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Coastal upwelling brings cooler, saltier, and nutrient-rich deep water upward to the surface. Upwelling fronts support enriched phytoplankton and zooplankton populations, thus having great influences on ocean ecosystems. We have developed a method to enable a Wave Glider (an autonomous surface vehicle) to autonomously detect and track an upwelling front. Unlike an autonomous underwater vehicle (AUV) which runs on a yo-yo trajectory to measure vertical profiles of water properties, a Wave Glider's measurements are confined to the surface (from the “float”) and a fixed depth of only several meters (from the submerged “glider”). However, an upwelling front presents a strong surface signature that a Wave Glider can detect. Because the upwelling process brings up cold water from depth, surface temperature in an upwelling region is considerably lower than that in stratified water. A Wave Glider can detect the upwelling front based on the horizontal gradient of the near-surface temperature. We have tested the algorithm by using previous AUV data (only using near-surface temperature measurements) and Wave Glider data. We plan to run field experiments in the summer of 2016 and report the results in the presentation.

There is a growing interest to develop microfluidic bioreactors and organ-on-chip platforms with integrated sensors to monitor their physicochemical properties and to maintain a well-controlled microenvironment for cultured organoids. Conventional sensing devices cannot be easily integrated with microfluidic organ-on-chip systems with low-volume bioreactors for continual monitoring. This paper reports on the development of a multi-analyte optical sensing module for dynamic measurements of pH and dissolved oxygen levels in the culture medium. The sensing system was constructed using low-cost electro-optics including light-emitting diodes and silicon photodiodes. The sensing module includes an optically transparent window for measuring light intensity, and the module could be connected directly to a perfusion bioreactor without any specific modifications to the microfluidic device design. A compact, user-friendly, and low-cost electronic interface was developed to control the optical transducer and signal acquisition from photodiodes. The platform enabled convenient integration of the optical sensing module with a microfluidic bioreactor. Human dermal fibroblasts were cultivated in the bioreactor, and the values of pH and dissolved oxygen levels in the flowing culture medium were measured continuously for up to 3 days. Our integrated microfluidic system provides a new analytical platform with ease of fabrication and operation, which can be adapted for applications in various microfluidic cell culture and organ-on-chip devices.

In this paper the spectrometer constructed by the E665 Collaboration is described. The spectrometer was built during the period 1982–87 and the first data were taken during the 1987–88 Fixed Target run of the Fermi National Accelerator Laboratory (FNAL) Tevatron. This is the first of a series of runs in which a comprehensive program of high energy muon scattering experiments will be performed.

Ocean sunfishes, Molidae, comprise the world’s heaviest bony fishes. They include the short mola,Mola ramsayi(Giglioli 1883), an important tourist draw at Nusa Penida and Nusa Lembongan, Bali, where SCUBA divers can observe ectoparasite-laden individuals being cleaned by smaller reef fishes. Despite widespread appeal, little is known about these fishes relative to regional oceanography. We present the first behavioral information for this species anywhere in the world. Satellite tag data indicate a wide thermal range (10–27.5°C) with depth occupation mostly (95%) in the upper 250 m and habitat preference near the bottom of the warm surface layer. One tag popped off as scheduled after 6 months off Nusa Penida, M. ramsayiin eastern regions of Indonesia, such as Alor, behavioral information of this species is essential for effective management and conservation of this valuable marine ecotourism asset.

Coastal upwelling occurs under the combined effect of wind stress and Earth's rotation. The nutrients carried up by upwelling have great impact on primary production and fisheries. For using autonomous underwater vehicles (AUVs) to investigate complex coastal upwelling ecosystems, we have developed algorithms for an AUV to autonomously distinguish between upwelling and stratified water columns based on the vertical temperature difference between shallow and deep depths, and to accurately detect an upwelling front based on the horizontal gradient of the vertical temperature difference in the water column. During a June 2011 experiment in Monterey Bay, California, the Dorado AUV flew on a transect from an upwelling shadow region (stratified water column), through an upwelling front, and into an upwelling water column. Running our algorithms, the AUV successfully classified the three distinct water types, accurately located the narrow front, and acquired targeted water samples from the three water types. Molecular analysis of the AUV-acquired water samples shows that mussels, calanoid copepods, and podoplean copepods were most abundant in the upwelling shadow region and nonexistent in the upwelling water column. Calanoid copepods were moderately abundant in the water samples collected from the upwelling front. These results are largely consistent with previous findings from zooplankton population surveys conducted with the Dorado AUV in Monterey Bay in 2009. The novel detecting and targeted sampling capabilities permit an AUV to autonomously conduct “surgical sampling” of a complex marine ecosystem.

The thermocline plays a key role in underwater acoustics and marine ecology. In oceanographic surveys, it is often desirable to detect the thermocline and track its spatio-temporal variation. Mobility of an autonomous underwater vehicle (AUV) makes it an efficient platform for thermocline tracking. In this paper, we present an autonomous algorithm for detecting and tracking the thermocline by an AUV. The key is detection and close tracking of the maximum vertical gradient of temperature. On August 31 and September 1, 2010, the Tethys AUV ran the algorithm to closely track the thermocline across a sharp temperature front in Monterey Bay, CA.

Coastal upwelling is a wind-driven ocean process. It brings cooler, saltier, and usually nutrient-rich deep water upward to replace surface water displaced offshore due to Ekman transport. The nutrients carried up by upwelling are important for primary production and fisheries. Ocean life can aggregate at the boundary between stratified water and upwelling water-the upwelling front. In an upwelling water column, temperature, salinity, and other water properties are much more homogeneous over depth than in stratified water. Drawing on this difference, we set up a key measure for differentiating upwelling and stratified water columns-the vertical temperature difference between shallow and deep depths. The vertical temperature difference is large in stratified water but small in upwelling water. Based on this classifier, we developed a method for an autonomous underwater vehicle (AUV) to autonomously detect and track an upwelling front. During the Controlled, Agile, and Novel Observing Network (CANON) Experiment in April 2011, the Tethys long-range AUV ran the algorithm to autonomously track an upwelling front in a dynamic coastal upwelling region in Monterey Bay, CA. The AUV transected the upwelling front 14 times over two days, providing a very high-resolution depiction of the front.

OBJECTIVE Insulin resistance (IR) confers risk for Type 2 diabetes and is associated with depressed mood. Neurons within the ventral striatum (VS) are sensitive to insulin levels and show altered function in the context of both IR and depression. Hence, VS may represent a critical component of a neural circuitry linking IR to depressed mood. METHODS Ninety adults (aged 30-50 years) free from major psychiatric illnesses and diabetes participated. Fasting blood was sampled, and participants completed a set of questionnaires (including the Beck Depression Inventory-II). Participants also underwent resting-state functional magnetic resonance imaging of the brain. Seed-based connectivity analyses, centered on VS, were conducted to examine how resting-state interregional connectivity patterns covaried with IR and depressed mood. RESULTS Higher levels of IR covaried with increased connective strength between the left VS and two regions: the insula and the anterior midcingulate cortex (aMCC). Moreover, aMCC-VS connectivity predicted depressed mood (b = 0.93, standard error = 0.36, F(change)(1,81) = 6.54, p = .01). Finally, aMCC-VS connectivity was shown by Monte Carlo analysis to mediate the relationship between IR and depressed mood (a*b indirect effect = 0.16, confidence interval = 0.005-0.39, p = .03). CONCLUSIONS IR relates to changes in the functional connectivity between VS and aMCC. These changes in interregional communication partly account for the coupling of IR to depressed mood in otherwise healthy adults. These findings are relevant for understanding bidirectional associations between diabetes risk and depressed mood.

