An Analysis by Synthesis Approach for Automatic Vertebral Shape Identification in Clinical QCT

Quantitative computed tomography (QCT) is a widely used tool for osteoporosis diagnosis and monitoring. The assessment of cortical markers like cortical bone mineral density (BMD) and thickness is a demanding task, mainly because of the limited spatial resolution of QCT. We propose a direct model based method to automatically identify the surface through the center of the cortex of human vertebra. We develop a statistical bone model and analyze its probability distribution after the imaging process. Using an as-rigid-as-possible deformation we find the cortical surface that maximizes the likelihood of our model given the input volume. Using the European Spine Phantom (ESP) and a high resolution \mu CT scan of a cadaveric vertebra, we show that the proposed method is able to accurately identify the real center of cortex ex-vivo. To demonstrate the in-vivo applicability of our method we use manually obtained surfaces for comparison.Comment: Presented on German Conference on Pattern Recognition (GCPR) 2018 in Stuttgar

Identification of hip fracture patients from radiographs using Fourier analysis of the trabecular structure: a cross-sectional study

Peer reviewedPublisher PD

Influence of gold nanoparticles on collagen fibril morphology quantified using transmission electron microscopy and image analysis

BACKGROUND: Development of implantable biosensors for disease detection is challenging because of poor biocompatibility of synthetic materials. A possible solution involves engineering interface materials that promote selfassembly and adhesion of autologous cells on sensor surfaces. Crosslinked type-I collagen is an acceptable material for developing engineered basement membranes. In this study, we used functionalized gold nanoparticles as the crosslinking agent. Functionalized nanoparticles provide sites for crosslinking collagen as well as sites to deliver signaling compounds that direct selfassembly and reduce inflammation. The goal of this study was to obtain a quantitative parameter to objectively determine the presence of crosslinks. METHODS: We analyzed TEM images of collagen fibrils by two methods: Run length analysis and topology analysis after medial axis transform. RESULTS: Run length analysis showed a significant reduction of the interfibril spaces in the presence of nanoparticles (change of 40%, P < 0.05), whereas the fibril thickness remained unchanged. In the topological network, the number of elements, number of branches and number of sides increased significantly in the presence of nanoparticles (P < 0.05). Other parameters, especially the number of loops showed only a minimal and nonsignificant change. We chose a ratiometric parameter of the number of branches normalized by the number of loops to achieve independence from gross fibril density. This parameter is lower by a factor of 2.8 in the presence of nanoparticles (P < 0.05). CONCLUSION: The numerical parameters presented herein allow not only to quantify fibril mesh complexity and crosslinking, but also to help quantitatively compare cell growth and adhesion on collagen matrices of different degree of crosslinking in further studies

Apparent Shear Sensitivity of Molecular Rotors in Various Solvents

Fluorescent environment-sensitive dyes often change their spectral properties concomitantly with multiple solvent properties, such as polarity, protonation, hydrogen bond formation, or viscosity. Careful consideration of the response is needed when a fluorescent dye is used to report a single property. Recently, we observed an increase of emission intensity of viscosity-sensitive molecular rotors in fluids subject to flow and speculated that either polar-polar interaction or hydrogen bond formation play a role in the apparent flow sensitivity. In this study, we show experimental evidence that photoisomerization to an isomer with a lower quantum yield, first proposed by Rumble et al. (J Phys Chem A 116(44):10786-10792, 2012), plays a key role in the observed phenomenon. We subjected four molecular rotors with different electron acceptor motifs to fluid flow in solvents of different polarity and ability to form hydrogen bonds. We also measured the isomerization dynamics in a custom fluorophotometer with extremely low light exposure. Our results indicate that the photoisomerization rate depends both on the solvent and on the electron acceptor group, as does the recovery of the original isomer in the dark. In most solvents, recovery of the dark isomer is much more rapid than originally reported, and a state of quasi-equilibrium between both isomers is possible. Moreover, the sensitivity (i.e., relative intensity increase at the same flow rate) is also solvent-dependent. The intensity increase can be detected at very low velocities (as low as 0.06 mm/s). Characteristic for fluorescent dyes is the high spatial resolution, and no flow measurement device with comparable sensitivity and spatial resolution exists, although the nature of the solvent needs to be taken into account for quantitative flow measurement

