Species introduction promotes hybridization and introgression in Coregonus: is there sign of selection against hybrids?

Species introductions are considered one of the major drivers of biodiversity loss via ecological interactions and genetic admixture with local fauna. We examined two well-recognized fish species, native whitefish (Coregonus lavaretus) and introduced vendace (Coregonus albula), as well as their morphological hybrids in a single lake to test for selection against hybrids and backcrosses in the wild. A representative random subsample of 693 individuals (27.8%) was taken from the total catch of coregonids. This subsample was examined with the aim to select c. 50 individuals of pure whitefish (n = 52), pure vendace (n = 55) and putative hybrid (n = 19) for genetic analyses. The subsequent microsatellites and mitochondrial (mt) DNA analyses provided compelling evidence of hybridization and introgression. Of the 126 fish examined, four were found to be F-1, 14 backcrosses to whitefish and seven backcrosses to vendace. The estimates of historical gene flow suggested higher rates from introduced vendace into native whitefish than vice versa, whereas estimates of contemporary gene flow were equal. Mitochondrial introgression was skewed, with 18 backcrosses having vendace mtDNA and only three with whitefish mtDNA. Hybrids and backcrosses had intermediate morphology and niche utilization compared with parental species. No evidence of selection against hybrids or backcrosses was apparent, as both hybrid and backcross growth rates and fecundities were high. Hybrids (F-1) were only detected in 2 year-classes, suggesting temporal variability in mating between vendace and whitefish. However, our data show that hybrids reached sexual maturity and reproduced actively, with backcrosses recorded from six consecutive year-classes, whereas no F-2 individuals were found. The results indicate widespread introgression, as 10.8% of coregonids were estimated to be backcrosses.

Micro-scale biopitting by endolithic lichen and their role in meso-scale solution basin development on limestone

Data are reported demonstrating the potential role of microscale morphologies, induced by endolithic lichen communities, specifically Verrucaria baldensis, in the initiation and development of mesoscale solution basin formation on limestone in the Burren, Co. Clare. A biophysical model is proposed outlining the different microscale stages leading to solution basin initiation with a progression from initial lichen colonisation and growth, associated biopitting followed by biopit coalescence to form biotroughs, their subsequent enlargement and eventual incipient solution basin formation. This model provides one explanation for solution basin development as this end state may also be achieved through simple solutional means without biological input. The complexity of interactions at the rock / lichen interface are identified with emphasis on the spatial and temporal variability of these underlining the point that, as with macro-topographies at the landscape scale, rock surface micro-topographies also reflect historical weathering legacies.

Development of a novel experimental model to investigate radiobiological implications of respiratory motion in advanced radiotherapy

Respiratory motion introduces complex spatio-temporal variations in the dosimetry of radiotherapy. There is a paucity of literature investigating the radiobiological consequences of intrafraction motion and concerns regarding the impact of movement when applied to cancer cell lines in vitro exist. We have addressed this by developing a novel model which accurately replicates respiratory motion under experimental conditions to allow clinically relevant irradiation of cell lines. A bespoke phantom and motor driven moving platform was adapted to accommodate flasks containing medium and cells in order to replicate respiratory motion using varying frequencies and amplitude settings. To study this effect on cell survival in vitro, dose response curves were determined for human lung cancer cell lines H1299 and H460 exposed to a uniform 6 MV radiation field under moving or stationary conditions. Cell survival curves showed no significant difference between irradiation at different dose points for these cell lines in the presence or absence of motion. These data indicate that motion of unshielded cells in vitro does not affect cell survival in the presence of uniform irradiation. This model provides a novel research platform to investigate the radiobiological consequences of respiratory motion in radiotherapy.

