303 research outputs found
On polymorphic logical gates in sub-excitable chemical medium
In a sub-excitable light-sensitive Belousov-Zhabotinsky chemical medium an
asymmetric disturbance causes the formation of localized traveling
wave-fragments. Under the right conditions these wave-fragment can conserve
their shape and velocity vectors for extended time periods. The size and life
span of a fragment depend on the illumination level of the medium. When two or
more wave-fragments collide they annihilate or merge into a new wave-fragment.
In computer simulations based on the Oregonator model we demonstrate that the
outcomes of inter-fragment collisions can be controlled by varying the
illumination level applied to the medium. We interpret these wave-fragments as
values of Boolean variables and design collision-based polymorphic logical
gates. The gate implements operation XNOR for low illumination, and it acts as
NOR gate for high illumination. As a NOR gate is a universal gate then we are
able to demonstrate that a simulated light sensitive BZ medium exhibits
computational universality
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
Beyond Gross-Pitaevskii equation for 1D gas: Quasiparticles and solitons
Describing properties of a strongly interacting quantum many-body system
poses a serious challenge both for theory and experiment. In this work, we
study excitations of one-dimensional repulsive Bose gas for arbitrary
interaction strength using a hydrodynamic approach. We use linearization to
study particle (type-I) excitations and numerical minimization to study hole
(type-II) excitations. We observe a good agreement between our approach and
exact solutions of the Lieb-Liniger model for the particle modes and
discrepancies for the hole modes. Therefore, the hydrodynamical equations find
to be useful for long-wave structures like phonons and of a limited range of
applicability for short-wave ones like narrow solitons. We discuss potential
further applications of the method.Comment: 27 pages, 11 figures. Submission to SciPos
Maximum likelihood models and algorithms for gene tree evolution with duplications and losses
<p>Abstract</p> <p>Background</p> <p>The abundance of new genomic data provides the opportunity to map the location of gene duplication and loss events on a species phylogeny. The first methods for mapping gene duplications and losses were based on a parsimony criterion, finding the mapping that minimizes the number of duplication and loss events. Probabilistic modeling of gene duplication and loss is relatively new and has largely focused on birth-death processes.</p> <p>Results</p> <p>We introduce a new maximum likelihood model that estimates the speciation and gene duplication and loss events in a gene tree within a species tree with branch lengths. We also provide an, in practice, efficient algorithm that computes optimal evolutionary scenarios for this model. We implemented the algorithm in the program DrML and verified its performance with empirical and simulated data.</p> <p>Conclusions</p> <p>In test data sets, DrML finds optimal gene duplication and loss scenarios within minutes, even when the gene trees contain sequences from several hundred species. In many cases, these optimal scenarios differ from the lca-mapping that results from a parsimony gene tree reconciliation. Thus, DrML provides a new, practical statistical framework on which to study gene duplication.</p
Preliminary studies of sediments from the Dobczyce drinking water reservoir
The analysis of river and lake sediments indicates that the physical, chemical, biochemical and geochemical
processes that influence the fate of toxic compounds and elements in sediments are numerous and complex
(for example: sorption - desorption, oxidation - reduction, ion-exchange, biological activity). Due to the
above-mentioned general statement, only a long term and complex research programme can lead to satisfactory
answers to the questions relating to possible changes of water and environmental quality in the future.
The aim of our study consisted in physical and chemical characterisation of sediments in in-depth profiles
taken from the Dobczyce reservoir in southern Poland that is a main source of drinking water for the city
of Kraków. Due to morphological reasons, 7 layers of sediment samples were distinguished from the ground
level to about 90 cm below (total thickness of the sediments in the sampling site). Analysis of grain size distribution
and application of x-ray diffraction method, enabled mineralogical description of sediments.
The use of proton-induced x-ray emission (PIXE) and atomic absorption spectrometry (AAS) revealed
elemental composition of the samples (Al, P, K, Ca, Sc, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, Zn). Concentrations
of natural 40K and artificial 137Cs radionuclides were determined by the use of gamma spectrometry.
