Complete Matrices Research Articles

Comparative Population Genomics of African Montane Forest Mammals Support Population Persistence across a Climatic Gradient and Quaternary Climatic Cycles

The Eastern Afromontane biodiversity hotspot (EABH) has the highest concentration of biodiversity in tropical Africa, yet few studies have investigated recent historical diversification processes in EABH lineages. Herein, we analyze restriction-site associated DNA-sequences (RAD-Seq) to study recent historical processes in co-distributed mouse (Hylomyscus) and shrew (Sylvisorex) species complexes, with an aim to better determine how historical paleoenvironmental processes might have contributed to the EABH’s high diversity. We analyzed complete SNP matrices of > 50,000 RAD loci to delineate populations, reconstruct the history of isolation and admixture, and discover geographic patterns of genetic partitioning. These analyses demonstrate that persistently unsuitable habitat may have isolated multiple populations distributed across montane habitat islands in the Itombwe Massif and Albertine Rift to the west as well as Mt Elgon and Kenyan Highlands to the east. We detected low genetic diversity in Kenyan Highland populations of both genera, consistent with smaller historical population sizes in this region. We additionally tested predictions that Albertine Rift populations are older and more persistently isolated compared to the Kenyan Highlands. Phylogenetic analyses support greater historical isolation among Albertine Rift populations of both shrews and mice compared to the Kenyan Highlands and suggest that there are genetically isolated populations from both focal genera in the Itombwe Massif, Democratic Republic of Congo. The Albertine Rift ecoregion has the highest mammalian tropical forest species richness per unit area on earth. Our results clearly support accelerating efforts to conserve this diversity.

Effects of missing data on topological inference using a Total Evidence approach.

To fully understand macroevolutionary patterns and processes, we need to include both extant and extinct species in our models. This requires phylogenetic trees with both living and fossil taxa at the tips. One way to infer such phylogenies is the Total Evidence approach which uses molecular data from living taxa and morphological data from living and fossil taxa. Although the Total Evidence approach is very promising, it requires a great deal of data that can be hard to collect. Therefore this method is likely to suffer from missing data issues that may affect its ability to infer correct phylogenies. Here we use simulations to assess the effects of missing data on tree topologies inferred from Total Evidence matrices. We investigate three major factors that directly affect the completeness and the size of the morphological part of the matrix: the proportion of living taxa with no morphological data, the amount of missing data in the fossil record, and the overall number of morphological characters in the matrix. We infer phylogenies from complete matrices and from matrices with various amounts of missing data, and then compare missing data topologies to the "best" tree topology inferred using the complete matrix. We find that the number of living taxa with morphological characters and the overall number of morphological characters in the matrix, are more important than the amount of missing data in the fossil record for recovering the "best" tree topology. Therefore, we suggest that sampling effort should be focused on morphological data collection for living species to increase the accuracy of topological inference in a Total Evidence framework. Additionally, we find that Bayesian methods consistently outperform other tree inference methods. We therefore recommend using Bayesian consensus trees to fix the tree topology prior to further analyses.

EPR investigation of local structure for the [Mn(H2O)6]2+cluster in M(ClO4)2· 6H2O:Mn2+(M = Cd, Hg) systems at different temperatures

Local lattice structure distortion studies of the octahedral Mn 2+ center in M(ClO 4 ) 2 · 6H 2 O:Mn 2+ (M = Cd, Hg) systems have been performed systematically based on the diagonalization of the complete energy matrices of electron-electron repulsion, spin-orbit coupling and trigonal ligand-field interaction for a d 5 configuration ion in a trigonal ligand field. From the EPR calculation, the local structure distortion parameters R and θ are determined, respectively. Results show that the local lattice structure around a trigonal Mn 2+ center has a compressed distortion along the crystalline C 3 axis. The compression distortion may be ascribed to the fact that the radius of the Mn 2+ ion is smaller than that of the Hg 2+ ion and the Cd 2+ ion. The local lattice structure parameters for Mn 2+ in M(ClO 4 ) 2 · 6H 2 O:Mn 2+ (M = Cd, Hg) systems are determined at liquid-nitrogen temperature and room temperature.