Investigating the influence of respiratory motion on the radiation induced bystander effect in modulated radiotherapy

Respiratory motion introduces complex spatio-temporal variations in the dosimetry of radiotherapy and may contribute towards uncertainties in radiotherapy planning. This study investigates the potential radiobiological implications occurring due to tumour motion in areas of geometric miss in lung cancer radiotherapy. A bespoke phantom and motor-driven platform to replicate respiratory motion and study the consequences on tumour cell survival in vitro was constructed. Human non-small-cell lung cancer cell lines H460 and H1299 were irradiated in modulated radiotherapy configurations in the presence and absence of respiratory motion. Clonogenic survival was calculated for irradiated and shielded regions. Direction of motion, replication of dosimetry by multi-leaf collimator (MLC) manipulation and oscillating lead shielding were investigated to confirm differences in cell survival. Respiratory motion was shown to significantly increase survival for out-of-field regions for H460/H1299 cell lines when compared with static irradiation (p <0.001). Significantly higher survival was found in the in-field region for the H460 cell line (p <0.030). Oscillating lead shielding also produced these significant differences. Respiratory motion and oscillatory delivery of radiation dose to human tumour cells has a significant impact on in- and out-of-field survival in the presence of non-uniform irradiation in this in vitro set-up. This may have important radiobiological consequences for modulated radiotherapy in lung cancer. 

Longitudinal proton probing of ultrafast and high-contrast laser-solid interactions

We have performed an experiment aimed at measuring self-generated magnetic fields produced in solids by high electron currents following high-intensity and high contrast short-pulse laser irradiation. This was done using longitudinal high resolution proton deflectometry. The experiment was performed at the Titan-JLF laser facility with a high-power short-pulse beam (700 fs, ~ 110 J) split into two beams irradiating two solid targets. One beam is used for the generation of protons and the other beam for the generation of the ultra-high currents of electrons and of the associated magnetic fields. This capability allows us to study the spatio-temporal evolution of the magnetic fields and its dependence on the laser intensity and target material. © Owned by the authors, published by EDP Sciences, 2013.

Holocene “turn-on” and evolution of the Southern Great Barrier Reef: Revisiting reef cores from the Capricorn Bunker Group

Extensive drilling of the Great Barrier Reef (GBR) in the 70s and 80s illuminated the main factors controlling reef growth during the Holocene. However, questions remain about: (1) the precise nature and timing of reef "turnon" or initiation, (2) whether consistent spatio-temporal patterns occur in the bio-sedimentologic response of the reef to Holocene sea-level rise then stability, and (3) how these factors are expressed in the context of the different evolutionary states (juvenile-mature-senile reefs). Combining 21 new C14-AMS and 146 existing recalibrated radiocarbon and U/Th ages, we investigated the detailed spatial and temporal variations in sedimentary facies and coralgal assemblages in fifteen cores across four reefs (Wreck, Fairfax, One Tree and Fitzroy) from the Southern GBR. Our newly defined facies and assemblages record distinct chronostratigraphic patterns in the cores, displaying both lateral zonation across the different reefs and shallowing upwards sequences, characterised by a transition from deep (Porites/faviids) to shallow (Acropora/Isopora) coral types. The revised reef accretion curves show a significant lag period, ranging from 0.7-2 ka, between flooding of the antecedent Pleistocene substrate and Holocene reef turn-on. This lag period and dominance of more environmentally tolerant early colonizers (e.g., domal Porites and faviids), suggests initial conditions that were unfavourable for coral growth. We contend that higher input of fine siliciclastic material from regional terrigenous sources, exposure to hydrodynamic forces and colonisation in deeper waters are the main factors influencing initially reduced growth and development. All four reefs record a time lag and we argue that the size and shape of the antecedent platform is most important in determining the duration between flooding and recolonisation of the Holocene reef. Finally, our study of Capricorn Bunker Group Holocene reefs suggests that the size and shape of the antecedent substrate has a greater impact on reef evolution and final evolutionary state (mature vs. senile), than substrate depth alone. 

Towards a general framework for social media research using big data

The increasing adoption of cloud computing, social networking, mobile and big data technologies provide challenges and opportunities for both research and practice. Researchers face a deluge of data generated by social network platforms which is further exacerbated by the co-mingling of social network platforms and the emerging Internet of Everything. While the topicality of big data and social media increases, there is a lack of conceptual tools in the literature to help researchers approach, structure and codify knowledge from social media big data in diverse subject matter domains, many of whom are from nontechnical disciplines. Researchers do not have a general-purpose scaffold to make sense of the data and the complex web of relationships between entities, social networks, social platforms and other third party databases, systems and objects. This is further complicated when spatio-temporal data is introduced. Based on practical experience of working with social media datasets and existing literature, we propose a general research framework for social media research using big data. Such a framework assists researchers in placing their contributions in an overall context, focusing their research efforts and building the body of knowledge in a given discipline area using social media data in a consistent and coherent manner.

