NEU-MODEL : a multi-level object-oriented dynamic emulation laboratory

Computational neuroscience aims to elucidate the mechanisms of neural information processing and population dynamics, through a methodology of incorporating biological data into complex mathematical models. Existing simulation environments model at a particular level of detail; none allow a multi-level approach to neural modelling. Moreover, most are not engineered to produce compute-efficient solutions, an important issue because sufficient processing power is a major impediment in the field. This project aims to apply modern software engineering techniques to create a flexible high performance neural modelling environment, which will allow rigorous exploration of model parameter effects, and modelling at multiple levels of abstraction.

The Long and Short of It: Branch Lengths and the Problem of Placing the New Zealand Short-Tailed Bat, Mystacina

The taxonomic position of the endemic New Zealand bat genus Mystacina has vexed systematists ever since its erection in 1843. Over the years the genus has been linked with many microchiropteran families and superfamilies. Most recent classifications place it in the Vespertilionoidea, although some immunological evidence links it with the Noctilionoidea (=Phyllostomoidea). We have sequenced 402 bp of the mitochondrial cytochrome b gene for M. tuberculata (Gray in Dieffenbach, 1843), and using both our own and published DNA sequences for taxa in both superfamilies, we applied different tree reconstruction methods to find the appropriate phylogeny and different methods of estimating confidence in the parts of the tree. All methods strongly support the classification of Mystacina in the Noctilionoidea. Spectral analysis suggests that parsimony analysis may be misleading for Mystacina's precise placement within the Noctilionoidea because of its long terminal branch. Analyses not susceptible to long-branch attraction suggest that the Mystacinidae is a sister family to the Phyllostomidae. Dating the divergence times between the different taxa suggests that the extant chiropteran families radiated around and shortly after the Cretaceous-Tertiary boundary. We discuss the biogeographical implications of classifying Mystacina within the Noctilionoidea and contrast our result with those classifications placing Mystacina in the Vespertilionoidea, concluding that evidence for the latter is weak.

Topical pattern based document modelling and relevance ranking

For traditional information filtering (IF) models, it is often assumed that the documents in one collection are only related to one topic. However, in reality users’ interests can be diverse and the documents in the collection often involve multiple topics. Topic modelling was proposed to generate statistical models to represent multiple topics in a collection of documents, but in a topic model, topics are represented by distributions over words which are limited to distinctively represent the semantics of topics. Patterns are always thought to be more discriminative than single terms and are able to reveal the inner relations between words. This paper proposes a novel information filtering model, Significant matched Pattern-based Topic Model (SPBTM). The SPBTM represents user information needs in terms of multiple topics and each topic is represented by patterns. More importantly, the patterns are organized into groups based on their statistical and taxonomic features, from which the more representative patterns, called Significant Matched Patterns, can be identified and used to estimate the document relevance. Experiments on benchmark data sets demonstrate that the SPBTM significantly outperforms the state-of-the-art models.

Differential processing of thematic and categorical conceptual relations in spoken word production

Studies of semantic context effects in spoken word production have typically distinguished between categorical (or taxonomic) and associative relations. However, associates tend to confound semantic features or morphological representations, such as whole-part relations and compounds (e.g., BOAT-anchor, BEE-hive). Using a picture-word interference paradigm and functional magnetic resonance imaging (fMRI), we manipulated categorical (COW-rat) and thematic (COW-pasture) TARGET-distractor relations in a balanced design, finding interference and facilitation effects on naming latencies, respectively, as well as differential patterns of brain activation compared with an unrelated distractor condition. While both types of distractor relation activated the middle portion of the left middle temporal gyrus (MTG) consistent with retrieval of conceptual or lexical representations, categorical relations involved additional activation of posterior left MTG, consistent with retrieval of a lexical cohort. Thematic relations involved additional activation of the left angular gyrus. These results converge with recent lesion evidence implicating the left inferior parietal lobe in processing thematic relations and may indicate a potential role for this region during spoken word production.

The fossil calibration database - A new resource for divergence dating

Fossils provide the principal basis for temporal calibrations, which are critical to the accuracy of divergence dating analyses. Translating fossil data into minimum and maximum bounds for calibrations is the most important, and often least appreciated, step of divergence dating. Properly justified calibrations require the synthesis of phylogenetic, paleontological, and geological evidence and can be difficult for non-specialists to formulate. The dynamic nature of the fossil record (e.g., new discoveries, taxonomic revisions, updates of global or local stratigraphy) requires that calibration data be updated continually lest they become obsolete. Here, we announce the Fossil Calibration Database (http://fossilcalibrations.org), a new open-access resource providing vetted fossil calibrations to the scientific community. Calibrations accessioned into this database are based on individual fossil specimens and follow best practices for phylogenetic justification and geochronological constraint. The associated Fossil Calibration Series, a calibration-themed publication series at Palaeontologia Electronica, will serve as one key pipeline for peer-reviewed calibrations to enter the database.

