor ( $Q_{m})$ , relative permeability, and magnetomechanical coupling coefficient were investigated as a function of $H_{mathrm{ dc}}$ . Many novel characteristics were observed under the drive of a small-signal field (7.96 A/m). The change tendency of the strain coefficient at resonance differs from that at low frequency, and the resonant strain coefficients are significantly high (>85 nm/A) in a wide range of bias field from 4.78 to 55.72 kA/m. Both the negative- $Delta E$ and positive- $Delta E$ effects are observed, and the negative- $Delta E$ effect in the low field range is also remarkable. In particular, $Q_{m}$ sharply decreases from the initial value of 104 to a minimum value of 11.4 and, then, increases slowly, and the ratio of the maximum variation of $Q_{m}$ over $H_{mathrm{ dc}}$ to the minimum value of $Q_{m}$ exceeds $sim 812.3$ %. This is an important systematic investigation on the small-signal dynamic magnetomechanical behavior of Tb x Dy 1– x Fe y , and the results are highly beneficial to the designing of magnetostrictive devices.
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    Simulations of Particle Trajectories in Hard Disk Drives Considering the Trapping Criterion (2016)
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    Publication Date: 2016-07-19
    Description: The presence of particles, which can intrude into the air bearing, is one of the most common factors in the failure of hard disk drives (HDDs). Previous studies have investigated particles trajectories with the assumption of ideal trapping or reflecting boundary conditions in air-filled drives. However, only the colliding particle with insufficient energy to escape the potential well will be trapped by the surface. In this paper, considering the particle-surface energy during the collision, the trapping criterion of the incident normal critical velocity ( $V_{text {ni}}^{mathrm {ast }})$ for Al 2 O 3 particles is developed as the boundary conditions for different colliding surfaces inside a 2.5 in drive. Then, trapping status for Al 2 O 3 particles and particles trajectories inside the drive are simulated by using the commercial computational fluid dynamics solver FLUENT with user-defined functions. The results reveal that the particles will travel longer distances until trapped by HDD components when considering the trapping criterion. In addition, smaller particles will more likely degrade the head–disk interface reliability, since they easily stick on the disk surface.
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    High-Speed, Low-Power, and Error-Free Asynchronous Write Circuit for STT-MRAM and Logic (2016)
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    Publication Date: 2016-07-19
    Description: Benefiting from its simple switching scheme (only a bidirectional current source), high-speed and low-power spin-transfer torque (STT) has been regarded as one of the most promising switching mechanisms for a magnetic tunnel junction (MTJ)-based non-volatile memory and logic circuits. However, it suffers from a number of reliability issues like write error induced by its intrinsic stochasticity, process variation, and so on. In order to reduce the write error rate, the mainstream solution is to enlarge the write pulse duration at the expense of write energy dissipation. Some self-terminated write circuits have been proposed to avoid the wasted write energy. But the hardware cost of these write circuits is especially large. In this paper, a novel cost-efficient self-terminated write circuit is proposed using two simple built-in sensing circuits. The proposed write circuit is simulated with a physics-based STT-MTJ compact model and a commercial CMOS 40 nm design kit. The simulation result shows about 35% reduction of circuit area and 10% lower energy consumption in comparison with that in prior work. In addition, the Error-Free write operation under process variation of both the CMOS transistor and the STT-MTJ is achieved due to its large sense margin ( $sim 320$ mV).
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    IEEE Technology and Engineering Management Society (2016)
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    Publication Date: 2016-07-19
    Description: Provides a listing of board members, committee members, editors, and society officers.
    Print ISSN: 0018-9391
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    A Tunable Majority Gate-Based Full Adder Using Current-Induced Domain Wall Nanomagnets (2016)
    Institute of Electrical and Electronics Engineers (IEEE)
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    Publication Date: 2016-07-19
    Description: Domain wall nanomagnet (DWNM)-based devices have been extensively studied as a promising alternative to the conventional CMOS technology in both the memory and logic implementations due to their non-volatility, near-zero standby power, and high integration density characteristics. In this paper, we leverage a physics-based model of a DWNM device to design a highly scalable current-mode majority gate to achieve a novel one bit full-adder (FA) circuit. The modeled DWNM specifications are calibrated with the experimentally measured data. The functionality of the proposed DWNM-based FA (DWNM-FA) is verified using a SPICE circuit simulator. The detailed analysis and the calculations have been performed to realize the proposed DWNM-FA delay and power consumption corresponding to the various induced input currents at different operating temperatures. The power-delay product of DWNM-FA is examined to tune the operation within the optimum induced input current region to obtain desired power-delay requirements over a range of 200 $mu text{A}$ to 1 mA at temperatures from 298 to 378 K. Finally, the comparison results exhibit 52% and 49% area improvement as well as 41% and 31% improvement in device count complexity over CMOS-based and magnetic tunnel junction-based FA designs, respectively.
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    Magnetic Transitions in Chemically Synthesized Nanoparticles of CoCr 2 O 4 (2016)
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    Publication Date: 2016-07-19
    Description: Bulk CoCr 2 O 4 undergoes a transition from paramagnetic to long-range ferrimagnetic phase at $T_{c}$ (94 K) to a long-range and/or short-range spiral order at $T_{s}$ ( $sim 24$ K), and finally shows a lock-in-transition below 15 K. The spiral component induces an electric polarization and also a spontaneous magnetization for which it is said to be multiferroic. Reducing the size of a CoCr 2 O 4 multiferroic material to $sim 50$ nm by a coprecipitation method, we obtain a pure cubic phase with space group, Fd3m and lattice parameter (8.334 ± 0.003 °A). A rich sequence of magnetic transitions are examined by measuring temperature and field-dependent magnetization and diffused neutron scattering (DNS) using polarized neutron at different temperatures. While paramagnetic to ferrimagnetic transition is enhanced from 97 K in bulk to 99 K at 0.5 kOe field, followed by a decrease in lock-in-transition ( $T_{L}$ ) from 15 K in bulk to 8 K, spiral ordering temperature does not show a significant change. A strong disagreement between paramagnetic moment obtained from the fitting of $chi ^{-1}=({T}/{C})+({1}/{chi _{o}})-({b}/{T-theta })$ and ferrimagnetic moment obtained from the $M$ versus $H$ loop taken at 2 K, nonsaturated magnetization at 50–100 kOe field, two order of magnitude higher coercivity ( $H_{c}$ ), and splitting of ac susceptibly confirm the core–shell structure of the particles. Furthermore, a magnetic scattering analysis clearly shows that while the paramagnetic to ferrimagnetic transition is continuous, the spiral ordering is sharp, short range, and commensurate in contrast to incommensurate spiral order observed single crystal of CoCr 2 O 4 .
