A NotI restriction map of the entire long arm of human chromosome 21

A variety of maps of the human genome have been constructed, including cloned DNA maps. We have isolated 40 of the 42 NotI sites that exist on the long arm of human chromosome 21, as NotI linking clones and constructed a complete NotI restriction map spanning the entire region. This map, which provides the most reliable ordering and distance estimation in the region from a pericentromeric locus to the terminus, demonstrates the usefulness of linking clone mapping for analysing human chromosomes.     

Long-term impact of reproductive factors on cancer risk

In the program ODS we provide a methodology for quickly ordering random clones into a physical map. The process of ordering individual clones with respect to their position along a chromosome is based on the similarity of binary signatures assigned to each clone. This binary signature is obtained by hybridizing each clone to a panel of oligonucleotide probes. By using the fact that the amount of overlap between any two clones is reflected in the similarity of their binary signatures, it is possible to reconstruct a chromosome by minimizing the sum of linking distances between an ordered sequence of clones. Unlike other programs for physical mapping, ODS is very general in the types of data that can be utilized for chromosome reconstruction. Any trait that can be scored in a presence--absence manner, such as hybridized synthetic oligonucleotides, restriction endonuclease recognition sites or single copy landmarks, can be used for analysis. Furthermore, the computational requirements for the construction of large physical maps can be measured in a matter of hours on work-stations such as the VAX2000.     

坐标展点测图精度分析与探讨

对采用坐标展点器展绘碎部点坐标所测绘的大比例尺地形图的精度进行了系统地分析，并定量地给出了采用不同测距方式展点测图的点位中误差．对大比例尺地形图的测绘和使用具有一定的指导意义．     

Effects of age on virtual environment place navigation and allocentric cognitive mapping.

This study assessed age differences in navigational behavior in a virtual Morris water maze (vMWM) and examined the ability of older adults to develop cognitive maps after vMWM experience. Compared with younger participants, older volunteers traversed a longer linear distance to locate the hidden platform. On the probe trial, younger volunteers spent a greater proportion of their total distance traveled in proximity to the platform and had more platform intersections. Analysis of map reproductions demonstrated that older participants used proximal objects to locate the goal but did not use room-geometry cues to aid navigation. These findings demonstrate age-related deficits on a laboratory measure of place learning and suggest that deficiencies in allocentric mapping may contribute to these deficits. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Unpacking the cognitive map: The parallel map theory of hippocampal function.

In the parallel map theory, the hippocampus encodes space with 2 mapping systems. The bearing map is constructed primarily in the dentate gyrus from directional cues such as stimulus gradients. The sketch map is constructed within the hippocampus proper from positional cues. The integrated map emerges when data from the bearing and sketch maps are combined. Because the component maps work in parallel, the impairment of one can reveal residual learning by the other. Such parallel function may explain paradoxes of spatial learning, such as learning after partial hippocampal lesions, taxonomic and sex differences in spatial learning, and the function of hippocampal neurogenesis. By integrating evidence from physiology to phylogeny, the parallel map theory offers a unified explanation for hippocampal function. (PsycINFO Database Record (c) 2011 APA, all rights reserved)     

Parallel computing of physical maps--a comparative study in SIMD and MIMD parallelism

Ordering clones from a genomic library into physical maps of whole chromosomes presents a central computational problem in genetics. Chromosome reconstruction via clone ordering is usually isomorphic to the NP-complete Optimal Linear Arrangement problem. Parallel SIMD and MIMD algorithms for simulated annealing based on Markov chain distribution are proposed and applied to the problem of chromosome reconstruction via clone ordering. Perturbation methods and problem-specific annealing heuristics are proposed and described. The SIMD algorithms are implemented on a 2048 processor MasPar MP-2 system which is an SIMD 2-D toroidal mesh architecture whereas the MIMD algorithms are implemented on an 8 processor Intel iPSC/860 which is an MIMD hypercube architecture. A comparative analysis of the various SIMD and MIMD algorithms is presented in which the convergence, speedup, and scalability characteristics of the various algorithms are analyzed and discussed. On a fine-grained, massively parallel SIMD architecture with a low synchronization overhead such as the MasPar MP-2, a parallel simulated annealing algorithm based on multiple periodically interacting searches performs the best. For a coarse-grained MIMD architecture with high synchronization overhead such as the Intel iPSC/860, a parallel simulated annealing algorithm based on multiple independent searches yields the best results. In either case, distribution of clonal data across multiple processors is shown to exacerbate the tendency of the parallel simulated annealing algorithm to get trapped in a local optimum.     

