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The sustainable management of fisheries and aquaculture requires an understanding of how these activities interact with natural fish populations. GoPro cameras were used to collect an underwater video data set on and around shellfish aquaculture farms in an estuary in the NE Pacific from June to August 2017 and June to August 2018 to better understand habitat use by the local fish and crab communities. Images extracted from these videos were labeled to produce a data set that is suitable for use in training computer vision models. The labeled data set contains 77,739 images sampled from the collected video; 67,990 objects (fishes and crustaceans) have been annotated in 30,384 images (the remainder have been annotated as “empty”). The metadata of the data set also indicates whether a physical magenta filter was used during video collection to counteract reduced visibility. These data have the potential to help researchers address system-level and in-depth regional shellfish aquaculture questions related to ecosystem services and shellfish aquaculture interactions.

We applied Qualitative Network Models (QNMs) to evaluate the potential community effects of ocean acidification (OA) in a major shellfish-producing estuary (Willapa Bay, Washington). QNMs are well-suited to data-limited systems and only require information on the sign (+, –, 0) of the interactions between species. We examined qualitative predictions of community responses to 13 different OA scenarios that corresponded to 3 broad categories of hypothesized OA effects: (1) increased primary productivity, (2) reductions in bivalve populations, and (3) enhanced predation interactions between bivalves and their crab and gastropod predators. The cultivated bivalve Manila clam tended to respond negatively across scenarios, while primary producers (phytoplankton and eelgrasses) and Chinook salmon tended to respond positively. Tradeoffs between species were also assessed: Manila clam and Pacific oyster were predicted to decrease and increase, respectively, when direct OA effects were limited to eelgrasses and the reverse occurred when phytoplankton alone was stimulated by OA. We analyzed the QNMs to identify key linkages that influenced the sign outcome of community members and might therefore warrant future quantitative study. QNMs may be particularly relevant to researchers as a simple method for identifying conditions under which the sign response of species to OA, as inferred from single-species OA experiments, will likely hold in the wild. Given data limitations in most systems, QNMs are a practical alternative or complement to data-intensive quantitative approaches and may help accelerate our understanding of the community-wide effects of OA in marine systems.

Antarctic blue and fin whales were once abundant in the southeastern Atlantic Ocean, yet their occurrence and ecology in this region is still poorly understood. Seasonal acoustic occurrence and behaviour of Antarctic blue and fin whales off the South African west coast were determined using bio-acoustic data collected through two autonomous acoustic recorders between December 2015 and January 2017. Blue whale Z-calls were detected year-round with a peak in July, while fin whale 20 Hz pulses were detected seasonally with a peak in June by a recorder deployed at 1118 m water depth. Blue and fin whale calls were detected seasonally with a similar peak in May by a recorder deployed at 4481 m water depth. The blue whale 27 Hz chorus, and blue and fin whale 18–28 Hz chorus followed a similar trend as the seasonal acoustic occurrence of individual Z-calls and 20 Hz pulses. A maximum detection range of 800 km estimated by acoustic propagation modelling suggests that detected calls originate from whales within the South African west coast waters. Random forest models classified month of the year, wind speed, log-transformed chlorophyll-a, and sea surface temperature anomaly as the most important predictors of blue and fin whale acoustic occurrence and behaviour. Our study highlights the South African west coast as an important year-round habitat and seasonal breeding or overwintering habitat of these whales. Additionally, the year-round acoustic occurrence in this region supports the notion that blue whale migration patterns are more dynamic than previously perceived.

