Heat-induced retrieval of immunogold labeling for nucleobindin and osteoadherin from Lowicryl sections of bone

The main purpose of this study was to examine whether antigens can be retrieved by heating Lowicryl sections of paraformaldehyde-fixed (PFF) tissues. Thus the intensity of the immunogold signal for two bone proteins (Nucleobindin (Nuc) and osteoadherin (OSAD)) was compared in retrieved and non-retrieved sections of PFF rat bone. As an additional experiment, the effect of antigen retrieval (for Nuc) in sections of tissue primary stabilized by high pressure freezing with subsequent freeze substitution (HPF-FS) was studied. Finally, the tissue distribution patterns of Nuc labeling were compared in non-retrieved HPF-FS sections to that of retrieved and non-retrieved PFF sections. Antigen retrieval in Lowicryl sections of PFF tissues showed significantly enhanced labeling intensity for both proteins in all compartments where they are known to occur. Retrieved PFF Lowicryl sections showed only minor ultrastructural differences compared to non-retrieved ones. Retrieval of HPF-FS sections exhibited no enhancement of labeling but rather a slight reduction, which was significant in the cytoplasm and in cartilage. Furthermore, striking ultrastructural differences were observed in retrieved HPF-FS sections compared to non-retrieved ones with loss of coherence and structure in sections subjected to heating. Comparison of the distribution patterns of Nuc in the sections of PFF and HPF-FS tissues showed discrepancy in most compartments. Antigen retrieval by heating Lowicryl sections of PFF tissues significantly enhances immunogold labeling in all cell compartments where the bone proteins are known to occur. However, the procedure may distort the tissue distribution pattern of bone proteins.     

Tautomeric populations of the charged species of 1,12‐diamino‐3,6,9‐triazadodecane (SpmTrien) studied with computer simulations and cluster expansions

Correct net charge and protonation pattern in the polyamine backbone is one of the major factors that define the interactions of this class of compounds. 1,12‐diamino‐3,6,9‐triazadodecane (SpmTrien) is a isosteric charge deficient analogue of naturally occurring spermine (Spm) with different biological features. The tautomeric populations of each SpmTrien charge state were estimated with computer simulations, molecular dynamics (MD) and quantum mechanical calculations, and cluster expansions separately. In the computer simulations, tautomeric populations of each charge state were obtained by constrained least‐squares fitting the theoretically calculated (GIAO B3LYP/6‐311 + G**) ¹⁵ N NMR chemical shieldings of SpmTrien tautomers to the experimentally measured chemical shifts. Theoretical chemical shieldings were calculated for water complexes of SpmTrien obtained from MD simulations in explicit water. Both methods gave highly similar realistic results. SpmTrien has many major populations of tautomers at biologically relevant charge states of three (+3) and four (+4) thus enabling a large variety of structures for specific ionic interactions. Copyright © 2013 John Wiley & Sons, Ltd.     

Narrowband bulk Bragg grating optical parametric oscillator

A narrowband, pulsed optical parametric oscillator (OPO) whose output coupler is a bulk glass Bragg grating is demonstrated. The OPO is based on periodically poled KTiOPO4 and is pumped by a pulsed, frequency-doubled Nd:YAG laser at 532 nm, generating a signal at 975 nm with a total efficiency of 35%. This novel and compact device shows a spectral bandwidth of 0.16 nm (50 GHz), a decrease by a factor of 20 compared with that when a conventional mirror is used. By using a folded cavity, we demonstrate tunable radiation with a tuning range of 60 nm and maintained spectral bandwidth.     

Diffusion-direction-dependent imaging: a novel MRI approach for peripheral nerve imaging

A novel magnetic resonance imaging approach, called diffusion-direction-dependent imaging (DDI), is introduced. Due to inherent anisotropic diffusion properties, peripheral nerves can be visualized on diffusion tensor imaging (DTI). The largest signal attenuation on DTI correlates with the direction of a nerve fiber, and the least signal attenuation correlates with the direction perpendicular to the nerve fiber. Since low signal-to-noise ratio is a concern in peripheral nerve DTI, we explored a new approach focusing on the perpendicular diffusion direction. A 36-gradient diffusion direction scheme was used. A mean expected curve specific for peripheral nerves was calculated based on the sciatic nerve and its division into the common peroneal nerve and the tibial nerve in three healthy volunteers. By a simple postprocessing method, a comparison of the mean expected curve and the measured curve was made voxel by voxel, and the sciatic nerve and its division were reconstructed, excluding other tissues. More studies are needed to investigate whether other postprocessing methods or other diffusion direction schemes are more suited for peripheral nerve imaging with DDI. Further studies may also be of interest to investigate whether DDI can be a complementary method to conventional T(1)-weighted and T(2)-weighted sequences in the imaging of peripheral nerve pathology or even in the visualization of other tissues, possibly with different diffusion direction schemes.     

Modelling of a city canyon problem in a turbulent atmosphere using an equivalent sources approach

The sound propagation into a courtyard shielded from direct exposure is predicted using an equivalent sources approach. The problem is simplified into that of a two-dimensional city canyon. A set of equivalent sources are used to couple the free half-space above the canyon to the cavity inside the canyon. Atmospheric turbulence causes an increase in the expected value of the sound pressure level compared to a homogeneous case. The level increase is estimated using a von Kármán turbulence model and the mutual coherences of all equivalent sources' contributions. For low frequencies the increase is negligible, but at 1.6 kHz it reaches 2-5 dB for the geometries and turbulence parameters used here. A comparison with a ray-based model shows reasonably good agreement.     

Neural Estimator of Information for Time-Series Data with Dependency

Novel approaches to estimate information measures using neural networks are well-celebrated in recent years both in the information theory and machine learning communities. These neural-based estimators are shown to converge to the true values when estimating mutual information and conditional mutual information using independent samples. However, if the samples in the dataset are not independent, the consistency of these estimators requires further investigation. This is of particular interest for a more complex measure such as the directed information, which is pivotal in characterizing causality and is meaningful over time-dependent variables. The extension of the convergence proof for such cases is not trivial and demands further assumptions on the data. In this paper, we show that our neural estimator for conditional mutual information is consistent when the dataset is generated with samples of a stationary and ergodic source. In other words, we show that our information estimator using neural networks converges asymptotically to the true value with probability one. Besides universal functional approximation of neural networks, a core lemma to show the convergence is Birkhoff’s ergodic theorem. Additionally, we use the technique to estimate directed information and demonstrate the effectiveness of our approach in simulations.     

Dimensions and Lyapunov exponents from exchange rate series

Detecting the presence of deterministic chaos in economic time series is an important problem that may be solved by measuring the largest Lyapunov exponent. In this paper we present estimates of the largest Lyapunov exponent in daily data for the Swedish Krona vs Deutsche Mark, ECU, U.S. Dollar and Yen exchange rates. In order to estimate the dimension of the systems producing these exchange rate series, we also present estimates of the correlation dimension. We found indications of deterministic chaos in all exchange rate series. However, the estimates for the largest Lyapunov exponents are not reliable, except in the Swedish Krona-ECU case, because of the limited number of data points. In the Swedish Krona-ECU case, we found indications of a low-order chaotic dynamical system.