Connecting soundscape to landscape: Which acoustic index best describes landscape configuration?

Soundscape assessment has been proposed as a remote ecological monitoring tool for measuring biodiversity, but few studies have examined how soundscape patterns vary with landscape configuration and condition. The goal of our study was to examine a suite of published acoustic indices to determine whether they provide comparable results relative to varying levels of landscape fragmentation and ecological condition in nineteen forest sites in eastern Australia. Our comparison of six acoustic indices according to time of day revealed that two indices, the acoustic complexity and the bioacoustic index, presented a similar pattern that was linked to avian song intensity, but was not related to landscape and biodiversity attributes. The diversity indices, acoustic entropy and acoustic diversity, and the normalized difference soundscape index revealed high nighttime sound, as well as a dawn and dusk chorus. These indices appear to be sensitive to nocturnal biodiversity which is abundant at night in warm, subtropical environments. We argue that there is need to better understand temporal partitioning of the soundscape by specific taxonomic groups, and this should involve integrated research on amphibians, insects and birds during a 24 h cycle. The three indices that best connected the soundscape with landscape characteristics, ecological condition and bird species richness were acoustic entropy, acoustic evenness and the normalized difference soundscape index. This study has demonstrated that remote soundscape assessment can be implemented as an ecological monitoring tool in fragmented Australian forest landscapes. However, further investigation should be dedicated to refining and/or combining existing acoustic indices and also to determine if these indices are appropriate in other landscapes and for other survey purposes.

Molecular data extend Australian Cricotopus midge (Chironomidae) species diversity, and provide a phylogenetic hypothesis for biogeography and freshwater monitoring

Resolving species relationships and confirming diagnostic morphological characters for insect clades that are highly plastic, and/or include morphologically cryptic species, is crucial for both academic and applied reasons. Within the true fly (Diptera) family Chironomidae, a most ubiquitous freshwater insect group, the genera CricotopusWulp, 1874 and ParatrichocladiusSantos-Abreu, 1918 have long been taxonomically confusing. Indeed, until recently the Australian fauna had been examined in just two unpublished theses: most species were known by informal manuscript names only, with no concept of relationships. Understanding species limits, and the associated ecology and evolution, is essential to address taxonomic sufficiency in biomonitoring surveys. Immature stages are collected routinely, but tolerance is generalized at the genus level, despite marked variation among species. Here, we explored this issue using a multilocus molecular phylogenetic approach, including the standard mitochondrial barcode region, and tested explicitly for phylogenetic signal in ecological tolerance of species. Additionally, we addressed biogeographical patterns by conducting Bayesian divergence time estimation. We sampled all but one of the now recognized Australian Cricotopus species and tested monophyly using representatives from other austral and Asian locations. Cricotopus is revealed as paraphyletic by the inclusion of a nested monophyletic Paratrichocladius, with in-group diversification beginning in the Eocene. Previous morphological species concepts are largely corroborated, but some additional cryptic diversity is revealed. No significant relationship was observed between the phylogenetic position of a species and its ecology, implying either that tolerance to deleterious environmental impacts is a convergent trait among many Cricotopus species or that sensitive and restricted taxa have diversified into more narrow niches from a widely tolerant ancestor.

The path less travelled: Vertical circulation spaces in apartment buildings in the subtropics

This paper presents data on residents’ use of common stairways and lifts (vertical circulation spaces) in multi-storey apartment buildings (MSABs) in Brisbane, Australia. Vertical movement is a defining aspect of multi-storey living and the energy consumed by lifts contributes significantly to the energy budget of the typical MSAB. The purpose is to investigate whether a reappraisal of vertical circulation design, through the lens of residents’ requirements, might contribute to energy reductions in this building type. Data was gathered on a theoretical sample of MSAB ranging from five decades old to very recent schemes. 90 residents were surveyed about their day-to-day experiences of circulation and access systems. The results showed that residents mainly chose to use the stairs for convenience and exercise. Building management regimes that limited residents’ access to collective spaces were the main impediment to discretionary stair use. Only two buildings did not have fully enclosed stairwells and these had the highest stair usage, suggesting that stair design, and building governance are two areas that might be worthy of attention. The more that circulation design is focussed on limiting access, the less opportunities there are for personal choice, incidental social interaction and casual surveillance of collective spaces. The more that design of vertical circulation spaces in MSAB meets residents’ needs the less likely they are to be reliant on continuous energy supply for normal functioning.

