QUASII: QUery-Aware Spatial Incremental Index.

With large-scale simulations of increasingly detailed models and improvement of data acquisition technologies, massive amounts of data are easily and quickly created and collected. Traditional systems require indexes to be built before analytic queries can be executed efficiently. Such an indexing step requires substantial computing resources and introduces a considerable and growing data-to-insight gap where scientists need to wait before they can perform any analysis. Moreover, scientists often only use a small fraction of the data - the parts containing interesting phenomena - and indexing it fully does not always pay off. In this paper we develop a novel incremental index for the exploration of spatial data. Our approach, QUASII, builds a data-oriented index as a side-effect of query execution. QUASII distributes the cost of indexing across all queries, while building the index structure only for the subset of data queried. It reduces data-to-insight time and curbs the cost of incremental indexing by gradually and partially sorting the data, while producing a data-oriented hierarchical structure at the same time. As our experiments show, QUASII reduces the data-to-insight time by up to a factor of 11.4x, while its performance converges to that of the state-of-the-art static indexes

The Functional Consequences of Variation in Transcription Factor Binding

One goal of human genetics is to understand how the information for precise and dynamic gene expression programs is encoded in the genome. The interactions of transcription factors (TFs) with DNA regulatory elements clearly play an important role in determining gene expression outputs, yet the regulatory logic underlying functional transcription factor binding is poorly understood. Many studies have focused on characterizing the genomic locations of TF binding, yet it is unclear to what extent TF binding at any specific locus has functional consequences with respect to gene expression output. To evaluate the context of functional TF binding we knocked down 59 TFs and chromatin modifiers in one HapMap lymphoblastoid cell line. We then identified genes whose expression was affected by the knockdowns. We intersected the gene expression data with transcription factor binding data (based on ChIP-seq and DNase-seq) within 10 kb of the transcription start sites of expressed genes. This combination of data allowed us to infer functional TF binding. On average, 14.7% of genes bound by a factor were differentially expressed following the knockdown of that factor, suggesting that most interactions between TF and chromatin do not result in measurable changes in gene expression levels of putative target genes. We found that functional TF binding is enriched in regulatory elements that harbor a large number of TF binding sites, at sites with predicted higher binding affinity, and at sites that are enriched in genomic regions annotated as active enhancers.Comment: 30 pages, 6 figures (7 supplemental figures and 6 supplemental tables available upon request to [email protected]). Submitted to PLoS Genetic

Correlating matched-filter model for analysis and optimisation of neural networks

A new formalism is described for modelling neural networks by means of which a clear physical understanding of the network behaviour can be gained. In essence, the neural net is represented by an equivalent network of matched filters which is then analysed by standard correlation techniques. The procedure is demonstrated on the synchronous Little-Hopfield network. It is shown how the ability of this network to discriminate between stored binary, bipolar codes is optimised if the stored codes are chosen to be orthogonal. However, such a choice will not often be possible and so a new neural network architecture is proposed which enables the same discrimination to be obtained for arbitrary stored codes. The most efficient convergence of the synchronous Little-Hopfield net is obtained when the neurons are connected to themselves with a weight equal to the number of stored codes. The processing gain is presented for this case. The paper goes on to show how this modelling technique can be extended to analyse the behaviour of both hard and soft neural threshold responses and a novel time-dependent threshold response is described

Proposal for a Mesoscopic Optical Berry-Phase Interferometer

We propose a novel spin-optronic device based on the interference of polaritonic waves traveling in opposite directions and gaining topological Berry phase. It is governed by the ratio of the TE-TM and Zeeman splittings, which can be used to control the output intensity. Because of the peculiar orientation of the TE-TM effective magnetic field for polaritons, there is no analogue of the Aharonov- Casher phase shift existing for electrons.Comment: 4 page

Pseudospin dynamics in multimode polaritonic Josephson junctions

We analyzed multimode Josephson junctions with exciton-polaritons (polaritonic Josephson junctions) when several coupling mechanisms of fundamental and excited states are present. The applied method is based on Keldysh-Green function formalism and takes into account polariton pseudospin. We found that mean value of circular polarization degree in intrinsic Josephson oscillations and microscopic quantum self-trapping follow an oscillator behavior whose renormalizes due to intermode interactions. The effect of an additional transfer of particles over junction barrier occurring in multimode approximation in combination with common Josephson tunneling is discussed in regime of dynamical separation of two polarizations.Comment: 12 pages, 4 figure

Actuality and perspectives of the wood industry development in western balkan countries

Wood mass represents a significant potential for the countries of the Adriatic region. Considering its geographic distribution, significant differences can be noticed. Those differences are mainly manifested regarding its quality and quantity. The aim of this paper is to emphasize the importance of territorial distribution of the wood mass from the aspect of its use in the wood industry. The result of the research procedure is to point out certain parts of the Adriatic region, where the development of the wood industry can be promoted

Variation of natural frequencies by circular saw blade rotation

In this paper the influence of circular saw blade rotation, slot shapes and number of slots on its natural frequencies and critical speeds is investigated. Firstly, the governing equation that describes the transverse vibrations of a stationary circular plate clamped at its centre is derived using Hamilton\u2019s principle and based on Kirchhoff-Love plate theory and von Karman strain theory. The results are then compared with the ones obtained using FEM method and the FEM method is then applied to the real circular saw blade model. Finally, influence of slot shapes and number of slots on natural frequencies and critical speeds is investigated

Highly efficient fe simulations by means of simplified corotational formulation

Finite Element Method (FEM) has deservedly gained the reputation of the most powerful numerical method in the field of structural analysis. It offers tools to perform various kinds of simulations in this field, ranging from static linear to nonlinear dynamic analyses. In recent years, a particular challenge is development of FE formulations that enable highly efficient simulations, aiming at real-time dynamic simulations as a final objective while keeping high simulation fidelity such as nonlinear effects. The authors of this paper propose a simplified corotational FE formulation as a possible solution to this challenge. The basic idea is to keep the linear behavior of each element in the FE assemblage, but to extract the rigid-body motion on the element level and include it in the formulation to cover geometric nonlinearities. This paper elaborates the idea and demonstrates it on static cases with three different finite element types. The objective is to check the achievable accuracy based on such a simplified geometrically nonlinear FE formulation. In the considered examples, the difference between the results obtained with the present formulation and those by rigorous formulations is less than 3% although fairly large deformations are induced