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Open Access Publications from the University of California

Scholarly Works (79 results)

  • Thesis
  • Peer Reviewed
UC San Diego Electronic Theses and Dissertations (2015)
Techniques for passive acoustic tracking in all three spatial dimensions of marine mammals and ships were developed for long-term acoustic datasets recorded continuously over months using custom-designed arrays of underwater microphones (hydrophones) with spacing ranging from meters to kilometers. From the three-dimensional tracks, the acoustical properties of toothed whales and ships, such as sound intensity and directionality, were estimated as they are needed for the passive acoustic abundance estimation of toothed whales and for a quantitative description of the contribution of ships to the underwater soundscape. In addition, the tracks of the toothed whales reveal their underwater movements and demonstrate the potential of the developed tracking techniques to investigate their natural behavior and responses to sound generated by human activity, such as from ships or military SONAR. To track the periodically emitted echolocation sounds of toothed whales in an acoustically refractive environment in the upper ocean, a propagation-model based technique was developed for a hydrophone array consisting of one vertical and two L- shaped subarrays deployed from the floating instrument platform R/P FLIP. The technique is illustrated by tracking a group of five shallow-diving killer whales showing coordinated behavior. The challenge of tracking the highly directional echolocation sounds of deep-diving (< 1 km) toothed whales, in particular Cuvier's beaked whales, was addressed by embedding volumetric small- aperture (̃ 1 m element spacing) arrays into a large- aperture (̃ 1 km element spacing) seafloor array to reduce the minimum number of required receivers from five to two. The capabilities of this technique are illustrated by tracking several groups of up to three individuals over time periods from 10 min to 33 min within an area of 20 km² in the Southern California Bight. To track and measure the underwater radiated sound of ships, a frequency domain beamformer was implemented for a volumetric hydrophone array (< 2 m element spacing) that was coupled to an autonomous acoustic seafloor recorder. This allows for the tracking and measurement of underwater radiated sound from ships of opportunity with a single instrument deployment and without depending on track information from the automatic information system (AIS)
    Cover page: Tracking marine mammals and ships with small and large- aperture hydrophone arrays
    • Thesis
    • Peer Reviewed
    UC San Diego Electronic Theses and Dissertations (2016)

    Two distinctive features of underwater light field in the upper ocean were examined: the wave-induced high-frequency light fluctuations within the near-surface layer under sunny skies, and the asymmetry of horizontal radiance within the photic layer of the ocean.

    To characterize the spatiotemporal statistical properties of the wave-induced light fluctuations, measurements of downward plane irradiance were made with novel instrumentation within the top 10 m layer of the ocean at depths as shallow as 10 cm under sunny skies, different solar zenith angles, and weak to moderate wind speeds. It was found that the maximum intensity of light fluctuations occurs at depths as shallow as 20 cm under the most favorable conditions for wave focusing, which correspond to high sun in a clear sky with weak wind. The strong frequency dependence of light fluctuations at shallow near-surface depths indicates dominant frequency range of 1 – 3 Hz under favorable conditions that shifts toward lower frequencies with increasing depth. The light fluctuations were found to be spatially correlated over horizontal distances varying from few up to 10 – 20 cm at temporal scales of 0.3 – 1 sec (at the dominant frequency of 1 – 3 Hz). The distance of correlation showed a tendency to increase with increasing depth, solar zenith angle, and wind speed. The observed variations in spatiotemporal statistical properties of underwater light fluctuations with depth and environmental conditions are driven largely by weakening of sunlight focusing which is associated with light scattering within the water column, in the atmosphere and at the air-sea interface.

    To investigate the underwater horizontal radiance field, measurements of horizontal spectral radiance in two opposite directions (solar and anti-solar azimuths) within the solar principal plane were made within the photic layer of the open ocean. The ratio of these two horizontal radiances represents the asymmetry of horizontal radiance field. In addition to measurements, the radiative transfer simulations were also conducted to examine variations in the asymmetry of horizontal radiance at different light wavelengths as a function of solar zenith angle at different depths within the water column down to 200 m. It was demonstrated that the asymmetry of horizontal radiance increases with increasing solar zenith angle, reaching a maximum at angles of 60° – 80° under clear skies at shallow depths (1 – 10 m). At larger depths the maximum of asymmetry occurs at smaller solar zenith angles. The asymmetry was also found to increase with increasing light wavelength. The results from radiative transfer simulations provided evidence that variations in the asymmetry with solar zenith angle are driven largely by the diffuseness of light incident upon the sea surface and the geometry of illumination of the sea surface, both associated with changing position of the sun.

    In addition to contributions to the field of ocean optics, the findings of this dissertation have relevance for oceanic animal camouflage and vision as well as photosynthesis and other photochemical processes.

