Andrzej Kruk

Long-Term Patterns in the Population Dynamics of Daphnia longispina, Leptodora kindtii and Cyanobacteria in a Shallow Reservoir: A Self-Organising Map (SOM) Approach.

The recognition of long-term patterns in the seasonal dynamics of Daphnia longispina, Leptodora kindtii and cyanobacteria is dependent upon their interactions, the water temperature and the hydrological conditions, which were all investigated between 1999 and 2008 in the lowland Sulejow Reservoir. The biomass of cyanobacteria, densities of D. longispina and L. kindtii, concentration of chlorophyll a and water temperature were assessed weekly from April to October at three sampling stations along the longitudinal reservoir axis. The retention time was calculated using data on the actual water inflow and reservoir volume. A self-organising map (SOM) was used due to high interannual variability in the studied parameters and their often non-linear relationships. Classification of the SOM output neurons into three clusters that grouped the sampling terms with similar biotic states allowed identification of the crucial abiotic factors responsible for the seasonal sequence of events: cluster CL-ExSp (extreme/spring) corresponded to hydrologically unstable cold periods (mostly spring) with extreme values and highly variable abiotic factors, which made abiotic control of the biota dominant; cluster CL-StSm (stable/summer) was associated with ordinary late spring and summer and was characterised by stable non-extreme abiotic conditions, which made biotic interactions more important; and the cluster CL-ExSm (extreme/summer), was associated with late spring/summer and characterised by thermal or hydrological extremes, which weakened the role of biotic factors. The significance of the differences between the SOM sub-clusters was verified by Kruskal-Wallis and post-hoc Dunn tests. The importance of the temperature and hydrological regimes as the key plankton-regulating factors in the dam reservoir, as shown by the SOM, was confirmed by the results of canonical correlation analyses (CCA) of each cluster. The demonstrated significance of hydrology in seasonal plankton dynamics complements the widely accepted pattern proposed by the plankton succession model for lakes, the PEG (Plankton Ecology Group), and may be useful for the formulation of management decisions in dam reservoirs.

Molecular subtyping of bladder cancer using Kohonen self-organizing maps.

Kohonen self‐organizing maps (SOMs) are unsupervised Artificial Neural Networks (ANNs) that are good for low‐density data visualization. They easily deal with complex and nonlinear relationships between variables. We evaluated molecular events that characterize high‐ and low‐grade BC pathways in the tumors from 104 patients. We compared the ability of statistical clustering with a SOM to stratify tumors according to the risk of progression to more advanced disease. In univariable analysis, tumor stage (log rank P = 0.006) and grade (P < 0.001), HPV DNA (P < 0.004), Chromosome 9 loss (P = 0.04) and the A148T polymorphism (rs 3731249) in CDKN2A (P = 0.02) were associated with progression. Multivariable analysis of these parameters identified that tumor grade (Cox regression, P = 0.001, OR.2.9 (95% CI 1.6–5.2)) and the presence of HPV DNA (P = 0.017, OR 3.8 (95% CI 1.3–11.4)) were the only independent predictors of progression. Unsupervised hierarchical clustering grouped the tumors into discreet branches but did not stratify according to progression free survival (log rank P = 0.39). These genetic variables were presented to SOM input neurons. SOMs are suitable for complex data integration, allow easy visualization of outcomes, and may stratify BC progression more robustly than hierarchical clustering.

Kohonen Artificial Neural Networks and the IndVal Index as Supplementary Tools for the Quantitative Analysis of Palaeoecological Data

Abstract We applied two widely-used methods for data partitioning - constrained incremental sum-of-squares (CONISS) and Optimal Partitioning (OP) along with two supplementary methods, a Kohonen artificial neural network (self-organising map, SOM) and the indicator value (IndVal) index, for the quantitative analysis of subfossil chironomid assemblages from a palaeolake in Central Poland. The samples, taken from 79 core depths, were divided into 5-11 groups (five by SOM, seven by CONISS, 11 by OP), for which different numbers of indicator taxa were determined with the use of the IndVal index (18 for CONISS, 15 for SOM, 11 for OP). Only six indicator taxa were common to all three methods. The number of highly specific (p < 0.001) taxa was highest for SOM. Only the SOM analysis clearly reflected the rate of the changes in chironomid assemblages, which occurred rapidly in the Late Glacial (as a result of greater climate variability) and slowly in the Holocene (as a reflection of slow long-term changes in the local habitat, such as paludification). In summary, we recommend using SOM and the IndVal index in combination with CONISS and/or OP in order to detect different aspects of temporal variability in complex multivariate palaeoecological data.

