Comparative evaluation of a new effective population size estimator based on approximate Bayesian computation

We describe and evaluate a new estimator of the effective population size (N-e), a critical parameter in evolutionary and conservation biology. This new "SummStat" N-e. estimator is based upon the use of summary statistics in an approximate Bayesian computation framework to infer N-e. Simulations of a Wright-Fisher population with known N-e show that the SummStat estimator is useful across a realistic range of individuals and loci sampled, generations between samples, and N-e values. We also address the paucity of information about the relative performance of N-e estimators by comparing the SUMMStat estimator to two recently developed likelihood-based estimators and a traditional moment-based estimator. The SummStat estimator is the least biased of the four estimators compared. In 32 of 36 parameter combinations investigated rising initial allele frequencies drawn from a Dirichlet distribution, it has the lowest bias. The relative mean square error (RMSE) of the SummStat estimator was generally intermediate to the others. All of the estimators had RMSE > 1 when small samples (n = 20, five loci) were collected a generation apart. In contrast, when samples were separated by three or more generations and Ne less than or equal to 50, the SummStat and likelihood-based estimators all had greatly reduced RMSE. Under the conditions simulated, SummStat confidence intervals were more conservative than the likelihood-based estimators and more likely to include true N-e. The greatest strength of the SummStat estimator is its flexible structure. This flexibility allows it to incorporate any, potentially informative summary statistic from Population genetic data.

A family study of co-morbidity between generalized social phobia and generalized anxiety disorder in a non-clinic sample

Background: High rates of co-morbidity between Generalized Social Phobia (GSP) and Generalized Anxiety Disorder (GAD) have been documented. The reason for this is unclear. Family studies are one means of clarifying the nature of co-morbidity between two disorders. Methods: Six models of co-morbidity between GSP and GAD were investigated in a family aggregation study of 403 first-degree relatives of non-clinical probands: 37 with GSP, 22 with GAD, 15 with co-morbid GSP/GAD, and 41 controls with no history of GSP or GAD. Psychiatric data were collected for probands and relatives. Mixed methods (direct and family history interviews) were utilised. Results: Primary contrasts (against controls) found an increased rate of pure GSP in the relatives of both GSP probands and co-morbid GSP/GAD probands, and found relatives of co-morbid GSP/GAD probands to have an increased rate of both pure GAD and comorbid GSP/GAD. Secondary contrasts found (i) increased GSP in the relatives of GSP only probands compared to the relatives of GAD only probands; and (ii) increased GAD in the relatives of co-morbid GSP/GAD probands compared to the relatives of GSP only probands. Limitations: The study did not directly interview all relatives, although the reliability of family history data was assessed. The study was based on an all-female proband sample. The implications of both these limitations are discussed. Conclusions: The results were most consistent with a co-morbidity model indicating independent familial transmission of GSP and GAD. This has clinical implications for the treatment of patients with both disorders. (C) 2006 Elsevier B.V. All fights reserved.

Sparse kernel density estimator using orthogonal regression based on D-optimality experimental design

A novel sparse kernel density estimator is derived based on a regression approach, which selects a very small subset of significant kernels by means of the D-optimality experimental design criterion using an orthogonal forward selection procedure. The weights of the resulting sparse kernel model are calculated using the multiplicative nonnegative quadratic programming algorithm. The proposed method is computationally attractive, in comparison with many existing kernel density estimation algorithms. Our numerical results also show that the proposed method compares favourably with other existing methods, in terms of both test accuracy and model sparsity, for constructing kernel density estimates.

Identification of nonlinear systems using generalized kernel models

Nonlinear system identification is considered using a generalized kernel regression model. Unlike the standard kernel model, which employs a fixed common variance for all the kernel regressors, each kernel regressor in the generalized kernel model has an individually tuned diagonal covariance matrix that is determined by maximizing the correlation between the training data and the regressor using a repeated guided random search based on boosting optimization. An efficient construction algorithm based on orthogonal forward regression with leave-one-out (LOO) test statistic and local regularization (LR) is then used to select a parsimonious generalized kernel regression model from the resulting full regression matrix. The proposed modeling algorithm is fully automatic and the user is not required to specify any criterion to terminate the construction procedure. Experimental results involving two real data sets demonstrate the effectiveness of the proposed nonlinear system identification approach.