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    Energy-Preserving Methods and Torque Computation From Energy Balance in Electrical Machine Simulations (2016)
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    Publication Date: 2016-07-19
    Description: The finite-element analysis for the simulation of magnetic fields in electrical machines leads to an index-1 differential-algebraic equation (DAE) (as opposed to a conventional ordinary differential equation), because the electrical conductivity can be zero in certain regions. First, we construct a DAE-compatible time integration scheme which is energy-balanced, meaning that in a linear system, the input stored and lost powers sum exactly to zero. Second, we use a method based on the energy balance to compute torque. We show that the energy balance method approaches the virtual work principle applied at remeshing layer, as the time step is refined. A similar result also holds if the rotation of the rotor is implemented by Nitsche’s method, which is an instance of the so-called mortar methods.
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    Application of Magneto-Quasi-Static Approximation in the Finite Difference Time Domain Method (2016)
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    Publication Date: 2016-07-19
    Description: Investigations about induction sensors, electromagnetic launchers, shields, transformers, and power line-induced currents address increased number of low-frequency research and industrial applications. In general, a magneto-quasi-static (MQS) approximation is considered for the solutions of low-frequency problems in electromagnetics. This approximation leads to a diffusion process when displacement currents are neglected. However, keeping the displacement currents, Maxwell’s equations are valid at low frequencies. In this manner, the finite difference time domain (FDTD) method must be modified by the slowing down propagation velocity at low-frequency regime. In this paper, important and crucial points of the MQS approximation and its application in the FDTD method are clarified in the sense of analytical and numerical aspects. A material scaling technique of dielectric permittivity for the QS FDTD application is analyzed within comprehensive investigations. Furthermore, a criterion for choosing a proper value of scaling parameter will be revealed. Finally, effects of proper and improper values of the scaling parameter are presented with validated analytical and numerical results.
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    Electrode Design for Antiparallel Magnetization Alignment in Nanogap Devices (2016)
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    Publication Date: 2016-07-19
    Description: The ability to manipulate the relative magnetization alignment between ferromagnetic source and drain electrodes attached to a molecule or small quantum dot is a prerequisite for a number of spintronic device applications. The influence of electrode shape and field orientation on pairwise magnetization reversal mechanisms in nanogap and point-contact structures is investigated here using micromagnetic simulations. A favorable device geometry and setup are identified for enabling planar, monodomain source and drain electrodes with a magnetization alignment that may be controllably switched between a parallel and antiparallel configuration.
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    Impact of Ferrite Shield Properties on the Low-Power Inductive Power Transfer (2016)
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    Publication Date: 2016-07-19
    Description: In typical inductive power transfer (IPT) applications, soft magnetic materials are employed in both transmitter and receiver coils as low reluctance paths in order to improve the inductive coupling and support the guidance of magnetic flux. Considering their critical role in the overall performance, this paper investigates the impact of magnetic material properties on the basic features of inductive powering systems. To this end, a group of Ni–Zn and Ni–Cu–Zn spinel ferrite samples with a wide value range of magnetic properties is prepared. The materials are characterized in terms of their structural and magnetic properties, and they are used to build various substrate assemblies for the IPT transmitter (Tx) coil. Conducting Al and Cu sheets and biasing permanent magnets are combined with ferrite disks to simulate common Tx coil designs. This allows the identification of the correlation between the material properties, especially power losses, and the measured power transfer efficiency and shielding effectiveness.
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    IEEE Magnetics Society Information (2016)
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    Publication Date: 2016-07-19
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    Autonomous crabbing by estimating wind using only GPS velocity (2016)
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    Publication Date: 2016-07-19
    Description: This paper presents a method to estimate steady wind and a maneuvering strategy for loitering under a strong, steady wind. The wind estimation uses Global Positioning System velocity only through a novel filter design without airspeed measurement. The wind estimate is then used to guide the aircraft to crab in a direction perpendicular to the wind, thereby avoiding large changes in flight variables if an orbit-type maneuver is attempted. The proposed method is demonstrated through flight tests.
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    Biased estimators for spinning antenna DOA measurements (2016)
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    Publication Date: 2016-07-19
    Description: We propose biased estimators to find the direction of arrival of emitters present in the mainlobe of a spinning antenna-based electronic intelligence system. The proposed estimators were constructed by using Bayesian techniques and by performing a linear transformation and an affine transformation on the maximum likelihood estimator. From a Monte Carlo simulation and experimental results, we demonstrate that the proposed estimators outperform the limit set by the popular performance benchmark, the Cramer-Rao lower bound.
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    Novel Methods for Sensing Acoustical Emissions From the Knee for Wearable Joint Health Assessment (2016)
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    Publication Date: 2016-07-19
    Description: Objective: We present the framework for wearable joint rehabilitation assessment following musculoskeletal injury. We propose a multimodal sensing (i.e., contact based and airborne measurement of joint acoustic emission) system for at-home monitoring. Methods: We used three types of microphones—electret, MEMS, and piezoelectric film microphones—to obtain joint sounds in healthy collegiate athletes during unloaded flexion/extension, and we evaluated the robustness of each microphone's measurements via: 1) signal quality and 2) within-day consistency. Results: First, air microphones acquired higher quality signals than contact microphones (signal-to-noise-and-interference ratio of 11.7 and 12.4 dB for electret and MEMS, respectively, versus 8.4 dB for piezoelectric). Furthermore, air microphones measured similar acoustic signatures on the skin and 5 cm off the skin (∼4.5× smaller amplitude). Second, the main acoustic event during repetitive motions occurred at consistent joint angles (intra-class correlation coefficient ICC(1, 1) = 0.94 and ICC(1, k) = 0.99). Additionally, we found that this angular location was similar between right and left legs, with asymmetry observed in only a few individuals. Conclusion: We recommend using air microphones for wearable joint sound sensing; for practical implementation of contact microphones in a wearable device, interface noise must be reduced. Importantly, we show that airborne signals can be measured consistently and that healthy left and right knees often produce a similar pattern in acoustic emissions. Significance: These proposed methods have the potential for enabling knee joint acoustics measurement outside the clinic/lab and permitting long-term monitoring of knee health for patients rehabilitating an acute knee joint injury.
