Searching for structure (alias-AID-III) ; an approach to analysis of substantial bodies of micro-data and documentation for a computer program (successor to the Automatic Interaction Detector Program) /

Bibliography: p. [165]-166.

Searching for structure ; an approach to analysis of substantial bodies of micro-data and documentation for a computer program /

Mode of access: Internet.

Stock structure of Spanish mackerel Scomberomorus commerson along the Australian east coast deduced from parasite data

The parasite fauna of Spanish mackerel Scomberomorus commerson from three regions off eastern Australia was examined for evidence of separate stocks. The abundance of five metacestodes was very similar in all areas suggesting that extensive mixing of the fish occurs along the coast, unlike the Situation across northern Australia where large differences have been found between regions. The similarity in abundances of two metacestodes from Townsville fish and south-east Queensland fish Suggests that these two regions have fish with very similar histories. The data lead to the conclusion that the seasonal fishery for Spanish mackerel off south-east Queensland is based on a random group of fish from the same origin as fish sampled off Townsville and is not a subpopulation that moves south each year. (c) 2006 The Fisheries Society of the British Isles.

Block GTM: Incorporating prior knowledge of covariance structure in data visualisation

Visualising data for exploratory analysis is a big challenge in scientific and engineering domains where there is a need to gain insight into the structure and distribution of the data. Typically, visualisation methods like principal component analysis and multi-dimensional scaling are used, but it is difficult to incorporate prior knowledge about structure of the data into the analysis. In this technical report we discuss a complementary approach based on an extension of a well known non-linear probabilistic model, the Generative Topographic Mapping. We show that by including prior information of the covariance structure into the model, we are able to improve both the data visualisation and the model fit.

A generalized multidimensional index structure for multimedia data to support content-based similarity searches in a collaborative search environment

Since multimedia data, such as images and videos, are way more expressive and informative than ordinary text-based data, people find it more attractive to communicate and express with them. Additionally, with the rising popularity of social networking tools such as Facebook and Twitter, multimedia information retrieval can no longer be considered a solitary task. Rather, people constantly collaborate with one another while searching and retrieving information. But the very cause of the popularity of multimedia data, the huge and different types of information a single data object can carry, makes their management a challenging task. Multimedia data is commonly represented as multidimensional feature vectors and carry high-level semantic information. These two characteristics make them very different from traditional alpha-numeric data. Thus, to try to manage them with frameworks and rationales designed for primitive alpha-numeric data, will be inefficient. An index structure is the backbone of any database management system. It has been seen that index structures present in existing relational database management frameworks cannot handle multimedia data effectively. Thus, in this dissertation, a generalized multidimensional index structure is proposed which accommodates the atypical multidimensional representation and the semantic information carried by different multimedia data seamlessly from within one single framework. Additionally, the dissertation investigates the evolving relationships among multimedia data in a collaborative environment and how such information can help to customize the design of the proposed index structure, when it is used to manage multimedia data in a shared environment. Extensive experiments were conducted to present the usability and better performance of the proposed framework over current state-of-art approaches.

A review of road structure data in six European countries

The European Union has expanded significantly in recent years. Sustainable trade within the Union, leading to economic growth to the benefit of the ‘old’ and ‘new’ member states is thus extremely important. The road infrastructure is strategic and vital to such development since an uneven transport infrastructure, in terms of capacity and condition, has the potential to reinforce uneven development trends and hinder economic convergence of old and new member states. In the decades since their design and construction, loading conditions have significantly changed for many major highway infrastructure elements/networks owing primarily to increased freight volumes and vehicle sizes. This, coupled with the gradual deterioration of a significant number of highway structures due to their age, and the absence of a pan-European assessment framework, can be expected to affect the smooth functioning of the infrastructure in its as-built condition. Increased periods of reduced flow can be expected owing to planned and unplanned interventions for repair/rehabilitation. This paper reports the findings of a survey regarding the current status of the highway infrastructure elements in six countries within the European Union as reported by the owners/operators. The countries surveyed include a cross-section of ‘existing’ older countries and ‘new’ member states. The current situations for bridges, culverts, tunnels and retaining walls are reported, along with their potential replacement costs. The findings act as a departure point for further studies in support of a centralised and/or synchronised EU approach to infrastructure maintenance management. Information in the form presented in this paper is central to any future decision-making frameworks in terms of trade route choice and operations, monetary investment, optimised maintenance, management and rehabilitation of the built infrastructure and the economic integration of the newly joined member states.

