Biomarkers of Seizure Activity in Patients With Intracranial Metastases and Gliomas: A Wide Range Study of Correlated Regions of Interest

Abstract The limitations of 2D microscopy constrain our ability to observe and understand tissue-wide networks that are, by nature, 3-dimensional. Optical projection tomography enables the acquisition of large volumes (ranging from micrometres to centimetres) in various tissues, with label-free capacities for the observation of auto-fluorescent signals as well fluorescent-labelled targets of interest in multiple channels. We present a multi-modal workflow for the characterization of both structural and quantitative parameters of the mouse small intestine. As proof of principle, we evidence its applicability for imaging the mouse intestinal immune compartment and surrounding mucosal structures. We quantify the volumetric size and spatial distribution of Isolated Lymphoid Follicles (ILFs) and quantify density of villi throughout centimetre long segments of intestine. Furthermore, we exhibit the age- and microbiota-dependence for ILF development, and leverage a technique that we call reverse-OPT for identifying and homing in on regions of interest. Several quantification capabilities are displayed, including villous density in the autofluorescent channel and the size and spatial distribution of the signal of interest at millimetre-scale volumes. The concatenation of 3D image acquisition with the reverse-OPT sample preparation and a 2D high-resolution imaging modality adds value to interpretations made in 3D. This cross-modality referencing technique is found to provide accurate localisation of ROIs and to add value to interpretations made in 3D. Importantly, OPT may be used to identify sparsely-distributed regions of interest in large volumes whilst retaining compatibility with high-resolution microscopy modalities, including confocal microscopy. We believe this pipeline to be approachable for a wide-range of specialties, and to provide a new method for characterisation of the mouse intestinal immune compartment.

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Perineuronal Net Dynamics in the Pathophysiology of Epilepsy

Epilepsy Currents ◽

10.1177/15357597211018688 ◽

2021 ◽

pp. 153575972110186

Author(s):

Lata Chaunsali ◽

Bhanu P. Tewari ◽

Harald Sontheimer

Keyword(s):

Critical Period ◽

Seizure Activity ◽

Perineuronal Nets ◽

Rodent Models ◽

Central Nervous System Diseases ◽

Intrinsic Properties ◽

Perineuronal Net ◽

Ecm Remodeling ◽

Activity Inhibition ◽

Wide Range

Perineuronal nets (PNNs) are condensed extracellular matrix (ECM) assemblies of polyanionic chondroitin sulfate proteoglycans, hyaluronan, and tenascins that primarily wrap around GABAergic parvalbumin (PV) interneurons. During development, PNN formation terminates the critical period of neuroplasticity, a process that can be reversed by experimental disruption of PNNs. Perineuronal nets also regulate the intrinsic properties of the enclosed PV neurons thereby maintaining their inhibitory activity. Recent studies have implicated PNNs in central nervous system diseases as well as PV neuron dysfunction; consequently, they have further been associated with altered inhibition, particularly in the genesis of epilepsy. A wide range of seizure presentations in human and rodent models exhibit ECM remodeling with PNN disruption due to elevated protease activity. Inhibition of PNN proteolysis reduces seizure activity suggesting that PNN degrading enzymes may be potential novel therapeutic targets.

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TFmotifView: a webserver for the visualization of transcription factor motifs in genomic regions

Nucleic Acids Research ◽

10.1093/nar/gkaa252 ◽

2020 ◽

Vol 48 (W1) ◽

pp. W208-W217

Author(s):

Clémentine Leporcq ◽

Yannick Spill ◽

Delphine Balaramane ◽

Christophe Toussaint ◽

Michaël Weber ◽

...

Keyword(s):

Gene Expression ◽

Transcription Factor ◽

Transcription Factors ◽

Regulation Of Gene Expression ◽

Genomic Region ◽

Regions Of Interest ◽

P Value ◽

Wide Range ◽

Genomic Regions ◽

Motif Information

Abstract Transcription factors (TFs) regulate the expression of gene expression. The binding specificities of many TFs have been deciphered and summarized as position-weight matrices, also called TF motifs. Despite the availability of hundreds of known TF motifs in databases, it remains non-trivial to quickly query and visualize the enrichment of known TF motifs in genomic regions of interest. Towards this goal, we developed TFmotifView, a web server that allows to study the distribution of known TF motifs in genomic regions. Based on input genomic regions and selected TF motifs, TFmotifView performs an overlap of the genomic regions with TF motif occurrences identified using a dynamic P-value threshold. TFmotifView generates three different outputs: (i) an enrichment table and scatterplot calculating the significance of TF motif occurrences in genomic regions compared to control regions, (ii) a genomic view of the organisation of TF motifs in each genomic region and (iii) a metaplot summarizing the position of TF motifs relative to the center of the regions. TFmotifView will contribute to the integration of TF motif information with a wide range of genomic datasets towards the goal to better understand the regulation of gene expression by transcription factors. TFmotifView is freely available at http://bardet.u-strasbg.fr/tfmotifview/.

