Restriction site mapping is in separation theory

A computer algorithm for restriction-site mapping consists ofa generator of partial maps and a consistency checker. Thispaper examines consistency checking and argues that a methodbased on separation theory extracts the maximum amount of informationfrom fragment lengths in digest data. It results in the minimumnumber of false maps being generated. Received on July 17, 1987; accepted on December 13, 1987     

Construction of restriction maps

A computer program is described, which constructs maps of restrictionendonuclease cleavage sites in linear or circular DNA molecules,given the fragment lengths in single and double digestions withtwo enzymes. The algorithm is based upon a partition methodand a very simple rule to chain fragments. The program is writtenin Prolog II. Received on July 28, 1987; accepted on December 31, 1987     

An analysis of Kohonen's self-organizing maps using a system of energy functions

In this paper a new method for analyzing Kohonen's self-organizing feature maps is presented. The method makes use of a system of energy functions, one energy function for each processing unit. It is shown that the training process is equivalent to minimizing each energy function subject to constraints. The analysis is used to prove the formation of topologically correct maps when the inherent dimensionality of the input patterns matches that of the network. The energy equations can be used to compute the steady-state weight values of the network. In addition, the analysis allows bounds on the training parameters to be determined. Finally, examples of energy landscapes are presented to graphically show the behavior of the network.     

Restriction map construction using a 'complete sentences compatibility' algorithm

We have developed a new algorithm ‘Complete sentencescompatibility’ (CSC) which uses single and double digestionfragments to rapidly determine restriction maps of circularDNA. From possible combinations of fragments of each simpledigestion, which we call ‘sentences of decomposition’,we construct a restriction map which combines the sentenceswhile taking into account compatibility rules. The algorithmcan also deal with experimental errors of fragment weight andcan suggest solutions that account for non-readable bands (fragmentsof zero length or multiple bands) on the gel. Because experimentsusing pairs of restrictive enzymes often result in multiplesolutions, a complementary algorithm tries to reduce the numberof proposed solutions by establishing consensus maps. The restrictionmap construction algorithm was tested on real cases, some containingmore than fifteen fragments. Execution times range from 1 –10 s on an IBM PC compatible microcomputer. Received on July 21, 1987; accepted on December 31, 1987     

Mutual Information Rate and Bounds for It

The amount of information exchanged per unit of time between two nodes in a dynamical network or between two data sets is a powerful concept for analysing complex systems. This quantity, known as the mutual information rate (MIR), is calculated from the mutual information, which is rigorously defined only for random systems. Moreover, the definition of mutual information is based on probabilities of significant events. This work offers a simple alternative way to calculate the MIR in dynamical (deterministic) networks or between two time series (not fully deterministic), and to calculate its upper and lower bounds without having to calculate probabilities, but rather in terms of well known and well defined quantities in dynamical systems. As possible applications of our bounds, we study the relationship between synchronisation and the exchange of information in a system of two coupled maps and in experimental networks of coupled oscillators.     

The effects of groundwater discharge,mowing and eutrophication on fen vegetation evaluated over half a century

Questions: Were continued groundwater discharge and mowing regimes sufficient for vegetation preservation from 1944 to 1993? Which has a stronger effect on vegetation development; groundwater discharge or mowing? What is the role of surface water eutrophication as driver of vegetation change? Location: Het Hol, The Netherlands (ca. 92 ha, 52°13′N, 5°05′E). Methods: Hydrology was simulated for the late 1940s, early 1960s and 1987. Vegetation maps (1944, 1960, 1975 and 1993) were compared for biotope cover. Vegetation recordings in 1944 and 1987 were compared. Surface water quality was compared between 1950 and 1987. Which sites were mown was reconstructed from an interview. Effects of periodic mowing and groundwater discharge on vegetation development were tested for correlation. Results: Biotope diversity reduced significantly through decrease of semi‐aquatic and tall‐herb biotopes, and expansion of forest. The quagfen terrestrialization sere nearly disappeared from 1987 recordings, while the reed sere did well concerning abundance and species richness. Several typical (rich) fen species disappeared from recordings, while new species were mostly field margin species. Periodic mowing and discharge combined are correlated with increasing species numbers. The P‐concentration in surface water increased while N‐concentration decreased. Conclusions: Preservation of the reed sere was successful, whereas preservation of the quagfen sere was not. Periodic mowing and discharge stimulate species richness, discharge more so than periodic mowing. But slight eutrophication likely induced a shift from P‐limitation to N‐limitation, which stimulated the reed sere at the expense of the quagfen sere.     

