CopyVAE: a variational autoencoder-based approach for copy number variation inference using single-cell transcriptomics.

MOTIVATION: Copy number variations (CNVs) are common genetic alterations in tumour cells. The delineation of CNVs holds promise for enhancing our comprehension of cancer progression. Moreover, accurate inference of CNVs from single-cell sequencing data is essential for unravelling intratumoral heterogeneity. However, existing inference methods face limitations in resolution and sensitivity. RESULTS: To address these challenges, we present CopyVAE, a deep learning framework based on a variational autoencoder architecture. Through experiments, we demonstrated that CopyVAE can accurately and reliably detect CNVs from data obtained using single-cell RNA sequencing. CopyVAE surpasses existing methods in terms of sensitivity and specificity. We also discussed CopyVAE's potential to advance our understanding of genetic alterations and their impact on disease advancement. AVAILABILITY AND IMPLEMENTATION: CopyVAE is implemented and freely available under MIT license at https://github.com/kurtsemih/copyVAE.

A morphological investigation of the tongue of roe deer (Capreolus capreolus Linnaeus, 1758).

The morphological structure of the tongue and papillae that occur on it vary according to an animal's lifestyle, nutrition, and adaptation to various environmental conditions. This study aimed to reveal in detail the morphological, histological, and electron microscopic structure of the tongue of roe deer (Capreolus capreolus Linnaeus, 1758). In this study, nine roe tongues were used. The tongue consists of three parts: the apex, body, and root. When the dorsal surface of the tongue was examined in detail, five different papillae were observed: filiform, lenticular, conical, fungiform, and vallate. Filiform papillae differed in having secondary papillae according to their localization. The opening holes of taste buds were observed on the surface of the round and flat fungiform papillae. The free ends of the filiform papillae were more pointed and thinner than those of the other papillae, while the width of the lenticular papillae was thicker, the surface was flat, and the free ends were blunt. Triangular-shaped conical papillae were observed differently regarding the presence or absence of secondary papillae. The vallate papillae were caudolateral to the lingual torus. On the surface of the vallate papillae, circumferenced by a deep groove, were the opening holes of the taste buds and microridges. From this analysis, it appears to be characteristic of roe deer that mechanical function, filiform, and conical papillae contain secondary papillae; lenticular papillae, absent in many deer species, are found; and a prominent papillary groove surrounds all mechanical and gustatory papillae. RESEARCH HIGHLIGHTS: The lingual papillae of roe deer (Capreolus capreolus Linnaeus, 1758) were examined with this study in detail for the first time. Similarities and differences with ruminant species were determined.

Comparison of sheep scapula models created with polylactic acid and thermoplastic polyurethane filaments by three-dimensional modelling.

Three-dimensional (3D) printing technology is a rapid prototyping method that has recently been increasingly used in anatomy education. Magnetic resonance imaging, computed tomography, and 3D scanners are generally used to create 3D models. The aim of this study, which was performed without using the aforementioned devices, is to design sheep scapula models in a computer environment and compare bone models created with different filaments printed by a 3D printer with real bone. Photographs of sheep scapula were taken for modelling, and measurements were made from certain points. After the photographs were transferred to a computer environment, they were transformed into 3D using the Cinema 4D software, a computer-aided design program. Models were created using a 3D printer employing polylactic acid (PLA) and thermoplastic polyurethane (TPU) filaments. By comparing the models created with PLA and TPU filaments to the real bone, it was found that they have a similar anatomical structure, with dimensional-morphometric differences found at some points. It was also observed that the scapula model created with PLA filaments was more resistant to impacts than the real bone and that the model created with TPU filaments was more flexible, with very low fragility as compared to PLA and real bone. Therefore, this method allows obtaining a large number of durable models as an alternative to the real bone without the need for much manpower or equipment and without the need for a 3D reconstruction device.

Rapid TAURUS for Relaxation-Based Color Magnetic Particle Imaging.

Magnetic particle imaging (MPI) is a rapidly developing medical imaging modality that exploits the non-linear response of magnetic nanoparticles (MNPs). Color MPI widens the functionality of MPI, empowering it with the capability to distinguish different MNPs and/or MNP environments. The system function approach for color MPI relies on extensive calibrations that capture the differences in the harmonic responses of the MNPs. An alternative calibration-free x-space-based method called TAURUS estimates a map of the relaxation time constant, τ , by recovering the underlying mirror symmetry in the MPI signal. However, TAURUS requires a back and forth scanning of a given region, restricting its usage to slow trajectories with constant or piecewise constant focus fields (FFs). In this work, we propose a novel technique to increase the performance of TAURUS and enable τ map estimation for rapid and multi-dimensional trajectories. The proposed technique is based on correcting the distortions on mirror symmetry induced by time-varying FFs. We demonstrate via simulations and experiments in our in-house MPI scanner that the proposed method successfully estimates high-fidelity τ maps for rapid trajectories that provide orders of magnitude reduction in scanning time (over 300 fold for simulations and over 8 fold for experiments) while preserving the calibration-free property of TAURUS.

Partial FOV Center Imaging (PCI): A Robust X-Space Image Reconstruction for Magnetic Particle Imaging.

Magnetic Particle Imaging (MPI) is an emerging medical imaging modality that images the spatial distribution of superparamagnetic iron oxide (SPIO) nanoparticles using their nonlinear response to applied magnetic fields. In standard x-space approach to MPI, the image is reconstructed by gridding the speed-compensated nanoparticle signal to the instantaneous position of the field free point (FFP). However, due to safety limits on the drive field, the field-of-view (FOV) needs to be covered by multiple relatively small partial field-of-views (pFOVs). The image of the entire FOV is then pieced together from individually processed pFOVs. These processing steps can be sensitive to non-ideal signal conditions such as harmonic interference, noise, and relaxation effects. In this work, we propose a robust x-space reconstruction technique, Partial FOV Center Imaging (PCI), with substantially simplified pFOV processing. PCI first forms a raw image of the entire FOV by mapping MPI signal directly to pFOV center locations. The corresponding MPI image is then obtained by deconvolving this raw image by a compact kernel, whose fully-known shape solely depends on the pFOV size. We analyze the performance of the proposed reconstruction via extensive simulations, as well as imaging experiments on our in-house FFP MPI scanner. The results show that PCI offers a trade-off between noise robustness and interference robustness, outperforming standard x-space reconstruction in terms of both robustness against non-ideal signal conditions and image quality.