Theoretical studies of the dependence of EPR parameters on local structure for the tetragonal Er3+ centres in YVO4 and ScVO4

The dependences of the EPR parameters on the local distortion parameters Δθ and ΔR as well as the crystal-field parameters have been studied by diagonalizing the 364×364 complete energy matrices for a tetragonal Er3+ centre in the YVO4 and ScVO4 crystals. The results show that the local distortion angle Δθ and the fourth-order crystal-field parameter Ā4 are most sensitive to the EPR g-factors g// and g⊥, whereas the local distortion length ΔR and the second-order parameter Ā2 are less sensitive to the g-factors. Furthermore, we found that the abnormal EPR g-factors for the Er3+ ion in the ScVO4 may be ascribed to the stronger nephelauxetic effect and covalent bonding effect, as a result of an expanded local distortion for the Er3+ centre in the ScVO4 crystal. Simultaneously, the contributions of the J–J mixing effects from the terms of excited states to the EPR parameters have been evaluated quantitatively.

Self-assembly of PEG-oligonucleotide-based matrices and lipoplexes as DNase-responsive delivery systems

This study proposes a new concept of DNase-triggered delivery systems using polyethylene glycol (PEG)-ssDNA matrices. To construct the matrices, firstly PEG molecules (4 k or 10 k or 35 kDa) were functionalized with single-strand oligonucleotides (PEG-ssDNA1). The complete self-assembled matrices were formed by cross-linking of complementary pairing with ssDNA2-conjugated model molecule and subsequent PEG-ssDNA2. The PEG-dsDNA-drug matrices achieved a prolonged release of the tracer molecule (6FAM) in presence of DNase. The release rate of 6FAM exhibited a dependence on the molecular weight of PEG used in matrix formation. A matrix with a higher Mw PEG would provide a slower release of 6FAM due to its denser tangled network being crossed-linked by longer PEG molecules against the approach of DNase. Remarkably, our results showed that nanoscaled complexes (lipoplexes) of lipid-coated PEG-dsDNA-6FAM can be formulated. These lipoplexes no longer release drugs in PBS with DNase but become an efficient vehicle for intracellular drug delivery. We observed a similar prolonged release of 6FAM inside COS-7 cells and noted that the released 6FAM would further distribute to extracellular surroundings. These results indicate that the PEG-ssDNA matrix is able to respond by either external or endogenous DNase activation and becomes an efficient candidate for extracellular or intracellular drug delivery.

Theoretical studies of the dependence of EPR g-factors on local structure for the trigonal Er3+–VK centres in KMgF3 and KZnF3

The dependence of the EPR g-factors on the local structural parameter for a 4f11 configuration ion Er3+ in a trigonal crystal-field has been studied by diagonalizing the 364×364 complete energy matrices. Our studies indicate that the EPR spectra of the trigonal Er3+–VK centers in KMgF3 and KZnF3 may be attributed to the translation of the cubic Kramers doublet Γ7. Furthermore, the EPR g-factors of the trigonal Er3+–VK centers may be interpreted reasonably by the shifts ΔZ≈0.340Å and ΔZ≈0.303Å of the Er3+ ions toward the charge compensator VK along the C3 axis for the KMgF3:Er3+ and the KZnF3:Er3+ systems respectively.

Imputação de dados climáticos utilizando a decomposição por valores singulares: uma comparação empírica

Um problema comum em dados climáticos é a informação ausente. Recentemente, foram desenvolvidos quatro métodos de imputação que têm como base a decomposição por valores singulares de uma matriz (DVS). O objetivo deste artigo é avaliar os novos desenvolvimentos fazendo uma comparação por meio de um estudo de simulação baseado em duas matrizes completas de dados reais. Uma matriz corresponde à precipitação histórica de Piracicaba/SP - Brasil, enquanto a outra matriz corresponde às características meteorológicas multivariadas na mesma cidade desde o ano 1997 até 2012. No estudo foram feitas retiradas aleatórias de diferentes porcentagens com posterior imputação, comparando as metodologias através de três critérios: a raiz quadrada normalizada do erro quadrático médio, a estatística de similaridade de Procrustes e o coeficiente de correlação não paramétrico de Spearman. Concluiu-se que a DVS deve ser utilizada unicamente quando sejam analisadas matrizes multivariadas e, no caso de matrizes de precipitação, a imputação pela média mensal supera o desempenho de métodos baseados na DVS.

