Social dominance and wheel running in females of Djungarian hamster (Phodopus sungorus)

Wheel running is a behaviour that has a rewarding effect on animals. There are not numerous papers investigating potential relationships between social rank and wheel running in mammals kept in groups, and the majority of published researches were conducted on male house mice (Mus musculus). The aim of our study was to investigate if social dominance and wheel running are related in female Djungarian hamsters (Phodopus sungorus). Hamsters were kept in groups, and social position of every animal was expressed as dominance index calculated on the basis of agonistic behaviour. We found significant positive correlation between dominance index and wheel running (rs = 0.809, n = 18, P < 0.0001), thus dominants used wheel more often than subordinates. Our results are consistent with those published on male mice. In conclusion, we claim that in majority of mammals (independent of their sex) kept in groups with restricted possibility of wheel running, dominants use wheel more often (or in optimal time) than subordinates, what is consistent with the fact that dominants have priority of access to resources

Behaviour of domestic rabbits during 2 weeks after weaning

Thirty three rabbits from five litters that were weaned at the age of 5 weeks were observed. The animals were kept in pens that were enriched with an elevation made of bricks. In total, 150&thinsp;h of observations made at feeding time (07:30–10:00 and 18:00–20:30&thinsp;LT, local time) were analysed. A number of affiliative, exploratory, comfort, eating, resting and locomotor behaviours were observed. Agonistic behaviour was not observed. Rabbits showed companion and location preferences: 56&thinsp;% of animals had a preferred companion, and 84&thinsp;% preferred a particular place in the pen. Significant effects of group size and time of day on the frequency of some forms of behaviour were found, e.g. rabbits performed comfort behaviours more often in the morning. Sex did not influence the rabbits' behaviour. Correlations were also found between different forms of behaviour, e.g. animals that performed more exploratory behaviours also showed more locomotor behaviours and affiliative interactions.</p

Time series classification with ensembles of elastic distance measures

Several alternative distance measures for comparing time series have recently been proposed and evaluated on time series classification (TSC) problems. These include variants of dynamic time warping (DTW), such as weighted and derivative DTW, and edit distance-based measures, including longest common subsequence, edit distance with real penalty, time warp with edit, and move–split–merge. These measures have the common characteristic that they operate in the time domain and compensate for potential localised misalignment through some elastic adjustment. Our aim is to experimentally test two hypotheses related to these distance measures. Firstly, we test whether there is any significant difference in accuracy for TSC problems between nearest neighbour classifiers using these distance measures. Secondly, we test whether combining these elastic distance measures through simple ensemble schemes gives significantly better accuracy. We test these hypotheses by carrying out one of the largest experimental studies ever conducted into time series classification. Our first key finding is that there is no significant difference between the elastic distance measures in terms of classification accuracy on our data sets. Our second finding, and the major contribution of this work, is to define an ensemble classifier that significantly outperforms the individual classifiers. We also demonstrate that the ensemble is more accurate than approaches not based in the time domain. Nearly all TSC papers in the data mining literature cite DTW (with warping window set through cross validation) as the benchmark for comparison. We believe that our ensemble is the first ever classifier to significantly outperform DTW and as such raises the bar for future work in this area

Evaluation of the suitability of the Waterloo Membrane Sampler for sample preconcentration before compound-specific isotope analysis

Compound-specific isotope analysis (CSIA) has been used extensively for fingerprinting applications and for the evaluation of the degradation processes in organic contaminant studies in groundwater. Recently, the potential applications of CSIA in unsaturated and vapour intrusion studies have been explored. A key challenge in these studies is the development of analytical protocols for CSIA that can handle the very low concentrations of organic compounds typically found in the unsaturated zone and indoor samples. The objective of this research was to evaluate the applicability of the Waterloo Membrane Sampler (WMS) for CSIA, with intended applications in the unsaturated zone and in vapour intrusion studies. Tests were performed to evaluate isotope effects associated with sorption and desorption of the analytes under active sampling and passive sampling conditions. A standard gas mixture containing three model analytes, hexane, benzene and trichloroethene, was used in the experiments. Tests were designed to evaluate the isotope effect as a function of the time of exposure (3 to 192 hours), amount of analytes sorbed, and exposure temperature (25°C and 12°C). The results obtained in all studies showed very good reproducibility with standard deviations within the accepted analytical error of ±0.5 ‰. The data also showed that the δ13C values of the analytes collected by passive sampling were more depleted than the values obtained by active sampling. However, the degree of fractionation, ranging from 0.4 to 1.4 ‰, was practically constant and independent of the sampling time, mass adsorbed and temperature in the ranges of variables studied. The lowest concentrations that could be detected were 0.65mg/m3for hexane, 0.88mg/m3benzene and 4.38mg/m3for TCE. The method developed was applied in a field study where the results obtained for benzene and toluene collected in the unsaturated zone showed the expected values compared to carbon isotope data obtained for benzene and toluene at the water table. Results obtained in this study confirmed good data reproducibility. This indicates that CSIA coupled with WMS has the potential to become a valuable tool in unsaturated zone studies and in the environmental forensics field