Mapping of sequenced genes (700 kbp) in the restriction map of the Escherichia coli chromosome

This paper describes software (written in Pascal and running on Macintosh computers) allowing localization of unknown DNA fragments from the Escherichia coli chromosome on the restriction map established by Kohara et al. (1987). The program identifies the segment's map position using a restriction pattern analysis obtained with all, or some, of the eight enzymes used by Kohara et al. (1987). Therefore, the sequenced genes available in the EMBL library may be localized on the E. coli chromosome restriction map. This allowed correction of the map (mainly by introducing missing sites in the published maps) at the corresponding positions. Analysis of the data indicates that there is only a very low level of polymorphism, at the nucleotide level, between the E. coli K12 strains used by the various laboratories involved in DNA sequencing. The program is versatile enough to be used with other genomes.     

受损沙地生态系统景观变化分析——以内蒙古浑善达克沙地为例

生态系统变化会引起景观结构及格局的改变,而景观格局及其演化可以作为评价环境变化的指标。为了揭示浑善达克沙地生态系统变化特征,该文使用陆地卫星(Landsat 5、7)的TM/ETM⁺资料及地面调查数据来分析沙地景观变化特征。通过计算机监督分类,获得了研究区1987和2000年景观类型数据,研究区的景观类型有草地、固定沙地、半固定沙地、流动沙地、灌木林及水体。通过对两期景观数据的基本特征、变化检测及转移矩阵分析发现:1)从1987到2000年,草原、固定沙地、半固定沙地都在减少,斑块破碎,而流动沙地显著增加,成为主要景观类型,同时斑块相互联合形成两条流动沙带;2)类型转移上,草原转为沙地,固定沙地主要转为半固定沙地,半固定沙地以绝对优势转为流动沙地,水体转为流动沙地及草原;3)变化监测显示,流动沙地增加面积远远大于减少的面积,而草原、固定沙地、半固定沙地呈现相反趋势,变化区域的空间分布也不尽相同。结果表明研究区沙地生态系统已经退化比较严重,特别是流动沙带的出现,需要采取积极有效的防治措施,防止进一步扩大。     

Modeling a solar radiation topoclimatology for the Rio Grande River Basin

Abstract. Key components in the climatology of the Earth are incoming and net solar radiation. Next to clouds, the major modulator of solar radiation at the surface is topography. Variability in elevation, slope, aspect, and shadowing can lead to large gradients in incoming and net solar radiation fields. The response of vegetation to these gradients can often be dramatic, as in the distribution of vegetation on south- and north-facing slopes. Recently much progress has been made in modeling the effects of topography on incoming and net solar radiation. Such models produce fields of radiation that have been adjusted for topography derived from digital elevation data. This paper presents a topographic solar radiation model that combines digital elevation data with surface and satellite measurements. Specifically, a monthly topoclimatology for the Rio Grande River Basin in Colorado is constructed for the hydrological years 1987 - 1990. Using digital elevation models with 30 m x 30 m grid spacing, representing a mosaic of 39 U.S. Geological Survey 1:24 000 Quadrangles, a digital representation of the watershed is created. Hourly pyranometer measurements taken nearby the basin are then used with satellite reflectances to drive the solar radiation model. The results are monthly maps at 30 m x 30 m grid spacing covering the entire basin that show considerable variability by location and season. Such maps may be useful for vegetation modeling, especially for pattern analysis and ecosystem process modeling.     

Confidence Intervals for fMRI Activation Maps

Neuroimaging activation maps typically color voxels to indicate whether the blood oxygen level-dependent (BOLD) signals measured among two or more experimental conditions differ significantly at that location. This data presentation, however, omits information critical for interpretation of experimental results. First, no information is represented about trends at voxels that do not pass the statistical test. Second, no information is given about the range of probable effect sizes at voxels that do pass the statistical test. This leads to a fundamental error in interpreting activation maps by naïve viewers, where it is assumed that colored, “active” voxels are reliably different from uncolored “inactive” voxels. In other domains, confidence intervals have been added to data graphics to reduce such errors. Here, we first document the prevalence of the fundamental error of interpretation, and then present a method for solving it by depicting confidence intervals in fMRI activation maps. Presenting images where the bounds of confidence intervals at each voxel are coded as color allows readers to visually test for differences between “active” and “inactive” voxels, and permits for more proper interpretation of neuroimaging data. Our specific graphical methods are intended as initial proposals to spur broader discussion of how to present confidence intervals for fMRI data.     

