Clara Bog: An ombotrophic groundwater dependant terrestrial ecosystem (Submitted)

Comparison of flow duration curves for a weir draining an undrained raised peat with those generated 20 years previously reveal that more recent curves reflect to be flatter with a lower Q95/Q5 ratio. Comparison of the bog topography for the same period revealed that although marginal drainage/peat reclamation had resulted in desiccation of peat around the bog margin and more frequent intense runoff, the central part of the bog had subsided to form an enclosed basin ,resulting in the creation of newly formed lakes that gave the central part of the bog an improved capacity to store, and more slowly discharge, water. Interrogation of groundwater monitoring data revealed a net decline in groundwater levels of up to three metres in the glacial tills underlying the bog associated with deepening and expansion of a marginal drain network which penetrated the base of the peat. Comparing organic carbon levels in peat the central part of the bog over a ten year period revealed an overall increase, with changes being most marked in deeper fen peat layers. These findings suggest that the decline in groundwater levels in the peat substrate resulted in an increase in effective stress in the peat causing greater subsidence in the central part of the bog due to greater overall thickness. Study results highlight how the hydrology of apparently isolated obotrophic raised bog ecosystems may be influenced by groundwater pressures in deeper deposits, and how marginal drains may have the capacity to impact areas at significant distances.

The effects of winter ice cover on the trophic ecology of whitefish (Coregonus lavaretus L.) in subarctic lakes

Lakes in Arctic and subarctic regions display extreme levels of seasonal variation in light, temperature and ice cover. Comparatively little is known regarding the effects of such seasonal variation on the diet and resource use of fish species inhabiting these systems. Variation in the diet of European whitefish Coregonus lavaretus (L.) during periods of ice cover in this region is often regarded as 'common knowledge'; however, this aspect of the species' ecology has not been examined empirically. Here, we outline the differences in invertebrate community structure, fish activity, and resource use of monomorphic whitefish populations between summer (August-September) and winter (February-March) in three subarctic lakes in Finnish Lapland. Benthic macroinvertebrate densities did not exhibit measurable differences between summer and winter. Zooplankton diversity and abundance, and activity levels of all fish species (measured as catch per unit effort) were lower in winter. The summer diet of C. lavaretus was typical of a generalist utilising a variety of prey sources. In winter, its dietary niche was significantly reduced, and the diet was dominated by chironomid larvae in all study sites. Pelagic productivity decreases during winter, and fish species inhabiting these systems are therefore restricted to feeding on benthic prey. Sampling time has strong effect on our understanding of resource utilisation by whitefish in subarctic lakes and should be taken into account in future studies of these systems. © 2012 John Wiley & Sons A/S.

Testate amoebae (thecamoebians) as water quality indicators in lakes: development of a modern distributional dataset from the Greater Toronto Area

Thecamoebians were examined from 123 surface sediment samples collected from 45 lakes in the Greater Toronto Area (GTA) and the surrounding region to i) elucidate the controls on faunal distribution in modern lake environments; and ii) to consider the utility of thecamoebians in quantitative studies of water quality change. This area was chosen because it includes a high density of lakes that are threatened by urban development and where water quality has deteriorated locally as a result of contaminant inputs, particularly nutrients. Canonical Correspondence analysis (CCA) and a series of partial CCAs were used to examine species-environment relationships. Twenty-four environmental variables were considered, including water properties (e.g. pH, DO, conductivity), substrate characteristics, nutrient loading, and environmentally available metals. The thecamoebian assemblages showed a strong association with Olsen's Phosphorus, reflecting the eutrophic status of many of the lakes, and locally to elevated conductivity measurements, which appear to reflect road salt inputs associated with winter de-icing operations. A transfer function was developed for Olsen P using this training set based on weighted averaging with inverse deshrinking (WA Inv). The model was applied to infer past changes in Phosphorus enrichment in core samples from several lakes, including eutrophic Haynes Lake within the GTA. Thecamoebian-inferred changes in sedimentary Phosphorus from a 210Pb dated core from Haynes Lake are related to i) widespread introduction of chemical fertilizers to agricultural land in the post WWII era; ii) a steep decline in Phosphorous with a change in agricultural practices in the late 1970s; and iii) the construction of a golf course in close proximity to the lake in the early 1990s. This preliminary study confirms that thecamoebians have considerable potential as indicators of eutrophication in lakes and can provide an estimate of baseline conditions.