Evidential event inference in transport video surveillance

This paper presents a new framework for multi-subject event inference in surveillance video, where measurements produced by low-level vision analytics usually are noisy, incomplete or incorrect. Our goal is to infer the composite events undertaken by each subject from noise observations. To achieve this, we consider the temporal characteristics of event relations and propose a method to correctly associate the detected events with individual subjects. The Dempster–Shafer (DS) theory of belief functions is used to infer events of interest from the results of our vision analytics and to measure conflicts occurring during the event association. Our system is evaluated against a number of videos that present passenger behaviours on a public transport platform namely buses at different levels of complexity. The experimental results demonstrate that by reasoning with spatio-temporal correlations, the proposed method achieves a satisfying performance when associating atomic events and recognising composite events involving multiple subjects in dynamic environments.

Vacuum birefringence in strong inhomogeneous electromagnetic fields

Birefringence is one of the fascinating properties of the vacuum of quantum electrodynamics (QED) in strong electromagnetic fields. The scattering of linearly polarized incident probe photons into a perpendicularly polarized mode provides a distinct signature of the optical activity of the quantum vacuum and thus offers an excellent opportunity for a precision test of nonlinear QED. Precision tests require accurate predictions and thus a theoretical framework that is capable of taking the detailed experimental geometry into account. We derive analytical solutions for vacuum birefringence which include the spatio-temporal field structure of a strong optical pump laser field and an x-ray probe. We show that the angular distribution of the scattered photons depends strongly on the interaction geometry and find that scattering of the perpendicularly polarized scattered photons out of the cone of the incident probe x-ray beam is the key to making the phenomenon experimentally accessible with the current generation of FEL/high-field laser facilities.

Indexing and matching trajectories under inconsistent sampling rates

Quantifying the similarity between two trajectories is a fundamental operation in analysis of spatio-temporal databases. While a number of distance functions exist, the recent shift in the dynamics of the trajectory generation procedure violates one of their core assumptions; a consistent and uniform sampling rate. In this paper, we formulate a robust distance function called Edit Distance with Projections (EDwP) to match trajectories under inconsistent and variable sampling rates through dynamic interpolation. This is achieved by deploying the idea of projections that goes beyond matching only the sampled points while aligning trajectories. To enable efficient trajectory retrievals using EDwP, we design an index structure called TrajTree. TrajTree derives its pruning power by employing the unique combination of bounding boxes with Lipschitz embedding. Extensive experiments on real trajectory databases demonstrate EDwP to be up to 5 times more accurate than the state-of-the-art distance functions. Additionally, TrajTree increases the efficiency of trajectory retrievals by up to an order of magnitude over existing techniques.

Time-lapse monitoring of climate effects on earthworks using surface waves

The UK’s transportation network is supported by critical geotechnical assets (cuttings/embankments/dams) that require sustainable, cost-effective management, while maintaining an appropriate service level to meet social, economic, and environmental needs. Recent effects of extreme weather on these geotechnical assets have highlighted their vulnerability to climate variations. We have assessed the potential of surface wave data to portray the climate-related variations in mechanical properties of a clay-filled railway embankment. Seismic data were acquired bimonthly from July 2013 to November 2014 along the crest of a heritage railway embankment in southwest England. For each acquisition, the collected data were first processed to obtain a set of Rayleigh-wave dispersion and attenuation curves, referenced to the same spatial locations. These data were then analyzed to identify a coherent trend in their spatial and temporal variability. The relevance of the observed temporal variations was also verified with respect to the experimental data uncertainties. Finally, the surface wave dispersion data sets were inverted to reconstruct a time-lapse model of S-wave velocity for the embankment structure, using a least-squares laterally constrained inversion scheme. A key point of the inversion process was constituted by the estimation of a suitable initial model and the selection of adequate levels of spatial regularization. The initial model and the strength of spatial smoothing were then kept constant throughout the processing of all available data sets to ensure homogeneity of the procedure and comparability among the obtained VS sections. A continuous and coherent temporal pattern of surface wave data, and consequently of the reconstructed VS models, was identified. This pattern is related to the seasonal distribution of precipitation and soil water content measured on site.