Deep Crustal Structure of the North-West African Margin from Combined Wide-angle and Reflection Seismic Data (MIRROR Seismic Survey)

The structure of the Moroccan and Nova Scotia conjugate rifted margins is of key importance for understanding the Mesozoic break-up and evolution of the northern central Atlantic Ocean basin. Seven combined multichannel reflection (MCS) and wide-angle seismic (OBS) data profiles were acquired along the Atlantic Moroccan margin between the latitudes of 31.5° and 33° N during the MIRROR seismic survey in 2011, in order to image the transition from continental to oceanic crust, to study the variation in crustal structure and to characterize the crust under the West African Coast Magnetic Anomaly (WACMA). The data were modeled using a forward modeling approach. The final models image crustal thinning from 36 km thickness below the continent to approximately 8 km in the oceanic domain. A 100 km wide zone characterized by rough basement topography and high seismic velocities up to 7.4 km/s in the lower crust is observed westward of the West African Coast Magnetic Anomaly. No basin underlain by continental crust has been imaged in this region, as has been identified north of our study area. Comparison to the conjugate Nova Scotian margin shows a similar continental crustal thickness and layer geometry, and the existence of exhumed and serpentinized upper mantle material on the Canadian side only. The oceanic crustal thickness is lower on the Canadian margin.

Censored Linear Regression Models For Irregularly Observed Longitudinal Data Using The Multivariate-t Distribution.

In acquired immunodeficiency syndrome (AIDS) studies it is quite common to observe viral load measurements collected irregularly over time. Moreover, these measurements can be subjected to some upper and/or lower detection limits depending on the quantification assays. A complication arises when these continuous repeated measures have a heavy-tailed behavior. For such data structures, we propose a robust structure for a censored linear model based on the multivariate Student's t-distribution. To compensate for the autocorrelation existing among irregularly observed measures, a damped exponential correlation structure is employed. An efficient expectation maximization type algorithm is developed for computing the maximum likelihood estimates, obtaining as a by-product the standard errors of the fixed effects and the log-likelihood function. The proposed algorithm uses closed-form expressions at the E-step that rely on formulas for the mean and variance of a truncated multivariate Student's t-distribution. The methodology is illustrated through an application to an Human Immunodeficiency Virus-AIDS (HIV-AIDS) study and several simulation studies.

On The Consistency Of Monte Carlo Track Structure Dna Damage Simulations.

Monte Carlo track structures (MCTS) simulations have been recognized as useful tools for radiobiological modeling. However, the authors noticed several issues regarding the consistency of reported data. Therefore, in this work, they analyze the impact of various user defined parameters on simulated direct DNA damage yields. In addition, they draw attention to discrepancies in published literature in DNA strand break (SB) yields and selected methodologies. The MCTS code Geant4-DNA was used to compare radial dose profiles in a nanometer-scale region of interest (ROI) for photon sources of varying sizes and energies. Then, electron tracks of 0.28 keV-220 keV were superimposed on a geometric DNA model composed of 2.7 × 10(6) nucleosomes, and SBs were simulated according to four definitions based on energy deposits or energy transfers in DNA strand targets compared to a threshold energy ETH. The SB frequencies and complexities in nucleosomes as a function of incident electron energies were obtained. SBs were classified into higher order clusters such as single and double strand breaks (SSBs and DSBs) based on inter-SB distances and on the number of affected strands. Comparisons of different nonuniform dose distributions lacking charged particle equilibrium may lead to erroneous conclusions regarding the effect of energy on relative biological effectiveness. The energy transfer-based SB definitions give similar SB yields as the one based on energy deposit when ETH ≈ 10.79 eV, but deviate significantly for higher ETH values. Between 30 and 40 nucleosomes/Gy show at least one SB in the ROI. The number of nucleosomes that present a complex damage pattern of more than 2 SBs and the degree of complexity of the damage in these nucleosomes diminish as the incident electron energy increases. DNA damage classification into SSB and DSB is highly dependent on the definitions of these higher order structures and their implementations. The authors' show that, for the four studied models, different yields are expected by up to 54% for SSBs and by up to 32% for DSBs, as a function of the incident electrons energy and of the models being compared. MCTS simulations allow to compare direct DNA damage types and complexities induced by ionizing radiation. However, simulation results depend to a large degree on user-defined parameters, definitions, and algorithms such as: DNA model, dose distribution, SB definition, and the DNA damage clustering algorithm. These interdependencies should be well controlled during the simulations and explicitly reported when comparing results to experiments or calculations.

