Making tourist guidance systems more intelligent, adaptive and personalised using crowd sourced movement data

Ambient intelligence (AmI) provides adaptive, personalized, intelligent, ubiquitous and interactive services to wide range of users. AmI can have a variety of applications, including smart shops, health care, smart home, assisted living, and location-based services. Tourist guidance is one of the applications where AmI can have a great contribution to the quality of the service, as the tourists, who may not be very familiar with the visiting site, need a location-aware, ubiquitous, personalised and informative service. Such services should be able to understand the preferences of the users without requiring the users to specify them, predict their interests, and provide relevant and tailored services in the most appropriate way, including audio, visual, and haptic. This paper shows the use of crowd sourced trajectory data in the detection of points of interests and providing ambient tourist guidance based on the patterns recognised over such data

Hadooping the genome: The impact of big data tools on biology

This essay examines the consequences of the so-called ‘big data’ technologies in biomedicine. Analyzing algorithms and data structures used by biologists can provide insight into how biologists perceive and understand their objects of study. As such, I examine some of the most widely used algorithms in genomics: those used for sequence comparison or sequence mapping. These algorithms are derived from the powerful tools for text searching and indexing that have been developed since the 1950s and now play an important role in online search. In biology, sequence comparison algorithms have been used to assemble genomes, process next-generation sequence data, and, most recently, for ‘precision medicine.’ I argue that the predominance of a specific set of text-matching and pattern-finding tools has influenced problem choice in genomics. It allowed genomics to continue to think of genomes as textual objects and to increasingly lock genomics into ‘big data’-driven text-searching methods. Many ‘big data’ methods are designed for finding patterns in human-written texts. However, genomes and other’ omic data are not human-written and are unlikely to be meaningful in the same way

Adaptation to climate in widespread eucalypt species

AbstractThe long term success of revegetation efforts will depend upon the planted species’ resilience to climate change. Many widespread species grow across a range of climatic conditions and, thus, may possess adaptations that could be utilised to improve climate resilience of restored ecosystems. Species can achieve a widespread distribution via two main mechanisms; (1) by diverging into a series of specialised populations, or (2) through high phenotypic plasticity. The extent to which populations are specialised or plastic in response to climate will determine the seed-sourcing strategy required for optimal restoration outcomes under a changing climate. We examined genetic divergence and phenotypic plasticity in two widespread Eucalyptus species (E. tricarpa in southeastern Australia, E. salubris in southwestern Australia), to determine the nature of adaptation to climate in these species, and whether genomic screening might be a useful tool to assess climate adaptation.We examined nine populations of each species across climate gradients and, for E. tricarpa, trees originating from the same populations were also studied in two common garden field trials. We characterised responses in functional traits relevant to climate adaptation, including leaf size, thickness, tissue density, and carbon isotope ratio (δ13C). Genetic variation was assessed with genome scans using DArTseq markers, and ‘outlier markers’ were identified as being linked to regions of the genome that are potentially under selection.Evidence of both plastic response and genetic specialisation for climate was found in both species, indicating that widespread eucalypts utilise a combination of both mechanisms for adaptation to spatial variation in climate. The E. tricarpa common garden data suggested high plasticity in most of the measured functional traits, and the extent of plasticity in some traits (e.g. leaf size and thickness) varied among provenances, suggesting genetic variation for plasticity itself. In E. salubris, most functional traits showed little variation across the gradient. However, water use efficiency appeared highly plastic, as determined from the strong correlation between δ13C and recent precipitation (R2 = 0.83). Both species showed spatial partitioning of genetic variation across the gradient, and data for E. salubris revealed two distinct lineages. The genome scans yielded 16,122 DArTseq markers for “Lineage 1” of E. salubris, of which 0.1% were potentially adaptive ‘outlier loci’, and 6,544 markers for E. tricarpa, of which 2.6% were outliers. Canonical Analysis of Principal Coordinates (CAP) analysis showed that the outlier markers were correlated with climatic variables, and some were also strongly correlated with functional traits. An ‘Aridity Index’ was also developed from the CAP analysis that has potential as a tool for environmental planners to use for matching seed sources to target climates.Widespread eucalypts are likely to possess a capacity to respond plastically to a changing climate to some extent, but selection of seed sources to match projected climate changes may confer even greater climate resilience. Further study of the mechanisms of plasticity in response to climate may improve our ability to assess climate adaptation in other species, and to determine optimal strategies for ecosystem restoration and management under climate change