Mapping the chicken genome: problems and perspectives

Various molecular methods are now used to map the chicken genome, including chromosome scraping, flow cytofluorimetry, zonal centrifugation, construction of chromosome-specific libraries, genetic analysis with polymorphic DNA markers, and in situ hybridization. Two main drawbacks are characteristic of existing maps of chicken chromosomes. First, classic genetic maps (i.e., linkage groups of genes for morphological, physiological, and biochemical characters), physical maps of chromosomes, and new genetic maps constructed on the basis of polymorphic DNA markers (RFLP, RAPD, VNTR, SSR, and CR1-PCR) do not coordinate with one another. Second, a relatively low number of genes is present in classic genetic maps and physical chromosome maps. Application of cytogenetic methods to chromosome mapping in birds is limited because of some specific features characteristic of the organization of avian genomes. For the same reason, studying the location and expression of avian genes is very important. Since mammalian and avian genomes differ in structure, revealing their possible common functional characteristics will provide for a better understanding of the general mechanisms that control biologically important characters in higher animals.     

Toward a cDNA map of the human genome

Advances in the Human Genome Project are shaping the strategies for identifying the 50,000-100,000 human genes. High-resolution genetic maps of the human genome combined with sequencing herald an era of rapid regional definition of disease genes. However, only once their chromosome band location is known will the systematic partial sequencing of thousands of random cDNA clones provide the reagents for teh rapid assessment of the genes responsible for the inherited disorders. We now present an approach to the rapid determination of map position and therefore to the creation of a transcribed map of the human genome. Sensitive fluorescence in situ hybridization has been combined with high-resolution chromosome banding and random cDNA sequencing to map 41 cDNAs with an average insert size of <2 kb to single human chromosome bands. The result provide 15 new genes, with database and functional information, as candidates for human disease. These include the large extracellular signal-related kinase (HUMERK), the ERK activator kinase (PRKMK1), a new member of the RAS oncogene family, protein phosphatase 2 regulatory subunit B alpha isoform (PPP2R2A), and a novel human gene with very high homology to a plant membrane transport family. Further, an analysis of expressed genes associated with pseudogenes showed that by using these techniques, it is possible to detect accurately the transcribed locus within a multigene or processed pseudogene family in most cases. These findings suggest that direct cDNA mapping using fluorescence in situ hybridization provides an accurate and rapid approach to the definition of a transcribed map of the human genome. This low-cost, high-resolution (2-5 Mb) mapping greatly enhances the speed with which these genes can be subsequently assigned to contigs. This assignment provides a necessary first step in understanding the relationship of the genes to both acquired and inherited human diseases.     

The psychological four-color mapping problem.

Mathematicians have proven that four colors are sufficient to color 2-D maps so that no neighboring regions share the same color. Here we consider the psychological 4-color problem: Identifying which 4 colors should be used to make a map easy to use. We build a model of visual search for this design task and demonstrate how to apply it to the task of identifying the optimal colors for a map. We parameterized the model with a set of 7 colors using a visual search experiment in which human participants found a target region on a small map. We then used the model to predict search times for new maps and identified the color assignments that minimize or maximize average search time. The differences between these maps were predicted to be substantial. The model was then tested with a larger set of 31 colors on a map of English counties under conditions in which participants might memorize some aspects of the map. Empirical tests of the model showed that an optimally best colored version of this map is searched 15% faster than the correspondingly worst colored map. Thus, the color assignment seems to affect search times in a way predicted by the model, and this effect persists even when participants might use other sources of knowledge about target location. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Automated high resolution optical mapping using arrayed, fluid-fixed DNA molecules