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    Topics: Medicine , Technology
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    Chirp signal detection using FFT peak frequency difference [Correspondence] (2016)
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    Publication Date: 2016-07-19
    Description: A new method was proposed for chirp signal detection and estimation built on the frame-based fast Fourier transform (FFT). The proposed method uses the peak frequency difference between FFT frames to detect a chirp signal and estimate chirp rate. This approach differs from conventional methods and is easy to implement. It generates more accurate chirp rate estimation especially under a low signal-to-noise ratio. Simulation and experimental data are used to verify the proposed methods.
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    MS-QI: A Modulation Spectrum-Based ECG Quality Index for Telehealth Applications (2016)
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    Publication Date: 2016-07-19
    Description: As telehealth applications emerge, the need for accurate and reliable biosignal quality indices has increased. One typical modality used in remote patient monitoring is the electrocardiogram (ECG), which is inherently susceptible to several different noise sources, including environmental (e.g., powerline interference), experimental (e.g., movement artifacts), and physiological (e.g., muscle and breathing artifacts). Accurate measurement of ECG quality can allow for automated decision support systems to make intelligent decisions about patient conditions. This is particularly true for in-home monitoring applications, where the patient is mobile and the ECG signal can be severely corrupted by movement artifacts. In this paper, we propose an innovative ECG quality index based on the so-called modulation spectral signal representation. The representation quantifies the rate of change of ECG spectral components, which are shown to be different from the rate of change of typical ECG noise sources. The proposed modulation spectral-based quality index, MS-QI, was tested on 1) synthetic ECG signals corrupted by varying levels of noise, 2) single-lead recorded data using the Hexoskin garment during three activity levels (sitting, walking, running), 3) 12-lead recorded data using conventional ECG machines (Computing in Cardiology 2011 dataset), and 4) two-lead ambulatory ECG recorded from arrhythmia patients (MIT-BIH Arrhythmia Database). Experimental results showed the proposed index outperforming two conventional benchmark quality measures, particularly in the scenarios involving recorded data in real-world environments.
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    Generation of Autologous Platelet-Rich Plasma by the Ultrasonic Standing Waves (2016)
    Institute of Electrical and Electronics Engineers (IEEE)
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    Publication Date: 2016-07-19
    Description: Platelet-rich plasma (PRP) is a volume of autologous plasma that has a higher platelet concentration above baseline. It has already been approved as a new therapeutic modality and investigated in clinics, such as bone repair and regeneration, and oral surgery, with low cost-effectiveness ratio. At present, PRP is mostly prepared using a centrifuge. However, this method has several shortcomings, such as long preparation time (30 min), complexity in operation, and contamination of red blood cells (RBCs). In this paper, a new PRP preparation approach was proposed and tested. Ultrasound waves (4.5 MHz) generated from piezoelectric ceramics can establish standing waves inside a syringe filled with the whole blood. Subsequently, RBCs would accumulate at the locations of pressure nodes in response to acoustic radiation force, and the formed clusters would have a high speed of sedimentation. It is found that the PRP prepared by the proposed device can achieve higher platelet concentration and less RBCs contamination than a commercial centrifugal device, but similar growth factor (i.e., PDGF-ββ). In addition, the sedimentation process under centrifugation and sonication was simulated using the Mason–Weaver equation and compared with each other to illustrate the differences between these two technologies and to optimize the design in the future. Altogether, ultrasound method is an effective method of PRP preparation with comparable outcomes as the commercially available centrifugal products.
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    Resolving aliasing effect in the QML estimation of PPSs (2016)
    Institute of Electrical and Electronics Engineers (IEEE)
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    Publication Date: 2016-07-19
    Description: The quasimaximum likelihood (QML) estimator of polynomial-phase signals (PPSs) is based on the maximization of the short-time Fourier transform and suffers from aliasing when signals are sampled below the Nyquist sampling rate. In this paper, a phase unwrapping procedure has been proposed as an additional step in the QML to estimate parameters of such signals. Statistical study has shown excellent performance of the proposed approach.
    Print ISSN: 0018-9251
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    Topics: Electrical Engineering, Measurement and Control Technology , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
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    A Wireless Sensor for Real-Time Monitoring of Tensile Force on Sutured Wound Sites (2016)
    Institute of Electrical and Electronics Engineers (IEEE)
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    Publication Date: 2016-07-19
    Description: A new wireless sensor was designed, fabricated, and applied for in situ monitoring of tensile force at a wound site. The sensor was comprised of a thin strip of magnetoelastic material with its two ends connected to suture threads for securing the sensor across a wound repair site. Since the sensor was remotely interrogated by applying an ac magnetic field and capturing the resulting magnetic field, it did not require direct wire connections to an external device or internal battery for long-term use. Due to its magnetoelastic property, the application of a tensile force changed the magnetic permeability of the sensor, altering the amplitude of the measured magnetic field. This study presents two sensor designs: one for high and one for low-force ranges. A sensor was fabricated by directly adhering the magnetoelastic strip to the suture. This sensor showed good sensitivity at low force, but its response saturated at about 1.5 N. To monitor high tensile force, the magnetoelastic strip was attached to a metal strip for load sharing. The suture thread was attached to the both ends of the metal strip so only a fraction of the applied force was directed to the sensor, allowing it to exhibit good sensitivity even at 44.5 N. The sensor was applied to two ex vivo models: a sutured section of porcine skin and a whitetail deer Achilles tendon. The results demonstrate the potential for in vivo force monitoring at a wound repair site.