A simple compliance modeling method for flexure hinges

Various types of flexure hinges have been introduced and implemented in a variety of fields due to their superior performances. The Castigliano’s second theorem, the Euler-Bernoulli beam theory based direct integration method and the unit-load method have been employed to analytically describe the elastic behavior of flexure hinges. However, all these methods require prior-knowledge of the beam theory and need to execute laborious integration operations for each term of the compliance matrix, thus highly decreasing the modeling efficiency and blocking practical applications of the modeling methods. In this paper, a novel finite beam based matrix modeling (FBMM) method is proposed to numerically obtain compliance matrices of flexure hinges with various shapes. The main concept of the method is to treat flexure hinges as serial connections of finite micro-beams, and the shearing and torsion effects of the hinges are especially considered to enhance the modeling accuracy. By means of matrix calculations, complete compliance matrices of flexure hinges can be derived effectively in one calculation process. A large number of numerical calculations are conducted for various types of flexure hinges with different shapes, and the results are compared with the ones obtained by conventional modeling methods. It demonstrates that the proposed modeling method is not only efficient but also accurate, and it is a more universal and more robust tool for describing elastic behavior of flexure hinges.

Convergence properties and practicalestimation of the probability of rankreversal in pairwisecomparisons for multi-criteria decisionmakingproblems

In this paper, we address the impact of uncertainty introduced when the experts complete pairwise comparison matrices, in the context of multi-criteria decision making. We first discuss how uncertainty can be quantified and modeled and then show how the probability of rank reversal scales with the number of experts. We consider the impact of various aspects which may affect the estimation of probability of rank reversal in the context of pairwise comparisons, such as the uncertainty level, alternative preference scales and different weight estimation methods. We also consider the case where the comparisons are carried out in a fuzzy manner. It is shown that in most circumstances, augmenting the size of the expert group beyond 15 produces a small change in the probability of rank reversal. We next address the issue of how this probability can be estimated in practice, from information gathered simply from the comparison matrices of a single expert group. We propose and validate a scheme which yields an estimate for the probability of rank reversal and test the applicability of this scheme under various conditions. The framework discussed in the paper can allow decision makers to correctly choose the number of experts participating in a pairwise comparison and obtain an estimate of the credibility of the outcome.

Imputação múltipla livre de distribuição em tabelas incompletas de dupla entrada

O objetivo deste trabalho foi propor um novo algoritmo de imputação múltipla livre de distribuição, por meio de modificações no método de imputação simples recentemente desenvolvido por Yan para contornar o problema de desbalanceamento de experimentos. O método utiliza a decomposição por valores singulares de uma matriz e foi testado por meio de simulações baseadas em duas matrizes de dados reais completos, provenientes de ensaios com eucalipto e cana-de-açúcar, com retiradas aleatórias de valores em diferentes percentagens. A qualidade das imputações foi avaliada por uma medida de acurácia geral que combina a variância entre imputações e o viés quadrático médio delas em relação aos valores retirados. A melhor alternativa para imputação múltipla é um modelo multiplicativo que inclui pesos próximos a 1 para os autovalores calculados com a decomposição. A metodologia proposta não depende de pressuposições distribucionais ou estruturais e não tem restrições quanto ao padrão ou ao mecanismo de ausência dos dados.

Acoustic and elastic anisotropy of acousto-optic Pb₂P₂Se₆ crystals.

We have determined experimentally the acoustic wave velocities for Pb₂P₂Se₆ crystals and obtained complete matrices of the elastic stiffness and elastic compliance coefficients on this basis. The anisotropy of the acoustic wave velocities has been analyzed, and the spatial directions of propagation and polarization of the slowest acoustic waves have been determined. In the case of acousto-optic (AO) interaction with these waves, the AO figure of merit can reach extremely high values, thus making Pb₂P₂Se₆ a promising AO material for the infrared spectral range.

VaR-implied tail-correlation matrices

Empirical evidence suggests that asset returns correlate more strongly in bear markets than conventional correlation estimates imply. We propose a method for determining complete tail-correlation matrices based on Value-at-Risk (VaR) estimates. We demonstrate how to obtain more efficient tail-correlation estimates by use of overidentification strategies and how to guarantee positive semidefiniteness, a property required for valid risk aggregation and Markowitz-type portfolio optimization. An empirical application to a 30-asset universe illustrates the practical applicability and relevance of the approach in portfolio management.

