Using a historical map as a baseline in a land-cover change study of northeast Tanzania

Vegetation data in an early 20th century map from northern Tanzania are presented and discussed for its potential of expanding the analytical time-frame in studies of land-use and land-cover change. The starting point is that much research on land-use and land-cover change suffers from a time-frame bias, caused by limitations in remote sensing data. At the same time, the use of historical maps as a complementary data-set is rather insignificant. Can information in historical maps be used to extend the baseline in land-use and land-cover change studies? The historical context of the vegetation data is evaluated, and as an illustration of its potential for interdisciplinary research on land-cover and ecosystems change, a section of the map is juxtaposed with a recent pollen record specifically addressing the impact of a 'large infrequent disturbance' (LID) event at the end of the 19th century. It is concluded that the vegetation data in the map are not likely to be reflecting an extreme situation due to the LID event. Finally, the historical vegetation data were visually compared with a national 1995 land-cover data set, illustrating the possibility of using the map data as a baseline in land-cover change studies.     

Phylogenetic mixtures on a single tree can mimic a tree of another topology

Phylogenetic mixtures model the inhomogeneous molecular evolution commonly observed in data. The performance of phylogenetic reconstruction methods where the underlying data are generated by a mixture model has stimulated considerable recent debate. Much of the controversy stems from simulations of mixture model data on a given tree topology for which reconstruction algorithms output a tree of a different topology; these findings were held up to show the shortcomings of particular tree reconstruction methods. In so doing, the underlying assumption was that mixture model data on one topology can be distinguished from data evolved on an unmixed tree of another topology given enough data and the "correct" method. Here we show that this assumption can be false. For biologists, our results imply that, for example, the combined data from two genes whose phylogenetic trees differ only in terms of branch lengths can perfectly fit a tree of a different topology.     

Collection and analysis of kinetic data from a stopped-flow spectrophotometer using a microcomputer

A method of interfacing an inexpensive microcomputer to a stopped-flow kinetics spectrophotometer is described. It allows software-selectable sampling frequencies between 0.1 ms and 8 s and large numbers of data points to be collected. Machine language routines to use the interface are described and these allow the sampling frequency to be altered during data collection to ensure adequate numbers of points in critical regions of the kinetic profile. BASIC programs for collection and analysis of multicomponent kinetic data using this system are also described. Due to the large number of data points that can be collected and the ability to selectively sample transmittance values in regions where the signal is rapidly changing with time, relatively unsophisticated methods of data analysis can be used. These methods are suitable for use by microcomputers and mean that data analysis and acquisition can be performed on the same microcomputer in real time. To illustrate this, multicomponent analysis of kinetic transients is performed on simulated data and on the dissociation kinetics of the ethidium-DNA complex.     

Statistics on continuous IBD data: Exact distribution evaluation for a pair of full(half)-sibs and a pair of a (great-) grandchild with a (great-) grandparent

Background  

Pairs of related individuals are widely used in linkage analysis. Most of the tests for linkage analysis are based on statistics associated with identity by descent (IBD) data. The current biotechnology provides data on very densely packed loci, and therefore, it may provide almost continuous IBD data for pairs of closely related individuals. Therefore, the distribution theory for statistics on continuous IBD data is of interest. In particular, distributional results which allow the evaluation of p-values for relevant tests are of importance.     

GEOBASE: a simple geographical information system on a personal computer

Spatially distributed data are often encountered in the biologicalsciences. Representation and analysis of such data requiresspecific tools. A simple geographical information system ispresented, which allows representation and elementary analysisof geographically coded information. The system handles twokinds of data: maps and facts, where map data describe the basison which the fact data are located. Maps consist of objectsdescribed through a set of coordinates, while for facts a coordinatepair is associated with an unlimited number of data recordscontaining five fields: a date, an element from a list, a two-charactercode, an integer number and a real number. The input data canbe displayed interactively on screen by logically combiningselection criteria for each field. The facts corresponding tothe selected criteria are either displayed as such, or are clusteredand displayed as polygons or pies. A short example showing apossible application of the program is presented and advantagesas well as limitations are discussed. Received on January 16, 1990; accepted on December 21, 1990     