Time-lapse monitoring of fluid induced geophysical property variations within an unstable earthwork using P-wave refraction

A significant portion of the UK’s transportation system relies on a network of geotechnical earthworks (cuttings and embankments) that were constructed more than 100 years ago, whose stability is affected by the change in precipitation patterns experienced over the past few decades. The vulnerability of these structures requires a reliable, cost- and time-effective monitoring of their geomechanical condition. We have assessed the potential application of P-wave refraction for tracking the seasonal variations of seismic properties within an aged clay-filled railway embankment, located in southwest England. Seismic data were acquired repeatedly along the crest of the earthwork at regular time intervals, for a total period of 16 months. P-wave first-break times were picked from all available recorded traces, to obtain a set of hodocrones referenced to the same spatial locations, for various dates along the surveyed period of time. Traveltimes extracted from each acquisition were then compared to track the pattern of their temporal variability. The relevance of such variations over time was compared with the data experimental uncertainty. The multiple set of hodocrones was subsequently inverted using a tomographic approach, to retrieve a time-lapse model of VPVP for the embankment structure. To directly compare the reconstructed VPVP sections, identical initial models and spatial regularization were used for the inversion of all available data sets. A consistent temporal trend for P-wave traveltimes, and consequently for the reconstructed VPVP models, was identified. This pattern could be related to the seasonal distribution of precipitation and soil-water content measured on site.

Time-lapse Monitoring of the Slopes of a Heritage Earthwork by Means of Near-surface Seismic Techniques

A significant portion of UK’s infrastructures earthworks was built more than 100 years ago, without modern construction standards: poor maintenance and the change of precipitations pattern experienced in the past decades are currently compromising their stability, leading to an increasing number of failures. To address the need for a reliable and time-efficient monitoring of earthworks at risk of failure we propose here the use of two established seismic techniques for the characterization of the near surface, MASW and P-wave refraction. We have regularly collected MASW and P-wave refraction data, from March 2014 to February 2015, along 4 reduced-scale seismic lines located on the flanks of a heritage railway embankment located in Broadway, SW of England. We have observed a definite temporal variability in terms of phase velocities of SW dispersion curves and of P-wave travel times. The accurate choice of ad-hoc inversion strategies has allowed to reconstruct reliable VP and VS models through which it is potentially possible to track the temporal variations of geo-mechanical properties of the embankment slopes. The variability over time of seismic data and seismic velocities seems to correlate well with rainfall data recorded in the days immediately preceding the date of acquisition.

Validating the use of intrinsic markers in body feathers to identify inter‑individual differences in non‑breeding areas of northern fulmars

Many wildlife studies use chemical analyses to explore spatio-temporal variation in diet, migratory patterns and contaminant exposure. Intrinsic markers are particularly valuable for studying non-breeding marine predators, when direct methods of investigation are rarely feasible. However, any inferences regarding foraging ecology are dependent upon the time scale over which tissues such as feathers are formed. In this study, we validate the use of body feathers for studying non-breeding foraging patterns in a pelagic seabird, the northern fulmar. Analysis of carcasses of successfully breeding adult fulmars indicated that body feathers moulted between September and March, whereas analyses of carcasses and activity patterns suggested that wing feather and tail feather moult occurred during more restricted periods (September to October and September to January, respectively). By randomly sampling relevant body feathers, average values for individual birds were shown to be consistent. We also integrated chemical analyses of body feather with geolocation tracking data to demonstrate that analyses of δ13C and δ15N values successfully assigned 88 % of birds to one of two broad wintering regions used by breeding adult fulmars from a Scottish study colony. These data provide strong support for the use of body feathers as a tool for exploring non-breeding foraging patterns and diet in wide-ranging, pelagic seabirds.

Geographic variation in sardine population traits: implications for stock assessment

Tese dout., Ciências e Tecnologias das Pescas, Universidade do Algarve, 2007