      Cover page: Characterization of the oceanic light field within the photic zone: Fluctuations of downward irradiance and asymmetry of horizontal radiance
      • Article
      • Peer Reviewed
      UC San Diego Previously Published Works (2017)
      Underwater radiated noise from merchant ships was measured opportunistically from multiple spatial aspects to estimate signature source levels and directionality. Transiting ships were tracked via the Automatic Identification System in a shipping lane while acoustic pressure was measured at the ships' keel and beam aspects. Port and starboard beam aspects were 15°, 30°, and 45° in compliance with ship noise measurements standards [ANSI/ASA S12.64 (2009) and ISO 17208-1 (2016)]. Additional recordings were made at a 10° starboard aspect. Source levels were derived with a spherical propagation (surface-affected) or a modified Lloyd's mirror model to account for interference from surface reflections (surface-corrected). Ship source depths were estimated from spectral differences between measurements at different beam aspects. Results were exemplified with a 4870 and a 10 036 twenty-foot equivalent unit container ship at 40%-56% and 87% of service speeds, respectively. For the larger ship, opportunistic ANSI/ISO broadband levels were 195 (surface-affected) and 209 (surface-corrected) dB re 1 μPa2 1 m. Directionality at a propeller blade rate of 8 Hz exhibited asymmetries in stern-bow (<6 dB) and port-starboard (<9 dB) direction. Previously reported broadband levels at 10° aspect from McKenna, Ross, Wiggins, and Hildebrand [(2012b). J. Acoust. Soc. Am. 131, 92-103] may be ∼12 dB lower than respective surface-affected ANSI/ISO standard derived levels.
        • Article
        • Peer Reviewed
        UC San Diego Previously Published Works (2015)
        Cuvier's beaked whales (Ziphius cavirostris) were tracked using two volumetric small-aperture (∼1 m element spacing) hydrophone arrays, embedded into a large-aperture (∼1 km element spacing) seafloor hydrophone array of five nodes. This array design can reduce the minimum number of nodes that are needed to record the arrival of a strongly directional echolocation sound from 5 to 2, while providing enough time-differences of arrivals for a three-dimensional localization without depending on any additional information such as multipath arrivals. To illustrate the capabilities of this technique, six encounters of up to three Cuvier's beaked whales were tracked over a two-month recording period within an area of 20 km(2) in the Southern California Bight. Encounter periods ranged from 11 min to 33 min. Cuvier's beaked whales were found to reduce the time interval between echolocation clicks while alternating between two inter-click-interval regimes during their descent towards the seafloor. Maximum peak-to-peak source levels of 179 and 224 dB re 1 μPa @ 1 m were estimated for buzz sounds and on-axis echolocation clicks (directivity index = 30 dB), respectively. Source energy spectra of the on-axis clicks show significant frequency components between 70 and 90 kHz, in addition to their typically noted FM upsweep at 40-60 kHz.
          • Article
          • Peer Reviewed
          UC San Diego Previously Published Works (2017)
          Underwater radiated noise from merchant ships was measured opportunistically from multiple spatial aspects to estimate signature source levels and directionality. Transiting ships were tracked via the Automatic Identification System in a shipping lane while acoustic pressure was measured at the ships keel and beam aspects. Port and starboard beam aspects were 15°, 30°, and 45° in compliance with ship noise measurements standards [ANSI/ASA S12.64 (2009) and ISO 17208-1 (2016)]. Additional recordings were made at a 10° starboard aspect. Source levels were derived with a spherical propagation (surface-affected) or a modified Lloyds mirror model to account for interference from surface reflections (surface-corrected). Ship source depths were estimated from spectral differences between measurements at different beam aspects. Results were exemplified with a 4870 and a 10 036 twenty-foot equivalent unit container ship at 40%-56% and 87% of service speeds, respectively. For the larger ship, opportunistic ANSI/ISO broadband levels were 195 (surface-affected) and 209 (surface-corrected) dB re 1 μPa2 1 m. Directionality at a propeller blade rate of 8 Hz exhibited asymmetries in stern-bow (<6 dB) and port-starboard (<9 dB) direction. Previously reported broadband levels at 10° aspect from McKenna, Ross, Wiggins, and Hildebrand [(2012b). J. Acoust. Soc. Am. 131, 92-103] may be ∼12 dB lower than respective surface-affected ANSI/ISO standard derived levels.
            Cover page: Deep-water measurements of container ship radiated noise signatures and directionality.
            • Article
            LBL Publications (1995)
              Cover page: Hollow-Anode Plasma Source for Molecular Beam Epitaxy of Gallium Nitride
              • Article
              • Peer Reviewed
              UC San Diego Previously Published Works (2013)
