VolumePeeler: a novel FIJI plugin for geometric tissue peeling to improve visualization and quantification of 3D image stacks.

MOTIVATION: Quantitative descriptions of multi-cellular structures from optical microscopy imaging are prime to understand the variety of three-dimensional (3D) shapes in living organisms. Experimental models of vertebrates, invertebrates and plants, such as zebrafish, killifish, Drosophila or Marchantia, mainly comprise multilayer tissues, and even if microscopes can reach the needed depth, their geometry hinders the selection and subsequent analysis of the optical volumes of interest. Computational tools to "peel" tissues by removing specific layers and reducing 3D volume into planar images, can critically improve visualization and analysis. RESULTS: We developed VolumePeeler, a versatile FIJI plugin for virtual 3D "peeling" of image stacks. The plugin implements spherical and spline surface projections. We applied VolumePeeler to perform peeling in 3D images of spherical embryos, as well as non-spherical tissue layers. The produced images improve the 3D volume visualization and enable analysis and quantification of geometrically challenging microscopy datasets. AVAILABILITY: ImageJ/FIJI software, source code, examples, and tutorials are openly available in https://cimt.uchile.cl/mcerda.

Cochlear dysfunction as an early biomarker of cognitive decline in normal hearing and mild hearing loss.

INTRODUCTION: Age-related hearing loss is an important risk factor for cognitive decline. However, audiogram thresholds are not good estimators of dementia risk in subjects with normal hearing or mild hearing loss. Here we propose to use distortion product otoacoustic emissions (DPOAEs) as an objective and sensitive tool to estimate the risk of cognitive decline in older adults with normal hearing or mild hearing loss. METHODS: We assessed neuropsychological, brain magnetic resonance imaging, and auditory analyses on 94 subjects > 64 years of age. RESULTS: We found that cochlear dysfunction, measured by DPOAEs-and not by conventional audiometry-was associated with Clinical Dementia Rating Sum of Boxes (CDR-SoB) classification and brain atrophy in the group with mild hearing loss (25 to 40 dB) and normal hearing (<25 dB). DISCUSSION: Our findings suggest that DPOAEs may be a non-invasive tool for detecting neurodegeneration and cognitive decline in the older adults, potentially allowing for early intervention.

Molecular dynamics simulations of the interactions between platinum clusters and carbon platelets.

Molecular dynamics simulations have been performed with two reactive force fields to investigate the structure of a Pt100 cluster adsorbed on the three distinct sides of a carbon platelet. A revised Reax force field for the carbon-platinum system is presented. In the simulations, carbon platelet edges both with and without hydrogen termination have been studied. It is found that the initial mismatch between the atomic structure of the platelet egde and the adsorbed face of the Pt100 cluster leads to a desorption of a few platinum atoms from the cluster and the subsequent restructuring of the cluster. Consequently, the average Pt-Pt bond length is enlarged in agreement with experimental results. This change in the bond length is supposed to play an important role in the enhancement of the catalytic activity, which is demonstrated by studying the changes in the bond order of the platinum atoms. We found an overall shift to lower values as well as a loss of the well-defined peak structure in the bond-order distribution.

Modelling the growth of ZnO thin films by PVD methods and the effects of post-annealing.

Results are presented for modelling of the evaporation and magnetron sputter deposition of Zn(x)O(y) onto an O-terminated ZnO (0001¯) wurtzite surface. Growth was simulated through a combination of molecular dynamics (MD) and an on-the-fly kinetic Monte Carlo (otf-KMC) method, which finds diffusion pathways and barriers without prior knowledge of transitions. We examine the effects of varying experimental parameters, such as substrate bias, distribution of the deposition species and annealing temperature. It was found when comparing evaporation and sputtering growth that the latter process results in a denser and more crystalline structure, due to the higher deposition energy of the arriving species. The evaporation growth also exhibits more stacking faults than the sputtered growth. Post-annealing at 770 K did not allow complete recrystallization, resulting in films which still had stacking faults where monolayers formed in the zinc blende phase, whereas annealing at 920 K enabled the complete recrystallization of some films to the wurtzite structure. At the latter temperature atoms could also sometimes be locked in the zinc blende phase after annealing. When full recrystallization did not take place, both wurtzite and zinc blende phases were seen in the same layer, resulting in a phase boundary. Investigation of the various distributions of deposition species showed that, during evaporation, the best quality film resulted from a stoichiometric distribution where only ZnO clusters were deposited. During sputtering, however, the best quality film resulted from a slightly O rich distribution. Two stoichiometric distributions, one involving mainly ZnO clusters and the other involving mainly single species, showed that the distribution of deposition species makes a huge impact on the grown film. The deposition of predominantly single species causes many more O atoms at the surface to be sputtered or reflected, resulting in an O deficiency of up to 18% in the deposited film and therefore resulting in more stacking faults and phase boundaries. The methods used allow analysis of key mechanisms that occur during the growth process and give hints as to the optimum conditions under which complete crystalline layers can form.

Carbon nanotubes as substrates for molecular spiropyran-based switches.

We present a joint theory-experiment study investigating the excitonic absorption of spiropyran-functionalized carbon nanotubes. The functionalization is promising for engineering switches on a molecular level, since spiropyrans can be reversibly switched between two different conformations, inducing a distinguishable and measurable change of optical transition energies in the substrate nanotube. Here, we address the question of whether an optical read-out of such a molecular switch is possible. Combining density matrix and density functional theory, we first calculate the excitonic absorption of pristine and functionalized nanotubes. Depending on the switching state of the attached molecule, we observe a red-shift of transition energies by about 15 meV due to the coupling of excitons with the molecular dipole moment. Then we perform experiments measuring the absorption spectrum of functionalized carbon nanotubes for both conformations of the spiropyran molecule. We find good qualitative agreement between the theoretically predicted and experimentally measured red-shift, confirming the possibility for an optical read-out of the nanotube-based molecular switch.