Comment on "A depth-based global envelope test for comparing two groups of functions with applications to biomedical data" by S. Lopez-Pintado and K. Qian.

This is a note describing nonparametric methodology of functional tests in the functional general linear models, which is more rich than the methodology presented in the commented paper.

New methods for multiple testing in permutation inference for the general linear model.

Permutation methods are commonly used to test the significance of regressors of interest in general linear models (GLMs) for functional (image) data sets, in particular for neuroimaging applications as they rely on mild assumptions. Permutation inference for GLMs typically consists of three parts: choosing a relevant test statistic, computing pointwise permutation tests, and applying a multiple testing correction. We propose new multiple testing methods as an alternative to the commonly used maximum value of test statistics across the image. The new methods improve power and robustness against inhomogeneity of the test statistic across its domain. The methods rely on sorting the permuted functional test statistics based on pointwise rank measures; still, they can be implemented even for large data. The performance of the methods is demonstrated through a designed simulation experiment and an example of brain imaging data. We developed the R package GET, which can be used for the computation of the proposed procedures.

Invasive round goby Neogobius melanostomus has sex-dependent locomotor activity and is under-represented in catches from passive fishing gear compared with seine catches.

The higher proportion of males of the invasive round goby Neogobius melanostomus in samples from two activity selective passive fishing gears compared with one activity non-selective fishing gear in three Dutch lakes is related to higher male locomotory activity and is a sex-dependent trait. This difference in activity reflects the different ecology of male and female N. melanostomus.

Fractal and stochastic geometry inference for breast cancer: a case study with random fractal models and Quermass-interaction process.

Fractals are models of natural processes with many applications in medicine. The recent studies in medicine show that fractals can be applied for cancer detection and the description of pathological architecture of tumors. This fact is not surprising, as due to the irregular structure, cancerous cells can be interpreted as fractals. Inspired by Sierpinski carpet, we introduce a flexible parametric model of random carpets. Randomization is introduced by usage of binomial random variables. We provide an algorithm for estimation of parameters of the model and illustrate theoretical and practical issues in generation of Sierpinski gaskets and Hausdorff measure calculations. Stochastic geometry models can also serve as models for binary cancer images. Recently, a Boolean model was applied on the 200 images of mammary cancer tissue and 200 images of mastopathic tissue. Here, we describe the Quermass-interaction process, which can handle much more variations in the cancer data, and we apply it to the images. It was found out that mastopathic tissue deviates significantly stronger from Quermass-interaction process, which describes interactions among particles, than mammary cancer tissue does. The Quermass-interaction process serves as a model describing the tissue, which structure is broken to a certain level. However, random fractal model fits well for mastopathic tissue. We provide a novel discrimination method between mastopathic and mammary cancer tissue on the basis of complex wavelet-based self-similarity measure with classification rates more than 80%. Such similarity measure relates to Hurst exponent and fractional Brownian motions. The R package FractalParameterEstimation is developed and introduced in the paper.

The Effect of Static Apnea Diving Training on the Physiological Parameters of People with a Sports Orientation and Sedentary Participants: A Pilot Study.

Diver training improves physical and mental fitness, which can also benefit other sports. This study investigates the effect of eight weeks of static apnea training on maximum apnea time, and on the physiological parameters of runners, swimmers, and sedentary participants, such as forced vital capacity (FVC), minimum heart rate (HR), and oxygen saturation (SpO2). The study followed 19 participants, including five runners, swimmers, sedentary participants, and four competitive divers for reference values. The minimum value of SpO2, HR, maximum duration of apnea, and FVC were measured. Apnea training occurred four times weekly, consisting of six apneas with 60 s breathing pauses. Apnea duration was gradually increased by 30 s. The measurement started with a 30 s apnea and ended with maximal apnea. There was a change in SpO2 decreased by 6.8%, maximum apnea length increased by 15.8%, HR decreased by 9.1%, and FVC increased by 12.4% for the groups (p < 0.05). There were intra-groups changes, but no significant inter-groups difference was observed. Eight weeks of apnea training improved the maximum duration of apnea, FVC values and reduced the minimum values of SpO2 and HR in all groups. No differences were noted between groups after training. This training may benefit cardiorespiratory parameters in the population.

Changing environmental conditions underpin long-term patterns of phytoplankton in a freshwater reservoir.