Atmospheric correction for remote sensing-based studies typically does not use information from spatio-temporally resolved meteorological models. We assessed the effect of using observations and mesoscale weather and chemical transport models on multispectral retrievals of land and ocean properties. We performed two atmospheric corrections on image data acquired by the Moderate Resolution Imaging Spectroradiometer (MODIS)/Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER) airborne simulator over Monterey Bay, California. One correction used local atmospheric profiles of meteorology and trace gases at overpass and the other used the 1976 US Standard default atmospheric profile in the MODTRAN4 radiative transfer model. We found only minor impacts from atmospheric correction in the Fluorescence Line Height index of ocean chlorophyll, but substantive differences in retrievals of surface temperature and the Normalized Difference Vegetation Index. Improvements in sea surface temperature retr...

We extend existing oceanographic sampling methodologies to sample an advecting feature of interest using autonomous robotic platforms. GPS-tracked Lagrangian drifters are used to tag and track a water patch of interest with position updates provided periodically to an autonomous underwater vehicle (AUV) for surveys around the drifter as it moves with ocean currents. Autonomous sampling methods currently rely on geographic waypoint track-line surveys that are suitable for static or slowly changing features. When studying dynamic, rapidly evolving oceanographic features, such methods at best introduce error through insufficient spatial and temporal resolution, and at worst, completely miss the spatial and temporal domain of interest. We demonstrate two approaches for tracking and sampling of advecting oceanographic features. The first relies on extending static-plan AUV surveys (the current state-of-the-art) to sample advecting features. The second approach involves planning of surveys in the drifter or patch frame of reference. We derive a quantitative envelope on patch speeds that can be tracked autonomously by AUVs and drifters and show results from a multi-day off-shore field trial. The results from the trial demonstrate the applicability of our approach to long-term tracking and sampling of advecting features. Additionally, we analyze the data from the trial to identify the sources of error that affect the quality of the surveys carried out. Our work presents the first set of experiments to autonomously observe advecting oceanographic features in the open ocean.

Recent advances in robotic technologies provide new opportunities to conduct high-resolution sampling of patchily distributed zooplankton and associated environmental variables. We used two robots and molecular probes to assess the temporal and spatial variability of zooplankton in water samples obtained from Monterey Bay, California. The Autonomous Underwater Vehicle (AUV) Dorado is a mobile platform that carries ten, 1.8-L bottles ("Gulpers") capable of rapidly acquiring discrete seawater samples, and an extensive sensor suite for gathering contextual environmental data during day-long expeditions. Molecular assays were conducted ex situ at a shore-based laboratory. In contrast, the Environmental Sample Processor (ESP) was deployed as a stationary (moored) device capable of repeatedly “sipping” water to conduct in situ molecular assays and record environmental data during month-long deployments. Molecular analyses were conducted with the sandwich hybridization assay (SHA), which employed 18S ribosomal RNA oligonucleotide probes designed to detect calanoid and podoplean copepods, and the larvae of barnacles, mussels, polychaete worms, brachyuran crabs, and invasive green crabs (Carcinus maenas). Both the stationary and mobile sampling protocols revealed the greatest zooplankton diversity and abundance in relatively warm waters, higher in chlorophyll and lower in salinity and nitrate. Diversity and abundance were least in recently upwelled waters with the inverse conditions. High-resolution sampling revealed that while calanoid copepods were generally associated with elevated chlorophyll, they were most abundant in upwelling fronts, in some cases. These narrow features appear to provide favorable conditions for the growth and aggregation of certain zooplankton.

Amoebophrya is a marine parasite recently found to infect and kill bloom-forming dinoflagellates in the California Current System (CCS). However, it is unknown whether parasitism by Amoebophrya can control dinoflagellate blooms in major eastern boundary upwelling systems, such as the CCS. We quantified the abundance of a common bloom-forming species Akashiwo sanguinea and prevalence of its parasite (i.e., % infected cells) in surface water samples collected weekly from August 2005 to December 2008 at the Santa Cruz Wharf (SCW), Monterey Bay, CA. Additionally, we measured physical and chemical properties at the SCW and examined regional patterns of wind forcing and sea surface temperature. Relative abundance of the net phytoplankton species was also analyzed to discern whether or not parasitism influences net phytoplankton community composition. Epidemic infection outbreaks (>20% parasite prevalence in the host species) may have contributed to the end or prevented the occurrence of A. sanguinea blooms, whereas low parasite prevalence was associated with short-term (≤2 weeks) A. sanguinea blooms. The complete absence of parasitism in 2007 was associated with an extreme A. sanguinea bloom. Anomalously strong upwelling conditions were detected in 2007, suggesting that A. sanguinea was able to outgrow Amoebophrya and ‘escape’ parasitism. We conclude that parasitism can strongly influence dinoflagellate bloom dynamics in upwelling systems. Moreover, Amoebophrya may indirectly influence net phytoplankton species composition, as species that dominated the net phytoplankton and developed algal blooms never appeared to be infected.

During the Gulf of Mexico Oil Spill Response Scientific Survey on the National Oceanic and Atmospheric Administration Ship Gordon Gunter Cruise GU-10-02 (27 May–4 June 2010), a Monterey Bay Aquarium Research Institute autonomous underwater vehicle (AUV) was deployed to make high-resolution surveys of the water column in targeted areas. There were 10 2-liter samplers on the AUV for acquiring water samples. An essential challenge was how to autonomously trigger the samplers when peak hydrocarbon signals were detected. In ship hydrocasts (measurements by lowered instruments) at a site to the southwest of the Deepwater Horizon wellhead, the hydrocarbon signal showed a sharp peak between 1,100- and 1,200-m depths, suggesting the existence of a horizontally oriented subsurface hydrocarbon plume. In response to this finding, we deployed the AUV at this site to make high-resolution surveys and acquire water samples. To autonomously trigger the samplers at peak hydrocarbon signals, we modified an algorithm that was previously developed for capturing peaks in a biological thin layer. The modified algorithm still uses the AUV's sawtooth (i.e., yo-yo) trajectory in the vertical dimension and takes advantage of the fact that in one yo-yo cycle, the vehicle crosses the horizontal plume (i.e., the strong-signal layer) twice. On the first crossing, the vehicle detects the peak and logs the corresponding depth (after correcting for the detection delay). On the second crossing, a sampling is triggered when the vehicle reaches the depth logged on the first crossing, based on the assumption that the depth of the horizontal oil layer does not vary much between two successive crossings that are no more than several hundred meters apart. In this paper, we present the algorithm and its performance in an AUV mission on 3 June 2010 in the Gulf of Mexico. In addition, we present an improvement to the algorithm and the corresponding results from postprocessing the AUV mission data. © 2011 Wiley Periodicals, Inc. © 2011 Wiley Periodicals, Inc.

Using autonomous molecular analytical devices embedded within an ocean observatory, we studied harmful algal bloom (HAB) ecology in the dynamic coastal waters of Monterey Bay, California. During studies in 2007 and 2008, HAB species abundance and toxin concentrations were quantified periodically at two locations by Environmental Sample Processor (ESP) robotic biochemistry systems. Concurrently, environmental variability and processes were characterized by sensors co-located with ESP network nodes, regional ocean moorings, autonomous underwater vehicle surveys, and satellite remote sensing. The two locations differed in their long-term average physical and biological conditions and in their degree of exposure to episodic wind-forced variability. While anomalously weak upwelling and strong stratification during the 2007 study favored toxigenic dinoflagellates (Alexandrium catenella), anomalously strong upwelling during the 2008 study favored toxigenic diatoms (Pseudo-nitzschia spp.). During both studies, raphidophytes (Heterosigma akashiwo) were detected within a similar range of concentrations, and they reached higher abundances at the relatively sheltered, stratified site. During 2008, cellular domoic acid reached higher concentrations and was far more variable at the shallower ESP node, where phytoplankton populations were influenced by resuspended sediments. Episodic variability caused by wind forcing, lateral mixing, internal waves, and subsurface phytoplankton layers influenced ESP detection patterns. The results illustrate the importance of mobilizing HAB detection on autonomous platforms that can intelligently target sample acquisition as a function of environmental conditions and biological patch encounter.