              To study delphinid near surface movements and behavior, two L-shaped hydrophone arrays and one vertical hydrophone line array were deployed at shallow depths (<125 m) from the floating instrument platform R/P FLIP, moored northwest of San Clemente Island in the Southern California Bight. A three-dimensional propagation-model based passive acoustic tracking method was developed and used to track a group of five offshore killer whales (Orcinus orca) using their emitted clicks. In addition, killer whale pulsed calls and high-frequency modulated (HFM) signals were localized using other standard techniques. Based on these tracks sound source levels for the killer whales were estimated. The peak to peak source levels for echolocation clicks vary between 170-205 dB re 1 μPa @ 1 m, for HFM calls between 185-193 dB re 1 μPa @ 1 m, and for pulsed calls between 146-158 dB re 1 μPa @ 1 m.
                • Article
                • Peer Reviewed
                UC Irvine Previously Published Works (2023)
                A landmark event in the transition from interphase to mitosis in metazoans is nuclear envelope breakdown (NEBD). Important mitotic events occur prior to NEBD, including condensation of replicated chromosomes and assembly of kinetochores to rapidly engage spindle microtubules. Here, we show that nuclear-enriched protein phosphatase 4 (PP4) ensures robust assembly of the microtubule-coupling outer kinetochore prior to NEBD. In the absence of PP4, chromosomes exhibit extended monopolar orientation after NEBD and subsequently mis-segregate. A secondary consequence of diminished outer kinetochore assembly is defective sister chromatid resolution. After NEBD, a cytoplasmic activity compensates for PP4 loss, leading to outer kinetochore assembly and recovery of chromosomes from monopolar orientation to significant bi-orientation. The Ndc80-Ska microtubule-binding module of the outer kinetochore is required for this recovery. PP4 associates with the inner kinetochore protein CENP-C; however, disrupting the PP4-CENP-C interaction does not perturb chromosome segregation. These results establish that PP4-dependent outer kinetochore assembly prior to NEBD is critical for timely and proper engagement of chromosomes with spindle microtubules.
                  Cover page: Nuclear-enriched protein phosphatase 4 ensures outer kinetochore assembly prior to nuclear dissolution.
                  • Article
                  • Peer Reviewed
                  UC San Diego Previously Published Works (2023)
                  The container shipping line Maersk undertook a Radical Retrofit to improve the energy efficiency of twelve sister container ships. Noise reduction, identified as a potential added benefit of the retrofitting effort, was investigated in this study. A passive acoustic recording dataset from the Santa Barbara Channel off Southern California was used to compile over 100 opportunistic vessel transits of the twelve G-Class container ships, pre- and post-retrofit. Post-retrofit, the G-Class vessels' capacity was increased from ~9,000 twenty-foot equivalent units (TEUs) to ~11,000 TEUs, which required a draft increase of the vessel by 1.5 m on average. The increased vessel draft resulted in higher radiated noise levels (<2 dB) in the mid- and high-frequency bands. Accounting for the Lloyd's mirror (dipole source) effect, the monopole source levels of the post-retrofit ships were found to be significantly lower (>5 dB) than the pre-retrofit ships in the low-frequency band and the reduction was greatest at low speed. Although multiple design changes occurred during retrofitting, the reduction in the low-frequency band most likely results from a reduction in cavitation due to changes in propeller and bow design.
                    Creative Commons 'BY' version 4.0 license
                    • Article
                    • Peer Reviewed
                    UC San Diego Previously Published Works (2015)
                    The clinical interest in farnesyltransferase inhibitors (FTIs) makes it important to understand how these compounds affect cellular processes involving farnesylated proteins. Mitotic abnormalities observed after treatment with FTIs have so far been attributed to defects in the farnesylation of the outer kinetochore proteins CENP-E and CENP-F, which are involved in chromosome congression and spindle assembly checkpoint signaling. Here we identify the cytoplasmic dynein adaptor Spindly as an additional component of the outer kinetochore that is modified by farnesyltransferase (FTase). We show that farnesylation of Spindly is essential for its localization, and thus for the proper localization of dynein and its cofactor dynactin, to prometaphase kinetochores and that Spindly kinetochore recruitment is more severely affected by FTase inhibition than kinetochore recruitment of CENP-E and CENP-F. Molecular replacement experiments show that both Spindly and CENP-E farnesylation are required for efficient chromosome congression. The identification of Spindly as a new mitotic substrate of FTase provides insight into the causes of the mitotic phenotypes observed with FTase inhibitors.
                      Cover page: Preventing farnesylation of the dynein adaptor Spindly contributes to the mitotic defects caused by farnesyltransferase inhibitors
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