Testing stochastic software using Pseudo-oracles

Stochastic models can be difficult to test due to their complexity and randomness, yet their predictions are often used to make important decisions, so they need to be correct. We introduce a new search-based technique for testing implementations of stochastic models by maximising the differences between the implementation and a pseudo-oracle. Our technique reduces testing effort and enables discrepancies to be found that might otherwise be overlooked. We show the technique can identify differences challenging for humans to observe, and use it to help a new user understand implementation differences in a real model of a citrus disease (Huanglongbing) used to inform policy and research.Wellcome TrustThis is the author accepted manuscript. The final version is available from the Association for Computing Machinery via http://dx.doi.org/10.1145/2931037.293106

Parental depressive symptoms, children’s emotional and behavioural problems, and parents’ expressed emotion - critical and positive comments

This is the final version of the article. Available from Public Library of Science via the DOI in this record.This longitudinal study examined whether mothers’ and fathers’ depressive symptoms predict, independently and interactively, children’s emotional and behavioural problems. It also examined bi-directional associations between parents’ expressed emotion constituents (parents’ child-directed positive and critical comments) and children’s emotional and behavioural problems. At time 1, the sample consisted of 160 families in which 50 mothers and 40 fathers had depression according to the Structured Clinical Interview for DSM-IV. Children’s mean age at Time 1 was 3.9 years (SD = 0.8). Families (n = 106) were followed up approximately 16 months later (Time 2). Expressed emotion constituents were assessed using the Preschool Five Minute Speech Sample. In total, 144 mothers and 158 fathers at Time 1 and 93 mothers and 105 fathers at Time 2 provided speech samples. Fathers’ depressive symptoms were concurrently associated with more child emotional problems when mothers had higher levels of depressive symptoms. When controlling for important confounders (children’s gender, baseline problems, mothers’ depressive symptoms and parents’ education and age), fathers’ depressive symptoms independently predicted higher levels of emotional and behavioural problems in their children over time. There was limited evidence for a bi-directional relationship between fathers’ positive comments and change in children’s behavioural problems over time. Unexpectedly, there were no bi-directional associations between parents’ critical comments and children’s outcomes. We conclude that the study provides evidence to support a whole family approach to prevention and intervention strategies for children’s mental health and parental depression

Effects of food type and abundance on begging and sharing in Asian small-clawed otters (Aonyx cinereus)

This is the final version. Available from PeerJ via the DOI in this record. The following information was supplied regarding data availability: Data and code are available at Figshare: https://figshare.com/authors/Madison_BowdenParry/9424769. Bowden-Parry, Madison; Postma, Erik; J. Boogert, Neeltje (2020): Bowden-ParryOtterdata.csv. figshare. Dataset. https://doi.org/10.6084/m9.figshare. 13017158.v2 Bowden-Parry, Madison; Postma, Erik; J. Boogert, Neeltje (2020): Bowden-ParryOtterRScript.R. figshare. Software. https://doi.org/10.6084/m9.figshare. 13016888.v2 Bowden-Parry, Madison; Postma, Erik; J. Boogert, Neeltje (2020): Bowden-ParryOtterDyadShare.csv. figshare. Dataset. https://doi.org/10.6084/m9.figshare. 13017137.v1.Begging for food, a conspicuous solicitation display, is common in a variety of taxa, and it has received extensive research attention in a parent-offspring context. Both theoretical models and empirical evidence suggest that offspring begging can be an honest signal of hunger or a mediator of competition between siblings. At a behavioural mechanistic level, begging for food can be a form of harassment aimed at persuading those in possession of food to share. Food sharing, defined as the transfer of a defendable food item from one individual to another, can vary considerably between species, age-classes and food type and abundance. We investigated the determinants of begging and food-sharing behaviours in Asian small-clawed otters (Aonyx cinereus), a group-living species that commonly exhibits begging in captivity. We presented two captive otter populations with three food types that varied in exploitation complexity, in three different abundances. We predicted that begging rates would be highest when food was in lowest abundance and hardest to exploit, and that increased begging would lead to increased food sharing. We found that, over time, increased begging rates were indeed correlated with increased food transfers, but neither food type complexity nor abundance affected begging or sharing rates. However, age category was significantly associated with begging and food sharing rates: juvenile otters begged more and shared less than adult otters. The results from this first experimental study on begging and food sharing within the Mustelid family begin to reveal some of the drivers of these behaviours