Glucose enhances memory in a variety of species. In humans, glucose administration enhances episodic memory encoding, although little is known regarding the neural mechanisms underlying these effects. Here we examined whether elevating blood glucose would enhance functional MRI (fMRI) activation and connectivity in brain regions associated with episodic memory encoding and whether these effects would differ depending on the emotional valence of the material. We used a double-blind, within-participants, crossover design in which either glucose (50 g) or a saccharin placebo were administered before scanning, on days approximately 1 week apart. We scanned healthy young male participants with fMRI as they viewed emotionally arousing negative pictures and emotionally neutral pictures, intermixed with baseline fixation. Free recall was tested at 5 min after scanning and again after 1 day. Glucose administration increased activation in brain regions associated with successful episodic memory encoding. Glucose also enhanced activation in regions whose activity was correlated with subsequent successful recall, including the hippocampus, prefrontal cortex, and other regions, and these effects differed for negative vs. neutral stimuli. Finally, glucose substantially increased functional connectivity between the hippocampus and amygdala and a network of regions previously implicated in successful episodic memory encoding. These findings fit with evidence from nonhuman animals indicating glucose modulates memory by selectively enhancing neural activity in brain regions engaged during memory tasks. Our results highlight the modulatory effects of glucose and the importance of examining both regional changes in activity and functional connectivity to fully characterize the effects of glucose on brain function and memory.

Exaggerated cardiovascular reactivity to stress is a risk factor for cardiovascular disease. Further, individual differences in stressor-evoked cardiovascular reactivity covary with the functionality of corticolimbic brain systems, particularly areas of the cingulate cortex. What remains unclear, however, is how individual differences in personality traits interact with cingulate functionality in the prediction of stressor-evoked cardiovascular reactivity. Accordingly, we tested the associations between (i) a particular personality trait, Agreeableness, which is associated with emotional reactions to conflict, (ii) resting state functional connectivity within the cingulate cortex, and (iii) stressor-evoked blood pressure (BP) reactivity. Participants (N = 39, 19 men, aged 20–37 years) completed a resting functional connectivity MRI protocol, followed by two standardized stressor tasks that engaged conflict processing and evoked BP reactivity. Agreeableness covaried positively with BP reactivity across individuals. Moreover, connectivity analyses demonstrated that a more positive functional connectivity between the posterior cingulate (BA31) and the perigenual anterior cingulate (BA32) covaried positively with Agreeableness and with BP reactivity. Finally, statistical mediation analyses demonstrated that BA31–BA32 connectivity mediated the covariation between Agreeableness and BP reactivity. Functional connectivity within the cingulate appears to link Agreeableness and a risk factor for cardiovascular disease, stressor-evoked BP reactivity.

Thin layers of phytoplankton have an important impact on coastal ocean ecology. The high spatial and temporal variability of such layers makes autonomous underwater vehicles (AUVs) ideal for their study. At the Monterey Bay Aquarium Research Institute (MBARI, Moss Landing, CA), the authors have used an AUV for obtaining repeated high-resolution surveys of thin layers in Monterey Bay, CA. The AUV is equipped with ten “gulpers” that can capture water samples when some feature is detected. In this paper, the authors present an adaptive triggering method for an AUV to capture water samples at chlorophyll fluorescence peaks in a thin layer. The algorithm keeps track of the fluorescence background level and the peaks' baseline in real time to ensure that detection is tuned to the ambient conditions. The algorithm crosschecks for concurrent high values of optical backscattering to ensure that sampling targets true particle peaks and not simply physiologically controlled fluorescence peaks. To let the AUV capture the thin layer's peak without delay, the algorithm takes advantage of the vehicle's sawtooth (i.e., yo-yo) trajectory: in one yo-yo cycle, the vehicle makes two crossings of the thin layer. On the first crossing, the vehicle detects the layer's fluorescence peak and saves the peak height; on the second crossing, as the fluorescence measurement reaches the saved peak height (plus meeting additional timing and depth conditions), a sampling is triggered. Based on the thin layer's vertical position in the vehicle's yo-yo profiles, the algorithm selects the pair of detection and triggering crossings so as to minimize the spacing between them. We use the algorithm to postprocess a data set of 20 AUV missions in the 2005 Layered Organization in the Coastal Ocean (LOCO) Experiment in Monterey Bay, CA, and compare its performance with that of a threshold triggering method. In October 2009, the presented method was field tested in an AUV mission in northern Monterey Bay, CA.

There are governmental (DFO, DND, NOAA, USN), commercial (typically proprietary), and non-governmental organization (NGO) passive acoustic ocean observing systems installed on the North East Pacific Coast. The NGO passive acoustic datasets span many years, four decades for OrcaLab. This presentation provides an overview of the data collected at various NGO acoustic observatories on the North East Pacific Coast. The dataset time windows, sampling rates, formats, and ancillary data are given for each NGO. Data availability, searchability, data use restrictions, and contact information are given to allow acoustic researchers to access this treasure of acoustic observatory data. NGO’s include Fin Island Marine Institute, CetaceaLab, Pacific Wild, OrcaLab, Ocean Networks Canada, Saturna Island Marine Research and Education Society, Orcasound, and the Monterey Bay Aquarium Research Institute.There are governmental (DFO, DND, NOAA, USN), commercial (typically proprietary), and non-governmental organization (NGO) passive acoustic ocean observing systems installed on the North East Pacific Coast. The NGO passive acoustic datasets span many years, four decades for OrcaLab. This presentation provides an overview of the data collected at various NGO acoustic observatories on the North East Pacific Coast. The dataset time windows, sampling rates, formats, and ancillary data are given for each NGO. Data availability, searchability, data use restrictions, and contact information are given to allow acoustic researchers to access this treasure of acoustic observatory data. NGO’s include Fin Island Marine Institute, CetaceaLab, Pacific Wild, OrcaLab, Ocean Networks Canada, Saturna Island Marine Research and Education Society, Orcasound, and the Monterey Bay Aquarium Research Institute.

The Monterey Bay Aquarium Research Institute has been recording since July 2015 almost continuously at the Monterey Accelerated Research System (MARS) cabled observatory in Monterey Bay, California, USA. This long-term recording contains thousands of whale calls to help further our understanding of interannual, seasonal, and diel patterns. Here we report on our highly accurate detection and classification method developed to classify blue whale A, B, and D calls and Fin whale 20 Hz pulses. The foundation of the method is a computationally efficient and tuned decimation filter to convert the broadband hydrophone 128 kHz signal to 2 kHz which preserves the low-frequency signal and avoids any high-frequency aliasing. Detection is done using a band-limited-energy-detection filter to find potential calls in the decimated data. Spectrograms are then generated for potential calls and enhanced with local image normalization followed by smoothing by convolving in either time or frequency. Classification is done using the Google Inception v3 model with a transfer learning method. Overall, false positive rates are very low despite variability in whale call shape and background noise.The Monterey Bay Aquarium Research Institute has been recording since July 2015 almost continuously at the Monterey Accelerated Research System (MARS) cabled observatory in Monterey Bay, California, USA. This long-term recording contains thousands of whale calls to help further our understanding of interannual, seasonal, and diel patterns. Here we report on our highly accurate detection and classification method developed to classify blue whale A, B, and D calls and Fin whale 20 Hz pulses. The foundation of the method is a computationally efficient and tuned decimation filter to convert the broadband hydrophone 128 kHz signal to 2 kHz which preserves the low-frequency signal and avoids any high-frequency aliasing. Detection is done using a band-limited-energy-detection filter to find potential calls in the decimated data. Spectrograms are then generated for potential calls and enhanced with local image normalization followed by smoothing by convolving in either time or frequency. Classification is done us...