The case for the plain packaging of tobacco products

AIMS: The Framework Convention on Tobacco Control (FCTC) requires nations that have ratified the convention to ban all tobacco advertising and promotion. In the face of these restrictions, tobacco packaging has become the key promotional vehicle for the tobacco industry to interest smokers and potential smokers in tobacco products. This paper reviews available research into the probable impact of mandatory plain packaging and internal tobacco industry statements about the importance of packs as promotional vehicles. It critiques legal objections raised by the industry about plain packaging violating laws and international trade agreements. METHODS: Searches for available evidence were conducted within the internal tobacco industry documents through the online document archives; tobacco industry trade publications; research literature through the Medline and Business Source Premier databases; and grey literature including government documents, research reports and non-governmental organization papers via the Google internet search engine. RESULTS: Plain packaging of all tobacco products would remove a key remaining means for the industry to promote its products to billions of the world's smokers and future smokers. Governments have required large surface areas of tobacco packs to be used exclusively for health warnings without legal impediment or need to compensate tobacco companies. CONCLUSIONS: Requiring plain packaging is consistent with the intention to ban all tobacco promotions. There is no impediment in the FCTC to interpreting tobacco advertising and promotion to include tobacco packs.

Consistent responses of soil microbial communities to elevated nutrient inputs in grasslands across the globe

Soil microorganisms are critical to ecosystem functioning and the maintenance of soil fertility. However, despite global increases in the inputs of nitrogen (N) and phosphorus (P) to ecosystems due to human activities, we lack a predictive understanding of how microbial communities respond to elevated nutrient inputs across environmental gradients. Here we used high-throughput sequencing of marker genes to elucidate the responses of soil fungal, archaeal, and bacterial communities using an N and P addition experiment replicated at 25 globally distributed grassland sites. We also sequenced metagenomes from a subset of the sites to determine how the functional attributes of bacterial communities change in response to elevated nutrients. Despite strong compositional differences across sites, microbial communities shifted in a consistent manner with N or P additions, and the magnitude of these shifts was related to the magnitude of plant community responses to nutrient inputs. Mycorrhizal fungi and methanogenic archaea decreased in relative abundance with nutrient additions, as did the relative abundances of oligotrophic bacterial taxa. The metagenomic data provided additional evidence for this shift in bacterial life history strategies because nutrient additions decreased the average genome sizes of the bacterial community members and elicited changes in the relative abundances of representative functional genes. Our results suggest that elevated N and P inputs lead to predictable shifts in the taxonomic and functional traits of soil microbial communities, including increases in the relative abundances of faster-growing, copiotrophic bacterial taxa, with these shifts likely to impact belowground ecosystems worldwide.

Re-valuing construction materials and components through design for disassembly

The construction industry accounts for a significant portion of the material consumption of our industrialised societies. That material consumption comes at an environmental cost, and when buildings and infrastructure projects are demolished and discarded, after their useful lifespan, that environmental cost remains largely unrecovered. The expected operational lifespan of modern buildings has become disturbingly short as buildings are replaced for reasons of changing cultural expectations, style, serviceability, locational obsolescence and economic viability. The same buildings however are not always physically or structurally obsolete; the materials and components within them are very often still completely serviceable. While there is some activity in the area of recycling of selected construction materials, such as steel and concrete, this is almost always in the form of down cycling or reprocessing. Very little of this material and component resource is reuse in a way that more effectively captures its potential. One significant impediment to such reuse is that buildings are not designed in a way that facilitates easy recovery of materials and components; they are designed and built for speed of construction and quick economic returns, with little or no consideration of the longer term consequences of their physical matter. This research project explores the potential for the recovery of materials and components if buildings were designed for such future recovery; a strategy of design for disassembly. This is not a new design philosophy; design for disassembly is well understood in product design and industrial design. There are also some architectural examples of design for disassembly; however these are specialist examples and there is no significant attempt to implement the strategy in the main stream construction industry. This paper presents research into the analysis of the embodied energy in buildings, highlighting its significance in comparison with operational energy. Analysis at material, component, and whole-of-building levels shows the potential benefits of strategically designing buildings for future disassembly to recover this embodied energy. Careful consideration at the early design stage can result in the deconstruction of significant portions of buildings and the recovery of their potential through higher order reuse and upcycling.

Palissya: A global review and reassessment of Eastern Gondwanan material

The conifer genus Palissya is reviewed giving special attention to assessing the reliability of Gondwanan material referred to this genus. The collection localities of Australasian specimens are mapped on palaeogeographic reconstructions of Eastern Gondwana at relevant times between 179 Ma and 119 Ma. Australasian and other Gondwanan material previously referred to Palissya is considered to differ substantially from the generic diagnosis. Specimens from the Toarcian of Australasia are shown to be allied to Knezourocarpon; this genus is only known from the Toarcian of eastern Australia. Middle Jurassic–Lower Cretaceous Australasian specimens previously referred to Palissya are likely allied to the Knezourocarponaceae fam. nov. The higher taxonomic affinity of this family is unknown but broadly, its structure is suggestive of ginkgoalean or pteridospermous affiliation. Southern hemisphere specimens were probably catkin-like and megascopically very different from the northern hemisphere Palissya and the two groups are unlikely to be closely related. Consequently, genuine Palissya cones and foliage appear to be restricted to the Rhaetian–Lower Jurassic of the northern hemisphere.