Solution structure of biopolymers: a new method of constructing a bead model

We propose a new, automated method of converting crystallographic data into a bead model used for the calculations of hydrodynamic properties of rigid macromolecules. Two types of molecules are considered: nucleic acids and small proteins. A bead model of short DNA fragments has been constructed in which each nucleotide is represented by two identical, partially overlapping spheres: one for the base and one for the sugar and phosphate group. The optimum radius sigma = 5.0 A was chosen on the basis of a comparison of the calculated translational diffusion coefficients (D(T)) and the rotational relaxation times (tau(R)) with the corresponding experimental data for B-DNA fragments of 8, 12, and 20 basepairs. This value was assumed for the calculation D(T) and tau(R) of tRNA(Phe). Better agreement with the experimental data was achieved for slightly larger sigma = 5.7 A. A similar procedure was applied to small proteins. Bead models were constructed such that each amino acid was represented by a single sphere or a pair of identical, partially overlapping spheres, depending on the amino acid's size. Experimental data of D(T) of small proteins were used to establish the optimum value of sigma = 4.5 A for amino acids. The lack of experimental data on tau(R) for proteins restricted the tests to the translational diffusion properties.     

Geospatially structured biodiversity information as a component of a regional biodiversity clearing house

To function effectively, the international biodiversity Clearing HouseMechanism (CHM), based on the Convention on Biological Diversity (CBD), needs tobe rooted at the regional and local levels. This article presents an example ofhow stakeholders of regional data and information can be encouraged to formnetworks linked to national biodiversity focal points (NFPs). We pay specialattention to exploiting the geospatial properties of biodiversity data andinformation, and demonstrate how data and information can best be filtered,classified and labelled to facilitate geographically based information retrievalon the Internet. The geocodability of bibliographic reports proved to be poor,indicating an urgent need to reconsider the geographical properties ofbiodiversity information under production. Also, it is useful to utilisenetworking processes with information from fields other than biodiversity wheninitiating the network. Finally, we present and discuss problems of integrityand interoperability of data, and also the process of biodiversity informationproduction from the point of view of general information theory and innovationsoffered by modern information technology.     

Modification of a Computer Simulation Model for a Plant-Nematode System

New data on egg development and death rates, and refinements of logic concerning interaction of the nematode and host, were incorporated into a simulation model of a Meloidogyne arenaria and grapevine system. Simulations of field data improved but other areas of weakness in the model were discovered. Two peaks in the egg population curve suggested that the nematode was able to complete two life cycles before host dormancy and declining temperatures limited physiological activity.     

Population genetic inference using a fixed number of segregating sites: a reassessment

Coalescent theory is commonly used to perform population genetic inference at the nucleotide level. Here, we examine the procedure that fixes the number of segregating sites (henceforth the FS procedure). In this approach a fixed number of segregating sites (S) are placed on a coalescent tree (independently of the total and internode lengths of the tree). Thus, although widely used, the FS procedure does not strictly follow the assumptions of coalescent theory and must be considered an approximation of (i) the standard procedure that uses a fixed population mutation parameter theta, and (ii) procedures that condition on the number of segregating sites. We study the differences in the false positive rate for nine statistics by comparing the FS procedure with the procedures (i) and (ii), using several evolutionary models with single-locus and multilocus data. Our results indicate that for single-locus data the FS procedure is accurate for the equilibrium neutral model, but problems arise under the alternative models studied; furthermore, for multilocus data, the FS procedure becomes inaccurate even for the standard neutral model. Therefore, we recommend a procedure that fixes the theta value (or alternatively, procedures that condition on S and take into account the uncertainty of theta) for analysing evolutionary models with multilocus data. With single-locus data, the FS procedure should not be employed for models other than the standard neutral model.     

A targeted maximum likelihood estimator of a causal effect on a bounded continuous outcome

Targeted maximum likelihood estimation of a parameter of a data generating distribution, known to be an element of a semi-parametric model, involves constructing a parametric model through an initial density estimator with parameter ? representing an amount of fluctuation of the initial density estimator, where the score of this fluctuation model at ? = 0 equals the efficient influence curve/canonical gradient. The latter constraint can be satisfied by many parametric fluctuation models since it represents only a local constraint of its behavior at zero fluctuation. However, it is very important that the fluctuations stay within the semi-parametric model for the observed data distribution, even if the parameter can be defined on fluctuations that fall outside the assumed observed data model. In particular, in the context of sparse data, by which we mean situations where the Fisher information is low, a violation of this property can heavily affect the performance of the estimator. This paper presents a fluctuation approach that guarantees the fluctuated density estimator remains inside the bounds of the data model. We demonstrate this in the context of estimation of a causal effect of a binary treatment on a continuous outcome that is bounded. It results in a targeted maximum likelihood estimator that inherently respects known bounds, and consequently is more robust in sparse data situations than the targeted MLE using a naive fluctuation model. When an estimation procedure incorporates weights, observations having large weights relative to the rest heavily influence the point estimate and inflate the variance. Truncating these weights is a common approach to reducing the variance, but it can also introduce bias into the estimate. We present an alternative targeted maximum likelihood estimation (TMLE) approach that dampens the effect of these heavily weighted observations. As a substitution estimator, TMLE respects the global constraints of the observed data model. For example, when outcomes are binary, a fluctuation of an initial density estimate on the logit scale constrains predicted probabilities to be between 0 and 1. This inherent enforcement of bounds has been extended to continuous outcomes. Simulation study results indicate that this approach is on a par with, and many times superior to, fluctuating on the linear scale, and in particular is more robust when there is sparsity in the data.     