Using two years of nearly continuous recordings from Monterey Bay National Marine Sanctuary, August 2015 through July 2017, variations in humpback whale song are examined on diel, seasonal, and interannual time scales. The cabled hydrophone is in humpback feeding and migratory habitat at 36.7128°N, 122.186°W. Diel analyses show 69% of song during night, 23% during day, and 8% during dusk or dawn. Seasonal analyses show song absence during summer (June–August), emergence during fall (September–October), peak during late fall/winter (November–January), and highly variable detection during spring (February–May). During both years >80% of song occurred during the November–January peak. Song detection within a month reached a maximum of 58% of the time during November 2016. Song length increased (p < 0.01) month-to-month from the start in fall through the end of the peak in January. The months of maximum song occurrence coincide with declining visual sighting of humpbacks within Monterey Bay, consistent with seasonal southward migration to breeding habitat and/or more offshore residence. Interannual variation in song was marked by a 51% increase between the first and second years. Habitat during the first year was strongly influenced by a prolonged regional oceanic warm anomaly and the largest toxic algal bloom ever recorded in the northeast Pacific. Alternative hypotheses for the interannual difference in song detection relate to differences in humpback regional abundance, behavior, and habitat occupancy.

Predicting when and where key oceanic processes will be encountered is problematic in dynamic coastal waters where diverse physical, chemical, and biological factors interact in varied and rapidly changing combinations. Defining key processes often requires efficient sampling of specific water masses and prompt sample return for subsequent analyses. This compound challenge motivated our efforts to develop mobile autonomous process sampling (MAPS) for use with autonomous underwater vehicles (AUVs). With this system, features are recognized by artificial intelligence that integrates AUV sensor data to estimate probabilistic states for adaptive control of survey navigation and triggering of targeted water samplers. To demonstrate the utility of the MAPS/AUV system, we focused on intermediate nepheloid layers (INLs), episodic transport events that may play a role in zooplankton ecology. During multiple field tests in Monterey Bay, California, the MAPS/AUV system recognized, mapped, and sampled INLs. Invertebrate larvae contained in the water samples were subsequently characterized with molecular probes developed for high-throughput screening. Preliminary results support the hypothesis that INLs function as vehicles for episodic larval transport. Applying MAPS within a greater coastal ocean observing system permitted description of regional oceanographic dynamics that influenced the patterns and scales of INL and larval transport.

Here, we describe the derivation of a novel human embryonic stem cell (hESC) line, Endeavour-2 (E-2), propagated on human fetal fibroblasts (HFF) in a serum-replacement media. The inner cell mass (ICM) was manually dissected from the blastocyst without using immunodissection and, therefore, antibodies from animal sources. A total of 20 embryos were thawed and cultured, eight embryos were hatched, and five ICMs were obtained. They were transferred onto HFF used as feeder layer, and one colony representing the initial cell proliferation of a new hESC line, E-2, was obtained. The newly emerged hESC colony was passaged first by physical dissection and subsequently by enzymatic dissociation. E-2 has been in culture for over 6 months and has been shown to possess typical features of a pluripotent hESC line including expression of stem cell surface markers (SSEA4, TRA-160, and integrin alpha-6), intracellular alkaline phosphatase, and pluripotency gene markers, OCT4 and NANOG. This hESC line shows lineage-specific differentiation into various representative cell types expressing markers characteristic of the three somatic germ layers under both in vitro and in vivo conditions. E-2 line shows a normal karyotype (46 XX) and has been successfully cryopreserved and thawed several times using slow-freezing procedures. E-2 adds to the repertoire of existing hESC lines for research and development purposes in the field of regenerative medicine.

During the 2005 Layered Organization in the Coastal Ocean (LOCO) field program in Monterey Bay, California, we integrated intensive water column surveys by an autonomous underwater vehicle (AUV) with satellite and mooring data to examine the spatiotemporal scales and processes of phytoplankton thin-layer development. Surveying inner to outer shelf waters repeatedly between August 18 and September 6, the AUV acquired 6841 profiles. By the criteria: [(1) thickness ≤3 m at the full-width half-maximum, (2) peak chlorophyll at least twice the local background concentrations, and (3) a corresponding peak in optical backscattering], thin layers were detected in 3978 (58%) of the profiles. Average layer thickness was 1.4 m, and average intensity was 13.5 μg l−1 above (3.2x) background. Thin layers were observed at depths between 2.6 and 17.6 m, and their depths showed diurnal vertical migration of the layer phytoplankton populations. Horizontal scales of thin-layer patches ranged from 10,000 m. A thin-layer index (TLI), computed from layer frequency, intensity and thinness, was highest in mid-shelf waters, coincident with a frontal zone between bay waters and an intrusion of low-salinity offshore waters. Satellite observations showed locally enhanced chlorophyll concentrations along the front, and in situ observations indicated that phytoplankton may have been affected by locally enhanced nutrient supply in the front and concentration of motile populations in a convergence zone. Minimum TLI was furthest offshore, in the area most affected by the intrusion of offshore, low-chlorophyll waters. Average thin-layer intensity doubled during August 25–29, in parallel with warming at the surface and cooling within and below the thermocline. During this apparent bloom of thin-layer populations, density oscillations in the diurnal frequency band increased by an order of magnitude at the shelfbreak and in near-bottom waters of the inner shelf, indicating the role of internal tidal pumping from Monterey Canyon onto the shelf. This nutrient transport process was mapped by the AUV. Peak TLI was observed on August 29 during a nighttime survey, when phytoplankton were concentrated in the nutricline. Empirical orthogonal function decomposition of the thin-layer particle size distribution data from this survey showed that throughout the inner to outer shelf survey domain, the layers were dominated by phytoplankton having a cross-section of ∼50 μm. This is consistent with the size of abundant Akashiwo sanguinea cells observed microscopically in water samples. During a subsequent and stronger intrusion of low-salinity offshore waters, spatially-averaged vertical density stratification decreased by > 50%, and phytoplankton thin layers disappeared almost completely from the AUV survey domain.

Coincident measurements of chlorophyll a (Chl a) and temperature microstructure from Monterey Bay, California, U.S.A., are used to investigate the dynamics of a phytoplankton thin layer in the context of vertical turbulent mixing. The thin layer was situated in the thermocline of a 20.5-m water column, between a strongly turbulent surface mixed layer and a weakly turbulent stratified interior. The differential mixing established an asymmetric layer with a stronger Chl a gradient at the base of the layer than at the top. Sinking by Akashiwo sanguinea could have balanced turbulent mixing above the layer, but cannot explain the mid-column convergence needed to maintain the thin layer. Swimming by A. sanguinea directed towards a mid-column nitracline could have balanced turbulent mixing on both sides of the layer and supported the observed Chl a gradients. Results from a Eulerian advection-diffusion model suggest that cell swimming may have varied over the lifetime of the layer, with stronger or more directed swimming required for layer formation and weaker or less directed swimming needed to maintain the layer. In-layer growth is unlikely to have played a primary role in supporting the observed Chl a gradients. From the one-dimensional (vertical) observations, the role of shear-induced straining cannot be evaluated, but shear instabilities appear important to forcing elevated rates of turbulent diffusion within the layer. Finally, a Lagrangian particle-tracking model is used to explore the implications of a balance of vertical velocity and turbulent diffusion on the vertical motions of individual cells that constitute the thin layer.

