The Knowlton-Graham partition problem

A set partition technique that is useful for identifying wires in cables can be recast in the language of 0--1 matrices, thereby resolving an open problem stated by R.~L. Graham in Volume 1 of this journal. The proof involves a construction of 0--1 matrices having row and column sums without gaps

Optimization of grow-out of bouldering coral microfragments: land vs. offshore nursery

Corals along the Florida Reef Tract and the wider Caribbean have been declining for decades. Low densities of adult colonies hinder the ability of corals to replenish themselves through sexual reproduction, thus reef managers are focusing on restoration actions that increase coral biomass. Microfragmentation is a way to quickly increase the biomass of bouldering corals by cutting the coral into small pieces which forces the coral to allocate its resources away from reproduction and back into growth, increasing its growth rate. This study assessed the optimal location for grow-out (land vs. offshore nursery) and its synergy with size of fragment in 4 bouldering coral species (Orbicella faveolata, Siderastrea siderea, Pseudodiploria clivosa and Diploria labyrinthiformis). Survival and growth rates were tracked through monthly pictures of the microfragments to determine differences between the locations, fragment sizes, species, and individuals. Coral microfragments of all species and sizes grown in the land-based nursery had increased survival and growth rates compared to the counterparts grown in the offshore nursery. These results help inform managers to make the best choices for growing coral microfragments. The longevity of coral reefs is dependent on techniques such as this succeeding in increasing coral cover quickly

Evolution into and out of the Andes: A Bayesian analysis of historical diversification in Thamnophilus antshrikes

The Andean uplift played important roles in the historical diversification of Neotropical organisms, both by producing new high-elevation habitats that could be colonized and by isolating organisms on either side of the mountains. Here, we present a molecular phylogeny of Thamnophlius antshrikes, a clade of 30 species whose collective distribution spans nearly the entirety of lowland habitats in tropical South America, the eastern slope foothills of the Andes, and the tepuis of northern South America. Our goal was to examine the role of the Andes in the diversification of lowland and foothill species. Using parsimony and Bayesian ancestral state reconstructions of a three-state distribution character (lowland-restricted, lowland-to-highland, highland-restricted), we found that the Andes were colonized twice independently and the tepuis once from lowland-restricted ancestors. Over the entire evolutionary history of Thamnophilus, the highest transition rates were between highland-restricted and lowland-to-highland distributions, with extremely low rates into and out of lowland-restricted distributions. This pattern suggests lowland-restricted distributions are limited not by physiological constraints, but by other forces, such as competition. These results highlight the need for additional comparative studies in elucidating processes associated with the colonization of high-elevation habitats and the differentiation of populations within them. © 2007 The Author(s)

Deep learning-enabled technologies for bioimage analysis.

Deep learning (DL) is a subfield of machine learning (ML), which has recently demonstrated its potency to significantly improve the quantification and classification workflows in biomedical and clinical applications. Among the end applications profoundly benefitting from DL, cellular morphology quantification is one of the pioneers. Here, we first briefly explain fundamental concepts in DL and then we review some of the emerging DL-enabled applications in cell morphology quantification in the fields of embryology, point-of-care ovulation testing, as a predictive tool for fetal heart pregnancy, cancer diagnostics via classification of cancer histology images, autosomal polycystic kidney disease, and chronic kidney diseases

Long Distance Dispersal and Connectivity in Amphi-Atlantic Corals at Regional and Basin Scales

Among Atlantic scleractinian corals, species diversity is highest in the Caribbean, but low diversity and high endemism are observed in various peripheral populations in central and eastern Atlantic islands and along the coasts of Brazil and West Africa. The degree of connectivity between these distantly separated populations is of interest because it provides insight into processes at both evolutionary and ecological time scales, such as speciation, recruitment dynamics and the persistence of coral populations. To assess connectivity in broadly distributed coral species of the Atlantic, DNA sequence data from two nuclear markers were obtained for six coral species spanning their distributional ranges. At basin-wide scales, significant differentiation was generally observed among populations in the Caribbean, Brazil and West Africa. Concordance of patterns in connectivity among co-distributed taxa indicates that extrinsic barriers, such as the Amazon freshwater plume or long stretches of open ocean, restrict dispersal of coral larvae from region to region. Within regions, dispersal ability appears to be influenced by aspects of reproduction and life history. Two broadcasting species, Siderastrea siderea and Montastraea cavernosa, were able to maintain gene flow among populations separated by as much as 1,200 km along the coast of Brazil. In contrast, brooding species, such as Favia gravida and Siderastrea radians, had more restricted gene flow along the Brazilian coast