The following facts were established: 1) the oldest (deepest) and newest, recently deposited layers of
sediments are similar in their physical and chemical properties. It means that the inflow of contaminants
and biogenic compounds to the reservoir has changed little since it was constructed and filled with water;
2) the severe flood in 1997 changed significantly sediment composition and, in fact, led to purification of
sediments in the Dobczyce reservoir
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
Range‑wide pattern of genetic variation in Colobanthus quitensis
There is only one species representing Magnoliopsida which is considered as native to the Antarctic, i.e., Antarctic pearlwort
(Colobanthus quitensis). Although it was intensively studied toward the morphophysiological adaptation to extreme environmental
conditions of that area, there is still a lack of sufficient data on its genetic variability. Nine C. quitensis populations
from Chile and the Maritime Antarctic were sampled to estimate the pattern of genetic variation in relation to the geographic
distribution of analyzed populations and postglacial history of the species. The retrotransposon-based DNA marker system
used in our studies appeared to be effective in revealing genetic polymorphism between individuals and genetic differentiation
among populations. Although the level of polymorphism was low (9.57%), the Analysis of Molecular Variance showed
that overall population differentiation was high (FST = 0.6241) and revealed significant differentiation between the Northern
and Southern Group of populations as well as the population from Conguillio Park. The observed genetic subdivision of
C. quitensis populations was confirmed by Bayesian clustering and results of Principal Coordinates Analysis. The Southern
Group of populations was characterized by generally higher genetic diversity, which was expressed by the values of
the effective number of alleles, expected heterozygosity and by the distribution of private alleles. Our results suggest that
the species may have survived the Last Glacial Maximum in refugia located both on the South American continent and in
geographically isolated islands of the Maritime Antarctic, i.e., they support the concept of the multiregional origin of C.
quitensis in Antarctica
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α-Dystrobrevin knockout mice have increased motivation for appetitive reward and altered brain cannabinoid receptor 1 expression
Abstract: α-Dystrobrevin (α-DB) is a major component of the dystrophin-associated protein complex (DAPC). Knockout (KO) of α-DB in the brain is associated with astrocytic abnormalities and loss of neuronal GABA receptor clustering. Mutations in DAPC proteins are associated with altered dopamine signaling and cognitive and psychiatric disorders, including schizophrenia. This study tested the hypothesis that motivation and associated underlying biological pathways are altered in the absence of α-DB expression. Male wildtype and α-DB KO mice were tested for measures of motivation, executive function and extinction in the rodent touchscreen apparatus. Subsequently, brain tissues were evaluated for mRNA and/or protein levels of dysbindin-1, dopamine transporter and receptor 1 and 2, mu opioid receptor 1 (mOR1) and cannabinoid receptor 1 (CB1). α-DB KO mice had significantly increased motivation for the appetitive reward, while measures of executive function and extinction were unaffected. No differences were observed between wildtype and KO animals on mRNA levels of dysbindin-1 or any of the dopamine markers. mRNA levels of mOR1were significantly decreased in the caudate-putamen and nucleus accumbens of α-DB KO compared to WT animals, but protein levels were unaltered. However, CB1 protein levels were significantly increased in the prefrontal cortex and decreased in the nucleus accumbens of α-DB KO mice. Triple-labelling immunohistochemistry confirmed that changes in CB1 were not specific to astrocytes. These results highlight a novel role for α-DB in the regulation of appetitive motivation that may have implications for other behaviours that involve the dopaminergic and endocannabinoid systems
Cold stress effects on organelle ultrastructure in polar Caryophyllaceae species
Abstract: This study investigated leaf mesophyll cells of Caryophyllaceae plants growing in polar regions -Cerastium alpinum and Silene involucrata from the Hornsund region of Spitsbergen island (Svalbard Archipelago, Arctic), and Colobanthus quitensis from the Ad− miralty Bay region on King George Island (South Shetland Islands, West Antarctic). Ultra− structural changes were analyzed in mesophyll protoplasts of plants growing in natural Arctic and Antarctic habitats and plants grown in a greenhouse, including plants exposed to short−term cold stress under semi−controlled conditions. Cell organelles of plants growing in natural polar habitats and greenhouse−grown plants were characterized by significant mor− phological plasticity. Chloroplasts of plants studied in this work formed variously shaped pro− trusions and invaginations that visibly increased the contact area between adjacent cell com− partments and reduced the distance between organelles. S. involucrata plants grown under greenhouse conditions, tested by us in this work, were characterized by highly dynamic cell nuclei with single or multiple invaginations of the nuclear membrane and the presence of channels and cisternae filled with cytoplasm and organelles. Crystalline inclusion proteins were observed in the cell nuclei of C. quitensis between nuclear membranes and in the direct proximity of heterochromatin. Our study revealed significant conformational dynamics of organelles, manifested by variations in the optical density of matrices, membranes and enve− lopes, in particular in C. quitensis, which could suggest that the analyzed Caryophyllaceae taxa are well adapted to severe climate and changing conditions in polar regions
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