The “dirty dozen” of freshwater science: Detecting then reconciling hydrological data biases and errors

Sound water policy and management rests on sound hydrometeorological and ecological data. Conversely, unrepresentative, poorly collected or erroneously archived data introduces uncertainty regarding the magnitude, rate and direction of environmental change, in addition to undermining confidence in decision-making processes. Unfortunately, data biases and errors can enter the information flow at various stages, starting with site selection, instrumentation, sampling/ measurement procedures, post-processing and ending with archiving systems. Techniques such as visual inspection of raw data, graphical representation and comparison between sites, outlier and trend detection, and referral to metadata can all help uncover spurious data. Tell-tale signs of ambiguous and/or anomalous data are highlighted using 12 carefully chosen cases drawn mainly from hydrology (‘the dirty dozen’). These include evidence of changes in site or local conditions (due to land management, river regulation or urbanisation); modifications to instrumentation or inconsistent observer behaviour; mismatched or misrepresentative sampling in space and time; treatment of missing values, post-processing and data storage errors. As well as raising awareness of pitfalls, recommendations are provided for uncovering lapses in data quality after the information has been gathered. It is noted that error detection and attribution are more problematic for very large data sets, where observation networks are automated, or when various information sources have been combined. In these cases, more holistic indicators of data integrity are needed that reflect the overall information life-cycle and application(s) of the hydrological data

A Quantitative, Non-Destructive Methodology for Habitat Characterisation and Benthic Monitoring at Offshore Renewable Energy Developments

Following governments' policies to tackle global climate change, the development of offshore renewable energy sites is likely to increase substantially over coming years. All such developments interact with the seabed to some degree and so a key need exists for suitable methodology to monitor the impacts of large-scale Marine Renewable Energy Installations (MREIs). Many of these will be situated on mixed or rocky substrata, where conventional methods to characterise the habitat are unsuitable. Traditional destructive sampling is also inappropriate in conservation terms, particularly as safety zones around (MREIs) could function as Marine Protected Areas, with positive benefits for biodiversity. Here we describe a technique developed to effectively monitor the impact of MREIs and report the results of its field testing, enabling large areas to be surveyed accurately and cost-effectively. The methodology is based on a high-definition video camera, plus LED lights and laser scale markers, mounted on a “flying array” that maintains itself above the seabed grounded by a length of chain, thus causing minimal damage. Samples are taken by slow-speed tows of the gear behind a boat (200 m transects). The HD video and randomly selected frame grabs are analysed to quantify species distribution. The equipment was tested over two years in Lyme Bay, UK (25 m depth), then subsequently successfully deployed in demanding conditions at the deep (>50 m) high-energy Wave Hub site off Cornwall, UK, and a potential tidal stream energy site in Guernsey, Channel Islands (1.5 ms−1 current), the first time remote samples from such a habitat have been achieved. The next stage in the monitoring development process is described, involving the use of Remote Operated Vehicles to survey the seabed post-deployment of MREI devices. The complete methodology provides the first quantitative, relatively non-destructive method for monitoring mixed-substrate benthic communities beneath MPAs and MREIs pre- and post-device deployment

Typhoid fever as a cause of opportunistic infection: case report

BACKGROUND: Typhoid fever is a systemic infection caused by the bacterium Salmonella enterica subspecies enterica serotype typhi, which is acquired by ingestion of contaminated food and water. Each year the disease affects at least 16 million persons world-wide, most of whom reside in the developing countries of Southeast Asia and Africa. In Italy the disease is uncommon with a greater number of cases in Southern regions than in Northern ones. CASE PRESENTATION: We report on a 57-year-old Sri-Lankan male affected by typhoid fever, the onset of which was accompanied by oropharyngeal candidiasis. This clinical sign was due to a transient cell-mediated immunity depression (CD4+ cell count was 130 cells/mm(3)) probably caused by Salmonella typhi infection. Human immunodeficiency virus infection was ruled out. Diagnosis of typhoid fever was made by the isolation of Salmonella typhi from two consecutive blood cultures. The patient recovered after a ten days therapy with ciprofloxacin and his CD4+ cell count improved gradually until normalization within 3 weeks. CONCLUSION: Our patient is the first reported case of typhoid fever associated with oropharyngeal candidiasis. This finding suggests a close correlation between Salmonella typhi infection and transitory immunodepression

