Submegabase-size topologically associating domains (TAD) have been observed in high-throughput chromatin interaction data (Hi-C). However, accurate detection of TADs depends on ultra-deep sequencing and sophisticated normalization procedures. Here we propose a fast and normalization-free method to decode the domains of chromosomes (deDoc) that utilizes structural information theory. By treating Hi-C contact matrix as a representation of a graph, deDoc partitions the graph into segments with minimal structural entropy. We show that structural entropy can also be used to determine the proper bin size of the Hi-C data. By applying deDoc to pooled Hi-C data from 10 single cells, we detect megabase-size TAD-like domains. This result implies that the modular structure of the genome spatial organization may be fundamental to even a small cohort of single cells. Our algorithms may facilitate systematic investigations of chromosomal domains on a larger scale than hitherto have been possible.
The ancestral recombination graph (ARG) is a structure that describes the joint genealogies of sampled DNA sequences along the genome. Recent computational methods have made impressive progress towards scalably estimating whole-genome genealogies. In addition to inferring the ARG, some of these methods can also provide ARGs sampled from a defined posterior distribution. Obtaining good samples of ARGs is crucial for quantifying statistical uncertainty and for estimating population genetic parameters such as effective population size, mutation rate, and allele age. Here, we use standard neutral coalescent simulations to benchmark the estimates of pairwise coalescence times from three popular ARG inference programs: ARGweaver, Relate, and tsinfer+tsdate. We compare 1) the true coalescence times to the inferred times at each locus; 2) the distribution of coalescence times across all loci to the expected exponential distribution; 3) whether the sampled coalescence times have the properties expected of a valid posterior distribution. We find that inferred coalescence times at each locus are most accurate in ARGweaver, and often more accurate in Relate than in tsinfer+tsdate. However, all three methods tend to overestimate small coalescence times and underestimate large ones. Lastly, the posterior distribution of ARGweaver is closer to the expected posterior distribution than Relate’s, but this higher accuracy comes at a substantial trade-off in scalability. The best choice of method will depend on the number and length of input sequences and on the goal of downstream analyses, and we provide guidelines for the best practices.
It is of significance to further improve the bioactivity of existing calcium phosphate (Ca–P) biomaterials to satisfy the needs of regenerative medicine.
We consider the following basic problem in phylogenetic tree construction. Let P = {T 1 , . . . , T k } be a collection of rooted phylogenetic trees over various subsets of a set of species. The tree compatibility problem asks whether there is a tree T with the following property: for each i ∈ {1, . . . , k}, T i can be obtained from the restriction of T to the species set of T i by contracting zero or more edges. If such a tree T exists, we say that P is compatible.We give aÕ(M P ) algorithm for the tree compatibility problem, where M P is the total number of nodes and edges in P. Unlike previous algorithms for this problem, the running time of our method does not depend on the degrees of the nodes in the input trees. Thus, it is equally fast on highly resolved and highly unresolved trees.
Spherical
calcium phosphate (Ca-P) granules show advantages in
filling bone cavity defects. In this study, gelatinizing technology
combined with microsphere-sintering and gas-foaming methods was applied
to fabricate porous spherical Ca-P bioceramic granules. The obtained
three kinds of Ca-P granules (i.e., hydroxyapatite, HA-G; biphasic
calcium phosphate, BCP-G; and tricalcium phosphate, TCP-G) exhibited
uniformly spherical shapes and interconnected pore structures with
controlled macropores (about 600 μm), and abundant minor- (10–100
μm) to microsized (<10 μm) pores. The obtained Ca-P
granules contained only the HA and β-TCP phases, but their phase
ratios (HA/β-TCP) had some changes in the sintering process.
All of the Ca-P granules were favorable for serum protein adsorption
and bonelike apatite formation, and TCP-G was superior to the other
two. Cell-culturing results showed that these Ca-P granules could
promote cell adhesion, proliferation, and expression of a series of
osteogenic genes. These findings demonstrated that these Ca-P granules
had good bioactivity and pro-osteogenic ability, especially for BCP-G
and TCP-G. Therefore, the porous spherical Ca-P bioceramic granules
fabricated by the novel method show great potential to serve as good
candidates for bone defect filling materials.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.