The C-terminal Region Of The Human P23 Chaperone Modulates Its Structure And Function.

The p23 protein is a chaperone widely involved in protein homeostasis, well known as an Hsp90 co-chaperone since it also controls the Hsp90 chaperone cycle. Human p23 includes a β-sheet domain, responsible for interacting with Hsp90; and a charged C-terminal region whose function is not clear, but seems to be natively unfolded. p23 can undergo caspase-dependent proteolytic cleavage to form p19 (p231-142), which is involved in apoptosis, while p23 has anti-apoptotic activity. To better elucidate the function of the human p23 C-terminal region, we studied comparatively the full-length human p23 and three C-terminal truncation mutants: p23₁₋₁₁₇; p23₁₋₁₃₁ and p23₁₋₁₄₂. Our data indicate that p23 and p19 have distinct characteristics, whereas the other two truncations behave similarly, with some differences to p23 and p19. We found that part of the C-terminal region can fold in an α-helix conformation and slightly contributes to p23 thermal-stability, suggesting that the C-terminal interacts with the β-sheet domain. As a whole, our results suggest that the C-terminal region of p23 is critical for its structure-function relationship. A mechanism where the human p23 C-terminal region behaves as an activation/inhibition module for different p23 activities is proposed.

Is size structure a good measure of future trends of plant populations? an empirical approach using five woody species from the Cerrado (Brazilian savanna)

Size distributions in woody plant populations have been used to assess their regeneration status, assuming that size structures with reverse-J shapes represent stable populations. We present an empirical approach of this issue using five woody species from the Cerrado. Considering count data for all plants of these five species over a 12-year period, we analyzed size distribution by: a) plotting frequency distributions and their adjustment to the negative exponential curve and b) calculating the Gini coefficient. To look for a relationship between size structure and future trends, we considered the size structures from the first census year. We analyzed changes in number over time and performed a simple population viability analysis, which gives the mean population growth rate, its variance and the probability of extinction in a given time period. Frequency distributions and the Gini coefficient were not able to predict future trends in population numbers. We recommend that managers should not use measures of size structure as a basis for management decisions without applying more appropriate demographic studies.

Evaluation of the dental structure loss produced during maintenance and replacement of occlusal amalgam restorations

The aim of this in vitro study was to evaluate four different approaches to the decision of changing or not defective amalgam restorations in first primary molar teeth concerning the loss of dental structure. Ditched amalgam restorations (n = 11) were submitted to four different treatments, as follows: Control group - polishing and finishing of the restorations were carried out; Amalgam group - the ditched amalgam restorations were replaced by new amalgam restorations; Composite resin group - the initial amalgam restorations were replaced by composite resin restorations; Flowable resin group - the ditching around the amalgam restorations was filled with flowable resin. Images of the sectioned teeth were made and the area of the cavities before and after the procedures was determined by image analysis software to assess structural loss. The data were submitted to ANOVA complemented by the Student Newman Keuls test (p < 0.05). The cavities in all the groups presented significantly greater areas after the procedures. However, the amalgam group showed more substantial dental loss. The other three groups presented no statistically significant difference in dental structure loss after the re-treatments. Thus, replacing ditched amalgam restorations by other similar restorations resulted in a significant dental structure loss while maintaining them or replacing them by resin restorations did not result in significant loss.