It has recently been shown that inner shelf waters of NE Monterey Bay, California function as an “extreme bloom incubator”, frequently developing dense “red tide” blooms that can rapidly spread. Located within the California Current upwelling system, this open bay is strongly influenced by oceanographic dynamics resulting from cycles of upwelling favorable winds and their relaxation and/or reversal. Different wind forcing causes influx of different water types that originate outside the bay: cold nutrient-rich waters during upwelling and warm nutrient-poor waters during relaxation. In this study, we examine how the bay's bloom incubation area can interact with highly variable circulation to cause red tide spreading, dispersal and retention. This examination of processes is supported by satellite, airborne and in situ observations of a major dinoflagellate bloom during August and September of 2004. Remote sensing of high spatial, temporal and spectral resolution shows that the bloom originated in the NE bay, where it was highly concentrated in a narrow band along a thermal front. Upwelling circulation rapidly spread part of the bloom, mixing cool waters of an upwelling filament with warm bloom source waters as they spread. Vertical migration of the dinoflagellate populations was mapped by autonomous underwater vehicle surveys through the spreading bloom. Following bloom expansion, a two-day wind reversal forced intrusion of warm offshore waters that dispersed much of the bloom. Upwelling winds then resumed, and the bloom was further dispersed by an influx of cold water. Throughout these oceanographic responses to changing winds, an intense bloom persisted in sheltered waters of the NE bay, where extreme blooms are most frequent and intense. Microscopic examination of surface phytoplankton samples from the central bay showed that spreading of the bloom from the NE bay and mixing with regional water masses resulted in significantly increased abundance of dinoflagellates and decreased abundance of diatoms. Similar dinoflagellate bloom incubation sites are indicated in other areas of the California Current system and other coastal upwelling systems. Through frequent bloom development and along-coast transports, relatively small incubation sites may significantly influence larger regions of the coastal marine ecosystems in which they reside.

The red tide forming dinoflagellate genus Cochlodinium appears to be expanding globally, as well as blooming and/or causing more economic losses within its previously reported geographic distribution. Despite the widespread occurrence of this organism in the Pacific, Atlantic, and Indian oceans, relatively few studies of its ecophysiology have been conducted. Here we summarize the ecophysiological characteristics through both a literature review and by assessing recent bloom events in Monterey Bay, CA, USA. Using this comparative approach, we identify the basic characteristics of this organism: Cochlodinium is found in both warm and cool (11–30 °C) waters in the western and eastern Pacific, respectively, at moderate salinities (30–34). The production of pelagic vegetative seed banks or benthic seed beds by this organism and ability to survive ballast water transport likely facilitate its ability to colonize and establish itself in new habitats. It is a strong vertical migrator capable of utilizing both inorganic and organic nitrogen sources as well as mixotrophy and may be associated with moderate nutrient loading. These characteristics provide Cochlodinium with an adaptive capability conducive to rapid colonization of newly opened ecological niches, which may partially explain the apparent global expansion of its geographic range and bloom frequency.

A primary limitation of phytoplankton ecology research is the difficulty of describing patchiness and distributions of different phytoplankton groups. Chlorophyll fluorescence and optical backscatter are useful measurements that provide information about phytoplankton, but these measurements do not allow distinction of phytoplankton taxa. Traditional phytoplankton identification methods (such as microscopy, HPLC analysis, and flow cytometry) are labor intensive and therefore can provide only very limited coverage and resolution. Through lab experiments we show that the Laser In Situ Scattering and Transmissometer (LISST-100) instrument can accurately quantify phytoplankton cell dimensions for some cell shapes. Pseudo-spherical dinoflagellates are described with a single peak in the particle size distribution (PSD) at the cross-sectional dimension of the cells. Pennate diatoms are described with peaks in the PSD at the major and minor axis dimensions of the cells. Diatom cells with minor axis dimensions that vary along the major axis are described with one peak across the range of minor axis dimensions and a second peak at the major axis dimension. Through field experiments, we show that mapping the PSD in situ at high resolution permits description of patchiness and evolution of phytoplankton populations. We present two examples: (1) growing dominance of Ceratium species during a red tide bloom, and (2) concentration of Pseudo-nitzschia australis, a harmful algal bloom (HAB) species, at a water mass front. We conclude that synoptic mapping of the PSD can significantly advance phytoplankton ecology research in the coastal ocean.

Using multidisciplinary observations from regional- to small-scale, we examined the development of thin phytoplankton layers in water mass frontal zones of a coastal upwelling system. Two fronts developed successively in the same region of Monterey Bay, California, USA, during August and September 2003: (1) when warm, fresh offshore waters flowed into the bay following relaxation and reversal of upwelling favorable winds, and (2) when a cold upwelling filament flowed into the bay after upwelling favorable winds resumed. Thin phytoplankton layers were observed dur- ing the presence of both fronts. The layers exhibited peaks in chlorophyll fluorescence and optical backscattering, indicating biomass maxima in the layers. Maximum chlorophyll concentrations in the layers ranged from 11 to 37 µg l -1 and were 4 to 55 times greater than background levels. Layer ver- tical thickness ranged from 1 to 5 m, averaging 2.3 m. All thin layers were in the thermocline, near the 12.5°C isotherm, and the depth of the layers varied between 12 and 33 m, in parallel with varia- tions in thermocline depth. Synoptic mapping of the first frontal zone shortly before the thin layers developed showed strong phytoplankton patchiness. The role of vertical shear in thin layer formation from phytoplankton patches is supported by multiple results: (1) most thin layers (92%) were associ- ated with sharp changes in the direction of horizontal currents; (2) layer thickness was significantly (p < 0.03) negatively correlated with shear; (3) the median shear profile, computed from all thin layer velocity profiles, peaked sharply at the center of thin layers.

Here we describe the derivation of a novel human embryonic stem (hES) cell line, Endeavour-1 (E1), its four new clonal lines (E1C1, E1C2, E1C3, E1C4), and their characterization. E1 and its clonal lines are propagated on human fetal fibroblasts (HFFs) derived and grown in a largely serum-free medium. Seven inner cell masses were isolated from 34 donated human embryos (27 survived), and one new hES cell line was obtained. E1 has been in culture for over 1 year and possesses all the typical features of stem cells, i.e., expression of stem cell surface markers (stage-specific embryonic antigens SSEA-3 and SSEA-4, and tumor recognition antigens TRA-1-60 and TRA-1-81), staining for alkaline phosphatase, and the presence of the pluripotent gene marker (nanog). This line shows pluripotency both under in vitro and in vivo conditions. E1 has a normal karyotype (46XX). Using our optimized procedure for cloning, four new clonal lines were derived from E1: E1C1, E1C2, E1C3, and E1C4. These clonal lines show normal characteristics: karyotype of that of the parent line (46XX) except for E1C3, which showed reciprocal translocation involving chromosomes 15 and 17; stem cell surface markers SSEA-4, TRA-1-60, and TRA-1-81; and gene expression for pluripotency (Nanog). All of these clonal lines formed embryoid bodies (EBs) in suspension cultures. After seeding, the EBs differentiated, forming cell lineages derived from all three germ layers as indicated by immunolocalization for the ectodermal marker beta-III tubulin, the mesodermal marker CD34, and the endodermal marker alpha-fetoprotein (AFP). There were subtle differences in the expression of these markers between clones. These clonal lines showed pluripotency in vivo. E1 and its clonal lines can differentiate to definitive endoderm after treatment with activin A, and, as indicated by expression of SOX17, FOXa2, and GATA-4 by RT-PCR, there are some subtle differences between these clonal lines. This may help in selecting clonal lines for specific lineage specification and for developing future cell therapy for various diseases.