Deterministic Imputation in Multienvironment Trials

This paper proposes five new imputation methods for unbalanced experiments with genotype by-environment interaction (G×E). The methods use cross-validation by eigenvector, based on an iterative scheme with the singular value decomposition (SVD) of a matrix. To test the methods, we performed a simulation study using three complete matrices of real data, obtained from G×E interaction trials of peas, cotton, and beans, and introducing lack of balance by randomly deleting in turn 10%, 20%, and 40% of the values in each matrix. The quality of the imputations was evaluated with the additive main effects and multiplicative interaction model (AMMI), using the root mean squared predictive difference (RMSPD) between the genotypes and environmental parameters of the original data set and the set completed by imputation. The proposed methodology does not make any distributional or structural assumptions and does not have any restrictions regarding the pattern or mechanism of missing values.

Subnational migration in the United Kingdom: producing a consistent time series using a combination of available data and estimates

There is no single framework in place in the United Kingdom for collating and harmonizing the data on migration taking place between the subnational administrative units that constitute the home nations, together with the flows of international migration between these areas and the ‘rest of the world’. This paper proposes the construction of complete matrices of subnational migration statistics on an annual basis which can then be used to monitor migration trends throughout the UK in a comprehensive manner. The paper reviews how various ‘known’ flows are estimated by the national statistics agencies and develops estimates to fill in the gaps in the matrices. It then looks at changing patterns of migration in the UK between 2001/2002 and 2010/2011, showing that migration exhibits most activity in the middle of the decade. Flows within the home nations are the most consistent over time, while the patterns of international migration and migration across the borders of the home nations exhibit more substantial change. The latter flows, although relatively small in magnitude, have not previously been studied at the subnational level in any detail. Patterns of subnational internal and international net migration are found to be negatively correlated.

From viral genome to specific peptide epitopes: methods for identifying porcine T cell epitopes based on in silico predictions, in vitro identification and ex vivo verification (P6098)

Abstract The affinity with which major histocompatibility complex (MHC) class I molecules bind peptides is instrumental to presentation of viral epitopes to cytotoxic T lymphocytes (CTLs). We analyzed three swine leukocyte antigen (SLA) molecules for complete nonamer peptide-based binding matrices in order to predict likely candidates for peptide-SLA binding. These results were combined with binding predictions generated by the algorithm, NetMHCpan (http://www.cbs.dtu.dk/services/NetMHCpan/) in order to select peptide candidates for in vitro analysis. The correlation between high affinity and high stability was determined using luminescence oxygen channeling (LOCI) and scintillation proximity assay (SPA) for peptides bound by the commonly occurring SLA molecules, SLA-1*0401, SLA-2*0401, and SLA-3*0401. Using these tools, peptides bound by SLA with high affinity and stability were identified from a library of 10.000 peptides. T cell epitopes were identified using peptide-SLA complexes assembled into fluorescent tetramers to stain swine influenza specific CTLs derived from immunized animals and MHC-defined pigs vaccinated against foot-and-mouth disease virus. These results demonstrate the broad applicability of methods originally developed for analysis of human leukocyte antigen (HLA) presentation of peptides. The methods presented provide a timely and cost-effective approach to CTL epitope discovery that can be applied to diseases of swine and of other mammalian species of interest.

Investigation of the local structure and EPR spectra for Nd3+ in Bi4Ge3O12

On the basis of complete energy matrices for a 4f3 configuration ion in trigonal symmetry ligand-field, the optical and EPR spectra of Nd3+ center in Bi4Ge3O12 have been reasonably explained. The results indicate that the Nd3+ ion do not occupy the actual Bi3+ site, but departure from the ideal host position along the C3 axis by about 0.07Å. The new set of crystal-field parameters that can well account for the Stark levels and EPR parameters have been obtained from the superposition model. Moreover, the influence of orbital reduction factor k and local distortion parameter ΔZ on EPR parameters is analyzed.

