Designing boosting ensemble of relational fuzzy systems

A method frequently used in classification systems for improving classification accuracy is to combine outputs of several classifiers. Among various types of classifiers, fuzzy ones are tempting because of using intelligible fuzzy if-then rules. In the paper we build an AdaBoost ensemble of relational neuro-fuzzy classifiers. Relational fuzzy systems bond input and output fuzzy linguistic values by a binary relation; thus, fuzzy rules have additional, comparing to traditional fuzzy systems, weights - elements of a fuzzy relation matrix. Thanks to this the system is better adjustable to data during learning. In the paper an ensemble of relational fuzzy systems is proposed. The problem is that such an ensemble contains separate rule bases which cannot be directly merged. As systems are separate, we cannot treat fuzzy rules coming from different systems as rules from the same (single) system. In the paper, the problem is addressed by a novel design of fuzzy systems constituting the ensemble, resulting in normalization of individual rule bases during learning. The method described in the paper is tested on several known benchmarks and compared with other machine learning solutions from the literature.     

How does metal soil pollution change the plant mycobiome?

Microorganisms play a key role in plant adaptation to the environment. The aim of this study was to evaluate the effect of toxic metals present in the soil on the biodiversity of plant-related, endophytic mycobiota. The mycobiome of plants and soil from a Zn–Pb heap and a metal-free ruderal area were compared via Illumina sequencing of the ITS1 rDNA. The biodiversity of plants and fungi inhabiting mine dump substrate was lower than that of the metal free site. In the endosphere of Arabidopsis arenosa from the mine dump the number of endophytic fungal taxa was comparable to that in the reference population, but the community structure significantly differed. Agaricomycetes was the most notably limited class of fungi. The results of plant mycobiota evaluation from the field study were verified in terms of the role of toxic metals in plant endophytic fungi community assembly in a reconstruction experiment. The results presented in this study indicate that metal toxicity affects the structure of the plant mycobiota not by changing the pool of microorganisms available in the soil from which the fungal symbionts are recruited but most likely by altering plant and fungi behaviour and the organisms' preferences towards associating in symbiotic relationships.     

Accounting for differential migration strategies between age groups to monitor raptor population dynamics in the eastern Black Sea flyway

Migration counts can offer a cost-effective method for monitoring the state of migrant raptor populations. However, differential migration strategies between inexperienced juveniles and experienced non-juveniles are rarely accounted for when inferring population trends from raptor migration counts. Since 2011, the Batumi Raptor Count (BRC) monitors the autumn migration of more than 1 million raptors along the eastern Black Sea coast in the Republic of Georgia. We also systematically sampled age information to assess differential migration timing between age groups and estimate age-specific linear trends in abundance between 2011 and 2018 for eight focal species. In so doing we aimed (1) to reassess the global relevance of BRC counts for each species and the potential for monitoring abundance of juveniles and non-juveniles, and (2) to identify demographic changes underlying recent trends in overall abundance. We found that the mean annual passage of non-juveniles at Batumi represents at least 1% of the estimated global breeding population of five study species. As expected, counts of juveniles were more variable than counts of non-juveniles. Yet despite our short monitoring period our models had sufficient statistical power to detect changes in abundance of 10%/year or less for at least one age group in all species except Pallid Harrier Circus macrourus. Our results indicate stable abundance and demography for half of the study species. We also found strong and significant increases in the abundance of Black Kites Milvis migrans and Short-toed Eagles Circaetus gallicus that were primarily due to increasing numbers of non-juveniles. By contrast, juvenile Montagu's Harriers Circus pygargus and Booted Eagles Hieraaetus pennatus significantly decreased in abundance. The first decade of BRC surveys offers an important benchmark for monitoring raptor populations using the eastern African–Palearctic flyway in the 21st century. We discuss possible causes of the observed trends and hope our work will stimulate demographic monitoring at migration count sites.     

Profiling the physiological pitfalls of anti-hepatitis C direct-acting agents in budding yeast

Sofosbuvir and Daclatasvir are among the direct-acting antiviral (DAA) medications prescribed for the treatment of chronic hepatitis C (CHC) virus infection as combination therapy with other antiviral medications. DAA-based therapy achieves high cure rates, reaching up to 97% depending on the genotype of the causative hepatitis C virus (HCV). While DAAs have been approved as an efficient and well-tolerated therapy for CHC, emerging concerns about adverse cardiac side effects, higher risk of recurrence and occurrence of hepatocellular carcinoma (HCC) and doubts of genotoxicity have been reported. In our study, we investigated in detail physiological off-targets of DAAs and dissected the effects of these drugs on cellular organelles using budding yeast, a unicellular eukaryotic organism. DAAs were found to disturb the architecture of the endoplasmic reticulum (ER) and the mitochondria, while showing no apparent genotoxicity or DNA damaging effect. Our study provides evidence that DAAs are not associated with genotoxicity and highlights the necessity for adjunctive antioxidant therapy to mitigate the adverse effects of DAAs on ER and mitochondria.     