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    Detection of the Third Heart Sound Based on Nonlinear Signal Decomposition and Time–Frequency Localization (2016)
    Institute of Electrical and Electronics Engineers (IEEE)
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    Publication Date: 2016-07-19
    Description: This study presents a precise way to detect the third ( $S_{3}$ ) heart sound, which is recognized as an important indication of heart failure, based on nonlinear single decomposition and time–frequency localization. The detection of the $S_{3}$ is obscured due to its significantly low energy and frequency. Even more, the detected $S_{3}$ may be misunderstood as an abnormal second heart sound with a fixed split, which was not addressed in the literature. To detect such $S_{3}$ , the Hilbert vibration decomposition method is applied to decompose the heart sound into a certain number of subcomponents while intactly preserving the phase information. Thus, the time information of all of the decomposed components are unchanged, which further expedites the identification and localization of any module/section of a signal properly. Next, the proposed localization step is applied to the decomposed subcomponents by using smoothed pseudo Wigner–Ville distribution followed by the reassignment method. Finally, based on the positional information, the $S_{3}$ is distinguished and confirmed by measuring time delays between the $S_{2}$ and $S_{3}$ . In total, 82 sets of cardiac cycles collected from different databases including Texas Heart Institute database are examined for evaluation of the proposed method. The result analysis shows that the proposed method can detect the $S_{3}$ correctly, even when the - ormalized temporal energy of $S_{3}$ is larger than 0.16, and the frequency of those is larger than 34 Hz. In a performance analysis, the proposed method demonstrates that the accuracy rate of $S_{3}$ detection is as high as 93.9%, which is significantly higher compared with the other methods. Such findings prove the robustness of the proposed idea for detecting substantially low-energized $S_{3}$ .
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    Simultaneous Electromagnetic Tracking and Calibration for Dynamic Field Distortion Compensation (2016)
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    Publication Date: 2016-07-19
    Description: Electromagnetic (EM) tracking systems are highly susceptible to field distortion. The interference can cause measurement errors up to a few centimeters in clinical environments, which limits the reliability of these systems. Unless corrected for, this measurement error imperils the success of clinical procedures. It is therefore fundamental to dynamically calibrate EM tracking systems and compensate for measurement error caused by field distorting objects commonly present in clinical environments. We propose to combine a motion model with observations of redundant EM sensors and compensate for field distortions in real time. We employ a simultaneous localization and mapping technique to accurately estimate the pose of the tracked instrument while creating the field distortion map. We conducted experiments with six degrees-of-freedom motions in the presence of field distorting objects in research and clinical environments. We applied our approach to improve the EM tracking accuracy and compared our results to a conventional sensor fusion technique. Using our approach, the maximum tracking error was reduced by 67% for position measurements and by 64% for orientation measurements. Currently, clinical applications of EM trackers are hampered by the adverse distortion effects. Our approach introduces a novel method for dynamic field distortion compensation, independent from preoperative calibrations or external tracking devices, and enables reliable EM navigation for potential applications.
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    A Wearable Device for Monitoring Sweat Rates via Image Analysis (2016)
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    Publication Date: 2016-07-19
    Description: A feasibility study on a new technique capable of monitoring localized sweat rate is explored in this paper. Wearable devices commonly used in clinical practice for sweat sampling (i.e., Macroducts) were positioned on the body of an athlete whose sweat rate was then monitored during cycling sessions. The position at which the sweat fills the Macroduct was indicated by a contrasting marker and captured via a series of time-stamped photos or a video recording of the device during an exercise period. Given that the time of each captured image/frame is known (either through time stamp on photos or the constant frame rate of the video capture), it was, therefore, possible to estimate the sweat flow rate through a simple calibration model. The importance of gathering such valuable information is described, together with the results from a number of exercise trials to investigate the viability of this approach.
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    A Novel Analysis Technique for Transcutaneous Measurement of Glomerular Filtration Rate With Ultralow Dose Marker Concentrations (2016)
    Institute of Electrical and Electronics Engineers (IEEE)
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    Publication Date: 2016-07-19
    Description: Objective: A novel high-precision approach [lifetime-decomposition measurement (LTDM)] for the assessment of the glomerular filtration rate (GFR) based on clearance measurements of exogenous filtration marker. Methods: The time-correlated single photon counting (TCSPC) acquisition in combination with a new decomposition method allows the separation of signal and background from transcutaneous measurements of GFR. Results: The performance of LTDM is compared versus the commercially available NIC-kidney patch-based system for transcutaneous GFR measurement. Measurements are performed in awake Sprague Dawley (SD) rats. Using the standard concentration required for the NIC-kidney system [7-mg/100-g body weight (b.w.) FITC-Sinistrin] as reference, the mean difference (bias) of the elimination curves GFR between LTDM and NIC-kidney was 4.8%. On the same animal and same day, the capability of LTDM to measure GFR with a FITC-Sinistrin dose reduced by a factor of 200 (35-μg/100-g b.w.) was tested as well. The mean differences (half lives with low dose using LTDM compared with those using first, the NIC-Kidney system and its standard concentration, and second, LTDM with the same concentration as for the NIC-Kidney system) were 3.4% and 4.5%, respectively. Conclusion: We demonstrate that with the LTDM strategy substantial reductions in marker concentrations are possible at the same level of accuracy. Significance: LTDM aims to resolve the issue of the currently necessary large doses of fluorescence tracer required for transcutaneous GFR measurement. Due to substantially less influences from autofluorescence and artifacts, the proposed method outperforms other existing techniques for accurate percutaneous organ function measurement.