M-estimator, and D-optimality model construction using orthogonal forward regression

This correspondence introduces a new orthogonal forward regression (OFR) model identification algorithm using D-optimality for model structure selection and is based on an M-estimators of parameter estimates. M-estimator is a classical robust parameter estimation technique to tackle bad data conditions such as outliers. Computationally, The M-estimator can be derived using an iterative reweighted least squares (IRLS) algorithm. D-optimality is a model structure robustness criterion in experimental design to tackle ill-conditioning in model Structure. The orthogonal forward regression (OFR), often based on the modified Gram-Schmidt procedure, is an efficient method incorporating structure selection and parameter estimation simultaneously. The basic idea of the proposed approach is to incorporate an IRLS inner loop into the modified Gram-Schmidt procedure. In this manner, the OFR algorithm for parsimonious model structure determination is extended to bad data conditions with improved performance via the derivation of parameter M-estimators with inherent robustness to outliers. Numerical examples are included to demonstrate the effectiveness of the proposed algorithm.

Generalized matching networks and their properties

In this paper, we introduce two kinds of graphs: the generalized matching networks (GMNs) and the recursive generalized matching networks (RGMNs). The former generalize the hypercube-like networks (HLNs), while the latter include the generalized cubes and the star graphs. We prove that a GMN on a family of k-connected building graphs is -connected. We then prove that a GMN on a family of Hamiltonian-connected building graphs having at least three vertices each is Hamiltonian-connected. Our conclusions generalize some previously known results.

Minimum neighborhood in a generalized cube

Generalized cubes are a subclass of hypercube-like networks, which include some hypercube variants as special cases. Let theta(G)(k) denote the minimum number of nodes adjacent to a set of k vertices of a graph G. In this paper, we prove theta(G)(k) >= -1/2k(2) + (2n - 3/2)k - (n(2) - 2) for each n-dimensional generalized cube and each integer k satisfying n + 2 <= k <= 2n. Our result is an extension of a result presented by Fan and Lin [J. Fan, X. Lin, The t/k-diagnosability of the BC graphs, IEEE Trans. Comput. 54 (2) (2005) 176-184]. (c) 2005 Elsevier B.V. All rights reserved.

Generalized honeycomb torus is Hamiltonian

Generalized honeycomb torus is a candidate for interconnection network architectures, which includes honeycomb torus, honeycomb rectangular torus, and honeycomb parallelogramic torus as special cases. Existence of Hamiltonian cycle is a basic requirement for interconnection networks since it helps map a "token ring" parallel algorithm onto the associated network in an efficient way. Cho and Hsu [Inform. Process. Lett. 86 (4) (2003) 185-190] speculated that every generalized honeycomb torus is Hamiltonian. In this paper, we have proved this conjecture. (C) 2004 Elsevier B.V. All rights reserved.

A lower bound on the size of k-neighborhood in generalized cubes

The determination of the minimum size of a k-neighborhood (i.e., a neighborhood of a set of k nodes) in a given graph is essential in the analysis of diagnosability and fault tolerance of multicomputer systems. The generalized cubes include the hypercube and most hypercube variants as special cases. In this paper, we present a lower bound on the size of a k-neighborhood in n-dimensional generalized cubes, where 2n + 1 <= k <= 3n - 2. This lower bound is tight in that it is met by the n-dimensional hypercube. Our result is an extension of two previously known results. (c) 2005 Elsevier Inc. All rights reserved.

A novel radix-3/9 algorithm for type-III generalized discrete Hartley transform

A novel radix-3/9 algorithm for type-III generalized discrete Hartley transform (GDHT) is proposed, which applies to length-3(P) sequences. This algorithm is especially efficient in the case that multiplication is much more time-consuming than addition. A comparison analysis shows that the proposed algorithm outperforms a known algorithm when one multiplication is more time-consuming than five additions. When combined with any known radix-2 type-III GDHT algorithm, the new algorithm also applies to length-2(q)3(P) sequences.