The utility of repeated presence data as a surrogate for counts: a case study using butterflies

Abundance data are widely used to monitor long-term population trends for management and conservation of species of interest. Programs that collect count data are often prohibitively expensive and time intensive, limiting the number of species that can be simultaneously monitored. Presence data, on the other hand, can often be collected in less time and for multiple species simultaneously. We investigate the relationship of counts to presence using 49 butterfly species across 4 sites over 9 years, and then compare trends produced from each index. We also employed simulated datasets to test the effect of reduced sampling on the relationship of counts to presence data and to investigate changes in each index’s power to reveal population trends. Presence and counts were highly correlated for most species tested, and population trends based on each index were concordant for most species. The effect of reduced sampling was species-specific, but on a whole, sensitivity of both indices to detect population trends was reduced. Common and rare species, as well as those with a range of life-history and behavioral traits performed equally well. The relationship between presence and count data may break down in cases of very abundant and widespread species with extended flight seasons. Our results suggest that when used cautiously, presence data has the potential to be used as a surrogate for counts. Collection of presence data may be useful for multi-species monitoring or to reduce the duration of monitoring visits without fully sacrificing the ability to infer population trends.     

The Mobility of The Coordinates of a Subjective Semantic Space As a Manifestation of Categorical Set

The perception and objective semantic interpretation of an object depend on categorical set. Categorical set is the readiness of the subject to interact with objects of a specified category. A multitude of experimental evidence confirms the existence of categorical set. This evidence can be divided into three groups: (a) data indicating that perception depends on experimental instructions; (b) data indicating that perception depends on the category to which the preceding stimulation belongs; and, finally, (c) data indicating that perception depends on individual differences in motivation, which are a priori with regard to the experiment. The reasons for the appearance of sets vary; but in the end they all lead to one and the same result: the evocation of diverse expectations (hypotheses) in different subjects in the same situation, or in the same subject at different moments in time (Bruner, 1977).     

Hybrid neural simulation of a fed-batch bioreactor for a nonideal recombinant fermentation

Fermentations employing genetically modified microbes under industrial conditions are difficult to monitor on line or to describe by simple, good mathematical models. So, a practically convenient approach is to combine mathematical models of some aspects with artificial neural networks of those aspects which are difficult to measure or model. Such hybrid models have been applied earlier to laboratory-scale bioreactors. In the present work, a model based on laboratory data for the synthesis of recombinant #-galactosidase was corrupted by adding imperfect mixing and noise in the feed stream to generate data mimicking a real nonideal operation. These data were used to train a recurrent Elman neural network and a hybrid neural network, and it was seen that a hybrid network provides more accurate estimates of both extra-cellular and intra-cellular variables. The benefit is enhanced by the hybrid network's superiority being more pronounced for the intra-cellular recombinant protein, #-galactosidase, which is the main product of interest.     

Application of the lod method to the detection of linkage between a quantitative trait and a qualitative marker: a simulation experiment.

Simulation experiments were performed to assess the power of the lod method for detecting linkage between a quantitative trait and a qualitative marker. Using family data on the Amy2-Duffy linkage, it was found that linkage detection is feasible in certain limited circumstances. The same qualitative data yielded no evidence for a significant difference in male and female recombination fractions.     

Single-nucleotide polymorphism versus microsatellite markers in a combined linkage and segregation analysis of a quantitative trait

Increasingly, single-nucleotide polymorphism (SNP) markers are being used in preference to microsatellite markers. However, methods developed for microsatellites may be problematic when applied to SNP markers. We evaluated the results of using SNPs vs. microsatellites in Monte Carlo Markov chain (MCMC) oligogenic combined segregation and linkage analysis methods. These methods were developed with microsatellite markers in mind. We selected chromosome 7 from the Collaborative Study on the Genetics of Alcoholism dataset for analysis because linkage to an electrophysiological trait had been reported there. We found linkage in the same region of chromosome 7 with the Affymetrix SNP data, the Illumina SNP data, and the microsatellite marker data. The MCMC sampler appears to mix with both types of data. The sampler implemented in this MCMC oligogenic combined segregation and linkage analysis appears to handle SNP data as well as microsatellite data and it is possible that the localizations with the SNP data are better.     