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    Tracking Neural Modulation Depth by Dual Sequential Monte Carlo Estimation on Point Processes for Brain–Machine Interfaces (2016)
    Institute of Electrical and Electronics Engineers (IEEE)
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    Publication Date: 2016-07-19
    Description: Classic brain–machine interface (BMI) approaches decode neural signals from the brain responsible for achieving specific motor movements, which subsequently command prosthetic devices. Brain activities adaptively change during the control of the neuroprosthesis in BMIs, where the alteration of the preferred direction and the modulation of the gain depth are observed. The static neural tuning models have been limited by fixed codes, resulting in a decay of decoding performance over the course of the movement and subsequent instability in motor performance. To achieve stable performance, we propose a dual sequential Monte Carlo adaptive point process method, which models and decodes the gradually changing modulation depth of individual neuron over the course of a movement. We use multichannel neural spike trains from the primary motor cortex of a monkey trained to perform a target pursuit task using a joystick. Our results show that our computational approach successfully tracks the neural modulation depth over time with better goodness-of-fit than classic static neural tuning models, resulting in smaller errors between the true kinematics and the estimations in both simulated and real data. Our novel decoding approach suggests that the brain may employ such strategies to achieve stable motor output, i.e., plastic neural tuning is a feature of neural systems. BMI users may benefit from this adaptive algorithm to achieve more complex and controlled movement outcomes.
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    IEEE Transactions on Biomedical Engineering (T-BME) (2016)
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    Publication Date: 2016-07-19
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    DeMixGen: Deterministic Mixed-Signal Layout Generation With Separated Analog and Digital Signal Paths (2016)
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    Publication Date: 2016-07-19
    Description: With shrinking process technology, decreasing supply voltage, and increasing clock frequency, noise reduction becomes more and more crucial to the success of modern mixed-signal system-on-chip design. To eliminate the switching noise due to crosstalk coupling between analog and digital signals, it is essential to fully separate the routing paths of analog and digital nets when generating mixed-signal layouts. Different from previous works which cannot fully separate analog and digital routing paths, this paper presents a novel hierarchical deterministic mixed-signal layout synthesis approach with the separation of analog and digital signal paths for switching noise elimination. Experimental results based on a third-order $ {Sigma Delta }$ modulator show that the proposed approach can result in various layouts with separated analog and digital signal paths while achieving better signal-to-noise and distortion ratio, and overall performance specifications.
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    Bayesian Model Fusion: Large-Scale Performance Modeling of Analog and Mixed-Signal Circuits by Reusing Early-Stage Data (2016)
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    Publication Date: 2016-07-19
    Description: Efficient performance modeling of today’s analog and mixed-signal circuits is an important yet challenging task, due to the high-dimensional variation space and expensive circuit simulation. In this paper, we propose a novel performance modeling algorithm that is referred to as Bayesian model fusion (BMF) to address this challenge. The key idea of BMF is to borrow the information collected from an early stage (e.g., schematic level) to facilitate efficient performance modeling at a late stage (e.g., post layout). Such a goal is achieved by statistically modeling the performance correlation between early and late stages through Bayesian inference. Furthermore, to make the proposed BMF method of practical utility, four implementation issues, including: 1) prior mapping; 2) missing prior knowledge; 3) fast solver; and 4) prior and hyper-parameter selection, are carefully considered in this paper. Two circuit examples designed in a commercial 32 nm CMOS silicon on insulator process demonstrate that the proposed BMF method achieves up to $9times $ runtime speed-up over the traditional modeling technique without surrendering any accuracy.
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    IEEE International Symposium on Biomedical Imaging (2016)
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    Publication Date: 2016-07-19
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    Ieee transactions on computer-aided design of integrated circuits and systems society information (2016)
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    Publication Date: 2016-07-19
    Description: Provides a listing of the editors, board members, and current staff for this issue of the publication.
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    Layout-Dependent Effects-Aware Analytical Analog Placement (2016)
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    Publication Date: 2016-07-19
    Description: Layout-dependent effects (LDEs) have become a critical issue in modern analog and mixed-signal circuit designs. The three major sources of LDEs, well proximity, length of oxide diffusion, and oxide-to-oxide spacing, significantly affect the threshold voltage and mobility of devices in advanced technology nodes. In this paper, we propose the first work to consider the three major sources of LDEs during analog placement. We first transform the three LDE models into nonlinear analytical placement models. Then an LDE-aware analytical analog placement algorithm is presented to mitigate the influence of the LDEs while improving circuit performance. Experimental results show that our placement algorithm can effectively and efficiently reduce the LDE-induced variations and improve circuit performance.
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    A Computationally Efficient Reconfigurable FIR Filter Architecture Based on Coefficient Occurrence Probability (2016)
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    Publication Date: 2016-07-19
    Description: Reconfigurable digital filter is being widely used in applications such as communication and signal processing. Its performance, power consumption, and logic resource utilization are the major factors to be taken into consideration when designing the filters. This paper proposes a concise canonic signed digit coefficient grouping method aiming at reducing the number of common subexpressions (CSs). Further, we statistically analyze every CS occurance for numerous sorts of the finite-impulse response (FIR) filters and obtain characterization of the distribution behavior for all the possible CS patterns in a 16-bit coefficient. Thus, a novel processing element structure is proposed to form a medium-grain array for computationally efficient realization of reconfigurable FIR filter. The experiment results suggest such design implementations typically achieve 21% reduction in silicon area, 20% decrease in power consumption, and 14% improvement in operation speed in comparison to other conventional FIR architectures.
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    Integrated Functional and Washing Routing Optimization for Cross-Contamination Removal in Digital Microfluidic Biochips (2016)
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    Publication Date: 2016-07-19
    Description: Digital microfluidic biochips (DMFBs) are gaining increasing attention with promising applications for automating and miniaturizing laboratory procedures in biochemistry. In DMFBs, cross-contamination of droplets with different biomolecules is a major issue, which causes significant errors in bioassays. Washing operations are introduced to clean the cross-contamination spots. However, existing works have oversimplified assumptions on the washing behavior, which either assume infinite washing capacity, or ignore the routing conflicts between functional and washing droplets. This paper proposes the first integrated functional and washing droplet routing flow, which considers practical issues including the finite washing capacity constraint, and the routing conflicts between functional and washing droplets. Washing droplets of different sizes are also proposed to wash the congested cross-contamination spots. Effectiveness of the proposed method is validated by real-life biochemical applications.
