A Fast Counting Method for 6-motifs with Low Connectivity

A $k$-motif (or graphlet) is a subgraph on $k$ nodes in a graph or network. Counting of motifs in complex networks has been a well-studied problem in network analysis of various real-word graphs arising from the study of social networks and bioinformatics. In particular, the triangle counting problem has received much attention due to its significance in understanding the behavior of social networks. Similarly, subgraphs with more than 3 nodes have received much attention recently. While there have been successful methods developed on this problem, most of the existing algorithms are not scalable to large networks with millions of nodes and edges. The main contribution of this paper is a preliminary study that genaralizes the exact counting algorithm provided by Pinar, Seshadhri and Vishal to a collection of 6-motifs. This method uses the counts of motifs with smaller size to obtain the counts of 6-motifs with low connecivity, that is, containing a cut-vertex or a cut-edge. Therefore, it circumvents the combinatorial explosion that naturally arises when counting subgraphs in large networks

Colored Motifs Reveal Computational Building Blocks in the C. elegans Brain

Background: Complex networks can often be decomposed into less complex sub-networks whose structures can give hints about the functional organization of the network as a whole. However, these structural motifs can only tell one part of the functional story because in this analysis each node and edge is treated on an equal footing. In real networks, two motifs that are topologically identical but whose nodes perform very different functions will play very different roles in the network. Methodology/Principal Findings: Here, we combine structural information derived from the topology of the neuronal network of the nematode C. elegans with information about the biological function of these nodes, thus coloring nodes by function. We discover that particular colorations of motifs are significantly more abundant in the worm brain than expected by chance, and have particular computational functions that emphasize the feed-forward structure of information processing in the network, while evading feedback loops. Interneurons are strongly over-represented among the common motifs, supporting the notion that these motifs process and transduce the information from the sensor neurons towards the muscles. Some of the most common motifs identified in the search for significant colored motifs play a crucial role in the system of neurons controlling the worm's locomotion. Conclusions/Significance: The analysis of complex networks in terms of colored motifs combines two independent data sets to generate insight about these networks that cannot be obtained with either data set alone. The method is general and should allow a decomposition of any complex networks into its functional (rather than topological) motifs as long as both wiring and functional information is available

From ductile to brittle: evolution and localization of deformation below a crustal detachment (Tinos, Cyclades, Greece)

International audienceThe Cycladic Oligo-Miocene detachment of Tinos island is an example of a flat-lying extensional shear zone evolving into a low-angle brittle detachment. A clear continuum of extensional strain from ductile to brittle regime is observed in the footwall. The main brittle structures marking extension are shallow- and steeply dipping normal faults associated with subvertical extensional joints and veins. The earliest brittle structures are lowangle normal faults which commonly superimpose on, and reactivate, earlier (precursory) ductile shear bands, but newly formed low-angle normal faults could also be observed. Low-angle normal faults are cut by late steeply dipping normal faults. The inversion of fault slip data collected within, and away from, the main detachment zone shows that the direction of the minimum stress axis is strictly parallel to the NE-SW stretching lineation and that the maximum principal stress axis remained subvertical during the whole brittle evolution, in agreement with the subvertical attitude of veins throughout the island. The high angle of s1 to the main detachment suggests that the detachment was weak. This observation, together with the presence of a thick layer of cataclasites below the main detachment and the kinematic continuum from ductile to brittle, leads us to propose a kinematic model for the formation of the detachment. Boudinage at the crustal scale induces formation, near the brittle-ductile transition, of ductile shear zones near the edges of boudins. Shear zones are progressively exhumed and replaced by shallowdipping cataclastic shear zones when they reached the brittle field. Most of the displacement is achieved through cataclastic flow in the upper crust and only the last increment of strain gives rise to the formation of brittle faults. The formation of the low-angle brittle detachment is thus ''prepared'' by the ductile shear zone and the cataclasites and favored by the circulation of surface-derived fluids in the shear zone

Effective problem solving using SAT solvers

In this article we demonstrate how to solve a variety of problems and puzzles using the built-in SAT solver of the computer algebra system Maple. Once the problems have been encoded into Boolean logic, solutions can be found (or shown to not exist) automatically, without the need to implement any search algorithm. In particular, we describe how to solve the $n$-queens problem, how to generate and solve Sudoku puzzles, how to solve logic puzzles like the Einstein riddle, how to solve the 15-puzzle, how to solve the maximum clique problem, and finding Graeco-Latin squares.Comment: To appear in Proceedings of the Maple Conference 201

A proposal for a coordinated effort for the determination of brainwide neuroanatomical connectivity in model organisms at a mesoscopic scale