Comparison of the three-dimensional structures of human, yeast, and oat ubiquitin

The crystal structure of human ubiquitin has been solved by x-ray diffraction methods and refined by standard procedures to a conventional crystallographic R factor of 0.176 at 1.8-A resolution (Vijay-Kumar, S., Bugg, C.E., and Cook, W.J. (1987) J. Mol. Biol. 194, 525-538). Crystals of yeast and oat ubiquitin have been grown using human ubiquitin crystals as seeds. Diffraction data for yeast and oat ubiquitin have been collected to a resolution of 1.9 and 1.8 A, respectively. Difference Fourier electron-density maps reveal that the structures of yeast and oat ubiquitin are quite similar to human ubiquitin. All the amino acid changes are clustered in two small patches on one surface of the molecule. This surface is probably not involved in conjugation with proteins destined for ATP-dependent proteolysis.     

Evaluation of Noether's Method of Sample Size Determination for the Wilcoxon-Mann-Whitney Test

NOETHER (1987) proposed a method of sample size determination for the Wilcoxon-Mann-Whitney test. To obtain a sample size formula, he restricted himself to alternatives that differ only slightly from the null hypothesis, so that the unknown variance o² of the Mann-Whitney statistic can be approximated by the known variance under the null hypothesis which depends only on n. This fact is frequently forgotten in statistical practice. In this paper, we compare Noether's large sample solution against an alternative approach based on upper bounds of σ² which is valid for any alternatives. This comparison shows that Noether's approximation is sufficiently reliable with small and large deviations from the null hypothesis.     

基于边界特征的山地森林景观碎裂化研究

景观边界特征与景观碎裂化过程之间的相互关系研究已经引起了广泛的关注。利用 1 987年和 1 997年两个时段遥感景观资料 ,编制了卧龙自然保护区的景观类型图 ,以验证景观碎裂化过程导致边界数量 ,特别是短边界数量增加这一假说。研究工作包括 4个方面的内容 :(1 )利用每年的 2 0个 2 0 0× 2 0 0像元的正方形样地 ,分析工作区内景观边界的一般特征 ;(2 )对每个样地边界数量的长度谱分布特征进行拟合 ,确定能够反映边界属性特征的拟合方程参数 ;(3 )将边界属性特征参数与样地的景观碎裂化指数进行比较研究 ,建立景观边界特征与景观碎裂化程度之间的量化关系模型 ;(4 )利用每个时段的 1 0个验证样地来检验关系模型的有效性。研究结果表明 ,所有样地边界数量的长度谱分布特征可以使用对数方程 y=bln(x) +c进行拟合。景观的碎裂化过程将同时导致拟合方程参数 b的绝对值和 c值线性增加 ,景观碎裂化水平的增加将导致景观边界数量和短边界数量均呈指数增长方式。从研究的结果中还可以推断出 ,生境碎裂化水平对于生物多样性的影响也将呈现出明显的放大效应。     

Some patterns of spatial-ontogenetic structure in populations of tuber orchids

Population dynamics, density, and aggregation size of tuberoid orchids have been identified based on mapping, electronic maps constructed with “point processes,” and Ripley function and pair-correlation function. Discrete and discrete-continuous types of spatial structure dominate in populations in optimal ecological conditions. The bounded aggregations of levels I (radius 0.45–0.75 m) and II (radius 1.2–2.5 m) are formed at 3 to 7.5 m². The spatial pattern depends on generative specimens which are related with the “group effect.” The microloci have full ontogenetic structure and may be regarded as elemental populations. They form larger aggregations of levels III and IV with random spatial distribution and continuous bounds. Aggregations of higher level are not formed under worse ecological conditions. Random spatial distribution and incomplete ontogenetic spectrum of microloci are indicators of critical population status.     

A program for the graphic representation and manipulation of DNA sequences

We have developed a program for the graphic representation andmanipulation of DNA sequences. The program (named CARTE fromthe French for ‘map’) is intended as a tool in theplanning and analysis of recombinant DNA experiments. DNA sequencesare represented as standard restriction maps, using any desiredcombination of restriction enzymes. Features of interest, suchas promoters or coding sequences, can be highlighted. The sequencecan be manipulated to mimic cloning, using deletions, insertionsor replacements at specified sites. This process is facilitatedby the simultaneous display of a graphic map of the entire sequence,a detailed picture of the work in progress, and a menu of functions. Received on November 17, 1986; accepted on March 12, 1987     

Bayesian estimation of species divergence times under a molecular clock using multiple fossil calibrations with soft bounds