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    Efficient Layer Assignment of Bus-Oriented Nets in High-Speed PCB Designs (2016)
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    Publication Date: 2016-07-19
    Description: It is known that bus-oriented escape routing and area routing are necessary in a high-speed printed circuit board (PCB) design. In this paper, given a set of global routed buses in a high-speed PCB design, it is assumed that the routed nets in a single bus are represented as a bus-oriented net between two escaped boundary pins. Based on the construction of a virtual wall between two circuit components, the connection transformation of the given bus-oriented nets inside a closed region and the construction of a covering graph for the represented intervals, an iterative modified left-edge algorithm is proposed to minimize the number of the assigned layers and assign all the bus-oriented nets onto the available layers. Compared with Tsai’s algorithm, the experimental results show that our proposed algorithm reduces 15.0% of the layer number and 21.9% of CPU time for six tested examples on the average, respectively. Compared with Chin’s algorithm, the experimental results show that our proposed algorithm use less CPU time to reduce 15.0% of the layer number for six tested examples on the average.
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    IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems publication information (2016)
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    Publication Date: 2016-07-19
    Description: Provides a listing of the editors, board members, and current staff for this issue of the publication.
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    Innovation and technology management in the entrepreneurial era (2016)
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    Publication Date: 2016-07-19
    Description: Prospective authors are requested to submit new, unpublished manuscripts for inclusion in the upcoming event described in this call for papers.
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    Workload Change Point Detection for Runtime Thermal Management of Embedded Systems (2016)
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    Publication Date: 2016-07-19
    Description: Applications executed on multicore embedded systems interact with system software [such as the operating system (OS)] and hardware, leading to widely varying thermal profiles which accelerate some aging mechanisms, reducing the lifetime reliability. Effectively managing the temperature therefore requires: 1) autonomous detection of changes in application workload and 2) appropriate selection of control levers to manage thermal profiles of these workloads. In this paper, we propose a technique for workload change detection using density ratio-based statistical divergence between overlapping sliding windows of CPU performance statistics. This is integrated in a runtime approach for thermal management, which uses reinforcement learning to select workload-specific thermal control levers by sampling on-board thermal sensors. Identified control levers override the OSs native thread allocation decision and scale hardware voltage–frequency to improve average temperature, peak temperature, and thermal cycling. The proposed approach is validated through its implementation as a hierarchical runtime manager for Linux, with heuristic-based thread affinity selected from the upper hierarchy to reduce thermal cycling and learning-based voltage–frequency selected from the lower hierarchy to reduce average and peak temperatures. Experiments conducted with mobile, embedded, and high performance applications on ARM-based embedded systems demonstrate that the proposed approach increases workload change detection accuracy by an average ${3.4times }$ , reducing the average temperature by 4 °C–25 °C, peak temperature by 6 °C–24 °C, and thermal cycling by 7%–35% over state-of-the-art approaches.
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    Three-Tier Modular Structural Health Monitoring Framework Using Environmental and Operational Condition Clustering for Data Normalization: Validation on an Operational Wind Turbine System (2016)
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    Publication Date: 2016-07-19
    Description: This paper proposes a three-tier algorithmic framework as the basis for the flexible design of data-driven structural health monitoring (SHM) systems. The three major functions of the SHM system, including data normalization, feature extraction, and hypothesis testing (HT), are mapped to the three layers of the framework. The first tier of the framework is devoted to data normalization. Machine learning (ML) methods are adopted to normalize available data sets by binning data sets to similar environmental and operational conditions (EOCs) of the system. Specifically, affinity propagation clustering is used to delineate data into groups of similar EOC. Once data are normalized by EOC, the second tier of the framework extracts features from the data to serve as condition parameters (CPs) for damage assessment. To ascertain the health state of the structure, the third tier of the framework is devoted to statistical analysis of the CP through HT. An intrinsic goal of the study is to explore the modularity of the three tier framework as a means of offering SHM system designers opportunity to explore and test different computational block sets at each layer to maximize the detection capability of the SHM system. Various realizations of the three-tier modular framework are presented and applied to acceleration and EOC data collected from an operational 3-kW wind turbine. In total, 354 data sets are collected from the turbine, including tower lateral accelerations in two orthogonal directions at six heights, wind speed and wind direction; 317 of the data sets correspond to the wind turbine in a healthy state and 37 with the wind turbine in a damage state. Using quantitative metrics derived from receiver operating characteristic (ROC) curves, the damage classification capabilities of the framework are validated and shown to accurately identify intentionally introduced damage in the turbine.
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    Open Access (2016)
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    how can you get your idea to market first (2016)
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    Print ISSN: 0018-9219
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    Back Cover (2016)
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    Measuring Crack Movement in Reinforced Concrete Using Digital Image Correlation: Overview and Application to Shear Slip Measurements (2016)
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    Publication Date: 2016-07-19
    Description: Reinforced concrete infrastructure assets built during the last century are required to stay in-service beyond their intended design lives, which requires techniques that allow the effects of deterioration and overloading to be monitored to ensure these assets are still fit for purpose. One such indicator of distress in a reinforced concrete structure is crack movement; models have been proposed that allow the internal stresses within a structure to be estimated if crack width and slip can be measured. This paper introduces a technique that uses digital image correlation (DIC) to measure not only crack width but also crack slip. The effect of curvature on this measurement technique is discussed and a method for minimizing the errors due to curvature is presented. The technique is used to measure crack width and slip in reinforced concrete beams with both small crack slip and significant crack slip. The results suggest that the technique can be used to measure crack movement in beams once the effects of curvature are accounted for. Future research in this area will focus on development of this technique for use in the field.
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    Topics: Electrical Engineering, Measurement and Control Technology
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    Predictive Guided Wave Models Through Sparse Modal Representations (2016)
    Institute of Electrical and Electronics Engineers (IEEE)
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    Publication Date: 2016-07-19
    Description: Ultrasonic guided waves are an attractive tool for structural health monitoring due to their capability to rapidly assess large regions of a structure. Yet, most guided wave based methods for detecting, locating, and classifying structural damage rely on our ability to accurately predict guided wave behavior. Characterizing and predicting guided wave behavior is difficult, particularly in mechanically complex materials such as fiber-reinforced composites. In this paper, we address this challenge through a sparse wavenumber analysis framework. Sparse wavenumber analysis integrates physics-based models, signal processing algorithms for compressive sensing, and a small number of local measurements to predict global wave behavior. We implement sparse wavenumber analysis for three wave systems: standing waves on a string, Lamb waves in an isotropic plate, and guided waves in a unidirectional, anisotropic plate. Through the use of simulation and experimental data, we show that sparse wavenumber analysis can accurately recover the sparse representations (i.e., the eigenmodes) of each system and then use these representations to predict global wave behavior. For the anisotropic plate, we accurately predict 149765 experimental time-domain measurements from only 36 local measurements.
