Dataset Information

Automated map sharpening by maximization of detail and connectivity.

ABSTRACT: An algorithm for automatic map sharpening is presented that is based on optimization of the detail and connectivity of the sharpened map. The detail in the map is reflected in the surface area of an iso-contour surface that contains a fixed fraction of the volume of the map, where a map with high level of detail has a high surface area. The connectivity of the sharpened map is reflected in the number of connected regions defined by the same iso-contour surfaces, where a map with high connectivity has a small number of connected regions. By combining these two measures in a metric termed the `adjusted surface area', map quality can be evaluated in an automated fashion. This metric was used to choose optimal map-sharpening parameters without reference to a model or other interpretations of the map. Map sharpening by optimization of the adjusted surface area can be carried out for a map as a whole or it can be carried out locally, yielding a locally sharpened map. To evaluate the performance of various approaches, a simple metric based on map-model correlation that can reproduce visual choices of optimally sharpened maps was used. The map-model correlation is calculated using a model with B factors (atomic displacement factors; ADPs) set to zero. This model-based metric was used to evaluate map sharpening and to evaluate map-sharpening approaches, and it was found that optimization of the adjusted surface area can be an effective tool for map sharpening.

SUBMITTER: Terwilliger TC

PROVIDER: S-EPMC6096490 | biostudies-literature | 2018 Jun

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Automated map sharpening by maximization of detail and connectivity.

Terwilliger Thomas C TC Sobolev Oleg V OV Afonine Pavel V PV Adams Paul D PD

Acta crystallographica. Section D, Structural biology 20180518 Pt 6

An algorithm for automatic map sharpening is presented that is based on optimization of the detail and connectivity of the sharpened map. The detail in the map is reflected in the surface area of an iso-contour surface that contains a fixed fraction of the volume of the map, where a map with high level of detail has a high surface area. The connectivity of the sharpened map is reflected in the number of connected regions defined by the same iso-contour surfaces, where a map with high connectivit ...[more]

PMID: 29872005

Similar Datasets

Project description:BackgroundRecovering individual genomes from metagenomic datasets allows access to uncultivated microbial populations that may have important roles in natural and engineered ecosystems. Understanding the roles of these uncultivated populations has broad application in ecology, evolution, biotechnology and medicine. Accurate binning of assembled metagenomic sequences is an essential step in recovering the genomes and understanding microbial functions.ResultsWe have developed a binning algorithm, MaxBin, which automates the binning of assembled metagenomic scaffolds using an expectation-maximization algorithm after the assembly of metagenomic sequencing reads. Binning of simulated metagenomic datasets demonstrated that MaxBin had high levels of accuracy in binning microbial genomes. MaxBin was used to recover genomes from metagenomic data obtained through the Human Microbiome Project, which demonstrated its ability to recover genomes from real metagenomic datasets with variable sequencing coverages. Application of MaxBin to metagenomes obtained from microbial consortia adapted to grow on cellulose allowed genomic analysis of new, uncultivated, cellulolytic bacterial populations, including an abundant myxobacterial population distantly related to Sorangium cellulosum that possessed a much smaller genome (5 MB versus 13 to 14 MB) but has a more extensive set of genes for biomass deconstruction. For the cellulolytic consortia, the MaxBin results were compared to binning using emergent self-organizing maps (ESOMs) and differential coverage binning, demonstrating that it performed comparably to these methods but had distinct advantages in automation, resolution of related genomes and sensitivity.ConclusionsThe automatic binning software that we developed successfully classifies assembled sequences in metagenomic datasets into recovered individual genomes. The isolation of dozens of species in cellulolytic microbial consortia, including a novel species of myxobacteria that has the smallest genome among all sequenced aerobic myxobacteria, was easily achieved using the binning software. This work demonstrates that the processes required for recovering genomes from assembled metagenomic datasets can be readily automated, an important advance in understanding the metabolic potential of microbes in natural environments. MaxBin is available at https://sourceforge.net/projects/maxbin/.

Project description:The ability to generate episodic details while recollecting autobiographical events is believed to depend on a collection of brain regions that form a posterior medial network (PMN). How age-related differences in episodic detail generation relate to the PMN, however, remains unclear. The present study sought to examine individual differences, and the role of age, in PMN resting state functional connectivity (rsFC) associations with episodic detail generation. Late middle-aged and older adults (N = 41, ages 52-81), and young adults (N = 21, ages 19-35) were asked to describe recent personal events, and these memory narratives were coded for episodic, semantic and 'miscellaneous' details. Independent components analysis and regions-of-interest analyses were used to assess rsFC within the PMN separately for anterior connections (hippocampal and medial prefrontal) and posterior connections (hippocampal, parahippocampal and parieto-occipital), as these connections purportedly serve different functional roles in episodic detail generation. Compared to younger adults, older adults produced memory narratives with lower episodic specificity (ratio of episodic:total details) and a greater amount of semantic detail. Among the older adults, episodic detail amounts and episodic specificity were reduced with increasing age. There were no significant age differences in PMN rsFC. Stronger anterior PMN rsFC was related to lower episodic detail in the older adult group, but not in the young. Among the older adults, increasing age brought on an association between increased anterior PMN rsFC and reduced episodic specificity. In contrast, increasing age brought on an association between increased posterior PMN rsFC and increased semantic detail. The present study provides evidence that functional connectivity within the PMN, particularly anterior PMN, tracks individual differences in the amount of episodic details retrieved by older adults. Furthermore, these brain-behavior relationships appear to be age-specific, indicating that some process within aging alters the nature of how anterior PMN rsFC and episodic detail relate to each other. Whether this process entails an age-related loss of integrity to the PMN, or an age-related shift toward semantic retrieval, remains to be determined.

Dataset Information

Automated map sharpening by maximization of detail and connectivity.

Publications

Automated map sharpening by maximization of detail and connectivity.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets