Discriminant Function Analysis in Marine Ecology: Some Oversights and their Solutions

Marine ecologists commonly use discriminant function analysis (DFA) to evaluate the similarity of distinct populations and to classify individuals of unknown origin to known populations. However, investigators using DFA must account for (1) the possibility of correct classification due to chance alone, and (2) the influence of prior probabilities of group membership on classification results. A search of the recent otolith chemistry literature showed that these two concerns are sometimes ignored, so we used simulated data sets to explore the potential pitfalls of such oversights. We found that when estimating reclassification success for a training data set, small sample sizes or unbalanced sampling designs can produce remarkably high reclassification success rates by chance alone, especially when prior probabilities are estimated from sample size. When using a training data set to classify unknown individuals, maximum likelihood estimation of mixture proportions and group membership afforded up to 20% improvement over DFA with uninformative priors when groups contributed to the sample unequally. Given these results, we recommend the use of (1) randomization tests to estimate the probability that reclassification success is better than random, and (2) maximum likelihood estimation of mixture proportions in place of uninformative priors

PPI Questionnaire on Adaptive Wearable Appropriateness as an Autistic Intervention

Autism Spectrum Condition (ASC) is a life-long diagnosis, which has a subset of features including hyper-, seeking- and/or hypo-reactivity to sensory inputs or unusual interests (APA, 2013). These qualities are evident across environmental (e.g. response to specific sounds, visual fascination with lights or movements) and physiological domains (e.g. anxiety, respiration or euthermia). Scholars report that ninety (90%) of autistic adults experience sensory issues causing significant barriers at school/work (Leekam et al., 2007). As part of a larger PhD Research Project, this pilot study establishes designs, processes and measures that may establish if autistic individuals find value utilising adaptive/wearable interventions that possibly alter, redirect and/or attenuate disruptive stimuli. This study incorporates benign information not yet containing practical data, other than to provision and trial space where real data is nominally present. This pilot loads systems functionality for future use (e.g. consent, demographic collection, measures, post-mortem/survey feedback, storage, sorting, query, statistical analyses and reporting). Finally, this pilot provisions a follow-on and full-fledge Participant Public Involvement (PPI) designed to exploit data from focus group and co-produced surveys/designs. In turn, these may be used to inform an as-yet-to-be developed interventional prototype. Hence, the forthcoming PPI—by leveraging this pilot—aims to describe what degree sensory distractions occur among adolescent and adult ASC participants. Both pilot and PPI aspire to whether focus, anxiety and attentional concerns are perceived as negative issues and if individuals prefer assistance (vis à vis assistive wearables) to reduce anxiety, distractions and increase focus at school and at work (Bagley et al., 2016). This study results yield promise; in that, a subsequent PPI can be leveraged to obtain co-designed autistic data leading to a randomised clinical trial

Sound Impairment Effect on Cognitive Skill Performance

Autism Spectrum Condition (ASC) is a life-long diagnosis, which has a subset of individualized characteristics consisting of hyper-, seeking- and/or hypo-reactivity to sensory inputs or unusual interests (APA, 2013). These sensitivities are evident in both environmental (e.g. apparent response to specific sounds, visual fascination with lights or movements) and physiological domains (e.g. anxiety, respiration or euthermia). As part of a larger PhD Research Project (SensorAble), this pilot study proposes that autistic individuals who exhibit greater distractibility and reduced focus/attention resulting stimuli may benefit from interventions that alter, redirect and/or attenuate stimuli. In particular, Irrelevant-Sound Effect (ISE) consisting of un-targeted and/or modulated sonics cause greater disruption of performance of simultaneous and visual simple tasks compared to baseline ISE that are merely directed. Using gold-standard Stroop experiments, data collected among neurotypical (NT) and ASC individuals at baseline and at various ISE modes result in greater reaction time (RT) improvements among ASC than NT participants. In this study, which focuses on aural distractibility only, data supports that signal processing may provide a gateway to enhancing focus and attention while reduce distractibility and anxiety in other domains

Ontology and the Future of Dental Research Informatics.