Studies of EPR spectra and defect structure for Er3+ ions in BaF2 and SrF2 crystals

The local lattice structure and electron paramagnetic resonance (EPR) spectra have been studied systematically by diagonalizing 364×364 complete energy matrices for a f11 ion in a trigonal ligand-field. By simulating the calculated Stark levels and EPR parameters to the experimental results, the shift parameters are determined for Er3+ ions in BaF2 and SrF2. The results show that the trigonal center is attributed to an interstitial F− ion located at the [111] axis of the cube, and the nearest ligand close to the charge compensator has a displacement towards central ion by 0.042Å for L center in BaF2:Er3+ and 0.026Å for J center in SrF2:Er3+, respectively. Moreover, the relationships between g-factors and shift parameter ΔZ as well as orbit reduction factor k′ are discussed.

Theoretical studies of EPR parameters and defect structures for Ni2+ ions in corundum

In this paper, fourth-order perturbation formulae of zero-field splitting (ZFS) parameter D and g -factors g // , g ⊥ for ground state 3 A 2g of 3d 8 ions in the trigonal crystal field (CF) have been derived by perturbation theory method (PTM), and the complete energy matrices (45×45) including low symmetry ligand field ( C 3v ), Coulomb interactions and spin-orbital (SO) coupling interaction for 3d 8 ions have been constructed, in the strong-field scheme. In these formulae, both the contributions from the SO of the central 3d ion and the ligands taken into account by using the two SO coupling parameter model, and the contributions to the ZFS from all excited states are included. These PTM formulae and complete energy matrices are applied to investigate the EPR parameters D and g -factors for Ni 2+ ions in Al 2 O 3 crystals unifiedly, and the calculated results of PTM and complete diagonalization method (CDM) are not only close to each other but also in good agreement with the experimental data, and the local structure of [NiO 6 ] 10− cluster is determined quantitatively. Furthermore, the validities of the present formulae are tested further by the comparison of calculated results of the formula and these of CDM based on intermediate –CF scheme, and the comparison shows that the calculated results with these two different methods are in mutually good agreement with each other in all different trigonal crystal environments, which also suggest that these fourth-order perturbation formulae are suitable for explaining both D and g -factors for 3d 8 ions in trigonally distorted octahedral field.

Noncollinear Magnetism in Ultrathin Films with Strong Spin-Orbit Coupling from Ab Initio

Fe and Pt are paradigms for ferromagnetism and strong spin-orbit coupling, respectively. Their combination--in an ultrathin Fe film on a Pt(111) substrate--is thus expected to modify the magnetic structures. We report on a theoretical investigation of a monolayer of Fe on Pt(111), using a generalized Heisenberg model that includes the complete spin interaction matrices I(ij) computed from first principles. We find a noncollinear periodic configuration that is strongly determined by the Dzyaloshinskii-Moriya interaction. Taking into account a magnetic field to mimic recent experiments, this noncollinear structure solves the disagreement between the experimental magnetization and the average magnetization for a ferromagnetic system. The critical temperature decreases from 670 K to 590 K due to spin-orbit coupling.

Integration of Spatial and Social Network Analysis in Disease Transmission Studies

This study presents a case study of how social network and spatial analytical methods can be used simultaneously for disease transmission modeling. The article first reviews strategies employed in previous studies and then offers the example of transmission of two bacterial diarrheal diseases in rural Bangladesh. The goal is to understand how diseases vary socially above and beyond the effects of the local neighborhood context. Patterns of cholera and shigellosis incidence are analyzed in space and within kinship-based social networks in Matlab, Bangladesh. Data include a spatially referenced longitudinal demographic database that consists of approximately 200,000 people and laboratory-confirmed cholera and shigellosis cases from 1983 to 2003. Matrices are created of kinship ties among households using a complete network design and distance matrices are also created to model spatial relationships. Moran's I statistics are calculated to measure clustering within both social and spatial matrices. Combined spatial effects and spatial disturbance models are built to simultaneously analyze spatial and social effects while controlling for local environmental context. Results indicate that cholera and shigellosis always cluster in space and only sometimes within social networks. This suggests that the local environment is most important for understanding transmission of both diseases, although kinship-based social networks also influence their transmission. Simultaneous spatial and social network analysis can help us better understand disease transmission and this study offers several strategies on how.