Modern ocean microbial research utilizes advanced molecular analytical techniques, such as polymerase chain reaction (PCR), DNA and protein probe arrays, and nucleic acid sequencing (etc.). Applying or at least initiating these techniques at the point and time of sample collection can enhance their effectiveness. To that end, in-situ sample processing and real-time molecular detection schemes have been implemented using deployable autonomous systems that can be operated in diverse ocean environments from shallow coastal waters to the deep sea. Such devices have been termed “ecogenomic sensors.” The size of these instruments currently requires that they be moored in a fixed location or passively mobile, drifting at fixed depth and observing microbial communities in a moving frame of reference with ocean currents. With the highly dynamic motion of open water and microbial life, the next frontier of ocean microbial research requires the improved capability of an actively mobile asset. A mobile ecogenomic sensor encompasses a fully maneuverable vehicle with weeks of persistence, environmental data analysis, detection of physical and biological features, autonomous sampling and in situ analysis, and near-real-time data reporting. This system is now being developed by integrating three components: a compact molecular analytical instrument (the 3rd generation Environmental Sample Processor), a long-range autonomous underwater vehicle, and software algorithms for AUV-based feature detection and sampling. A summary of the system and its initial application is presented.

Objectives The development of Type 1 diabetes mellitus (T1DM) within the first 7 years of life has been linked to poorer cognitive performance. Adults with T1DM have altered functional brain connectivity, but no studies have examined whether earlier age of T1DM onset is associated with functional connectivity later in life. Accordingly, we tested the relationship between age of onset and resting state functional connectivity in a cohort of middle-aged adults with childhood-onset T1DM. Methods Participants were from a subsample of the Pittsburgh Epidemiology of Diabetes Complications cohort and included 66 adults (mean age = 47.54 years, 32 men). Resting state blood oxygen level-dependent activity was used to calculate mean connectivity for eight functional brain networks. A multivariate analysis of variance examined associations between age of onset and network connectivity. Diffusion tensor and fluid-attenuated inversion recovery images were analyzed to identify microstructural alterations and white-matter hyperintensity volumes. Results Later childhood onset of T1DM was associated with lower connectivity (F(8,57) = 2.40, p = .026). A significant interaction was present for current age such that an inverse association with age of onset for functional connectivity was present in older individuals (F(8,55) = 2.88, p = .035). Lower connectivity was associated with older age, increased white-matter hyperintensity volume, and lower microstructural integrity. Conclusions Diagnosis of T1DM later in childhood may be associated with lower brain functional connectivity, particularly in those surviving into older ages. These alterations may be an early marker for subsequent cognitive decrements. Future studies are warranted to understand the pathways underlying these associations.

In social neuroscience research, startle eyeblink modification can serve as a marker of emotion, but it is less clear whether it can also serve as a marker of prejudice. In Experiment 1, 30 White students viewed photographs of White and Black targets while the startle eyeblink reflex and facial EMG from the brow and cheek regions were recorded. Prejudice was related to facial EMG activity, but not to startle modification, which instead appeared to index attention to race. To test further whether racial categorizations are associated with differential attention, a dual-task paradigm was used in Experiment 2. Fifty-four White and fifty-five Black participants responded more slowly to a tone presented when viewing a racial outgroup member or a negative stimulus, indicating that both draw more attention than ingroup members or positive stimuli. We conclude that startle modification is useful to index differential attention to groups when intergroup threat is low.

As brainstem nuclei are interconnected with several cortical structures and regulate several autonomic, cognitive, and behavioral functions, it might be important to place the brainstem within an important pathologic core in the progression of Alzheimer’s disease (AD). Although there have been several postmortem studies reporting neuropathological alterations of the brainstem in AD, there has been no in-vivo structural neuroimaging study of the brainstem in the patients with AD. The aim of this study was to investigate differences in the brainstem volume and shape between patients with AD and elderly normal controls. Fifty AD patients (the Clinical Dementia Rating Scale ≥ 1) and 50 normal controls were recruited, and the brainstem volumes and deformations were compared between the AD and the controls. Patients with AD showed significant total volume [(mean ± SD) 21007 ± 1640 mm3]reduction in the brainstem compared with the controls [(mean ± SD) 22530 ± 1750 mm3] (P < 0.001). In addition, AD patients showed significant brainstem deformations in the upper posterior brainstem corresponding to the midbrain compared with the healthy individuals (false discovery rate corrected P < 0.05). This study is the first to explore brainstem volume change and deformations in AD. These structural changes in the midbrain areas might be at the core of the underlying neurobiological mechanisms of brainstem dysfunction with relevance to their various cognitive and behavioral symptoms such as memory impairment, sleep, and emotional disturbance in AD. However, further longitudinal studies might be needed to confirm these findings.

Diabetes and obesity, two major public health concerns, are associated with increased risk for problems in multiple organ systems, including the central nervous system. The adverse effects of diabetes and obesity on cognitive functioning are increasingly well recognized. This special issue of Psychosomatic Medicine features the latest research linking diabetes, obesity, and brain structure, function, and metabolism and follows a special meeting on this topic organized by the American Psychosomatic Society in October 2013. Evidence for the increased prevalence of diabetes and obesity is reviewed as it relates to cognitive decline. These articles indicate that the age of onset of Type 1 diabetes may be relevant to future cognitive function and that disease duration of Type 2 diabetes and sociocultural factors are related to cognitive decline during the aging process. The hypothalamus and other neural circuits, notably the dopaminergic system that underlies feeding and reward-related aspects of food intake, are among the key factors involved in obesity. Research on the associations between obesity and cognitive function is described using the positive effects of weight reduction following bariatric surgery or behavioral methods. This special issue concludes with a conceptual framework for linking obesity and diabetes with accelerated cognitive decline as related to the aging process. The collection of articles highlights the importance of using a life span perspective to understand the influence of both Type 1 and Type 2 diabetes on brain metabolism, function, and structure. Moreover, these studies show that distressing environmental circumstances can adversely influence neurocognitive dysfunction associated with obesity and diabetes.

The need for major infrastructure renewal in the US is widely recognized. The amount of private-sector capital willing to invest in this renewal through innovative public-private partnerships (P3s) is at unprecedented levels. The latter is often talked about as an obvious way to address the former. Yet at every level of US government and across all infrastructure sectors progress in actually enacting P3s is frustratingly slow. Why?This short paper (written as a key-issues briefing memo for an upcoming P3 conference organized by the Cornell Program in Infrastructure Policy) proposes that the answer to this question is found in the inadequacy of current P3 measurement methodology with respect to the currently most relevant potential use of P3s in the US. The current standard P3 evaluation methodology, Value for Money (VfM), is primarily focused on measuring cost-efficiency, which was an important metric in the original, primarily European, application of the P3 approach. However, for most US state and local government cost-efficiency is not the most relevant factor in the infrastructure decision. Rather, the perception of increased funding risk in the post-2008 economic environment is currently preventing a higher level of needed public-sector infrastructure investment. Funding risk can be efficiently transferred to the private sector through P3 transactions. But since VfM does not measure the value of transferring funding risk adequately, it is difficult to make a compelling case for P3 transactions in the face of stakeholder skepticism and resistance.The paper proposes that P3 evaluation methodologies be improved to include (1) better measurement of public sector cost of capital in the VfM framework and (2) the addition of another analytical dimension focused on funding risk transfer, called ‘Value for Funding’. Federal infrastructure policy can support the development and adoption of improved P3 measurement methodologies.