How do we find what is clinically significant in the swarms of data being generated by today’s diagnostic technologies? As electronic records become ever more prevalent – and digital imaging and genomic, proteomic, salivaomics, metabalomics, pharmacogenomics, phenomics and transcriptomics techniques become commonplace – fdifferent clinical and biological disciplines are facing up to the need to put their data houses in order to avoid the consequences of an uncontrolled explosion of different ways of describing information. We describe a new strategy to advance the consistency of data in the dental research community. The strategy is based on the idea that existing systems for data collection in dental research will continue to be used, but proposes a methodology in which past, present and future data will be described using a consensus-based controlled structured vocabulary called the Ontology for Dental Research (ODR)

Herbivory and the Resilience of Caribbean Coral Reefs: Knowledge Gaps and Implications for Management

Herbivory is a key process on coral reefs that can facilitate reef-building corals by excluding algae that otherwise negatively impact coral settlement, growth, and survivorship. Over the last several decades, coral cover on Caribbean reefs has declined precipitously. On many reefs, large structurally complex corals have been replaced by algae and other non-reef-building organisms, resulting in the collapse of physical structure and the loss of critical ecosystem services. The drivers of coral decline on Caribbean reefs are complex and vary among locations. On many reefs, populations of key herbivores have been greatly reduced by disease and overfishing, and this has resulted in the proliferation of algae that hinder coral recovery following major disturbances. Yet, evidence that increases in herbivory can promote coral recovery on Caribbean reefs has been mixed. Here, we discuss key contingencies that will modify the relationships between herbivores, algae, and corals and identify critical knowledge gaps that limit our ability to predict when and where herbivores are most likely to facilitate coral persistence and recovery. Impacts of herbivores on coral reef ecosystems will vary greatly in space and time and will depend on herbivore diversity and species identity. While there are still a large number of knowledge gaps, we make several management recommendations based on our current understanding of the processes that structure reef ecosystems. Reversing the fate of Caribbean coral reefs will require the development of integrated management strategies that simultaneously address multiple stressors in addition to the impacts of fisheries on herbivore assemblages

Patterns, Causes and Consequences of Regional Variation in the Ecology and Life History of a Reef Fish

Many species vary in their ecology across their geographic ranges in response to gradients in environmental conditions. Such variation, which can influence life history traits and subsequent demography of populations, usually occurs over large spatial scales. However, describing and understanding the causes of such variation is difficult precisely because it occurs over such large spatial scales. In this study, we document spatial variation in the ecology of a common reef fish, Stegastes beebei, in the Gala´pagos Islands and test a number of potential causal mechanisms. The pattern resembles that seen in latitudinal variation: individuals are larger, occur in higher densities, and live longer in the coldest region of the islands than those in the warmest region. However, in this system, demography varies among regional populations separated bytemperature, despite differences in the gross magnitude and timing of reproduction in different regions. A model of reproductive output suggests that fish in the warmest region are allocating a greater proportion of available energy to reproduction, resulting in apparent regional life history tradeoffs. Our data suggest that regional demographic differences in S. beebei may be driven by a combination of variation in food availability and an environmentally mediated life history tradeoff

Bacterially mediated removal of phosphorus and cycling of nitrate and sulfate in the waste stream of a "zero-discharge" recirculating mariculture system

Simultaneous removal of nitrogen and phosphorus by microbial biofilters has been used in a variety of water treatment systems including treatment systems in aquaculture. In this study, phosphorus, nitrate and sulfate cycling in the anaerobic loop of a zero-discharge, recirculating mariculture system was investigated using detailed geochemical measurements in the sludge layer of the digestion basin. High concentrations of nitrate and sulfate, circulating in the overlying water (~15 mM), were removed by microbial respiration in the sludge resulting in a sulfide accumulation of up to 3 mM. Modelling of the observed S and O isotopic ratios in the surface sludge suggested that, with time, major respiration processes shifted from heterotrophic nitrate and sulfate reduction to autotrophic nitrate reduction. The much higher inorganic P content of the sludge relative to the fish feces is attributed to conversion of organic P to authigenic apatite. This conclusion is supported by: (a) X-ray diffraction analyses, which pointed to an accumulation of a calcium phosphate mineral phase that was different from P phases found in the feces, (b) the calculation that the pore waters of the sludge were highly oversaturated with respect to hydroxyapatite (saturation index = 4.87) and (c) there was a decrease in phosphate (and in the Ca/Na molar ratio) in the pore waters simultaneous with an increase in ammonia showing there had to be an additional P removal process at the same time as the heterotrophic breakdown of organic matter