The impact of spatial data redundancy on SOLAP query performance

Geographic Data Warehouses (GDW) are one of the main technologies used in decision-making processes and spatial analysis, and the literature proposes several conceptual and logical data models for GDW. However, little effort has been focused on studying how spatial data redundancy affects SOLAP (Spatial On-Line Analytical Processing) query performance over GDW. In this paper, we investigate this issue. Firstly, we compare redundant and non-redundant GDW schemas and conclude that redundancy is related to high performance losses. We also analyze the issue of indexing, aiming at improving SOLAP query performance on a redundant GDW. Comparisons of the SB-index approach, the star-join aided by R-tree and the star-join aided by GiST indicate that the SB-index significantly improves the elapsed time in query processing from 25% up to 99% with regard to SOLAP queries defined over the spatial predicates of intersection, enclosure and containment and applied to roll-up and drill-down operations. We also investigate the impact of the increase in data volume on the performance. The increase did not impair the performance of the SB-index, which highly improved the elapsed time in query processing. Performance tests also show that the SB-index is far more compact than the star-join, requiring only a small fraction of at most 0.20% of the volume. Moreover, we propose a specific enhancement of the SB-index to deal with spatial data redundancy. This enhancement improved performance from 80 to 91% for redundant GDW schemas.

The Relationship between Population Structure and Aluminum Tolerance in Cultivated Sorghum

Background: Acid soils comprise up to 50% of the world's arable lands and in these areas aluminum (Al) toxicity impairs root growth, strongly limiting crop yield. Food security is thereby compromised in many developing countries located in tropical and subtropical regions worldwide. In sorghum, SbMATE, an Al-activated citrate transporter, underlies the Alt(SB) locus on chromosome 3 and confers Al tolerance via Al-activated root citrate release. Methodology: Population structure was studied in 254 sorghum accessions representative of the diversity present in cultivated sorghums. Al tolerance was assessed as the degree of root growth inhibition in nutrient solution containing Al. A genetic analysis based on markers flanking Alt(SB) and SbMATE expression was undertaken to assess a possible role for Alt(SB) in Al tolerant accessions. In addition, the mode of gene action was estimated concerning the Al tolerance trait. Comparisons between models that include population structure were applied to assess the importance of each subpopulation to Al tolerance. Conclusion/Significance: Six subpopulations were revealed featuring specific racial and geographic origins. Al tolerance was found to be rather rare and present primarily in guinea and to lesser extent in caudatum subpopulations. Alt(SB) was found to play a role in Al tolerance in most of the Al tolerant accessions. A striking variation was observed in the mode of gene action for the Al tolerance trait, which ranged from almost complete recessivity to near complete dominance, with a higher frequency of partially recessive sources of Al tolerance. A possible interpretation of our results concerning the origin and evolution of Al tolerance in cultivated sorghum is discussed. This study demonstrates the importance of deeply exploring the crop diversity reservoir both for a comprehensive view of the dynamics underlying the distribution and function of Al tolerance genes and to design efficient molecular breeding strategies aimed at enhancing Al tolerance.

An assessment of population structure in eight breeds of cattle using a whole genome SNP panel

Background: Analyses of population structure and breed diversity have provided insight into the origin and evolution of cattle. Previously, these studies have used a low density of microsatellite markers, however, with the large number of single nucleotide polymorphism markers that are now available, it is possible to perform genome wide population genetic analyses in cattle. In this study, we used a high-density panel of SNP markers to examine population structure and diversity among eight cattle breeds sampled from Bos indicus and Bos taurus. Results: Two thousand six hundred and forty one single nucleotide polymorphisms ( SNPs) spanning all of the bovine autosomal genome were genotyped in Angus, Brahman, Charolais, Dutch Black and White Dairy, Holstein, Japanese Black, Limousin and Nelore cattle. Population structure was examined using the linkage model in the program STRUCTURE and Fst estimates were used to construct a neighbor-joining tree to represent the phylogenetic relationship among these breeds. Conclusion: The whole-genome SNP panel identified several levels of population substructure in the set of examined cattle breeds. The greatest level of genetic differentiation was detected between the Bos taurus and Bos indicus breeds. When the Bos indicus breeds were excluded from the analysis, genetic differences among beef versus dairy and European versus Asian breeds were detected among the Bos taurus breeds. Exploration of the number of SNP loci required to differentiate between breeds showed that for 100 SNP loci, individuals could only be correctly clustered into breeds 50% of the time, thus a large number of SNP markers are required to replace the 30 microsatellite markers that are currently commonly used in genetic diversity studies.