New mapping approaches construct ordered restriction maps from fluorescence microscope images of individual, endonuclease-digested DNA molecules. In optical mapping, molecules are elongated and fixed onto derivatized glass surfaces, preserving biochemical accessibility and fragment order after enzymatic digestion. Measurements of relative fluorescence intensity and apparent length determine the sizes of restriction fragments, enabling ordered map construction without electrophoretic analysis. The optical mapping system reported here is based on our physical characterization of an effect using fluid flows developed within tiny, evaporating droplets to elongate and fix DNA molecules onto derivatized surfaces. Such evaporation-driven molecular fixation produces well elongated molecules accessible to restriction endonucleases, and notably, DNA polymerase I. We then developed the robotic means to grid DNA spots in well defined arrays that are digested and analyzed in parallel. To effectively harness this effect for high-throughput genome mapping, we developed: (i) machine vision and automatic image acquisition techniques to work with fixed, digested molecules within gridded samples, and (ii) Bayesian inference approaches that are used to analyze machine vision data, automatically producing high-resolution restriction maps from images of individual DNA molecules. The aggregate significance of this work is the development of an integrated system for mapping small insert clones allowing biochemical data obtained from engineered ensembles of individual molecules to be automatically accumulated and analyzed for map construction. These approaches are sufficiently general for varied biochemical analyses of individual molecules using statistically meaningful population sizes.     

Computer technology for genogenographic study of the gene pool. V. Evaluation of the reliability of maps

An important aspect of gene geography, the estimation of the reliability of interpolation maps, is considered. The introduced quantitative parameter, map reliability, was estimated as the probability of predicted character values in interpolated map regions. The obtained estimates characterize the statistic significance of the mapped values of the character. The estimation algorithm is based on concepts and mathematical methods of the reliability theory. The proposed approach involved the estimation of the reliability at each point of the mapped area and resulted in a new map (a reliability map) expressing the reliability of gene geographic mapping in probability terms. Approaches to estimate the reliability of mapping, as dependent on various parameters of the initial data, were proposed, a general computer-based technology was elaborated, and a standardized reliability scale was proposed. Reliability maps are considered necessary for the correct interpretation of gene geographic maps. The estimation of reliability as dependent on the number and distribution of initially tested populations was illustrated by the example of frequency maps of individual genes (HP*1, HLA*A1) and synthetic maps (100 alleles of 34 polymorphic loci) of Eastern Europe.     

Comprehension of arithmetic word problems: Evidence from students' eye fixations.

Students have difficulty solving arithmetic word problems containing a relational term that is inconsistent with the required arithmetic operation (e.g., containing the term less, yet requiring addition) rather than consistent. To investigate this consistency effect, students' eye fixations were recorded as they read arithmetic word problems on a computer monitor and stated a solution plan for each problem. As predicted, low-accuracy students made more reversal errors on inconsistent than consistent problems, students took more time for inconsistent than consistent problems, this additional time was localized in the integration/planning stages of problem solving rather than in the initial reading of the problem, these response-time patterns were obtained for high-accuracy but not for low-accuracy students, and high-accuracy students required more rereadings of previously fixated words for inconsistent than for consistent problems. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

