Mathematical methods for visualization and anomaly detection in telemetry datasets.

Recent developments in both biological data acquisition and analysis provide new opportunities for data-driven modelling of the health state of an organism. In this paper, we explore the evolution of temperature patterns generated by telemetry data collected from healthy and infected mice. We investigate several techniques to visualize and identify anomalies in temperature time series as temperature relates to the onset of infectious disease. Visualization tools such as Laplacian Eigenmaps and Multidimensional Scaling allow one to gain an understanding of a dataset as a whole. Anomaly detection tools for nonlinear time series modelling, such as Radial Basis Functions and Multivariate State Estimation Technique, allow one to build models representing a healthy state in individuals. We illustrate these methods on an experimental dataset of 306 Collaborative Cross mice challenged with Salmonella typhimurium and show how interruption in circadian patterns and severity of infection can be revealed directly from these time series within 3 days of the infection event.

Effect of Pseudokirchneriella subcapitata (Chlorophyceae) exudates on metal toxicity and colloid aggregation.

The effects of Pseudokirchneriella subcapitata exudates on the acute toxicity of metals (Cd, Cu, Pb and Zn) were studied using (1h) algal photosynthesis inhibition tests. The metal concentrations tested were 30, 60, 120, 250 and 500microgL(-1) for Cd and Zn; and 500, 1000, 2000, 3000, 4000microgL(-1) for Cu and Pb. It was established that P. subcapitata exudates markedly decreased metal toxicity. This effect was ascribed to: (i) the presence of organic ligands that bind metals and reduce the concentration of free ionic metal, and/or (ii) interaction of exudates with the cell surface with a subsequent decrease in metal uptake. The effects of the exudates on colloid aggregation were also examined using two different types of single particle counters (SPC). Exudates facilitated the colloid removal, likely via acceleration of aggregation (bridging). The results clearly demonstrate that algal exudates play an important role in the biogeochemical cycling of metals in natural surface water: (1) by reducing free metal concentrations and toxicity to living organisms and (2) by favoring colloid aggregation leading to the removal of colloid-bound metals (colloidal pumping). Such results highlight one potential application of the algae in the remediation of metal-contaminated waters. The results also suggest that current algal toxicity testing protocols, in particular long-term and static tests, may underestimate metal toxicity because of the presence of algal exudates.

Comparative performance of membrane filters vs. high-surface area filtration cartridges for the determination of element concentrations in freshwater systems.

Interdisciplinary studies on trace element cycles in aquatic environments may require the simultaneous use of small- and large-scale filtration devices to collect all the necessary sample aliquots for the different scientific objectives (e.g. trace element and organic carbon analysis, chronic toxicity testing, and characterization of colloidal matter). This study compares the performance of membrane filters (MF, Millipore-approx. surface area 0.002 m2) and two large-surface area filtration cartridges (Calyx, MSI and Polypro, CUNO approx. surface area 1 m2) in three freshwater systems with contrasting characteristics. Membrane filters and filtration cartridges fractionate water samples in a comparable way except for some elements (Al, Mn, Pb, and Ti) and when dealing with high-turbidity, organic-rich matrices. Estimation of the actual filters' pore size using the single particle counting technique gives cut-offs of 0.2-0.3, 0.7 and 2 microm for membrane filters, Polypro cartridge and Calyx cartridge respectively, explaining many of the differences observed between membrane and cartridge filters. Direct involvement of filter manufacturers to determine actual filter cut-offs during environmental applications would be highly beneficial to increase the comparability of the measurements of filterable element concentrations. Better harmonization of filtration procedures (filter type, actual filter cut-off, in situ vs. ex situ filtration) among laboratories in different countries is also necessary in order to improve consistency of environmental databases.

Kinetics of mass and DNA decomposition in tomato leaves.

This laboratory study investigated the kinetics of leaf and DNA content decomposition in two varieties of tomato (Palmiro and Admiro) after incubation in soil for 35 days. Results revealed that the decrease of dry matter in leaves in both varieties did not follow a single exponential function and was better described by a double exponential model. Composite half-decrease times were 3.4 and 2.4 days for Palmiro and Admiro respectively. The same pattern was observed for DNA mass loss, although this was closer to a single exponential model with composite half-decrease times of 1.5 and 1.4 days. Genomic analysis showed that DNA in dried leaves at room temperature (not inoculated in the soil), remains intact or presents a weak degradation, and DNA extracted from leaves inoculated in non-sterile soil showed degradation after two days. These results indicate that before release an important quantity of DNA may be degraded inside plant tissues during decomposition in soil.