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The application of a workflow integrating the variable reproducibility and harmonizability of radiomic features on a phantom dataset

PLoS ONE ◽

10.1371/journal.pone.0251147 ◽

2021 ◽

Vol 16 (5) ◽

pp. e0251147

Author(s):

Abdalla Ibrahim ◽

Turkey Refaee ◽

Ralph T. H. Leijenaar ◽

Sergey Primakov ◽

Roland Hustinx ◽

...

Keyword(s):

High Throughput ◽

Medical Images ◽

Image Acquisition ◽

Regions Of Interest ◽

Analysis Framework ◽

Wide Range ◽

The Subject

Radiomics–the high throughput extraction of quantitative features from medical images and their correlation with clinical and biological endpoints- is the subject of active and extensive research. Although the field shows promise, the generalizability of radiomic signatures is affected significantly by differences in scan acquisition and reconstruction settings. Previous studies reported on the sensitivity of radiomic features (RFs) to test-retest variability, inter-observer segmentation variability, and intra-scanner variability. A framework involving robust radiomics analysis and the application of a post-reconstruction feature harmonization method using ComBat was recently proposed to address these challenges. In this study, we investigated the reproducibility of RFs across different scanners and scanning parameters using this framework. We analysed thirteen scans of a ten-layer phantom that were acquired differently. Each layer was subdivided into sixteen regions of interest (ROIs), and the scans were compared in a pairwise manner, resulting in seventy-eight different scenarios. Ninety-one RFs were extracted from each ROI. As hypothesized, we demonstrate that the reproducibility of a given RF is not a constant but is dependent on the heterogeneity found in the data under analysis. The number (%) of reproducible RFs varied across the pairwise scenarios investigated, having a wide range between 8 (8.8%) and 78 (85.7%) RFs. Furthermore, in contrast to what has been previously reported, and as hypothesized in the robust radiomics analysis framework, our results demonstrate that ComBat cannot be applied to all RFs but rather on a percentage of those–the “ComBatable” RFs–which differed depending on the data being harmonized. The number (%) of reproducible RFs following ComBat harmonization varied across the pairwise scenarios investigated, ranging from 14 (15.4%) to 80 (87.9%) RFs, and was found to depend on the heterogeneity in the data. We conclude that the standardization of image acquisition protocols remains the cornerstone for improving the reproducibility of RFs, and the generalizability of the signatures developed. Our proposed approach helps identify the reproducible RFs across different datasets.

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Image Segmentation and the Projections of Graphic Centred Approaches in Medical Image Processing

10.46532/jmic.20200904 ◽

2020 ◽

pp. 74-81

Author(s):

Anandakumar Haldorai ◽

Shrinand Anandakumar

Keyword(s):

Image Segmentation ◽

Medical Image ◽

Real Life ◽

Medical Image Processing ◽

Medical Image Segmentation ◽

Regions Of Interest ◽

Object Categorization ◽

Range Image ◽

Image Evaluation ◽

Wide Range

– Medical image segmentation is considered the most precarious element in the analysis and processing of real-life images in the clinical sector. Actually, segmentation effects affect the subsequent procedures of image evaluation, life object illustration and description, feature dimensions and the subsequent considerable task levels such as object categorization. In that case, medical image segmentation is the most essential and crucial aspect for aiding the visualization, delineation and depiction of regions of interest for any particular image. The aspect of physical segmentation of a picture is not just challenging and time-consuming task to do, but also problematic to assure accuracy considering the wide-range image modalities and unguided image quantities which have to be observed. In that case, it now becomes fundamental to evaluate the present approaches of image segmentation based on the application of computing algorithms which require the interaction of users with evaluating medical images. In the process of image segmentation, an anatomic classification requires to be extracted or defined to be projected effectively and independently. In that case, this contribution is focused on image segmentation to extract details for decision-making in the clinical sector. The paper presents generalized and relative techniques that have been categorized into three groups: pixel-centre, edge-centred and region-centred techniques. The paper also provides a highlight of the strengths and weaknesses of these techniques in reference to the appropriateness of a wide-range application in medical image segmentation.

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Asteroid and Comet Impact Speeds upon Mars: Significance for Panspermia and the Supply of Organics

International Astronomical Union Colloquium ◽

10.1017/s0252921100014718 ◽

1997 ◽

Vol 161 ◽

pp. 197-201 ◽

Cited By ~ 1

Author(s):

Duncan Steel

Keyword(s):

Probability Distributions ◽

Regions Of Interest ◽

Significant Fraction ◽

Organic Chemicals ◽

Impact Speed ