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Lu Ashley   2013
The branchsite model is a widely popular approach that accommodates for the lineage and the sitespecific heterogeneity of natural selection regimes among coding sequences. This model relies on prior knowledge of the (foreground) lineage(s) evolving under positive selection at some sites. Unfortunately, such prior information is not always available in ...


San Phyo Phyo   2013
This paper focuses on the hybridization technology using rough sets concepts and neural computing for decision and classification purposes. Based on the rough set properties, the lower region and boundary region are defined to partition the input signal to a consistent (predictable) part and an inconsistent (random) part. In this ...


Koh P P   2013
Gap acceptance of violating pedestrians was studied at seven stretches of signalised pedestrian crossings in Singapore. The provision of the traffic light signals provide a 'safer' crossing option to these pedestrians, as compared to uncontrolled crossings and midblock arterial roads. However, there are still people choosing to cross at the ...


Heled Joseph   2013
Bayesian phylogenetic analysis generates a set of trees which are often condensed into a single treerepresenting the whole set. Many methods exist for selecting a representative topology for a setof unrooted trees, few exist for assigning branch lengths to a fixed topology, and even fewer forsimultaneously setting the topology and ...


Moore Ryan T   2013
In typical political experiments, researchers randomize a set of households, precincts, or individuals to treatments all at once, and characteristics of all units are known at the time of randomization. However, in many other experiments, subjects "trickle in" to be randomized to treatment conditions, usually via complete randomization. To take ...


Buttenheim Alison M   2013
High rates of household participation are critical to the success of doortodoor vector control campaigns. We used the Health Belief Model to assess determinants of participation, including neighbour participation as a cue to action, in a Chagas disease vector control campaign in Peru. We evaluated clustering of participation among neighbours; ...


Massoudieh Arash   2013
A Bayesian parameter estimation approach is developed for the estimation of joint probability distribution functions for colloid and bacterial fate and transport model parameters describing breakthrough curves (BTCs) obtained through porous media column studies, and is applied to data involving different ionic strength solutions to fit models of differing complexity. ...


Xiang Shuo   2013
Bioimaging technologies allow scientists to collect large amounts of highdimensional data from multiple heterogeneous sources for many biomedical applications. In the study of Alzheimer's Disease (AD), neuroimaging data, gene/protein expression data, etc., are often analyzed together to improve predictive power. Joint learning from multiple complementary data sources is advantageous, but ...


Bogacki Rachael   2013
A preparatively accessible route to a series of conformationallylocked bicyclic morpholines has been developed. This flexible approach allows for diversification in order for a small array of leadlike scaffolds to be synthesised from readily available key building blocks.


Haller Benjamin C   2013
Abstract Divergent adaptation to different environments can promote speciation, and it is thus important to consider spatial structure in models of speciation. Earlier theoretical work, however, has been limited to particularly simple types of spatial structure (linear environmental gradients and spatially discrete metapopulations), leaving unaddressed the effects of more realistic ...


Kergosien Yannick L   2013
We describe reversible adaptive trees, a class of stochastic algorithms modified from the formerly described adaptive trees. They evolve in time a finite subset of an ambient Euclidean space of any dimension, starting from a seed point and, accreting points to the evolving set, they grow branches towards a target ...


Mader Malenka   2013
Statistical inference of signals is key to understand fundamental processes in the neurosciences. It is essential to distinguish true from random effects. To this end, statistical concepts of confidence intervals, significance levels and hypothesis tests are employed. Bootstrapbased approaches complement the analytical approaches, replacing the latter whenever these are not ...


Zu Jian   2013
In this paper, with the methods of adaptive dynamics and critical function analysis, we investigate the evolutionary branching phenomenon of predator species. We assume that both the prey and predators are densitydependent and the predator's attack ability can adaptively evolve, but this has a cost in terms of its death ...


Winkler Marco   2013
Conventionally, pairwise relationships between nodes are considered to be the fundamental building blocks of complex networks. However, over the last decade, the overabundance of certain subnetwork patterns, i.e., the socalled motifs, has attracted much attention. It has been hypothesized that these motifs, instead of links, serve as the building blocks ...


Johnston Barbara M   2013
A method for accurately finding cardiac bidomain conductivity parameters is a crucial part of efforts to study and understand the electrical functioning of the heart. The bidomain model considers current flowing along (longitudinal) and across (transverse) sheets of cardiac fibres, as well as between these sheets (normal), in both the ...


Zhang Xinfeng   2013
Block transform coded images usually suffer from annoying artifacts at low bit rates, caused by the coarse quantization of transform coefficients. In this paper, we propose a new method to reduce compression artifacts by overlappedblock transform coefficient estimation from nonlocal blocks. In the proposed method, the DCT coefficients of each ...


Miekley Bettina   2013
This study analyzed the methodology and applicability of multivariate cumulative sum (MCUSUM) charts for early mastitis and lameness detection. Data used were recorded on the Karkendamm dairy research farm, Germany, between August 2008 and December 2010. Data of 328 and 315 cows in their first 200 d in milk were ...


Barthelemy Marc   2013
Interventions of central, topdown planning are serious limitations to the possibility of modelling the dynamics of cities. An example is the city of Paris (France), which during the 19th century experienced large modifications supervised by a central authority, the 'Haussmann period'. In this article, we report an empirical analysis of ...


Miekley Bettina   2013
This investigation analysed the applicability of principal component analysis (PCA), a latent variable method, for the early detection of mastitis and lameness. Data used were recorded on the Karkendamm dairy research farm between August 2008 and December 2010. For mastitis and lameness detection, data of 338 and 315 cows in ...


Chai BianFang   2013
Latent community discovery that combines links and contents of a textassociated network has drawn more attention with the advance of social media. Most of the previous studies aim at detecting densely connected communities and are not able to identify general structures, e.g., bipartite structure. Several variants based on the stochastic ...


Pardo Edison   2013
The construction of an atlas of the human brain connectome, in particular, the cartography of fiber bundles of superficial white matter (SWM) is a complex and unachieved task. Its description is essential for the understanding of human brain function and the study of several pathologies. In this work we applied ...


DuxSantoy Lydia   2013
The cardiac conduction system is divided in different sections that play an important role in the cardiac depolarization sequence and define the morphology of the electrocardiogram. In this study we have built several configurations for each section based on anatomical descriptions. The effect of the morphology of the bundle branches, ...


A programmable analog subthreshold biomimetic model for bidirectional communication with the brain.
Ghaderi Viviane S   2013
In this paper, we present a hardware implementation of a second order Laguerre Expansion of Volterra Kernel (LEV) model with four basis functions. The model is versatile enough to be applied at different abstraction levels (synapse, neuron, or network of neurons) and is implemented with analog building blocks in a ...


Szilagyi Laszlo   2013
In this paper we propose an efficient reformulation of a Markov clustering algorithm, suitable for fast and accurate grouping of protein sequences, based on pairwise similarity information. The proposed modification consists of optimal reordering of rows and columns in the similarity matrix after every iteration, transforming it into a matrix ...


Demir Ali   2013
We consider the problem of clustering neural fiber pathways, produced from diffusion MRI data via tractography, into different bundles. Existing clustering methods often suffer from the burden of computing pairwise fiber (dis)similarities, which escalates quadratically as the number of fiber pathways increases. To address this challenge, we adopt the scenario ...


Crevecoeur Guillaume   2013
This paper proposes a modification of the subspace correlation cost function and the Recursively Applied and Projected Multiple Signal Classification (RAPMUSIC) method for electroencephalography (EEG) source analysis in epilepsy. This enables to reconstruct neural source locations and orientations that are less degraded due to the uncertain knowledge of the head ...


Weiskopf Nicole G   2013
We demonstrate the importance of explicit definitions of electronic health record (EHR) data completeness and how different conceptualizations of completeness may impact findings from EHRderived datasets. This study has important repercussions for researchers and clinicians engaged in the secondary use of EHR data. We describe four prototypical definitions of EHR ...


Laattoe Tariq   2013
Smallscale hyporheic zone (HZ) models often use a spatial periodic boundary (SPB) pair to simulate an infinite repetition of bedforms. SPB's are common features of commercially available multiphysics modeling packages. MODFLOW's lack of this boundary type has precluded it from being effectively utilized in this area of HZ research. We ...


Bentley Lisa Patrick   2013
Several theories predict wholetree function on the basis of allometric scaling relationships assumed to emerge from traits of branching networks. To test this key assumption, and more generally, to explore patterns of external architecture within and across trees, we measure branch traits (radii/lengths) and calculate scaling exponents from five functionally ...


Li Xinye   2013
Consider the revenuemaximizing problem in which a single seller wants to sell k different items to a single buyer, who has independently distributed values for the items with additive valuation. The $$k=1$$ case was completely resolved by Myerson's classical work in 1981, whereas for larger k the problem has been ...


Hajdu Eduardo   2013
This is the first phylogenetic analysis integrating both morphological and molecular data of the sponge suborder Mycalina (Poecilosclerida), which was erected in 1994. A cladistic analysis of morphology supported the monophyly of Cladorhizidae (including Euchelipluma), Guitarridae (excluding Euchelipluma), Isodictyidae, Latrunculiidae, and Podospongiidae but rejected monophyly for Desmacellidae, Esperiopsidae, Hamacanthidae, and ...


McCormack Lacey A   2013
This study was done in preparation for the launch of the National Children's Study (NCS) main study. The goal of this study was to examine the feasibility (completion rates and completeness of data), acceptability, staff time and costeffectiveness of three methods of data collection for the postnatal 3 and 9month ...


Saxena Ankur   2013
In this paper, we present a transform scheme where a secondary transform is applied after the conventional DCT for intra as well as inter prediction residues. Our approach is applicable to any blockbased video codec that employs transforms along the horizontal and vertical direction separably. The secondary transform is applied ...


Noland Robert B   2013
Pedestrian and motor vehicle casualties are analyzed for the State of New Jersey with the objective of determining how the income of an area may be associated with casualties. We develop a maximumlikelihood negative binomial model to examine how various spatially defined variables, including road, income, and vehicle ownership, may ...