An Update on Sedimentary Pigments in Victoria Land Lakes (East Antarctica)

Antarctic ice-free areas contain lakes and ponds that have interesting limnological features and are of wide global significance as early warning indicators of climatic and environmental change. However, most linmological and paleolimnological studies in continental Antarctica are limited to certain regions. There are several ice-free areas in Victoria Land that have not yet been studied well. There is therefore a need to extend limnological studies in space and time to understand how different geological and climatic features affect the composition and biological activity of freshwater communities. With the aim of contributing to a better limnological characterization of Victoria Land, this paper reports data on sedimentary pigments (used to identify the main algal taxa) obtained through a methodology that is more sensitive and selective than that of previous studies. Analyses were extended to 48 water bodies in ice-free areas with differing lithology, latitude, and altitude, and with different morphometry and physical, chemical, and biological characteristics in order to identify environmental factors affecting the distribution and composition of freshwater autotrophic communities. A wider knowledge of lakes in a limnologically important region of Antarctica was obtained. Cyanophyta was found to be the most important algal group, followed by Chlorophyta and Bacillariophyta, whereas latitude and altitude are the main factors affecting pigment distribution.

Temporal variation in the water chemistry of northern Victoria Land lakes (Antarctica)

Concentrations of major ions, silicate and nutrients (total N and P) were measured in samples of surface water from 28 lakes in ice-free areas of northern Victoria Land (East Antarctica). Sixteen lakes were sampled during austral summers 2001/02, 2003/04, 2004/05 and 2005/06 to assess temporal variation in water chemistry. Although samples showed a wide range in ion concentrations, their composition mainly reflected that of seawater. In general, as the distance from the sea increased, the input of elements from the marine environment (through aerosols and seabirds) decreased and there was an increase in nitrate and sulfate concentrations. Antarctic lakes lack outflows and during the austral summer the melting and/or ablation of ice cover, water evaporation and leaching processes in dry soils determine a progressive increase in water ion concentrations. During the five-year monitoring survey, no statistically significant variation in the water chemistry were detected, except for a slight (hardly significant) increase in TN concentrations. However, Canonical Correspondence Analysis (CCA) indicated that other factors besides distance from the sea, the presence of nesting seabirds, the sampling time and percentage of ice cover affect the composition of water in Antarctic cold desert environments.

The marginal willingness-to-pay for attributes of a hypothetical HIV vaccine

This paper estimates the marginal willingness-to-pay for attributes of a hypothetical HIV vaccine using discrete choice modeling. We use primary data from 326 respondents from Bangkok and Chiang Mai, Thailand, in 2008–2009, selected using purposive, venue-based sampling across two strata. Participants completed a structured questionnaire and full rank discrete choice modeling task administered using computer-assisted personal interviewing. The choice experiment was used to rank eight hypothetical HIV vaccine scenarios, with each scenario comprising seven attributes (including cost) each of which had two levels. The data were analyzed in two alternative specifications: (1) best-worst; and (2) full-rank, using logit likelihood functions estimated with custom routines in Gauss matrix programming language. In the full-rank specification, all vaccine attributes are significant predictors of probability of vaccine choice. The biomedical attributes of the hypothetical HIV vaccine (efficacy, absence of VISP, absence of side effects, and duration of effect) are the most important attributes for HIV vaccine choice. On average respondents are more than twice as likely to accept a vaccine with 99% efficacy, than a vaccine with 50% efficacy. This translates to a willingness to pay US$383 more for a high efficacy vaccine compared with the low efficacy vaccine. Knowledge of the relative importance of determinants of HIV vaccine acceptability is important to ensure the success of future vaccination programs. Future acceptability studies of hypothetical HIV vaccines should use more finely grained biomedical attributes, and could also improve the external validity of results by including more levels of the cost attribute.