Long-term effects of oestrogenic effluent exposure on wild fish populations

This thesis was submitted for the award of Doctor of Philosophy and was awarded by Brunel University London.Freshwater streams in the developed world are becoming increasingly dominated by treated wastewater. Continually discharged into most surface waters, these effluents contain a suite of bioactive man-made chemicals, including steroid and non-steroid oestrogens, which have been found to feminise male fish, skew sex ratios, and cause reproductive failure. However, the consequences of reproductive disruption remain poorly explored at the population level. This thesis was initiated to evaluate how oestrogenic contaminants might influence the population ecology of a common cyprinid, the roach (Rutilus rutilus). An investigation encompassing population structure, multigenerational exposure and the role of additional drivers of fish population dynamics was undertaken to contextualise the effects of oestrogenic effluents on wild fish populations. Population genetic analysis of UK roach found they exhibit moderately high levels of genetic diversity and significant intra-river genetic structure. Genetically differentiated local subpopulations indicate little interbreeding and limited gene flow, consistent with a typical metapopulation that has not been homogenised by restocking. Similarly, my thesis demonstrates no significant relationship between effluent exposure and Ne (effective population size) or genetic diversity of roach populations, albeit a 65% reduction in Ne is possible at highly polluted sites. River stretches contaminated with high levels of effluent can support breeding populations, which recruit successfully with minimal immigration from less contaminated sites. Multigenerational effects of effluent exposure on roach were also evaluated experimentally using reproductive success from breeding adults over three generations. Lifelong exposure to 100% treated effluent resulted in feminised phenotypes (ovarian cavities and intersex condition) in males but no observable effect on females. Additionally, despite gonadal disruption in males and effluent exposure of their mothers, I found no detrimental effect on their ability to compete with control fish. Instead, reproductive success was primarily determined by body size. A novel approach considering additional fish population drivers suggests that genetic diversity and species diversity decline in parallel with an increasing presence of disturbed land, when combined with geographical isolation. In conclusion, group assemblage and genetic structure of fish populations appears multi-causal and cannot be disaggregated, such that a single environmental characteristic can be shown to drive patterns of population success.NERC (NE/G019355/1) and DEFRA

Shotgun ion mobility mass spectrometry sequencing of heparan sulfate saccharides

Despite evident regulatory roles of heparan sulfate (HS) saccharides in numerous biological processes, definitive information on the bioactive sequences of these polymers is lacking, with only a handful of natural structures sequenced to date. Here, we develop a “Shotgun” Ion Mobility Mass Spectrometry Sequencing (SIMMS2) method in which intact HS saccharides are dissociated in an ion mobility mass spectrometer and collision cross section values of fragments measured. Matching of data for intact and fragment ions against known values for 36 fully defined HS saccharide structures (from di- to decasaccharides) permits unambiguous sequence determination of validated standards and unknown natural saccharides, notably including variants with 3O-sulfate groups. SIMMS2 analysis of two fibroblast growth factor-inhibiting hexasaccharides identified from a HS oligosaccharide library screen demonstrates that the approach allows elucidation of structure-activity relationships. SIMMS2 thus overcomes the bottleneck for decoding the informational content of functional HS motifs which is crucial for their future biomedical exploitation

How predictable are evolutionary responses to environment? Comparing trait-environment relationships among three species of Asteraceae forbs in the Great Basin

Restoring native forbs in the Great Basin Desert is an important part of regenerating a healthy landscape that benefits wildlife, plant communities, and humans. Despite their importance and contribution to plant diversity, forbs have been understudied relative to grasses and shrubs. To begin bridging this knowledge gap, we examined three Asteraceae species (Chaenactis douglasii, Dieteria canescens, Erigeron pumilus) collected from a wide geographic area and grown in common garden experiments, asking how variable these species and populations are, how their traits were associated with environment of origin, and how two of the three species responded to water addition in direct-seeding environments. We also asked if trait-environment relationships were similar among these three species. As expected, we found that populations were extremely variable, and that much of this variation was significantly different among populations, with some variation explained by the ecoregion where populations were gathered. All three species had at least one trait strongly correlated with an environmental variable, sometimes in similar ways. For example, we found a consistent relationship where plants from higher elevation locations flowered earlier across all species, as well as a relationship with plant height and mean annual temperature, with taller plants sourced from warmer areas. Across species, the strongest trait-environment relationships we found were found for plant height, flowering phenology, and flower production, though there was variation in which environmental variables were most correlated with these responses. Our results suggest that approaches that generalize across species, even closely related ones, may not be adequate when determining whether a potential seed-source is well-matched to a target restoration site. Instead, our results support the idea that species-specific seed zones (areas where seeds can be moved without loss of performance) should be developed to help make this decision. Additionally, we found that environmental variables such as mean annual temperature and elevation were highly associated with traits that are typically considered important in restoration, i.e. phenology, number of inflorescences, and plant size. Therefore, before species-specific seed zones are available, we may be able to use these environmental factors as proxies to help us better match seed sources to target restoration sites. Finally, we also found that at least one species (C. douglasii) emerged from seed more readily when it was sourced from a drier origin, in both ambient and water addition conditions. Although more research needs to be done in this area, this suggests that seeds sourced from drier locations may be better suited for restoration projects that are being direct-seeded

Lipid analysis of CO2-rich subsurface aquifers suggests an autotrophy-based deep biosphere with lysolipids enriched in CPR bacteria.

Sediment-hosted CO2-rich aquifers deep below the Colorado Plateau (USA) contain a remarkable diversity of uncultivated microorganisms, including Candidate Phyla Radiation (CPR) bacteria that are putative symbionts unable to synthesize membrane lipids. The origin of organic carbon in these ecosystems is unknown and the source of CPR membrane lipids remains elusive. We collected cells from deep groundwater brought to the surface by eruptions of Crystal Geyser, sequenced the community, and analyzed the whole community lipidome over time. Characteristic stable carbon isotopic compositions of microbial lipids suggest that bacterial and archaeal CO2 fixation ongoing in the deep subsurface provides organic carbon for the complex communities that reside there. Coupled lipidomic-metagenomic analysis indicates that CPR bacteria lack complete lipid biosynthesis pathways but still possess regular lipid membranes. These lipids may therefore originate from other community members, which also adapt to high in situ pressure by increasing fatty acid unsaturation. An unusually high abundance of lysolipids attributed to CPR bacteria may represent an adaptation to membrane curvature stress induced by their small cell sizes. Our findings provide new insights into the carbon cycle in the deep subsurface and suggest the redistribution of lipids into putative symbionts within this community