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    Independent Component Analysis for Improved Defect Detection in Guided Wave Monitoring (2016)
    Institute of Electrical and Electronics Engineers (IEEE)
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    Publication Date: 2016-07-19
    Description: Guided wave sensors are widely used in a number of industries and have found particular application in the oil and gas industry for the inspection of pipework. Traditionally this type of sensor was used for one-off inspections, but in recent years there has been a move towards permanent installation of the sensor. This has enabled highly repeatable readings of the same section of pipe, potentially allowing improvements in defect detection and classification. This paper proposes a novel approach using independent component analysis to decompose repeat guided wave signals into constituent independent components. This separates the defect from coherent noise caused by changing environmental conditions, improving detectability. This paper demonstrates independent component analysis applied to guided wave signals from a range of industrial inspection scenarios. The analysis is performed on test data from pipe loops that have been subject to multiple temperature cycles both in undamaged and damaged states. In addition to processing data from experimental damaged conditions, simulated damage signals have been added to “undamaged” experimental data, so enabling multiple different damage scenarios to be investigated. The algorithm has also been used to process guided wave signals from finite element simulations of a pipe with distributed shallow general corrosion, within which there is a patch of severe corrosion. In all these scenarios, the independent component analysis algorithm was able to extract the defect signal, rejecting coherent noise.
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    Statistical Performance Assessment of an NDE-Based SHM-DP Methodology for the Remaining Fatigue Life Prediction of Monitored Structural Components and Systems (2016)
    Institute of Electrical and Electronics Engineers (IEEE)
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    Publication Date: 2016-07-19
    Description: Integrated structural health monitoring and damage prognosis (SHM-DP) methodologies, coupled with sensor-based nondestructive evaluation (NDE) techniques, are becoming increasingly important for the near-real-time condition assessment (i.e., SHM) and future performance predictions (i.e., DP) of aging mechanical systems, civil structures, and infrastructure networks, as well as automotive, naval, and aerospace vehicles. A successful SHM-DP strategy, capable of identifying all critical damage mechanisms while accounting for all relevant sources of uncertainty, can be used as an advanced tool to effectively and optimally manage the life-cycle of the monitored system, recursively forecast its remaining useful life (RUL), and ultimately reduce the overall ownership cost through dynamic reliability-based inspection and maintenance (RBIM) plans, system downtime minimization, catastrophic failure prevention, and potential RUL extension. In this perspective, fatigue damage propagation is one of the most critical and unpredictable deterioration processes for a large variety of structural and mechanical systems that are subjected repeatedly to cyclic and/or random operational loading during their service life. Within this limited scope, the authors developed a comprehensive NDE-based SHM-DP framework for recursively predicting the time-varying system reliability and the remaining fatigue life (RFL) of monitored systems subjected to deterioration by multi-site fatigue damage propagation. This paper provides a brief overview of the proposed framework and then uses a set of experimental fatigue test data to perform a thorough statistical performance assessment of the developed methodology at the local reliability component level (i.e., single damage mechanism and single damage location) including NDE detectability and measurement uncertainty as well as both load and model parameter uncertainty.
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    What the Public Knew About Wireless Before Titanic (2016)
    Institute of Electrical and Electronics Engineers (IEEE)
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    Publication Date: 2016-07-19
    Print ISSN: 0018-9219
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    Strain Sensing Sheets for Structural Health Monitoring Based on Large-Area Electronics and Integrated Circuits (2016)
    Institute of Electrical and Electronics Engineers (IEEE)
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    Publication Date: 2016-07-19
    Description: Accurate and reliable damage characterization (i.e., damage detection, localization, and evaluation of extent) in civil structures and infrastructure is an important objective of structural health monitoring (SHM). Highly accurate and reliable characterization of damage at early stages requires continuous or quasi-continuous direct sensing of the critical parameters. Direct sensing requires deploying dense arrays of sensors, to enhance the probability that damage will result in signals that can be directly acquired by the sensors. However, coverage by dense arrays of sensors over the large areas that are of relevance represents an enormous challenge for current technologies. Large area electronics (LAE) is an emerging technology that can enable the formation of dense sensor arrays spanning large areas (several square meters) on flexible substrates. This paper explores the requirements and technology for a sensing sheet for SHM based on LAE and crystalline silicon CMOS integrated circuits (ICs). The sensing sheet contains a dense array of thin-film full-bridge resistive strain sensors, along with the electronics for strain readout, full-system self-powering, and communication. Research on several stages is presented for translating the sensing sheet to practical SHM applications. This includes experimental characterization of an individual sensor’s response when exposed to cracks in concrete and steel; theoretical and experimental performance evaluation of various geometrical parameters of the sensing sheet; and development of the electronics necessary for sensor readout, power management, and sensor-data communication. The concept of direct sensing has been experimentally validated, and the potential of a sensing sheet to provide direct sensing and successful damage characterization has been evaluated in the laboratory setting. A prototype of the sensing sheet has also been successfully developed and independently characterized in the laboratory, meeting the- required specifications. Thus, a sensing sheet for SHM applications shows promise both in terms of practicality and effectiveness.
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    Bayesian Inference for Inversion in Synthetic Aperture Imaging Radiometry (2016)
    Institute of Electrical and Electronics Engineers (IEEE)
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    Publication Date: 2016-07-22
    Description: The inverse problem of synthetic aperture imaging radiometers (SAIRs) has been demonstrated to be not well posed. The regularization methods are crucial for providing unique and stable solutions in the reconstruction of radiometric brightness temperature (BT) maps. Different to deterministic ones, a new approach is presented by referring to the rule of Bayesian inference, providing a probability model of regularized constraints to combat the ill-posedness of finite-dimensional discrete inverse problems. In addition, the SAIR inverse problem can be converted into the probability estimation of the reconstructed BT. Furthermore, in application to both uniformly and nonuniformly spaced arrays, our method can obtain the optimal solution adaptively and avoid the dilemma of choosing the optimal regularization parameter. Finally, simulation results illustrating the effectiveness and performance of the proposed method are provided.