Environmental changes can exert strong pressure on freshwater biota and lead to unwanted alterations of local communities and deterioration of ecosystem services. Disentangling the links between environmental and community changes is, therefore, essential to understand and predict the impact of human activities on freshwater ecosystems. This is particularly relevant for man-made freshwater reservoirs that represent a nexus between anthropogenic, environmental, and biotic effects. Reservoir food webs depend strongly on phytoplankton dynamics, which are affected by abiotic conditions, nutrient availability and grazing pressure by zooplankton. We studied the effects of relevant environmental drivers (hydrochemistry, hydrodynamics and zooplankton) on the composition, diversity and community stability of main morpho-functional phytoplankton groups over 32 years in the Rímov Reservoir (Czech Republic). Environmental conditions in the reservoir are characterised by three distinct periods (1983-89, 1990-99, and 2000-14) defined by shifts and breakpoints in temporal trends in reservoir hydrochemistry and hydraulic conditions, and we examined if and how phytoplankton responded to these abrupt changes. We found significant differences in phytoplankton composition among the three periods. Phytoplankton underwent a substantial compositional shift towards a dominance of pennate diatoms. Time-lag analysis of dissimilarity in phytoplankton composition revealed higher and stochastic annual variations until 1999, followed by a lower variability and divergence in phytoplankton composition in subsequent years. Changes in overall phytoplankton assemblage and most abundant morpho-functional phytoplankton groups were driven mainly by hydrochemical (total nitrogen) and hydrodynamic variables (inflow rate, surface level and mixing depth) and less by zooplankton dynamics. These results suggest that phytoplankton are driven primarily by nutrient input and water regime, both of which can be appropriately managed to support valuable ecosystem services provided by phytoplankton in freshwater reservoirs.

Model of Risk of Exposure to Lyme Borreliosis and Tick-Borne Encephalitis Virus-Infected Ticks in the Border Area of the Czech Republic (South Bohemia) and Germany (Lower Bavaria and Upper Palatinate).

In Europe, Lyme borreliosis (LB) and tick-borne encephalitis (TBE) are the two vector-borne diseases with the largest impact on human health. Based on data on the density of host-seeking Ixodes ricinus ticks and pathogen prevalence and using a variety of environmental data, we have created an acarological risk model for a region where both diseases are endemic (Czech Republic-South Bohemia and Germany-Lower Bavaria, Upper Palatinate). The data on tick density were acquired by flagging 50 sampling sites three times in a single season. Prevalence of the causative agents of LB and TBE was determined. Data on environmental variables (e.g., altitude, vegetation cover, NDVI, land surface temperature) were obtained from various sources and processed using geographical information systems. Generalized linear models were used to estimate tick density, probability of tick infection, and density of infected ticks for the whole area. A significantly higher incidence of human TBE cases was recorded in South Bohemia compared to Bavarian regions, which correlated with a lower tick density in Bavaria. However, the differences in pathogen prevalence rates were not significant. The model outputs were made available to the public in the form of risk maps, indicating the distribution of tick-borne disease risk in space.

Multiple long-term trends and trend reversals dominate environmental conditions in a man-made freshwater reservoir.

Man-made reservoirs are common across the world and provide a wide range of ecological services. Environmental conditions in riverine reservoirs are affected by the changing climate, catchment-wide processes and manipulations with the water level, and water abstraction from the reservoir. Long-term trends of environmental conditions in reservoirs thus reflect a wider range of drivers in comparison to lakes, which makes the understanding of reservoir dynamics more challenging. We analysed a 32-year time series of 36 environmental variables characterising weather, land use in the catchment, reservoir hydrochemistry, hydrology and light availability in the small, canyon-shaped Rímov Reservoir in the Czech Republic to detect underlying trends, trend reversals and regime shifts. To do so, we fitted linear and piecewise linear regression and a regime shift model to the time series of mean annual values of each variable and to principal components produced by Principal Component Analysis. Models were weighted and ranked using Akaike information criterion and the model selection approach. Most environmental variables exhibited temporal changes that included time-varying trends and trend reversals. For instance, dissolved organic carbon showed a linear increasing trend while nitrate concentration or conductivity exemplified trend reversal. All trend reversals and cessations of temporal trends in reservoir hydrochemistry (except total phosphorus concentrations) occurred in the late 1980s and during 1990s as a consequence of dramatic socioeconomic changes. After a series of heavy rains in the late 1990s, an administrative decision to increase the flood-retention volume of the reservoir resulted in a significant regime shift in reservoir hydraulic conditions in 1999. Our analyses also highlight the utility of the model selection framework, based on relatively simple extensions of linear regression, to describe temporal trends in reservoir characteristics. This approach can provide a solid basis for a better understanding of processes in freshwater reservoirs.