A bagging-based correction for the mixture model estimator of population size

Estimation of a population size by means of capture-recapture techniques is an important problem occurring in many areas of life and social sciences. We consider the frequencies of frequencies situation, where a count variable is used to summarize how often a unit has been identified in the target population of interest. The distribution of this count variable is zero-truncated since zero identifications do not occur in the sample. As an application we consider the surveillance of scrapie in Great Britain. In this case study holdings with scrapie that are not identified (zero counts) do not enter the surveillance database. The count variable of interest is the number of scrapie cases per holding. For count distributions a common model is the Poisson distribution and, to adjust for potential heterogeneity, a discrete mixture of Poisson distributions is used. Mixtures of Poissons usually provide an excellent fit as will be demonstrated in the application of interest. However, as it has been recently demonstrated, mixtures also suffer under the so-called boundary problem, resulting in overestimation of population size. It is suggested here to select the mixture model on the basis of the Bayesian Information Criterion. This strategy is further refined by employing a bagging procedure leading to a series of estimates of population size. Using the median of this series, highly influential size estimates are avoided. In limited simulation studies it is shown that the procedure leads to estimates with remarkable small bias.

Thermodynamics of climate change: generalized sensitivities

Using a recent theoretical approach, we study how global warming impacts the thermodynamics of the climate system by performing experiments with a simplified yet Earth-like climate model. The intensity of the Lorenz energy cycle, the Carnot efficiency, the material entropy production, and the degree of irreversibility of the system change monotonically with the CO2 concentration. Moreover, these quantities feature an approximately linear behaviour with respect to the logarithm of the CO2 concentration in a relatively wide range. These generalized sensitivities suggest that the climate becomes less efficient, more irreversible, and features higher entropy production as it becomes warmer, with changes in the latent heat fluxes playing a predominant role. These results may be of help for explaining recent findings obtained with state of the art climate models regarding how increases in CO2 concentration impact the vertical stratification of the tropical and extratropical atmosphere and the position of the storm tracks.

Anticipatory activation in the amygdala and anterior cingulate in generalized anxiety disorder and prediction of treatment response

OBJECTIVE: The anticipation of adverse outcomes, or worry, is a cardinal symptom of generalized anxiety disorder. Prior work with healthy subjects has shown that anticipating aversive events recruits a network of brain regions, including the amygdala and anterior cingulate cortex. This study tested whether patients with generalized anxiety disorder have alterations in anticipatory amygdala function and whether anticipatory activity in the anterior cingulate cortex predicts treatment response. METHOD: Functional magnetic resonance imaging (fMRI) was employed with 14 generalized anxiety disorder patients and 12 healthy comparison subjects matched for age, sex, and education. The event-related fMRI paradigm was composed of one warning cue that preceded aversive pictures and a second cue that preceded neutral pictures. Following the fMRI session, patients received 8 weeks of treatment with extended-release venlafaxine. RESULTS: Patients with generalized anxiety disorder showed greater anticipatory activity than healthy comparison subjects in the bilateral dorsal amygdala preceding both aversive and neutral pictures. Building on prior reports of pretreatment anterior cingulate cortex activity predicting treatment response, anticipatory activity in that area was associated with clinical outcome 8 weeks later following treatment with venlafaxine. Higher levels of pretreatment anterior cingulate cortex activity in anticipation of both aversive and neutral pictures were associated with greater reductions in anxiety and worry symptoms. CONCLUSIONS: These findings of heightened and indiscriminate amygdala responses to anticipatory signals in generalized anxiety disorder and of anterior cingulate cortex associations with treatment response provide neurobiological support for the role of anticipatory processes in the pathophysiology of generalized anxiety disorder.

A geometric approach to generalized Stokes conjectures

We consider the Stokes conjecture concerning the shape of extreme two-dimensional water waves. By new geometric methods including a nonlinear frequency formula, we prove the Stokes conjecture in the original variables. Our results do not rely on structural assumptions needed in previous results such as isolated singularities, symmetry and monotonicity. Part of our results extends to the mathematical problem in higher dimensions.