High-Throughput Method of Whole-Brain Sectioning, Using the Tape-Transfer Technique

Cryostat sectioning is a popular but labor-intensive method for preparing histological brain sections. We have developed a modification of the commercially available CryoJane tape collection method that significantly improves the ease of collection and the final quality of the tissue sections. The key modification involves an array of UVLEDs to achieve uniform polymerization of the glass slide and robust adhesion between the section and slide. This report presents system components and detailed procedural steps, and provides examples of end results; that is, 20mum mouse brain sections that have been successfully processed for routine Nissl, myelin staining, DAB histochemistry, and fluorescence. The method is also suitable for larger brains, such as rat and monkey

Frequency-selective control of cortical and subcortical networks by central thalamus

Central thalamus plays a critical role in forebrain arousal and organized behavior. However, network-level mechanisms that link its activity to brain state remain enigmatic. Here, we combined optogenetics, fMRI, electrophysiology, and video-EEG monitoring to characterize the central thalamus-driven global brain networks responsible for switching brain state. 40 and 100 Hz stimulations of central thalamus caused widespread activation of forebrain, including frontal cortex, sensorimotor cortex, and striatum, and transitioned the brain to a state of arousal in asleep rats. In contrast, 10 Hz stimulation evoked significantly less activation of forebrain, inhibition of sensory cortex, and behavioral arrest. To investigate possible mechanisms underlying the frequency-dependent cortical inhibition, we performed recordings in zona incerta, where 10, but not 40, Hz stimulation evoked spindle-like oscillations. Importantly, suppressing incertal activity during 10 Hz central thalamus stimulation reduced the evoked cortical inhibition. These findings identify key brain-wide dynamics underlying central thalamus arousal regulation

Frequency-selective control of cortical and subcortical networks by central thalamus

Abstract Central thalamus plays a critical role in forebrain arousal and organized behavior. However, network-level mechanisms that link its activity to brain state remain enigmatic. Here, we combined optogenetics, fMRI, electrophysiology, and video-EEG monitoring to characterize the central thalamus-driven global brain networks responsible for switching brain state. 40 and 100 Hz stimulations of central thalamus caused widespread activation of forebrain, including frontal cortex, sensorimotor cortex, and striatum, and transitioned the brain to a state of arousal in asleep rats. In contrast, 10 Hz stimulation evoked significantly less activation of forebrain, inhibition of sensory cortex, and behavioral arrest. To investigate possible mechanisms underlying the frequencydependent cortical inhibition, we performed recordings in zona incerta, where 10, but not 40, Hz stimulation evoked spindle-like oscillations. Importantly, suppressing incertal activity during 10 Hz central thalamus stimulation reduced the evoked cortical inhibition. These findings identify key brain-wide dynamics underlying central thalamus arousal regulation

Role of mineral matrix composition and properties in the transformation of corn residues

The influence of the composition and properties of the mineral matrix in soils on the humification of corn residues was studied. The substrate (silica sand, loam, silica sand + 10% bentonite, or silica sand + 30% kaolinite) was mixed with 10% corn residues (milled to 3–5 mm) and incubated under stationary conditions for 6–19 months. Sampling for the analysis was performed every month, and a few times in the first month. The dynamics of mineralization and humification of plant residues was studied by applying elemental and bulk analyses of neogenic organic matter (OM), densitometric fractionation of substrates, FTIR spectroscopy, solid-phase 13C-NMR spectroscopy, and scanning electron microscopy with an electron microprobe. It was shown that the humification processes had a wavelike character for loam and sand substrates, which could be explained by the transformation of the microorganism populations together with the change in the amount and quality of OM in the system. The main mechanism for the stabilization of neogenic OM was adsorption on a mineral matrix with formation of relatively resistant compounds. This adsorption can be selective, depending on the composition and properties of the mineral matrix. The FTIR and 13C-NMR analyses of OM distribution in different substrates and densitometric fractions showed that sand and heavy fractions (HF >2.2 g/cm3) were enriched with compounds of an aromatic nature and polypeptides. Light fractions (LF-2, 1.4–2.2 g/cm3) accumulated compounds that also contained alkyl and carboxyl groups. The sandy substrate and HF have higher aromaticity indices than LF-2. Higher aromaticity index values of humus substances in the sandy substrate and HF in the loamy substrate, compared to LF-2, evidenced the formation of steady aromatic compounds, in which there may be kernels of humic acids (HA). We do not exclude the possibility of the matrix synthesis of the HA-like substances