Arcellacea (Testate Amoebae) as Bio-indicators of Road Salt Contamination in Lakes

Winter deicing operations occur extensively in mid- to high-latitude metropolitan regions around the world and result in a significant reduction in road accidents. Deicing salts can, however, pose a major threat to water quality and aquatic organisms. In this paper we examine the utility of Arcellacea (testate amoebae) for monitoring lakes that have become contaminated by winter deicing salts, particularly sodium chloride. We analysed 50 sediment samples and salt-related water-property variables (chloride concentrations; conductivity) from 15 lakes in the Greater Toronto Area and adjacent areas of southern Ontario, Canada. The sampled lakes included lakes in proximity to major highways and suburban roads, and control lakes in forested settings away from road influences. Samples from the most contaminated lakes, with chloride concentrations in excess of 400 mg/l and conductivities of >800 μS/cm, were dominated by species typically found in brackish and/or inhospitable lake environments and by lower faunal diversities (lowest Shannon Diversity Index values) than samples with lower readings. Q-R-mode cluster analysis and Detrended Correspondence Analysis (DCA) resulted in the recognition of four assemblage groupings. These reflect varying levels of salt contamination in the study lakes, along with other local influences, including nutrient loading. The response to nutrients can, however, be isolated if the planktic eutrophic indicator species Cucurbitella tricuspis is removed from the counts. The findings show that the group have considerable potential for biomonitoring in salt-contaminated lakes, and through application to lake sediment cores, may provide significant insights into long-term benthic community health, which is integral for remedial efforts.

mfx: Marginal Effects, Odds Ratios and Incidence Rate Ratios for GLMs

Estimates probit, logit, Poisson, negative binomial, and beta regression models, returning their marginal effects, odds ratios, or incidence rate ratios as an output.

Efficient Marginal Likelihood Computation for Gaussian Process Regression

In a Bayesian learning setting, the posterior distribution of a predictive model arises from a trade-off between its prior distribution and the conditional likelihood of observed data. Such distribution functions usually rely on additional hyperparameters which need to be tuned in order to achieve optimum predictive performance; this operation can be efficiently performed in an Empirical Bayes fashion by maximizing the posterior marginal likelihood of the observed data. Since the score function of this optimization problem is in general characterized by the presence of local optima, it is necessary to resort to global optimization strategies, which require a large number of function evaluations. Given that the evaluation is usually computationally intensive and badly scaled with respect to the dataset size, the maximum number of observations that can be treated simultaneously is quite limited. In this paper, we consider the case of hyperparameter tuning in Gaussian process regression. A straightforward implementation of the posterior log-likelihood for this model requires O(N^3) operations for every iteration of the optimization procedure, where N is the number of examples in the input dataset. We derive a novel set of identities that allow, after an initial overhead of O(N^3), the evaluation of the score function, as well as the Jacobian and Hessian matrices, in O(N) operations. We prove how the proposed identities, that follow from the eigendecomposition of the kernel matrix, yield a reduction of several orders of magnitude in the computation time for the hyperparameter optimization problem. Notably, the proposed solution provides computational advantages even with respect to state of the art approximations that rely on sparse kernel matrices.