Dynamics of an Acute Coral Disease Outbreak Associated with the Macroalgae \u3cem\u3eDictyota\u3c/em\u3e SPP. in Dry Tortugas National Park, Florida, USA

Reports of coral disease outbreaks have increased in recent decades, but often few details are known about these outbreaks, such as environmental triggers, associated biological variables, or even the precise temporal span of the outbreak. Here we document an acute outbreak of a rapid tissue loss disease on the highest live coral cover (15%–30%) reefs within Dry Tortugas National Park, Florida, USA. This disease exhibited similar signs to white plague disease with the notable exception that a white film often was observed on the recently denuded skeleton. The temporal span of the disease was short (\u3c2 mo). Partial mortality was recorded but there was no detectable impact to overall coral cover. A significant increase and then decrease in the cover of macroalgae, primarily of the genus Dictyota, occurred simultaneously with the increase and drop in disease lesion density (number of lesions per living tissue area), respectively. No other anomalous biological or physical factors (e.g., unusual temperature, turbidity, passage of storms) corresponded with the outbreak, although it is likely that some environmental anomaly that was undetectable with the methods employed favored both disease and Dictyota expansion. This is the first study to associate a rapid increase in a macroalgal population with a coral disease outbreak. We highlight the need for increased study of the initiation of such outbreaks in the caribbean

The OBO Foundry: Coordinated Evolution of Ontologies to Support Biomedical Data Integration

The value of any kind of data is greatly enhanced when it exists in a form that allows it to be integrated with other data. One approach to integration is through the annotation of multiple bodies of data using common controlled vocabularies or ‘ontologies’. Unfortunately, the very success of this approach has led to a proliferation of ontologies, which itself creates obstacles to integration. The Open Biomedical Ontologies (OBO) consortium has set in train a strategy to overcome this problem. Existing OBO ontologies, including the Gene Ontology, are undergoing a process of coordinated reform, and new ontologies being created, on the basis of an evolving set of shared principles governing ontology development. The result is an expanding family of ontologies designed to be interoperable, logically well-formed, and to incorporate accurate representations of biological reality. We describe the OBO Foundry initiative, and provide guidelines for those who might wish to become involved in the future

Rapid Invasion of Indo-Pacific Lionfishes (\u3cem\u3ePterois Volitans\u3c/em\u3e and \u3cem\u3ePterois Miles\u3c/em\u3e) in the Florida Keys, USA: Evidence from Multiple Pre- and Post-Invasion Data Sets

Over the past decade, Indo-Pacific lionfishes, Pterois volitans (Linnaeus, 1758) and Pterois miles (Bennett, 1828), venomous members of the scorpionfish family (Scorpaenidae), have invaded and spread throughout much of the tropical and subtropical northwestern Atlantic Ocean and Caribbean Sea. These species are generalist predators of fishes and invertebrates with the potential to disrupt the ecology of the invaded range. Lionfishes have been present in low numbers along the east coast of Florida since the 1980s, but were not reported in the Florida Keys until 2009. We document the appearance and rapid spread of lionfishes in the Florida Keys using multiple long-term data sets that include both pre- and post-invasion sampling. Our results are the first to quantify the invasion of lionfishes in a new area using multiple independent, ongoing monitoring data sets, two of which have explicit estimates of sampling effort. Between 2009 and 2011, lionfish frequency of occurrence, abundance, and biomass increased rapidly, increasing three- to six-fold between 2010 and 2011 alone. In addition, individuals were detected on a variety of reef and non-reef habitats throughout the Florida Keys. Because lionfish occurrence, abundance, and impacts are expected to continue to increase throughout the region, monitoring programs like those used in this study will be essential to document ecosystem changes that may result from this invasion