bioRxiv ScienceSearch

Biology subjects

Kelly, C. N.

Publications and source records attributed to Kelly, C. N..

2 recordsLinked to original sources

Computational and Image Processing Methods for Analysis and Automation of Anatomical Alignment and Joint Spacing in Reconstructive Surgery

PurposeReconstructive surgeries to treat a number of musculoskeletal conditions, from arthritis to severe trauma, involve implant placement and reconstructive planning components. Anatomically matched 3D printed implants are becoming increasingly patient-specific; however the preoperative planning and design process requires several hours of manual effort from highly trained engineers and clinicians. Our work mitigates this problem by proposing algorithms for the automatic re-alignment of unhealthy anatomies, leading to more efficient, affordable, and scalable treatment solutions. MethodsOur solution combines global alignment techniques such as iterative closest points (ICP) with novel joint space refinement algorithms. The latter is achieved by a low dimensional characterization of the joint space, computed from the distribution of the distance between adjacent points in a joint. ResultsExperimental validation is presented on real clinical data from human subjects. Compared with ground truth healthy anatomies, our algorithms can reduce misalignment errors by 22% in translation and 19% in rotation for the full foot-and-ankle and 37% in translation and 39% in rotation for the hind-foot only, achieving a performance comparable to expert technicians. ConclusionOur methods and histogram-based metric allow for automatic and unsupervised alignment of anatomies, a major step toward a fully automated and data driven re-positioning, designing, and diagnosing tool.

bioengineering

Metagenomic reconstruction of nitrogen and carbon cycling pathways in forest soil: Influence by different hardwood tree species

The soil microbiome plays an essential role in processing and storage of nitrogen (N) and carbon (C), and is influenced by vegetation above-ground through imparted differences in chemistry, structure, mass of plant litter, root physiology, and dominant mycorrhizal associations. We used shotgun metagenomic sequencing and bioinformatic analysis to quantify the abundance and distribution of gene families involved in soil microbial N and C cycling beneath three deciduous hardwood tree species: ectomycorrhizal (ECM)-associated Quercus rubra (red oak), ECM-associated Castanea dentata (American chestnut), and arbuscular mycorrhizal (AM)-associated Prunus serotina (black cherry). Chestnut exhibited the most distinct soil microbiome of the three species, both functionally and taxonomically, with a general suppression of functional genes in the nitrification, denitrification, and nitrate reduction pathways. These changes were related to low inorganic N availability in chestnut stands as soil was modified by poor, low-N litter quality relative to red oak and black cherry soils. IMPORTANCEPrevious studies have used field biogeochemical process rates, isotopic tracing, and targeted gene abundance measurements to study the influence of tree species on ecosystem N and C dynamics. However, these approaches do not enable a comprehensive systems-level understanding of the relationship between microbial diversity and metabolism of N and C below-ground. We analyzed microbial metagenomes from soils beneath red oak, American chestnut, and black cherry stands and showed that tree species can mediate the abundance of key microbial genes involved in N and (to a lesser extent) C metabolism pathways in soil. Our results highlight the genetic framework underlying tree species control over soil microbial communities, and below-ground C and N metabolism, and may enable land managers to select tree species to maximize C and N storage in soils.

ecology