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    Topics: Architecture, Civil Engineering, Surveying , Geography , Geosciences
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    Range-Cell-Focusing Algorithm Combined With Enhanced MUSIC for Close Target Imaging (2016)
    Institute of Electrical and Electronics Engineers (IEEE)
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    Publication Date: 2016-07-22
    Description: A range-cell-focusing algorithm is proposed in order to improve the quality of the target image. In a synthetic aperture radar (SAR) imaging system, the range resolution depends on the frequency bandwidth and determines the ability to distinguish between targets that are very close to each other. In cases where the resolution and the SNR from the environment are not adequate, targets cannot be accurately visualized. In order to successively classify targets that are close, we are combining an enhanced-multiple-signal-classification spectrum as a weighting function to reproduce the raw data. The proposed algorithm improves classification and separation for close targets while suppressing artifacts in the final images. The targets of interest are stationary point scatterers. The results are obtained from both simulated and experimental data to demonstrate that the proposed algorithm provides better performance than a conventional SAR imaging algorithm, the range migration algorithm.
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    Topics: Architecture, Civil Engineering, Surveying , Geography , Geosciences
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    Improved Multiscale Edge Detection Method for Polarimetric SAR Images (2016)
    Institute of Electrical and Electronics Engineers (IEEE)
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    Publication Date: 2016-07-22
    Description: This letter presents a multiscale edge detection method for multilook polarimetric synthetic aperture radar (PolSAR) images based on the nonsubsampled contourlet transform (NSCT). The NSCT can provide flexible multiscale and directional decomposition. In the multiscale decomposition, the coefficients of the nonsubsampled pyramid in the NSCT are calculated via maximizing the polarimetric contrast between the adjacent subband levels, instead of using the difference of the adjacent subbands as used in the additive noise model. By this way, we make the NSCT applicable to PolSAR data and multiband data. Then, the edges are detected in the NSCT domain based on a fusion of the directional subband coefficients at different scales. Experimental results with both simulated and real PolSAR data show that the present approach is robust to noise and the extracted edges are complete and continuous.
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    On the Spatial Resolution of GNSS Reflectometry (2016)
    Institute of Electrical and Electronics Engineers (IEEE)
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    Publication Date: 2016-07-22
    Description: A method for defining the spatial resolution of a Global Navigation Satellite System reflectometry delay–Doppler map (DDM) and of any derived geophysical product is proposed. An effective spatial resolution is derived as a function of measurement geometry and delay–Doppler (DD) interval, and as a more appropriate representation of resolution than the geometric resolution previously used in the literature. The definition more accurately accounts for variations in the scattered power across different pixels of the DDM and more accurately includes the power spreading effect caused by the Woodward ambiguity function. The dependence of the effective resolution on incidence angle, receiver altitude, and DD interval is analyzed and compared with the dependence of the geometric resolution with similar parameters.
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    Junction-Based Correspondence Estimation of Plant Point Cloud Data Using Subgraph Matching (2016)
    Institute of Electrical and Electronics Engineers (IEEE)
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    Publication Date: 2016-07-22
    Description: Laser scanner-captured 3-D point cloud data analysis is becoming more commonly used for remote sensing and plant science applications. Because of nonrigidity and complexity, reconstructing a 3-D model of a plant is extremely challenging. Existing algorithms often fail to find correct correspondences for plantlike thin structures. We address the problem of finding 3-D junction points in plant point cloud data as a first step of this correspondence matching process. Temporarily, we transform the 3-D problem into 2-D by performing appropriate coordinate transformations to the neighborhood of each 3-D point. Our proposed method has two steps. First, a statistical dip test of multimodality is performed to detect the nonlinearity of the local 2D structure. Then, each branch is approximated by sequential random-sample-consensus line fitting and a Euclidean clustering technique. The straight line parameters of each branch are extracted using total-least-squares estimation. Finally, the straight line equations are solved to determine if they intersect in the local neighborhood. Such junction points are good candidates for subsequent correspondence algorithms. Using these detected junction points, we formulate a correspondence algorithm as a subgraph matching problem and show that, without using traditional descriptor similarity-based matching, good correspondences can be obtained by simply considering geodesic distances among graph nodes. Experiments on synthetic and real ( Arabidopsis plant) data show that the proposed method outperforms the state of the art.
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    Improved Envisat Altimetry Ice Sheet Elevation Change Data Processing Algorithms Using Repeat-Track Analysis (2016)
    Institute of Electrical and Electronics Engineers (IEEE)
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    Publication Date: 2016-07-22
    Description: Repeat-track analysis is commonly utilized to generate elevation change time series from satellite radar altimetry over ice sheets. It requires surface gradient (SG) correction due primarily to orbital drifts and radar-related empirical corrections caused by radar scatters from ice surface and potential subsurface. In this letter, two approaches, namely, the use of a digital elevation model (DEM) and the modified repeat-track analysis, which uses the accumulated Envisat altimetry profiles, are applied to correct the SG over both Greenland ice sheet (GrIS) and Antarctic ice sheet (AIS). By comparing the root mean square (rms) of elevation change time series after SG correction, the percentage of data (rms< 1 m) obtained by using modified repeat-track analysis is found to be 85% and 88% for the GrIS and AIS, respectively, as opposed to 45% and 44% if the DEM method is used. Furthermore, three cases are studied to assess empirical corrections for elevation retrieved from both ice-1 and ice-2 algorithms over the AIS. We conclude that the modified repeat-track analysis is more effective to remove topographic induced error. For the ice-2 algorithm, waveform shape parameters are needed in addition to applying corrections from changes in backscatter coefficients. The trend of elevation changes from the ice-1 algorithm with only backscatter analysis agrees with that from the ice-2 algorithm with corrections from backscatter coefficient changes and waveform shape parameters. This study could provide a potential data processing recipe for generating improved satellite radar altimetry elevation time series over ice sheets.
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