ISWAC: proposed system for the integrated assembly of chromosomes

The generation of a physical map as an integral part of sequence project management is a problem that present computer systems do not address. Primarily, the analysis performed is based solely on the information available from a single knowledge level. Management systems that are currently available do not adequately model the multi-layer top down strategy that is most often utilized to manage large scale sequencing projects. Single layered approaches reflect an algorithmic inadequacy since interacting data sets are required to provide a good solution. The analysis tool that is currently under development termed ISWAC, the Integrated System for Wholistic Assembly of Chromosomes, overcomes these limitations by integrating information available from five layers of knowledge. These knowledge layers utilize information from the linkage map, physical map, restriction map, clone strategy map and the DNA sequence itself. The approach we are implementing, reviews current project status and continually refines the experimental strategy necessary to efficiently complete the sequencing task. To facilitate project completion the system is designed to interactively recommend strategies based on partial information. The utility of this tool is enhanced by implementing knowledge representation techniques that allow reasoning with approximate concepts characteristic of these data-sets. In addition, the raw physical data is maintained within an integrated map database to ease data verification. This paper presents the first discussion of the design specifications for a computer system to assimilate the various forms of data that are being generated as part of the human genome project. It was specifically written to stimulate discussion regarding data standardization, translation, analysis and most important, an understandable user-interphase for the molecular biologist. We would hope that interested readers would respond by assisting in the definition of a set of universal data standards and adopting them in their laboratories.     

Assembly of a 1-Mb restriction-mapped cosmid contig spanning the candidate region for Finnish congenital nephrosis (NPHS1) in 19q13.1

We describe the assembly of a 1-Mb cosmid contig and restriction map spanning the candidate region for Finnish congenital nephrosis (NPHS1) in 19q13.1. The map was constructed from 16 smaller contigs assembled by fingerprinting, a BAC and a PAC clone, and 42 previously unmapped cosmids. In most cases, single-step cosmid walks were sufficient to join two previously assembled contigs, and all but one gap was filled from this cosmid contig library. The remaining gap of about 19 kb was spanned with a single BAC and a single PAC clone. EcoRI mapping of a dense set of overlapping clones validated the assembly of the map and indicated a length of 1040 kb for the contig. This high-resolution clone map provides an ideal resource for gene identification through cDNA selection, exon trapping, and DNA sequencing.     

MapGIS制图中随意参数底图的矢量校正

基于MapGIS软件系统分析和东准噶尔地区空间多元地学信息找矿预测工作,针对无矢量化随意参数地质图件资料的矢量校正,提出了关键点配准法的底图矢量校正方法;对于无配准矢量化图件的矢量校正,提出了关键点坐标法和关键点距离法2种解决方案。研究表明,采用关键点配准法可有效解决传统单幅底图法存在的累计误差大及工作效率低等问题。对于无配准普通数字化图件的矢量校正,可采用关键点坐标法和关键点距离法实现,前者是解决无配准矢量化图校正的最佳方法,适用于原始底图中有4个或以上的关键点,校正后的图件图元信息准确,后期不需要进行点、线图元参数的调整,具有误差小、效率高的特点;当无配准矢量化图中关键点数量少,不适用关键点坐标法时,可采用关键点距离法进行校正。这3种方法对提高成果资料的利用水平,促进空间多元地学信息找矿预测的有效性和准确率有重要意义。     

Knowledge-Based Landslide Susceptibility Zonation System

The landslide susceptibility of a region is important for socioeconomic considerations and engineering applications. Thus, an automated system for mapping of landslide susceptibility could be of significant benefit for society. In this paper, a knowledge-based landslide susceptibility zonation (LSZ) system has been proposed. The system consists of input, understanding, expert, and output modules. The input module accepts thematic images of contributing factors for landslides. The understanding module interprets input images to extract relevant information as required by the expert module. The expert module consists of knowledge base and inference strategy to categorize a region into different landslide intensities. Finally the output module provides a LSZ map. It is a pixel-based system and provides output having the scale same as that of the input maps. The system has been tested to prepare a landslide susceptibility map for the Tehri-Garhwal region in India’s lower Himalayas, and further validated with studies for two other different regions. The proposed system provides output commensurate with that provided by experts. The categories of hazard zones have a discrepancy as little as 6.2% in high hazard zones and near to 1.5% and 4% in moderate and low hazard zones, respectively. The high hazard zones in the LSZ maps from the proposed system are supersets of that obtained by experts (i.e., the proposed system provides safer LSZ map). Thus, it can be concluded that the proposed system can be used for preparation of LSZ maps. In the future, the methodology may be extended for real time assessment and prediction of landslide hazards.