On assessing surrogacy in a single trial setting using a semicompeting risks paradigm

Summary .  There has been a recent emphasis on the identification of biomarkers and other biologic measures that may be potentially used as surrogate endpoints in clinical trials. We focus on the setting of data from a single clinical trial. In this article, we consider a framework in which the surrogate must occur before the true endpoint. This suggests viewing the surrogate and true endpoints as semicompeting risks data; this approach is new to the literature on surrogate endpoints and leads to an asymmetrical treatment of the surrogate and true endpoints. However, such a data structure also conceptually complicates many of the previously considered measures of surrogacy in the literature. We propose novel estimation and inferential procedures for the relative effect and adjusted association quantities proposed by Buyse and Molenberghs (1998, Biometrics 54, 1014–1029). The proposed methodology is illustrated with application to simulated data, as well as to data from a leukemia study.     

长江春大豆核心种质构建及分析

利用长江春大豆初选核心种质SSR(simple sequence repeat）标记和农艺性状表型等基础数据,对用不同个体取样方法以及不同数据类型建立的核心种质进行评价,目的是确定中国大豆（Glycine max）核心种质的最佳取样策略提供依据,结果表明,根据SSR分子数据聚类,采用类内随机取样,类内以遗传相似性系数取样以及仅依据遗传相似性系数取样都可用于大豆核心种质构建,但是综合不同评价参数发现,以类内随机取样最佳,类内按遗传相似性系数取样次之,单独以遗传相似性系数取样较差。分析不同SSR等位变异保留比例的遗传多样性指数发现,当保留90%和80%的SSR等位变异时,核心种质具有更高的遗传多样性,由于与SSR分子数据种质遗传关系评价的不一致性,农艺性状等基础数据虽然可用来构建核心种质,但其SSR分子水平代表性相对较低,本研究结果还表明,用不同方法或同一方法不同重复次数取样建立的核心种质具有异质性,且这种异质性随核心种质取样比例的降低而增大,因此,虽然可依据不同数据类型确定相应的方法建立核心种质,但综合表型和分子数据建立的核心种质更具有代表性。     

Efficient inference of haplotypes from genotypes on a pedigree

We study haplotype reconstruction under the Mendelian law of inheritance and the minimum recombination principle on pedigree data. We prove that the problem of finding a minimum-recombinant haplotype configuration (MRHC) is in general NP-hard. This is the first complexity result concerning the problem to our knowledge. An iterative algorithm based on blocks of consecutive resolved marker loci (called block-extension) is proposed. It is very efficient and can be used for large pedigrees with a large number of markers, especially for those data sets requiring few recombinants (or recombination events). A polynomial-time exact algorithm for haplotype reconstruction without recombinants is also presented. This algorithm first identifies all the necessary constraints based on the Mendelian law and the zero recombinant assumption, and represents them using a system of linear equations over the cyclic group Z2. By using a simple method based on Gaussian elimination, we could obtain all possible feasible haplotype configurations. A C++ implementation of the block-extension algorithm, called PedPhase, has been tested on both simulated data and real data. The results show that the program performs very well on both types of data and will be useful for large scale haplotype inference projects.     

Evaluation of a decision support system in a medical environment

This paper describes the impact of a decision support system on the quality of recorded diagnoses and the completeness of medical records. The assumption is that for quality assessment purposes enough data have to be recorded in an electronic medical record so that diagnostic decisions can be justified. The hypotheses were tested that active decision support will lead to better quality recorded diagnoses and more complete medical records. Three groups of ten GPs were presented with 10 cases each. The GPs had to enter the data about these cases in a GP information system. One group of GPs was not supported. The second group was presented with the ICHPPC-II-Defined criteria that had to be fulfilled when a diagnosis was entered. In a third group, the GPs were asked those data that were needed to justify an entered diagnosis (active support). It could be shown that the last group of GPs entered better quality diagnoses than the other two groups. These latter groups also entered so little data that most of their diagnoses could not be justified. It is concluded from the study that only active decision support will lead to better diagnoses and a more complete medical record that can be used for quality assessment.