The aim of this study is to investigate the potential use of reconstructed three-dimensional multi-detector computed tomography (3D MDCT) imagery to distinguish between perimortem cranial trauma and postmortem cranial damage. A total of 45 crania were initially examined for the purpose of this study. The postmortem group consists of 14 crania from a Medieval Scottish population while the perimortem group consists of 31 CT scans of perimortem trauma cases from the University Hospital of Heraklion, Crete. Six crania belonging to the perimortem group could not be assessed for the purposes of this study. Each of the remaining 39 crania was examined under the following criteria: preponderant texture, preponderant outline, edge morphology, fracture angle, fracture relationship to path of least resistance, evidence of plastic response and the presence of hinging. As edge morphology could not be determined for any of the crania this criterion was not considered for statistical computations. Statistical analysis demonstrated the five of the six criteria (preponderant texture, preponderant outline, fracture relationship to least resistance path, plastic response and the presence of hinging) subjected to statistical analysis bore statistical significance in distinguishing between perimortem trauma and postmortem damage when using 3D CT images. This study, therefore, demonstrated that the timing of cranial fractures can be determined using 3D CT images and thus can complement and add to existing methods for trauma assessment in both forensic and archaeological settings.

In this paper, data from 105 soil and groundwater remediation projects at BP gasoline service stations located in the state of Illinois were mined for lessons to reduce cost and improve management of remediation sites. Data mining software called D2K was used to train decision tree, stepwise linear regression and instance-based weighting models that relate hydrogeologic, sociopolitical, temporal and remedial factors in the site closure reports to remediation cost. The most important factors influencing cost were found to be the amount of soil excavated and the number of groundwater monitoring wells installed, suggesting that better management of excavation and well placement could result in significant cost savings. The best model for predicting cost classes (low, medium and high cost) was the decision tree, which had a prediction accuracy of approximately 73%. The misclassification of approximately 27% of the sites by even the best model suggests that remediation costs at service stations are influenced by other site-specific factors that may be difficult to accurately predict in advance.

This dissertation is a compilation of explorations of various methods related to mapping, methods and modeling. These methods are useful in the study of acoustic data. The exploration of data in this work from a Greenland fjord represents most (although not all) of these methods and therefore influences the title of this work. In this work, the background noise environment in a glacial fjord was measured and the data were analyzed. The work explores the utility of spectral probability density (SPD) in evaluating background noise characteristics in the frequency domain, models probability density functions (PDFs) of spectral levels and introduces a parameter σT that quantifies the character of noise in frequency bands of interest; this work demonstrates that the empirical PDFs used in the SPD can be replaced by analytical PDFs if the spectral estimates can be considered to be exponential random variables. It also explores the utility of k-medoids clustering as a pre-sorting method to inform the selection of features on which to base the training of more complex algorithms.

To inform cure in children living with HIV (CWH), we elucidated the dynamics and mechanisms underlying HIV persistence during antiretroviral therapy (ART). In 120 Kenyan CWH who initiated ART between 1-12 months of age, 55 had durable viral load suppression, and 65 experienced ART interruptions. We measured plasma HIV RNA levels, CD4+ T cell count, and levels of intact and defective HIV DNA proviruses via the cross-subtype intact proviral DNA assay (CS-IPDA). By modeling data from the durably suppressed subset, we found that during early ART (year 0-1 on ART), plasma RNA levels decayed rapidly and biphasically and intact and defective HIV DNA decayed with mean 3 and 9 month half-lives, respectively. After viral suppression was achieved (years 1-8 on ART), intact HIV DNA decay slowed to a mean 22 month half-life, whilst defective HIV DNA no longer decayed. In five CWH, we found individual CD4+ TCRβ clones wax and wane, but average kinetics resembled those of defective DNA and CD4 count, suggesting that differential decay of intact HIV DNA arises from selective pressures overlaying normal CD4+ T cell kinetics. Finally, by modeling HIV RNA and DNA in CWH with treatment interruptions, we linked temporary viremia to transient rises in HIV DNA, but long-term intact reservoirs were not strongly influenced, suggesting brief treatment interruptions may not significantly increase HIV reservoirs in children.