The taphonomy of Last Glacial–Interglacial Transition (LGIT) distal volcanic ash in small Scottish lakes

An extensive micro-tephrostratigraphic survey of three small lakes in the Scottish Inner Hebrides was conducted encompassing the Last Glacial–Interglacial Transition (LGIT). The lakes are highly contrasting in terms of lake area to catchment ratio, the presence or absence of stream inlets draining the catchment, and in the complexity of the catchment drainage network. A suite of distal Icelandic volcanic ashes was consistently detected in all three lakes, with three, namely Penifiler Tephra, Vedde Ash and Ashik Tephra, being common to all the lakes. These ashes were chosen to examine the taphonomic intercomparability of ash location and concentration among the lakes. Findings reveal that the part played by catchment inlets in determining ash concentration and within-basin location applies to microtephra layers as much as it does in studies of macrotephra layer thickness. The position of ash concentration maxima is also shown to vary significantly for different LGIT periods and may be a consequence of lake-level changes, especially during the early Holocene. High-resolution stratigraphic analysis through the Vedde Ash visible macrotephra at Loch Ashik reveals a high degree of complexity in taphonomic behaviour between the different geochemical components, with possible implications for the correct interpretation of the isochron position. The detection of multiple intact ash isochrons and the taphonomic processes responsible for their deposition should prove useful in future tephrostratigraphic surveys, as well as having applications within other palaeolimnological disciplines.

Sediment accumulation rates in subarctic lakes: insights into age-depth modeling from 22 dated lake records from the Northwest Territories, Canada

Age-depth modeling using Bayesian statistics requires well-informed prior information about the behavior of sediment accumulation. Here we present average sediment accumulation rates (represented as deposition times, DT, in yr/cm) for lakes in an Arctic setting, and we examine the variability across space (intra- and inter-lake) and time (late Holocene). The dataset includes over 100 radiocarbon dates, primarily on bulk sediment, from 22 sediment cores obtained from 18 lakes spanning the boreal to tundra ecotone gradients in subarctic Canada. There are four to twenty-five radiocarbon dates per core, depending on the length and character of the sediment records. Deposition times were calculated at 100-year intervals from age-depth models constructed using the ‘classical’ age-depth modeling software Clam. Lakes in boreal settings have the most rapid accumulation (mean DT 20 ± 10 years), whereas lakes in tundra settings accumulate at moderate (mean DT 70 ± 10 years) to very slow rates, (>100 yr/cm). Many of the age-depth models demonstrate fluctuations in accumulation that coincide with lake evolution and post-glacial climate change. Ten of our sediment cores yielded sediments as old as c. 9,000 cal BP (BP = years before AD 1950). From between c. 9,000 cal BP and c. 6,000 cal BP, sediment accumulation was relatively rapid (DT of 20 to 60 yr/cm). Accumulation slowed between c. 5,500 and c. 4,000 cal BP as vegetation expanded northward in response to warming. A short period of rapid accumulation occurred near 1,200 cal BP at three lakes. Our research will help inform priors in Bayesian age modeling.

Genome-wide DNA profiling of marginal zone lymphomas identifies subtype-specific lesions with an impact on the clinical outcome

Marginal zone B-cell lymphomas (MZLs) have been divided into 3 distinct subtypes (extranodal MZLs of mucosa-associated lymphoid tissue [MALT] type, nodal MZLs, and splenic MZLs). Nevertheless, the relationship between the subtypes is still unclear. We performed a comprehensive analysis of genomic DNA copy number changes in a very large series of MZL cases with the aim of addressing this question. Samples from 218 MZL patients (25 nodal, 57 MALT, 134 splenic, and 2 not better specified MZLs) were analyzed with the Affymetrix Human Mapping 250K SNP arrays, and the data combined with matched gene expression in 33 of 218 cases. MALT lymphoma presented significantly more frequently gains at 3p, 6p, 18p, and del(6q23) (TNFAIP3/A20), whereas splenic MZLs was associated with del(7q31), del(8p). Nodal MZLs did not show statistically significant differences compared with MALT lymphoma while lacking the splenic MZLs-related 7q losses. Gains of 3q and 18q were common to all 3 subtypes. del(8p) was often present together with del(17p) (TP53). Although del(17p) did not determine a worse outcome and del(8p) was only of borderline significance, the presence of both deletions had a highly significant negative impact on the outcome of splenic MZLs.