Chen ZhiZhong   2013
MOTIVATION: Haplotypes play a crucial role in genetic analysis and have many applications such as gene disease diagnoses, association studies, ancestry inference, etc. The development of DNA sequencing technologies makes it possible to obtain haplotypes from a set of aligned reads originated from both copies of a chromosome of a ...


Davies T Jonathan TJ Department of Biology, McGill University, Montreal, Quebec,   2013
The treeoflife represents the diversity of living organisms. Species extinction and the concomitant loss of branches from the treeoflife is therefore a major conservation concern. There is increasing evidence indicating that extinction is phylogenetically nonrandom, such that if one species is vulnerable to extinction so too are its close relatives. ...


Forman Christopher J   2013
Decorative domains force amyloid fibers to adopt spiral ribbon morphologies, as opposed to the more common twisted ribbon. We model the effect of decorating domains as a perturbation to the relative orientation of β strands in a bilayered extended βsheet. The model consists of minimal energy assemblies of rigid building ...


AgirrezabalTelleria I   2013
Among the furanbased compounds, furfural (FUR) shows interesting properties as buildingblock or industrial solvent. It is produced from pentosanrich biomass via xylose cyclodehydration. The current FUR production makes use of homogeneous catalysts and excessive amounts of steam. The development of greener furfural production and separation techniques implies the use of ...


Marrink Siewert J   2013
The Martini model, a coarsegrained force field for biomolecular simulations, has found a broad range of applications since its release a decade ago. Based on a building block principle, the model combines speed and versatility while maintaining chemical specificity. Here we review the current state of the model. We describe ...


Mattfeldt T   2013
This paper deals with the estimation of the intensity of a planar point process on the basis of a single point pattern, observed in a rectangular window. If the model assumptions of stationarity and isotropy hold, the method of block bootstrapping can be used to estimate the intensity of the ...


Kamisli Fatih   2013
In recent video coding standards, intra prediction of a block of pixels is performed by copying neighbor pixels of the block along an angular direction inside the block. Each block pixel is predicted from only one or few directionally aligned neighbor pixels of the block. Although this is a computationally ...


Oelz Dietmar   2013
A mathematical model in one dimension for a nonsarcomeric actomyosin bundle featuring antiparallel flows of antiparallel Factin is introduced. The model is able to relate these flows to the effect of crosslinking and bundling proteins, to the forces due to myosinII filaments and to external forces at the extreme tips ...


Stadler T   2013
Phylogenetic trees of only extant species contain information about the underlying speciation and extinction pattern. In this review, I provide an overview over the different methodologies that recover the speciation and extinction dynamics from phylogenetic trees. Broadly, the methods can be divided into two classes: (i) methods using the phylogenetic ...


Scotti Luciana   2013
The mosquito Aedes aegypti (Diptera, Culicidae) is the vector of yellow and dengue fever. In this study, chemometric tools, such as, Principal Component Analysis (PCA), Consensus PCA (CPCA), and Partial Least Squares Regression (PLS), were applied to a set of fifty five active compounds against Ae. aegypti larvae, which includes ...


Pang Herbert   2013
Abstract Highthroughput expression profiling allows simultaneous measure of tens of thousands of genes at once. These data have motivated the development of reliable biomarkers for disease subtypes identification and diagnosis. Many methods have been developed in the literature for analyzing these data, such as diagonal discriminant analysis, support vector machines, ...


HernandezAguilar R Adriana   2013
Data on chimpanzee (Pan troglodytes) nesting patterns were collected in Issa, Ugalla, western Tanzania. Ugalla is one of the driest, most open, and seasonal habitats inhabited by chimpanzees. We investigated the physical characteristics of nests and trees used for nesting to understand environmental influences on nest building and identify the ...


Ferreira Alexandre F P   2013
We study the adsorption equilibrium isotherms and differential heats of adsorption of hexane isomers on the zeolitic imidazolate framework ZIF8. The studies are carried out at 373 K using a manometric setup combined with a microcalorimeter. We see that the Langmuir model describes well the isotherms for all four isomers ...


Stenroos Matti   2013
The conductivity profile of the head has a major effect on EEG signals, but unfortunately the conductivity for the most important compartment, skull, is only poorly known. In dipole modelling studies, errors in modelled skull conductivity have been considered to have a detrimental effect on EEG source estimation. However, as ...


de Queiroz Kevin   2013
Adopting the perspective of graph theory, Martin et al. (2010) described two kinds of phylogenetic trees, which they termed nodebased and stem or branchbased, that differ with respect to the biological interpretations of their component nodes and branches. After establishing equivalency between the two different kinds of trees in terms ...


Kitsche Andreas   2013
Profile hidden Markov models (HMMs) were used to predict the configuration of secondary alcohols and αmethyl branches of modular polyketides. Based on the configurations of two chiral centers in these polyketides, 78 ketoreductases were classified into four different types of polyketide producers. The identification of positions that discriminate between these ...


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