Variability of the Left Atrial Appendage in Human Hearts

Atrial fibrillation increases the risk of thrombus formation. It is commonly responsible for cerebral stroke whereas less frequently for pulmonary embolism. The aim of the study was to describe the morphology of the left atrial appendage in the human heart with respect to sex, age and weight. Macroscopic examination was carried out on 100 left appendages taken from the hearts of the patients aged 18–77, both sexes. All hearts preserved in 4% water solution of formaldehyde carried neither marks of coronary artery disease nor congenital abnormalities. Three axes of appendage orientation were performed. After the appendage had been cut off, morphological examination was performed in long and perpendicular axes. Measurements of the appendages were taken from anatomical specimens and their silicone casts. We classified the left atrial appendage into 4 morphological groups according to the number of lobes. Most left atrial appendages in female population were composed of 2 lobes. In the male group typically 2 or 3-lobed appendages were observed. The mean left atrial appendage orifice ranged from 12.0 to 16.0 mm and the most significant difference in the orifices between males and females was observed in LAA type 2 (about 3.3 mm). A smaller orifice and narrower, tubular shape of the LAA lobes could explain a higher risk of thrombus formation during nonvalvular atrial fibrillation in women. Knowledge of anatomical variability of the LAA helps diagnose some undefined echoes in the appendage during transesophageal echocardiographic examination.     

Statistical evaluation of Ips typographus population density: a useful tool in protected areas and conservation-oriented forestry

Ips typographus (Col., Curculionidae, Scolytinae) occurring on Picea abies stems is a species characterised by large fluctuations in population numbers and causing frequent outbreaks. In protected areas, I. typographus is regarded as a sensitive bioindicator responsive to changes in forest health and vitality. In conservation-oriented forestry, attention is being paid to the ecological value of I. typographus beetles as ecosystem engineers and keystone species, driving forest natural regeneration and conversion. Despite many publications devoted to I. typographus, no accurate method for estimating the population density of this species has been developed. The objective of this study was to develop a statistical method for estimating I. typographus population density that enables calculation of estimation errors. The proposed method consists of two parts: tree-level analyses and stand-level analyses. Part one allows calculation of the total density of I. typographus infestation of each of P. abies selected stem (after selecting sample windfalls), part two allows estimation of the mean total infestation density of the stem in the area investigated. Linear regression functions were applied to part one and survey sampling to part two. The method is only marginally invasive because it involves debarking of one 0.5 m-long stem section on maximum 50 P. abies windfalls (trap trees can optionally be used). The developed method was employed to assess I. typographus population density in the ?wi?tokrzyskie Mountains in Central Poland in an area of ca. 4,000 ha. In 2010, in the area investigated, the mean total I. typographus infestation density of the P. abies stem was 440.6 maternal galleries/m² (from 358.7 to 522.6 maternal galleries/m² with ?? = 0.05; the relative error of estimation was 18.6%). The examined I. typographus population was in a progradation phase. The proposed method can be used in nature reserves, national parks and managed forests, mainly for scientific purposes.     

Assembling the SARS-CoV genome -- new method based on graph theoretical approach

Nowadays, scientists may learn a lot about the organisms studied just by analyzing their genetic material. This requires the development of methods of reading genomes with high accuracy. It has become clear that the knowledge of the changes occurring within a viral genome is indispensable for effective fighting of the pathogen. A good example is SARS-CoV, which was a cause of death of many people and frightened the entire world with its fast and hard to prevent propagation. Rapid development of sequencing methods, like shotgun sequencing or sequencing by hybridization (SBH), gives scientists a good tool for reading genomes. However, since sequencing methods can read fragments of up to 1000 bp only, methods for sequence assembling are required in order to read whole genomes. In this paper a new assembling method, based on graph theoretical approach, is presented. The method was tested on SARS-CoV and the results were compared to the outcome of other widely known methods.     

The molecular characterisation of the extended spectrum beta-lactamase (ESBL) producing strain of Salmonella enterica serovar Mbandaka isolated in Poland

The molecular attributes of the first ESBL producing isolate 267/99 of Salmonella enterica serovar Mbandaka isolated in 1999 in Poland were characterised. Tested strain produced CTX-M-3 and TEM-1 beta-lactamases, encoded by genes localised on the about 80 kb self-transferable plasmid, harbouring the 2 kb class 1 integron carrying aadA2 gene.