Real-time distribution of pelagic fish: combining hydroacoustics, GIS and spatial modelling at a fine spatial scale.

Understanding spatial distribution of organisms in heterogeneous environment remains one of the chief issues in ecology. Spatial organization of freshwater fish was investigated predominantly on large-scale, neglecting important local conditions and ecological processes. However, small-scale processes are of an essential importance for individual habitat preferences and hence structuring trophic cascades and species coexistence. In this work, we analysed the real-time spatial distribution of pelagic freshwater fish in the Rímov Reservoir (Czechia) observed by hydroacoustics in relation to important environmental predictors during 48 hours at 3-h interval. Effect of diurnal cycle was revealed of highest significance in all spatial models with inverse trends between fish distribution and predictors in day and night in general. Our findings highlighted daytime pelagic fish distribution as highly aggregated, with general fish preferences for central, deep and highly illuminated areas, whereas nighttime distribution was more disperse and fish preferred nearshore steep sloped areas with higher depth. This turnover suggests prominent movements of significant part of fish assemblage between pelagic and nearshore areas on a diel basis. In conclusion, hydroacoustics, GIS and spatial modelling proved as valuable tool for predicting local fish distribution and elucidate its drivers, which has far reaching implications for understanding freshwater ecosystem functioning.

Early life-history predator-prey reversal in two cyprinid fishes.

Predator-prey relationships are often perceived simply as a situation in which a predator enhances its own fitness while reducing the fitness of its prey. However, this relationship may become reversed when the prey feeds on the juvenile predator stages. We investigated this phenomenon in a model asp (Leuciscus aspius; predator)-bleak (Alburnus alburnus; prey) relationship. The adhesive asp eggs are available for bleak predation after a spawning event for only tens of seconds before they adhere to the stones, where bleak do not forage. Gut content analysis demonstrated that eggs were utilized in high quantities, especially in the spawning peak of the asp reproductive season. Furthermore, using underwater video, we recorded the bleak feeding efficiency on naturally drifting asp eggs as the percentage of eggs eaten. Within the 40 cm egg trajectory captured by our cameras, total egg mortality was 21.2 ± 2.2% on average. The highest survival chances occurred among eggs drifting in aggregations, since the short drifting distance together with their aggregated distribution satiated bleak and part of the egg aggregation could attach to the spawning ground. This study emphasizes the potential efficiency of predator egg utilization by prey, which may have further consequences in predator-prey dynamics.

Seasonal and daily protandry in a cyprinid fish.

In polygynandrous mating systems, in which females limit reproductive success, males can increase their success by investing in courtship. Earlier arrival at the spawning ground compared to when females arrive may increase their opportunities in competitive mating systems. In this study, we used passive telemetry to test whether a male minnow known as the asp, Leuciscus aspius, times its arrival at spawning grounds relative to the arrival of females. Males arrived in a model stream approximately five days earlier than females on average and left four to five days later than females over two years. Both sexes performed a daily migration between a staging ground (standing water, low energy costs) and the fluvial spawning ground (high energy costs). Fish abundance peaked twice a day, with a major peak at sunset and a minor peak at sunrise and with the evening peak abundance for males occurring 1 hour 40 minutes earlier than that of females. The number of females on the spawning ground never exceeded the number of males. While the degree of protandry is hypothesized to be influenced by the operational sex ratio (ranging from 0.5 to 1 in our study), our data did not support this theory.

A novel upward-looking hydroacoustic method for improving pelagic fish surveys.

For ethical reasons and animal welfare, it is becoming increasingly more important to carry out ecological surveys with a non-invasive approach. Information about fish distribution and abundance in the upper water column is often fundamental. However, this information is extremely hard to obtain using classical hydroacoustic methods. We developed a rigid frame system for pushing upward looking transducers of the scientific echo sounder (38 and 120 kHz) in front of the research vessel. The efficiency of the new approach for monitoring juvenile fish at night was investigated by comparing the results with a quantitative fry trawl in the Rímov Reservoir in the Czech Republic. The experimental setup enabled comparisons for the 0-3 m and 3-6 m depth layers, which are utilized by almost all juvenile fish in summer. No statistically significant differences in the estimated abundance of juveniles were found between the two sampling methods. The comparison of abundance estimates gathered by the two frequencies were also not significantly different. The predicted mean lengths from acoustic sampling and the trawl catches differed by less than 10 mm in all comparisons. Results suggest that mobile hydroacoustic upward-looking systems can fill the methodological gap in non-invasive surveying of surface fishes.