First record of Giardia assemblage D infection in farmed raccoon dogs (Nyctereutes procyonoides)

The presence of Giardia genotypes was investigated in 18 raccoon dogs ( Nyctereutes procyonoides ) and 80 red foxes ( Vulpes vulpes ) on one farm. To demonstrate Giardia cysts, fresh and trichrome stained smears were microscopically screened. Two molecular markers were used for Giardia genotyping: a fragment of the beta-giardin gene and a fragment of the glutamate dehydrogenase gene. All faecal samples obtained from red foxes were negative. Giardia cysts were identified only in 2 of the 18 raccoon dogs. The result of genotyping and phylogenetic analysis showed that the G. duodenalis from both raccoon dogs belonged to the D assemblage. This finding of a new animal reservoir of G. duodenalis canids-specific genotypes is important in order to eliminate the risk of infecting other animals bred for fur. Further molecular analyses of Giardia isolates in raccoon dogs are required. The present study represents the first contribution to knowledge of G. duodenalis genotypes in raccoon dogs

The great time series classification bake off: a review and experimental evaluation of recent algorithmic advances

In the last five years there have been a large number of new time series classification algorithms proposed in the literature. These algorithms have been evaluated on subsets of the 47 data sets in the University of California, Riverside time series classification archive. The archive has recently been expanded to 85 data sets, over half of which have been donated by researchers at the University of East Anglia. Aspects of previous evaluations have made comparisons between algorithms difficult. For example, several different programming languages have been used, experiments involved a single train/test split and some used normalised data whilst others did not. The relaunch of the archive provides a timely opportunity to thoroughly evaluate algorithms on a larger number of datasets. We have implemented 18 recently proposed algorithms in a common Java framework and compared them against two standard benchmark classifiers (and each other) by performing 100 resampling experiments on each of the 85 datasets. We use these results to test several hypotheses relating to whether the algorithms are significantly more accurate than the benchmarks and each other. Our results indicate that only 9 of these algorithms are significantly more accurate than both benchmarks and that one classifier, the Collective of Transformation Ensembles, is significantly more accurate than all of the others. All of our experiments and results are reproducible: we release all of our code, results and experimental details and we hope these experiments form the basis for more rigorous testing of new algorithms in the future

Beyond representing orthology relations by trees

Reconstructing the evolutionary past of a family of genes is an important aspect of many genomic studies. To help with this, simple relations on a set of sequences called orthology relations may be employed. In addition to being interesting from a practical point of view they are also attractive from a theoretical perspective in that e.\,g.\,a characterization is known for when such a relation is representable by a certain type of phylogenetic tree. For an orthology relation inferred from real biological data it is however generally too much to hope for that it satisfies that characterization. Rather than trying to correct the data in some way or another which has its own drawbacks, as an alternative, we propose to represent an orthology relation $\delta$ in terms of a structure more general than a phylogenetic tree called a phylogenetic network. To compute such a network in the form of a level-1 representation for $\delta$, we formalize an orthology relation in terms of the novel concept of a symbolic 3- dissimilarity which is motivated by the biological concept of a ``cluster of orthologous groups'', or COG for short. For such maps which assign symbols rather that real values to elements, we introduce the novel {\sc Network-Popping} algorithm which has several attractive properties. In addition, we characterize an orthology relation $\delta$ on some set $X$ that has a level-1 representation in terms of eight natural properties for $\delta$ as well as in terms of level-1 representations of orthology relations on certain subsets of $X$

Study on Phylogenetic Relationships, Variability, and Correlated Mutations in M2 Proteins of Influenza Virus A

M2 channel, an influenza virus transmembrane protein, serves as an important target for antiviral drug design. There are still discordances concerning the role of some residues involved in proton transfer as well as the mechanism of inhibition by commercial drugs. The viral M2 proteins show high conservativity; about 3/4 of the positions are occupied by one residue in over 95%. Nine M2 proteins from the H3N2 strain and possibly two proteins from H2N2 strains make a phylogenic cluster closely related to 2RLF. The variability range is limited to 4 residues/position with one exception. The 2RLF protein stands out by the presence of 2 serines at the positions 19 and 50, which are in most other M2 proteins occupied by cysteines. The study of correlated mutations shows that there are several positions with significant mutational correlation that have not been described so far as functionally important. That there are 5 more residues potentially involved in the M2 mechanism of action. The original software used in this work (Consensus Constructor, SSSSg, Corm, Talana) is freely accessible as stand-alone offline applications upon request to the authors. The other software used in this work is freely available online for noncommercial purposes at public services on bioinformatics such as ExPASy or NCBI. The study on mutational variability, evolutionary relationship, and correlated mutation presented in this paper is a potential way to explain more completely the role of significant factors in proton channel action and to clarify the inhibition mechanism by specific drugs