The muscarinic-cholinergic system is involved in the pathophysiology of bipolar disorder (BD), and contributes to attention and the top-down and bottom-up cognitive and affective mechanisms of emotional processing, functionally altered in BD. Emotion processing can be assessed by the ability to inhibit a response when the content of the image is emotional. Impaired regulatory capacity of cholinergic neurotransmission conferred by reduced M2-autoreceptor availability is hypothesized to play a role in elevated salience of negative emotional distractors in euthymic BD relative to individuals with no history of mood instability. Thirty-three euthymic BD type-I (DSM-V-TR) and 50 psychiatrically-healthy controls underwent functional magnetic resonance imaging (fMRI) and an emotion-inhibition paradigm before and after intravenous cholinergic challenge using the acetylcholinesterase inhibitor, physostigmine (1 mg), or placebo. Mood, accuracy, and reaction time on either recognizing or inhibiting a response associated with an image involving emotion and regional functional activation were examined for effects of cholinergic challenge physostigmine relative to placebo, prioritizing any interaction with the diagnostic group. Analyses revealed that (1) at baseline, impaired behavioral performance was associated with lower activation in the anterior cingulate cortex in BD relative to controls during emotion processing; (2) physostigmine (vs. placebo) affected behavioral performance during the inhibition of negative emotions, without altering mood, and increased activation in the posterior cingulate cortex in BD (vs. controls); (3) In BD, lower accuracy observed during emotion inhibition of negative emotions was remediated by physostigmine and was associated with cingulate cortex overactivation. Our findings implicate abnormal regulation of cholinergic neurotransmission in the cingulate cortices in BD, which may mediate exaggerated emotional salience processing, a core feature of BD.

Software verification is an important approach to establishing the reliability of critical systems. One important area of application is in the field of robotics, as robots take on more tasks in both day-to-day areas and highly specialised domains. Our particular interest is in checking the plans that robots are expected to follow to detect errors that would lead to unreliable behaviour. Python is a popular programming language in the robotics domain through the use of the Robot Operating System (ROS) and various other libraries. Python’s Turtle package provides a mobile agent, which we formally model here using Communicating Sequential Processes (CSP). Our interactive toolchain CSP2Turtle with CSP models and Python components enables plans for the turtle agent to be verified using the FDR model-checker before being executed in Python. This means that certain classes of errors can be avoided, providing a starting point for more detailed verification of Turtle programs and more complex robotic systems. We illustrate our approach with examples of robot navigation and obstacle avoidance in a 2D grid-world. We evaluate our approach and discuss future work, including how our approach could be scaled to larger systems.

Combining immunostimulatory chemotherapies with immunotherapy is an attractive strategy to enhance treatment responses in oesophagogastric junctional adenocarcinoma (OGJ). This study investigates the immunostimulatory properties of FLOT, CROSS and MAGIC chemotherapy regimens in the context of OGJ using in vitro and ex vivo models of the treatment-naïve and post-chemotherapy treated tumour microenvironment. FLOT and CROSS chemotherapy regimens increased surrogate markers of immunogenic cell death (HMGB1 and HLA-DR), whereas the MAGIC treatment regimen decreased HMGB1 and HLA-DR on OGJ cells (markedly for epirubicin). Tumour-infiltrating and circulating T cells had significantly lower CD27 expression and significantly higher CD69 expression post-FLOT and post-CROSS treatment. Similarly , the supernatant from FLOT- and CROSS-treated OGJ cell lines and from FLOT- and CROSS-treated OGJ biopsies cultured ex vivo also decreased CD27 and increased CD69 expression on T cells. Following 48 h treatment with post-FLOT and post-CROSS tumour conditioned media the frequency of CD69 + T cells in culture negatively correlated with the levels of soluble immunosuppressive pro-angiogenic factors in the conditioned media from ex vivo explants. Supernatant from FLOT- and CROSS-treated OGJ cell lines also increased the cytotoxic potential of healthy donor T cells ex vivo and enhanced OGJ patient-derived lymphocyte mediated-killing of OE33 cells ex vivo . Collectively, this data demonstrate that FLOT and CROSS chemotherapy regimens possess immunostimulatory properties, identifying these chemotherapy regimens as rational synergistic partners to test in combination with immunotherapy and determine if this combinatorial approach could boost anti-tumour immunity in OGJ patients and improve clinical outcomes.