Value for Money (VfM) is the standard evaluation framework for infrastructure public-private partnership (P3) alternatives to traditional public-sector project procurement and financing. VfM’s primary focus is on a net present value cost comparison between the alternatives. However, in light of the challenges that US state and local governments face in the current economic environment, an additional analytical framework that explicitly expands the focus to include public-sector funding and fiscal issues in the evaluation of an infrastructure P3 would be useful in many cases. We are calling this new framework a ‘Value for Funding’ (VfF) approach. This paper presents an example of a VfF approach applied to a specific topic, the risk-absorption features of various types of P3 contracts with respect to US state and local public-sector deficits. More generally, the paper outlines a stochastic methodology for the comparative assessment of P3 and traditional alternatives that will likely be the basis of much other VfF analysis, especially where the funding stream is relatively independent of specific project operation and the public sector is fiscally constrained.

Using field measurements and quantitative modeling, we demonstrate that red coloration of the sea surface is not associated with any particular group of phytoplankton and is strongly dependent on the physiology of the human visual system. Red or brown surface waters can be produced by high concentrations of most types of algae, colored dissolved organic matter, or suspended sediment. Even though light reflected by red tides commonly peaks in the yellow spectral region (570–580 nm), human color perception requires consideration of the entire spectrum of light relative to receptors within the human eye. The color shift from green to red is not due to any special optical properties of the algae but results from an overlap in spectral response of the eye’s red and green cones (centered at 564 and 534 nm, respectively). The spectral peak in light reflected from dense algal blooms coincides with a critical hinge point in color vision (570–580 nm), where fine-scale shifts in the spectral shape of water-leaving radiance due to algal absorption and backscattering properties lead to pronounced variations in the observed color. Of the taxa considered, only Chlorophytes and Prochlorophytes lacked sufficient accessory pigments to produce a red tide. Chlorophyll fluorescence and enhanced near-infrared reflectance (the ‘‘red edge’’) contribute negligibly to the perceived color. Black water events are produced when water is highly absorbing but lacks backscattering constituents.

Physical-biological couplings impacting phytoplankton ecology are examined with synoptic, high-resolution observations of Monterey Bay, California. Influences of submarine canyon and shelf break topography on the physical-biological couplings are supported by 2 case studies. In the first case study, benthic-pelagic coupling was observed in southern shelf waters where a turbid plume extended from the bottom at ~60 m deep to the base of a phytoplankton layer centered at ~10 m deep. The alongshelf scale of the plume ranged from ~5 km near the bottom to ~1 km at its intersection with the phytoplankton layer. In situ and remote sensing data support the influence of Monterey Canyon on circulation forcing the benthic-pelagic coupling. In the second case study, a frontal zone and adjacent waters were rapidly surveyed over ~20 km 2 of the northern shelf. The front was associated with an isopycnal ridge/trough structure, surface slick, and frontal eddy

We report measurements of dissolvable and particulate iron, particulate Al, nutrients and phytoplankton biomass in surface waters during the termination of one upwelling event and the initiation of a second event in August 2000. These events occurred in the area of the Ano Nuevo upwelling center off the coast of central California. The first event was observed after ∼8 days of continuous upwelling favorable winds, while the second event was observed through the onset of upwelling favorable winds to wind reversals ∼3 days later. Coincident with the upwelling signatures of low temperature and high salinity were significantly elevated concentrations of nitrate and silicate with average concentrations greater than 15 and 20 μM, respectively, during both upwelling events. Dissolvable Fe concentrations (TD-Fe) were significantly higher in the second event, 6.5 versus 1.2 nM Fe found in the first event. Nitrate was reduced by ∼5 μM day −1 within this second upwelled plume as compared to a drawdown of ∼2 μM day −1 within the first plume. Silicate was reduced in a ratio of 1.2 mol Si:mol NO 3 in the high Fe waters of the second plume as compared to a ratio of 2.2 in the lower Fe waters of the first plume. The observed differences in nutrient utilization are consistent with some degree of iron limitation. The area of increased dissolvable Fe in the second upwelling event was coincident with elevated particulate Fe concentrations, indicating the particulate pool as a possible source of the observed increase in TD-Fe. The elevated particulate Fe in surface waters was a result of resuspended sediments in the bottom boundary layer (BBL) of the shallow shelf being transported to the surface during upwelling. Particulate (and dissolvable) iron concentrations were significantly reduced as upwelling continued. This was most probably due to a decoupling of the BBL from upwelled source waters as the upwelling front moved offshore and/or reduced turbulence in the BBL as upwelling continued. The observed reduction in both particulate and dissolvable Fe, as upwelling continued to deliver macronutrients to surface waters, may result in varying levels of Fe limitation.

This manuscript contains a detailed description of the PHOBOS experiment as it is configured for the Year 2001 running period. It is capable of detecting charged particles over the full solid angle using a multiplicity detector and measuring identified charged particles near mid-rapidity in two spectrometer arms with opposite magnetic fields. Both of these components utilize silicon pad detectors for charged particle detection. The minimization of material between the collision vertex and the first layers of silicon detectors allows for the detection of charged particles with very low transverse momenta, which is a unique feature of the PHOBOS experiment. Additional detectors include a time-of-flight wall which extends the particle identification range for one spectrometer arm, as well as sets of scintillator paddle and Cherenkov detector arrays for event triggering and centrality selection.

In the Pacific Ocean, air and ocean temperatures, atmospheric carbon dioxide, landings of anchovies and sardines, and the productivity of coastal and open ocean ecosystems have varied over periods of about 50 years. In the mid-1970s, the Pacific changed from a cool “anchovy regime” to a warm “sardine regime.” A shift back to an anchovy regime occurred in the middle to late 1990s. These large-scale, naturally occurring variations must be taken into account when considering human-induced climate change and the management of ocean living resources.

The physical, chemical and biological perturbations in central California waters associated with the strong 1997–1998 El Nino are described and explained on the basis of time series collected from ships, moorings, tide gauges and satellites. The evolution of El Nino off California closely followed the pattern observed in the tropical Pacific. In June 1997 an anomalous influx of warm southerly waters, with weak signatures on coastal sea level and thermocline depth, marked the onset of El Nino in central California. The timing was consistent with propagation from the tropics via the equatorial and coastal wave-guide. By late 1997, the classical stratified ocean condition with a deep thermocline, high sea level, and warm sea surface temperature (SST) commonly associated with El Nino dominated the coastal zone. During the first half of 1998 the core of the California Current, which is normally detected several hundred kilometers from shore as a river of low salinity, low nutrient water, was hugging the coast. High nutrient, productive waters that occur in a north–south band from the coast to approximately 200 km offshore during cool years disappeared during El Nino. The nitrate in surface waters was less than 20% of normal and new production was reduced by close to 70%. The La Nina recovery phase began in the fall of 1998 when SSTs dropped below normal, and ocean productivity rebounded to higher than normal levels. The reduction in coastal California primary productivity associated with El Nino was estimated to be 50 million metric tons of carbon (5 × 10 13 g C). This reduction certainly had deleterious effects on zooplankton, fish, and marine mammals. The 1992–1993 El Nino was more moderate than the 1997–1998 event, but because its duration was longer, its overall chemical and biological impact may have been comparable. How strongly the ecosystem responds to El Nino appears related to the longer-term background climatic state of the Pacific Ocean. The 1982–1983 and 1992–1993 El Ninos occurred during the warm phase of the Pacific Decadal Oscillation (PDO). The PDO may have changed sign during the 1997–1998 El Nino, resulting in weaker ecological effects than would otherwise have been predicted based on the strength of the temperature anomaly.

