Biology subjects

Hempel, E.

Publications and source records attributed to Hempel, E..

3 recordsLinked to original sources

bioRxiv2024

A novel method for harmonization of PET image spatial resolution without phantoms

The most common approach for estimating the spatial resolution of PET images in multi-center studies typically uses Hoffman phantom data as a surrogate. Specifically, the phantom-based matching resolution approach assumes that scanned phantom PET images are well approximated by a ground truth, noise-free digital phantom convolved with a Gaussian kernel of unknown size. The size of the kernel is then estimated by an exhaustive search on the amount of blurring needed to match the smoothed digital phantom to a particular scanned phantom image. Unfortunately, Hoffman phantom images may not always be readily available, and phantom-based approaches may yield sub-optimal results. We propose a new, computational approach that allows estimation of spatial resolution directly from the PET image itself. We generalized the so-called logarithmic intensity plots method to the 3D case to perform a spatial resolution estimation in both axial and in-plane directions of the PET images. The proposed approach was applied to two different cohorts. The first cohort consisted of [18F]florbetapir amyloid PET images and matching phantoms coming from a Phase II clinical trial and includes different scanner models and/or orientation and grid reconstructions. The second cohort included {beta}-amyloid, FDG and tau PET images from the Alzheimers Disease Neuroimaging Initiative (ADNI) study. We obtained in-plane and axial resolution estimators that vary between 3.5 mm and 8.5 mm for both PET and matching phantom images. In both cases, we obtained small across-subject variability in groups of images sharing the same PET scanner model and reconstruction parameters. For human PET images, we also obtained a strong cross-tracer and longitudinal consistency in the spatial resolution estimators. Our novel approach does not only eliminate the need for surrogate brain phantom data, but also provides a general framework that can be applied to a wide range of tracers and other image modalities, such as SPECT.

neuroscience↗

bioRxiv2022

When blue turns to grey - Paleogenomic insights into the evolutionary history and extinction of the blue antelope (Hippotragus leucophaeus)

The blue antelope (Hippotragus leucophaeus) is the only large African mammal species to have become extinct in historical times, yet no nuclear genomic information is available for this species. A recent study showed that many alleged blue antelope museum specimens are either roan (H. equinus) or sable (H. niger) antelopes, further reducing the possibilities for obtaining genomic information for this extinct species. While the blue antelope has a rich fossil record from South Africa, climatic conditions in the region are unfavourable to the preservation of ancient DNA. Nevertheless, we recovered two blue antelope draft genomes, one at 3.4x mean coverage from a historical specimen (~200 years old) and one at 2.1x mean coverage from a fossil specimen dating to 9,800-9,300 cal BP, making it currently the oldest palaeogenome from Africa. Phylogenomics show that blue and sable antelope are sister species, confirming previous mitogenomic results, and demonstrate ancient gene flow from roan into blue antelope. We show that blue antelope genomic diversity was much lower than in roan and sable antelopes, indicative of a low population size since at least the early Holocene. This supports observations from the fossil record documenting major decreases in the abundance of blue antelope after the Pleistocene-Holocene transition. Finally, the persistence of this species throughout the Holocene despite low population size suggests that colonial-era human impact was likely a decisive factor in the blue antelopes extinction.

evolutionary biology↗

bioRxiv2018

Reticulate Evolutionary History of a Western Palaearctic Bat Complex Explained by Multiple mtDNA Introgressions in Secondary Contacts

AimThere is increasing evidence showing that species within various taxonomic groups have reticulate evolutionary histories with several cases of introgression events. Investigating the phylogeography of species complexes can provide insight about the introgressions, when and where these hybridizations occurred. In this study, we investigate the biogeography of a widely distributed Western Palaearctic bat species complex, namely Myotis nattereri sensu lato. This complex exhibits high genetic diversity and in its western distribution range is composed of deeply diverged genetical lineages. However, little is known about the genetic structure of the eastern populations. We also infer the conservation and taxonomical implications of the identified genetic divergences.\n\nLocationWestern Palaearctic\n\nMethodsWe analyzed 175 specimens collected from 67 locations and sequenced one mitochondrial and four nuclear DNA markers, and combined these with the available Gen-Bank sequences. We used haplotype networks, PCA, t-SNE, and Bayesian clustering algorithms to investigate the population structure and Bayesian trees to infer the phylogenetic relationship of the lineages.\n\nMain conclusionsWe identified deeply divergent genetical lineages. In some cases, nuclear and mitochondrial markers were discordant, which we interpret are caused by hybridization between lineages. We identified three such introgression events. Our findings suggest that the M. nattereri complex has a reticulate evolutionary history with multiple cases of hybridizations between some of the identified lineages. We also suggest a revision in the taxonomy of this species group, with two possible new taxa: M. hoveli and M. tschuliensis.

evolutionary biology↗