A comparative social network analysis of wasp colonies and classrooms: Linking network structure to functioning

A major question in current network science is how to understand the relationship between structure and functioning of real networks. Here we present a comparative network analysis of 48 wasp and 36 human social networks. We have compared the centralisation and small world character of these interaction networks and have studied how these properties change over time. We compared the interaction networks of (1) two congeneric wasp species (Ropalidia marginata and Ropalidia cyathiformis), (2) the queen-right (with the queen) and queen-less (without the queen) networks of wasps, (3) the four network types obtained by combining (1) and (2) above, and (4) wasp networks with the social networks of children in 36 classrooms. We have found perfect (100%) centralisation in a queen-less wasp colony and nearly perfect centralisation in several other queen-less wasp colonies. Note that the perfectly centralised interaction network is quite unique in the literature of real-world networks. Differences between the interaction networks of the two wasp species are smaller than differences between the networks describing their different colony conditions. Also, the differences between different colony conditions are larger than the differences between wasp and children networks. For example, the structure of queen-right R. marginata colonies is more similar to children social networks than to that of their queen-less colonies. We conclude that network architecture depends more on the functioning of the particular community than on taxonomic differences (either between two wasp species or between wasps and humans).

Ecology of uncultivated oscillospira species in the rumen of cattle, sheep, and reindeer as assessed by microscopy and molecular approaches

The ecology of the uncultured, but large and morphologically conspicuous, rumen bacterium Oscillospira spp. was studied. Oscillospira-specific 16S rRNA gene sequences were detected in North American domestic cattle, sheep from Australia and Japan, and Norwegian reindeer. Phylogenetic analysis of the sequences obtained allowed definition of three operational taxonomic units within the Oscillospira clade. Consistent with this genetic diversity, we observed atypical smaller morphotypes by using an Oscillospira-specific fluorescence in situ hybridization probe. Despite the visual disappearance of typical large Oscillospira morphotypes, the presence of Oscillospira spp. was still detected by Oscillospira-specific PCR in the rumen of cattle and sheep. These observations suggest the broad presence of Oscillospira species in various rumen ecosystems with the level, and most likely the morphological form, dependent on diet. An ecological analysis based on enumeration of the morphologically conspicuous, large-septate form confirms that the highest counts are associated with the feeding of fresh forage diets to cattle and sheep and in two different subspecies of reindeer investigated.

Suomen Taideyhdistyksestä Ateneumiin : Fredrik Cygnaeus, Carl Gustaf Estlander ja taidekokoelman roolit

From the Finnish Art Society to the Ateneum: Fredrik Cygnaeus, Carl Gustaf Estlander and the Roles of the Art Collection My dissertation deals with the Finnish Art Society and the development of its collection in the evolving field of the visual arts from the foundation of the society in 1846 to its exhibition in the Ateneum, a palace of art that was opened to the public in Helsinki in 1888. The main questions that it addresses are why and how the collection came into being, what its purpose was and what kind of future prospects were projected for it in the rapidly evolving field of the visual arts. I have examined the subject of my study from the perspectives of institutional history, the organisation of the field of art and the history of art collections. The prisms through which I have viewed the subject are the history of museums in Europe, the written history of art, the art association movement and the organisation of art education in relation to an ideology of enlightenment. Thus the activities of the Finnish Art Society are here mirrored for the first time in a wider context and the history of its collection located on the map of European collections. My research shows that the history of the collection of the Finnish Art Society initially depended on certain players in the visual arts and their particular leanings. The most important of these custodians were two long-serving chairmen of the society, Fredrik Cygnaeus (1807 1881) and Carl Gustaf Estlander (1834 1910). When the foundations for art activities had been laid through the establishment of the society, Cygnaeus and Estlander began to plan how the field of art might be moulded so as to improve the level of training for artists and to improve the quality of the collections and the opportunities for their display. Cygnaeus campaigned for the establishment of the Finnish Fine Arts Academy, while Estlander saw opportunities to combine the visual and applied arts. The findings of my research bring new information about the history of the collection of the Finnish Art Society, its profile, the professional abilities of those who were mainly responsible for developing it and the relationship between it and plans for reforming art education. The major findings are connected with the position of the collection in the field of art at different stages of its development. Despite the central monopoly of the Finnish Art Society in the field of art, the position of the collection was closely bound up with leading players in the field of art and their personal interests. This subservience also created an impediment to its full-blown enhancement and purposeful profiling, and it remained evident for a long time when the collection was seeking its own place in the Finnish art world.