We implement a Bayesian Markov chain Monte Carlo algorithm for estimating species divergence times that uses heterogeneous data from multiple gene loci and accommodates multiple fossil calibration nodes. A birth-death process with species sampling is used to specify a prior for divergence times, which allows easy assessment of the effects of that prior on posterior time estimates. We propose a new approach for specifying calibration points on the phylogeny, which allows the use of arbitrary and flexible statistical distributions to describe uncertainties in fossil dates. In particular, we use soft bounds, so that the probability that the true divergence time is outside the bounds is small but nonzero. A strict molecular clock is assumed in the current implementation, although this assumption may be relaxed. We apply our new algorithm to two data sets concerning divergences of several primate species, to examine the effects of the substitution model and of the prior for divergence times on Bayesian time estimation. We also conduct computer simulation to examine the differences between soft and hard bounds. We demonstrate that divergence time estimation is intrinsically hampered by uncertainties in fossil calibrations, and the error in Bayesian time estimates will not go to zero with increased amounts of sequence data. Our analyses of both real and simulated data demonstrate potentially large differences between divergence time estimates obtained using soft versus hard bounds and a general superiority of soft bounds. Our main findings are as follows. (1) When the fossils are consistent with each other and with the molecular data, and the posterior time estimates are well within the prior bounds, soft and hard bounds produce similar results. (2) When the fossils are in conflict with each other or with the molecules, soft and hard bounds behave very differently; soft bounds allow sequence data to correct poor calibrations, while poor hard bounds are impossible to overcome by any amount of data. (3) Soft bounds eliminate the need for "safe" but unrealistically high upper bounds, which may bias posterior time estimates. (4) Soft bounds allow more reliable assessment of estimation errors, while hard bounds generate misleadingly high precisions when fossils and molecules are in conflict.     

R0 bounds for worst-case endemic mixing models.

Upper and lower bounds are presented for the worst endemic prevalence possible in nonrandom mixing models. The bounds require only the value of the reproductive number R0 for the corresponding homogeneous epidemic model. For R0 values of 4 or larger, the difference between the upper and lower bounds on the worst-case prevalence is at most five percentage points.     

Bounds on controlled direct effects under monotonic assumptions about mediators and confounders

Adjusting for intermediate variables is a common analytic strategy for estimating a direct effect. Even if the total effect is unconfounded, the direct effect is not identified when unmeasured variables affect the intermediate and outcome variables. Therefore, some researchers presented bounds on the controlled direct effects via linear programming. They applied a monotonic assumption about treatment and intermediate variables and a no-interaction assumption to derive narrower bounds. Here, we improve their bounds without using linear programming and hence derive a bound under the monotonic assumption about an intermediate variable only. To improve the bounds, we further introduce the monotonic assumption about confounders. While previous studies assumed that an outcome is a binary variable, we do not make that assumption. The proposed bounds are illustrated using two examples from randomized trials.     

Modeling the effect of inbreeding among founders in linkage analysis

In this paper, we present a unified mathematical model for linkage analysis that allows for inbreeding among founders in all families. The identical by descent (IBD) configuration of each pedigree is modeled as a Markov process containing two parameters; the inverse inbreeding and kinship coefficient and a rate parameter proportional to the inverse expected length of chromosome segments shared IBD by two different founder haplotypes. We use hidden Markov models and define a forward-backward algorithm for computing the conditional IBD-distribution given marker data, thereby extending the multipoint method of Lander and Green [1987. Construction of multilocus genetic maps in humans, Proc. Natl. Acad. Sci. USA 84, 2363-2367] to situations where founders are inbred. Our methodology is valid for arbitrary pedigree structures. Simulation and theoretical approximations for nonparametric linkage (NPL) analysis based on affected sib pairs reveal that NPL scores are inflated and type 1 errors increased when the inbreeding coefficient or rate parameter is underestimated. When the parents are genotyped, we present a general way of modifying the score function to drastically reduce this effect.     

Unit-treatment interaction and its practical consequences

Most statistical characterizations of a treatment effect focus on the average effect of the treatment over an entire population. However, average effects may provide inadequate information, sometimes misleading information, when a substantial unit-treatment interaction is present in the population. It is even possible that a nonnegligible proportion of the individuals in the population experience an unfavorable treatment effect even though the treatment might appear to be beneficial when considering population averages. This paper examines the extent to which information about unit-treatment interaction can be extracted using observed data from a two-treatment completely randomized experiment. A method for utilizing the information from an available covariate is proposed. Although unit-treatment interaction is a nonidentifiable quantity, we show that mathematical bounds for it can be estimated from observed data. These bounds lead to estimated bounds for the probability of an unfavorable treatment effect. Maximum likelihood estimators of the bounds and their corresponding large-sample distributions are given. The use of the estimated bounds is illustrated in a clinical trials data example.