Diet overlap between two cyprinids: eurytopic roach and rheophilic dace in tailwater submersed macrophyte patches

Abstract From May to August 2004, the available food base and diet of two cyprinid species, eurytopic roach, represented by 75 small specimens, and rheophilic dace, represented by 37 small specimens, were investigated in seasonal patches of submersed aquatic macrophytes (SAM) in the impounded lowland Warta River, Poland. The aim of the study was to recognize spatial and temporal patterns in the feeding of both species in relation to available resources, and to evaluate their food niche overlap. To distinguish homogenous classes of fish alimentary tracts on the basis of their contents, a Kohonen artificial neural network (i.e., a self-organizing map, SOM) was used. Indicator food categories were identified using the IndVal index. Roach and dace partitioned the food niche, which was demonstrated in this study by 1) insignificant values of the Schoeners interspecific diet overlap index on particular sampling occasions, and two SOM sub-clusters (homogenous diet classes) with alimentary tracts almost exclusively of roach (axis of resources), 2) zero or low percentage of specimens of both fish species coming from the same sampling occasions and assigned to any of the remaining homogenous diet classes (axis of time), and 3) absence of roach in May and dace in August in the SAM patches, i.e., on almost half of the sampling occasions (axis of space). The diet overlap was highest when the SAM patches and food base were most developed, which is congruent with the niche overlap hypothesis saying that maximal tolerable niche overlap can be higher in less intensely competitive situations. We recommend the combined application of SOM and IndVal index, which have both previously been used in biocoenology, to the analyses of animal diets. They effectively allowed getting insight into the complex trophic relationships.

Significance of CDKN2A gene A148T variant in patients with bladder cancer.

Objectives The A148T polymorphism of CDKN2A gene is observed in various neoplasms with the incidence rate of 3-35%, however, rather little is known either about the frequency of its occurrence or of its significance in urinary bladder carcinoma. Materials and methods DNA was isolated from blood of 156 patients with urinary bladder carcinoma (130 men). In histopathology, 84 cases were classified as G1, 42 as G2, and 30 as G3. The clinical stage was in 81 cases estimated at Ta and in 75 cases at T1-T4. A148T polymorphism was detected by the MSSCP technique and by sequencing. Results A148T polymorphism was identified in 9/156 urinary bladder carcinoma cases (only in men). The obtained results were compared with the polymorphism incidence for the Polish population, estimated by Debniak et al. The occurrence in the group of the bladder cancer patients turned out higher (5.77%) from that in the control group (2.89%) (G test, table 2×2: NBLADDER CANCER = 156, NCONTROL = 1210, G = 4.298, p <0.05). Conclusion Summing up and taking into account the analysis of clinical parameters and the age of the disease occurrence, the A148T polymorphism of CDKN2A gene was identified in the study group only in men, in whom the disease was diagnosed above the age of 60, while the diagnosed neoplasms were in the majority of cases characterized by higher clinical stages and higher grades of malignancy. This has been the first study that attempted to show a potential association between A148T alterations and an increased risk for bladder cancer development.

Tailwater habitat stability after dam removal and return to a natural hydrological regime

Abstract The study was conducted from 2000 to 2003 in the tailwater of the Drzewieckie Lake, an artificial reservoir in Central Poland. Short-term peaks in water flow were generated for the purpose of the operation of a whitewater slalom canoeing track built just downstream of the dam. In 2002, the reservoir was drawn down. The patterns in habitat samples were recognized with a Kohonen’s unsupervised artificial neural network (SOM). The SOM spatial gradient was stronger than the SOM temporal gradient, which shows that the removal of the studied dam did not have a destructive impact on habitats’ features, as shown in other studies, and that the patchy nature of the riverbed has been maintained. The complete emptying of the Drzewieckie Lake took place at the beginning of the vegetation season, which allowed plants to cover the exposed bottom of the reservoir and, consequently, reduce the downstream flow of organic matter accumulated there. Patterns in the displacement of aquatic macrophytes, inorganic substratum and different fractions of particulate organic matter are discussed. The amount of dissolved oxygen decreased because of the lack of intensive water discharge from the reservoir into the river, which would result in high water turbulence. Results of this study are important for planning the ecologically sound dam removals.

Artificial neural network in predicting bladder cancer recurrence

The more we learn about human genetics and human variation, the more apparent it becomes that our individual make-up has a noticeble impact on the effectiveness of medications. Urinary bladder cancer is the sixth leading cause of mortality due to malignant neoplasm among Polish man in Lodz region. Many genetic and epigenetic alterations have been identified that contribute directly to the development of bladder tumors. The aim of the project was the creation of the individual risk calculator of bladder cancer recurrence using available clinical data and the results of the long term genetic research.

The A148T variant of CDKN2A gene in bladder cancer

Results We found common polymorphic variants reported in the literature at codon 148 in exon 2 (Arg148Thr) and at nucleotides 500 and 540 in the 3’untranslated region which were not considered to be functional variants. We compared the obtained frequencies for the particular CDKN2A variants with the control group for the Polish population examined by Debniak and colleagues (Cancer Research 2005) and we found a significant difference in A148T polymorphism occurrence in the group of the bladder cancer patients (G test, table 2 ×2: NBLADDER CANCER =80, NCONTROL=1210, G=10.214, p g, Nt540c>t polymorphisms recorded in the group of the bladder cancer patients in our study is not different from those recorded in the control group. Conclusion The A148T variant of CDKN2A gene seems to be associated with an increased risk of bladder cancer development.