Solvation and Protonation of Coumarin 102 in Aqueous Media - a Fluorescence Spectroscopic and Theoretical Study

The ground and excited state protonation of Coumarin 102 (C102), a fluorescent probe applied frequently in heterogeneous systems with an aqueous phase, has been studied in aqueous solutions by spectroscopic experiments and theoretical calculations. For the dissociation constant of the protonated form in the ground state, was obtained from the absorption spectra, for the excited state dissociation constant was obtained from the fluorescence spectra. These values were closely reproduced by theoretical calculations via a thermodynamic cycle – the value of also by calculations via the Förster cycle - using an implicit-explicit solvation model (polarized continuum model + addition of a solvent molecule). The theoretical calculations indicated that (i) in the ground state C102 occurs primarily as a hydrogen bonded water complex, with the oxo group as the binding site, (ii) this hydrogen bond becomes stronger upon excitation; (iii) in the ground state the amino nitrogen atom, in the excited state the carboxy oxygen atom is the protonation site. A comprehensive analysis of fluorescence decay data yielded the values kpr = 3.271010 M-1 s 1 for the rate constants of excited state protonation, and kdpr = 2.78108 s-1 for the rate constant of the reverse process (kpr and kdpr were treated as independent parameters). This, considering the relatively long fluorescence lifetimes of neutral C102 (6.02 ns) and its protonated form (3.06 ns) in aqueous media, means that a quasi-equilibrium state of excited state proton transfer is reached in strongly acidic solutions

Extrinsic Fluorescent Dyes as Tools for Protein Characterization

Noncovalent, extrinsic fluorescent dyes are applied in various fields of protein analysis, e.g. to characterize folding intermediates, measure surface hydrophobicity, and detect aggregation or fibrillation. The main underlying mechanisms, which explain the fluorescence properties of many extrinsic dyes, are solvent relaxation processes and (twisted) intramolecular charge transfer reactions, which are affected by the environment and by interactions of the dyes with proteins. In recent time, the use of extrinsic fluorescent dyes such as ANS, Bis-ANS, Nile Red, Thioflavin T and others has increased, because of their versatility, sensitivity and suitability for high-throughput screening. The intention of this review is to give an overview of available extrinsic dyes, explain their spectral properties, and show illustrative examples of their various applications in protein characterization

Predicting River Macroinvertebrate Communities Distributional Shifts under Future Global Change Scenarios in the Spanish Mediterranean Area

Several studies on global change over the next century predict increases in mean air temperatures of between 1°C to 5°C that would affect not only water temperature but also river flow. Climate is the predominant environmental driver of thermal and flow regimes of freshwater ecosystems, determining survival, growth, metabolism, phenology and behaviour as well as biotic interactions of aquatic fauna. Thus, these changes would also have consequences for species phenology, their distribution range, and the composition and dynamics of communities. These effects are expected to be especially severe in the Mediterranean basin due its particular climate conditions, seriously threatening Southern European ecosystems. In addition, species with restricted distributions and narrow ecological requirements, such as those living in the headwaters of rivers, will be severely affected. The study area corresponds to the Spanish Mediterranean and Balearic Islands, delimited by the Köppen climate boundary. With the application of the MEDPACS (MEDiterranean Prediction And Classification System) predictive approach, the macroinvertebrate community was predicted for current conditions and compared with three posible scenarios of watertemperature increase and its associated water flow reductions. The results indicate that the aquatic macroinvertebrate communities will undergo a drastic impact, with reductions in taxa richness for each scenario in relation to simulated current conditions, accompanied by changes in the taxa distribution pattern. Accordingly, the distribution area of most of the taxa (65.96%) inhabiting the mid-high elevations would contract and rise in altitude. Thus, families containing a great number of generalist species will move upstream to colonize new zones with lower water temperatures. By contrast, more vulnerable taxa will undergo reductions in their distribution area.This work was funded by GUADALMED-II (REN2001-3438-C07-06/HID), a project of excellence from “Junta de Andalucía” (RNM-02654/FEDER), the Spanish “Ministerio de Ciencia e Innovación” (CGL2007-61856/BOS), projects and a collaboration agreement between the “Spanish Ministerio de Medio Ambiente, Medio Rural y Marino” and the University of Granada (21.812-0062/8511)