An octree-based multiresolution approach supporting interactive rendering of very large volume data sets

Figure 1: Local re nement of nested ROIs in foot data set. Abstract We present an octree-based approach supporting multiresolution volume rendering of large data sets. Given a set of scattered points without connectivity information, we impose an octree data structure of low resolution in the preprocessing step. The construction of this initial octree structure is controlled by the original data resolution and cell-speci c error values. Using the octree nodes, rather than the data points, as elementary units for ray casting, we rst generate a crude rendering of a given data set. Keeping the pre-processing step independent from the rendering step, we allow a user to interactively explore a large data set by specifying a region of interest (ROI), where a higher level of rendering accuracy Center of Image Processing and Integrated Computing is desired. To re ne an ROI, we are making use of the octree constructed in the pre-processing step. Our approach is aimed at minimizing the number of computations and can be applied to large-scale data exploration tasks

The role of soil's particle-size fractions in the adsorption of heavy metals

The parameters of adsorption of Cu2+, Pb2+, and Zn2+ cations by southern chernozem and their particle-size fractions were studied. The adsorption of metals by soils and the strength of their fixation on the surface of soil particles under both mono- and poly-element contamination decreased with the decreasing proportion of fine fractions in the soil. The aim of this work was to study the effect of the particle-size distribution and the silt and physical clay fractions on the adsorption of copper, lead, and zinc by chernozems. The objects of study included the upper humus horizons of different southern chernozems of the Rostov oblast. To study the ion-exchange adsorption of the Cu2+, Pb2+, and Zn2+ cations, the soil in the natural ionic form was disaggregated using a pestle with a rubber head and sieved through a 1mm sieve. The soil samples were treated with solutions of Cu2+, Pb2+, and Zn2+ nitrates and acetates at the separate and simultaneous presence of heavy metals (HMs). In the solutions with the simultaneous presence of HMs, their molar concentrations were similar. The concentrations of the initial solutions varied in the range from 0.05 to 1 mM/l. The soil: solution ratio was 1:10. The contents of HMs in the filtrates were determined by atomic absorption spectrophotometry. The contents of adsorbed HM cations were calculated from the difference between the metal concentrations in the initial and equilibrium solutions. The increase in the degree of dispersion of the particle-size fractions in similar soils resulted not only in an increase in the content of adsorbed HMs but also in an enhancement of their fixation on the surface of the fine particles. Therefore, the adsorption capacity of the Lower Don soils for Cu2+, Pb2+, and Zn2+ decreased in the following sequence: clay loamy southern chernozem > loamy southern chernozem > loamy sandy southern chernozem. This was related to the qualitative differences in the mineralogy and chemistry of the separated fractions and the significant effect of their composition and properties on the parameters of the HMs adsorption

Constructing isosurfaces in a localized fashion using an underlying octree data structure

We present an octree-based approach for isosurface extraction from large volumetric scalar-valued data. Given scattered points with associated function values, we impose an octree structure of relatively low resolution. Octree construction is controlled by original data resolution and cell-specific error values. For each cell in the octree, we compute an average function value and additional statistical data for the original points inside the cell. Once a specific isovalue is specified, we adjust the initial octree by expanding its leaves based on a comparison of statistics with the isovalue. We tetrahedrize the centers of the octree's cells to determine tetrahedral meshes decomposing the entire spatial domain of the data, including a possibly specific region of interest (ROI). Extracted isosurfaces are crack-free inside an ROI, but cracks can appear at the boundary of an ROI. The inital isosurface is an approximation of the exact one, but its quality suffices for a viewer to identify an ROI where more accuracy is desirable. In the refinement process, we refine affected octree nodes and update the triangulation locally to produce better isosurface representations. This adaptive and user-driven refinement provides a means for interactive data exploration via real-time and local isosurface extraction