In this era of complete genomes, our knowledge of neuroanatomical circuitry remains surprisingly sparse. Such knowledge is however critical both for basic and clinical research into brain function. Here we advocate for a concerted effort to fill this gap, through systematic, experimental mapping of neural circuits at a mesoscopic scale of resolution suitable for comprehensive, brain-wide coverage, using injections of tracers or viral vectors. We detail the scientific and medical rationale and briefly review existing knowledge and experimental techniques. We define a set of desiderata, including brain-wide coverage; validated and extensible experimental techniques suitable for standardization and automation; centralized, open access data repository; compatibility with existing resources, and tractability with current informatics technology. We discuss a hypothetical but tractable plan for mouse, additional efforts for the macaque, and technique development for human. We estimate that the mouse connectivity project could be completed within five years with a comparatively modest budget.Comment: 41 page

Spatially-resolved optical and structural properties of semi-polar [Formula: see text] Al x Ga1-x N with x up to 0.56

Pushing the emission wavelength of efficient ultraviolet (UV) emitters further into the deep-UV requires material with high crystal quality, while also reducing the detrimental effects of built-in electric fields. Crack-free semi-polar [Formula: see text] Al x Ga1-x N epilayers with AlN contents up to x = 0.56 and high crystal quality were achieved using an overgrowth method employing GaN microrods on m-sapphire. Two dominant emission peaks were identified using cathodoluminescence hyperspectral imaging. The longer wavelength peak originates near and around chevron-shaped features, whose density is greatly increased for higher contents. The emission from the majority of the surface is dominated by the shorter wavelength peak, influenced by the presence of basal-plane stacking faults (BSFs). Due to the overgrowth technique BSFs are bunched up in parallel stripes where the lower wavelength peak is broadened and hence appears slightly redshifted compared with the higher quality regions in-between. Additionally, the density of threading dislocations in these region is one order of magnitude lower compared with areas affected by BSFs as ascertained by electron channelling contrast imaging. Overall, the luminescence properties of semi-polar AlGaN epilayers are strongly influenced by the overgrowth method, which shows that reducing the density of extended defects improves the optical performance of high AlN content AlGaN structures

Hydrothermal dolomitization of basinal deposits controlled by a synsedimentary fault system in Triassic extensional setting, Hungary

Dolomitization of relatively thick carbonate successions occurs via an effective fluid circulation mechanism, since the replacement process requires a large amount of Mg-rich fluid interacting with the CaCO3 precursor. In the western end of the Neotethys, fault-controlled extensional basins developed during the Late Triassic spreading stage. In the Buda Hills and Danube-East blocks, distinct parts of silica and organic matter-rich slope and basinal deposits are dolomitized. Petrographic, geochemical, and fluid inclusion data distinguished two dolomite types: (1) finely to medium crystalline and (2) medium to coarsely crystalline. They commonly co-occur and show a gradual transition. Both exhibit breccia fabric under microscope. Dolomite texture reveals that the breccia fabric is not inherited from the precursor carbonates but was formed during the dolomitization process and under the influence of repeated seismic shocks. Dolomitization within the slope and basinal succession as well as within the breccia zones of the underlying basement block is interpreted as being related to fluid originated from the detachment zone and channelled along synsedimentary normal faults. The proposed conceptual model of dolomitization suggests that pervasive dolomitization occurred not only within and near the fault zones. Permeable beds have channelled the fluid towards the basin centre where the fluid was capable of partial dolomitization. The fluid inclusion data, compared with vitrinite reflectance and maturation data of organic matter, suggest that the ascending fluid was likely hydrothermal which cooled down via mixing with marine-derived pore fluid. Thermal gradient is considered as a potential driving force for fluid flow

Construction and Analysis of an Integrated Regulatory Network Derived from High-Throughput Sequencing Data

We present a network framework for analyzing multi-level regulation in higher eukaryotes based on systematic integration of various high-throughput datasets. The network, namely the integrated regulatory network, consists of three major types of regulation: TF→gene, TF→miRNA and miRNA→gene. We identified the target genes and target miRNAs for a set of TFs based on the ChIP-Seq binding profiles, the predicted targets of miRNAs using annotated 3′UTR sequences and conservation information. Making use of the system-wide RNA-Seq profiles, we classified transcription factors into positive and negative regulators and assigned a sign for each regulatory interaction. Other types of edges such as protein-protein interactions and potential intra-regulations between miRNAs based on the embedding of miRNAs in their host genes were further incorporated. We examined the topological structures of the network, including its hierarchical organization and motif enrichment. We found that transcription factors downstream of the hierarchy distinguish themselves by expressing more uniformly at various tissues, have more interacting partners, and are more likely to be essential. We found an over-representation of notable network motifs, including a FFL in which a miRNA cost-effectively shuts down a transcription factor and its target. We used data of C. elegans from the modENCODE project as a primary model to illustrate our framework, but further verified the results using other two data sets. As more and more genome-wide ChIP-Seq and RNA-Seq data becomes available in the near future, our methods of data integration have various potential applications

Inter-observer variability in contouring the penile bulb on CT images for prostate cancer treatment planning

Several investigations have recently suggested the existence of a correlation between the dose received by the penile bulb (PB) and the risk of erectile dysfunction (ED) after radical radiotherapy for clinically localized prostate carcinoma