Satellite tracking of 27 whale sharks in the eastern tropical Pacific, examined in relation to environmental data, indicates preferential occupancy of thermo-biological frontal systems. In these systems, thermal gradients are caused by wind-forced circulation and mixing, and biological gradients are caused by associated nutrient enrichment and enhanced primary productivity. Two of the frontal systems result from upwelling, driven by divergence in the current systems along the equator and the west coast of South America; the third results from wind jet dynamics off Central America. All whale sharks were tagged near Darwin Island, Galápagos, within the equatorial Pacific upwelling system. Occupancy of frontal habitat is pronounced in synoptic patterns of shark locations in relation to serpentine, temporally varying thermal fronts across a zonal expanse > 4000 km. 80% of shark positions in northern equatorial upwelling habitat and 100% of positions in eastern boundary upwelling habitat were located within the upwelling front. Analysis of equatorial shark locations relative to thermal gradients reveals occupancy of a transition point in environmental stability. Equatorial subsurface tag data show residence in shallow, warm (>22°C) water 94% of the time. Surface zonal current speeds for all equatorial tracking explain only 16% of the variance in shark zonal movement speeds, indicating that passive drifting is not a primary determinant of movement patterns. Movement from equatorial to eastern boundary frontal zones occurred during boreal winter, when equatorial upwelling weakens seasonally. Off Peru sharks tracked upwelling frontal positions within ~100–350 km from the coast. Off Central America, the largest tagged shark (12.8 m TL) occupied an oceanic front along the periphery of the Panama wind jet. Seasonal movement from waning equatorial upwelling to productive eastern boundary habitat is consistent with underlying trophic dynamics. Persistent shallow residence in thermo-biological frontal zones suggests the role of physical-biological interactions that concentrate food resources.

© 2015 International Society for Microbial Ecology. The 'bacterial switch' is a proposed regulatory point in the global sulfur cycle that routes dimethylsulfoniopropionate (DMSP) to two fundamentally different fates in seawater through genes encoding either the cleavage or demethylation pathway, and affects the flux of volatile sulfur from ocean surface waters to the atmosphere. Yet which ecological or physiological factors might control the bacterial switch remains a topic of considerable debate. Here we report the first field observations of dynamic changes in expression of DMSP pathway genes by a single marine bacterial species in its natural environment. Detection of taxon-specific gene expression in Roseobacter species HTCC2255 during a month-long deployment of an autonomous ocean sensor in Monterey Bay, CA captured in situ regulation of the first gene in each DMSP pathway (dddP and dmdA) that corresponded with shifts in the taxonomy of the phytoplankton community. Expression of the cleavage pathway was relatively greater during a high-DMSP-producing dinoflagellate bloom, and expression of the demethylation pathway was greater in the presence of a mixed diatom and dinoflagellate community. These field data fit the prevailing hypothesis for bacterial DMSP gene regulation based on bacterial sulfur demand, but also suggest a modification involving oxidative stress response, evidenced as upregulation of catalase via katG, when DMSP is demethylated.

The Monterey Bay Aquarium Research Institute (MBARI) uses the Spatial Temporal Oceanographic Query System (STOQS) to manage data from its muli-platform observational campaigns. By using geospatial relational database technology STOQS solves the fundamental problem of providing efficient access to mobile platform data, while also handling in situ measurements from stationary platforms. Because it embraces existing standards and conventions it easily integrates into existing workflows. STOQS includes a modern web-based user interface providing sophisticated tools for deep exploration of multidisciplinary data sets. Direct programmatic access using the Python programming language allows for detailed visualization and analysis of large and diverse data sets. STOQS is a 100% open source project, free for anyone to use.

As a demonstrator for technologies for the next generation of ocean color sensors, the Hyperspectral Imager for the Coastal Ocean (HICO) provides enhanced spatial and spectral resolution that is required to understand optically complex aquatic environments. In this study we apply HICO, along with satellite remote sensing and in situ observations, to studies of phytoplankton ecology in a dynamic coastal upwelling environment-Monterey Bay, CA, USA. From a spring 2011 study, we examine HICO-detected spatial patterns in phytoplankton optical properties along an environmental gradient defined by upwelling flow patterns and along a temporal gradient of upwelling intensification. From a fall 2011 study, we use HICO's enhanced spatial and spectral resolution to distinguish a small-scale "red tide" bloom, and we examine bloom expansion and its supporting processes using other remote sensing and in situ data. From a spectacular HICO image of the Monterey Bay region acquired during fall of 2012, we present a suite of algorithm results for characterization of phytoplankton, and we examine the strengths, limitations, and distinctions of each algorithm in the context of the enhanced spatial and spectral resolution. © 2014 by the authors; licensee MDPI, Basel, Switzerland.

Studying ocean processes often requires observations made in a Lagrangian frame of reference, that is, a frame of reference moving with a feature of interest [1]. Often, the only way to understand a process is to acquire measurements at sufficient spatial and temporal resolution within a specific feature while it is evolving. Examples of coastal ocean features whose study requires Lagrangian observations include concentrated patches of microscopic algae (Fig. 1) that are toxic and may have impacts on fisheries, marine life and humans, or a patch of low-oxygen water that may cause marine life mortality depending on its movement and mixing.

Berdalet, Elisa ... et. al.-- Special issue Harmful Algal Blooms in Stratified Systems.-- 17 pages, 12 figures, The Global Ecology and Oceanography of Harmful Algal Blooms (GEOHAB) program of the Scientific Committee on Oceanic Research (SCOR) and the Intergovernmental Oceanographic Commission (IOC) of UNESCO, was created in 1999 to foster research on the ecological and oceanographic mechanisms underlying the population dynamics of harmful algal blooms (HABs). The ultimate goal of this research is to develop observational systems and models that will eventually enable the prediction of HABs and thereby minimize their impact on marine ecosystems, human health and economic activities. In August of 2012, a workshop was held under the umbrella of the GEOHAB program at the Monterey Bay Aquarium Research Institute (MBARI). The over arching goal of this workshop was to review the current understanding of the processes governing the structure and dynamics of HABs in stratified systems, and to identify how best to couple physical/chemical and biological measurements at appropriate spatial and temporal scales to quantify the dynamics of HABs in these systems, paying particular attention to thin layers. This contribution provides a review of recent progress in the field of HAB research in stratified systems including thin layers, and identifies the gaps in knowledge that our scientific community should strive to understand in the next decade, We are also grateful to the organizations that contributed financially to the meeting, specifically the Scientific Committee on Oceanic Research (SCOR), the Intergovernmental Oceanographic Commission (IOC) of UNESCO, and the Monterey Bay Aquarium Research Institution (MBARI. EB was funded by the Spanish Government through the ECOALFACS project (CTM2009-09581). ONR wishes to acknowledge financial support from the European Union Seventh Framework Programme (FP7/2007–2013)and Marie Curie IntraEuropean Fellowship for Career Development under Grant agreement no. 255396