Lithic technological responses to Late Pleistocene glacial cycling at Pinnacle Point Site 5-6, South Africa

There are multiple hypotheses for human responses to glacial cycling in the Late Pleistocene, including changes in population size, interconnectedness, and mobility. Lithic technological analysis informs us of human responses to environmental change because lithic assemblage characteristics are a reflection of raw material transport, reduction, and discard behaviors that depend on hunter-gatherer social and economic decisions. Pinnacle Point Site 5-6 (PP5-6), Western Cape, South Africa is an ideal locality for examining the influence of glacial cycling on early modern human behaviors because it preserves a long sequence spanning marine isotope stages (MIS) 5, 4, and 3 and is associated with robust records of paleoenvironmental change. The analysis presented here addresses the question, what, if any, lithic assemblage traits at PP5-6 represent changing behavioral responses to the MIS 5-4-3 interglacial-glacial cycle? It statistically evaluates changes in 93 traits with no a priori assumptions about which traits may significantly associate with MIS. In contrast to other studies that claim that there is little relationship between broad-scale patterns of climate change and lithic technology, we identified the following characteristics that are associated with MIS 4: increased use of quartz, increased evidence for outcrop sources of quartzite and silcrete, increased evidence for earlier stages of reduction in silcrete, evidence for increased flaking efficiency in all raw material types, and changes in tool types and function for silcrete. Based on these results, we suggest that foragers responded to MIS 4 glacial environmental conditions at PP5-6 with increased population or group sizes, 'place provisioning', longer and/or more intense site occupations, and decreased residential mobility. Several other traits, including silcrete frequency, do not exhibit an association with MIS. Backed pieces, once they appear in the PP5-6 record during MIS 4, persist through MIS 3. Changing paleoenvironments explain some, but not all temporal technological variability at PP5-6.Social Science and Humanities Research Council of Canada; NORAM; American-Scandinavian Foundation; Fundacao para a Ciencia e Tecnologia [SFRH/BPD/73598/2010]; IGERT [DGE 0801634]; Hyde Family Foundations; Institute of Human Origins; National Science Foundation [BCS-9912465, BCS-0130713, BCS-0524087, BCS-1138073]; John Templeton Foundation to the Institute of Human Origins at Arizona State Universit

Visualising biological data: a semantic approach to tool and database integration

<p>Abstract</p> <p>Motivation</p> <p>In the biological sciences, the need to analyse vast amounts of information has become commonplace. Such large-scale analyses often involve drawing together data from a variety of different databases, held remotely on the internet or locally on in-house servers. Supporting these tasks are <it>ad hoc </it>collections of data-manipulation tools, scripting languages and visualisation software, which are often combined in arcane ways to create cumbersome systems that have been customised for a particular purpose, and are consequently not readily adaptable to other uses. For many day-to-day bioinformatics tasks, the sizes of current databases, and the scale of the analyses necessary, now demand increasing levels of automation; nevertheless, the unique experience and intuition of human researchers is still required to interpret the end results in any meaningful biological way. Putting humans in the loop requires tools to support real-time interaction with these vast and complex data-sets. Numerous tools do exist for this purpose, but many do not have optimal interfaces, most are effectively isolated from other tools and databases owing to incompatible data formats, and many have limited real-time performance when applied to realistically large data-sets: much of the user's cognitive capacity is therefore focused on controlling the software and manipulating esoteric file formats rather than on performing the research.</p> <p>Methods</p> <p>To confront these issues, harnessing expertise in human-computer interaction (HCI), high-performance rendering and distributed systems, and guided by bioinformaticians and end-user biologists, we are building reusable software components that, together, create a toolkit that is both architecturally sound from a computing point of view, and addresses both user and developer requirements. Key to the system's usability is its direct exploitation of semantics, which, crucially, gives individual components knowledge of their own functionality and allows them to interoperate seamlessly, removing many of the existing barriers and bottlenecks from standard bioinformatics tasks.</p> <p>Results</p> <p>The toolkit, named Utopia, is freely available from <url>http://utopia.cs.man.ac.uk/</url>.</p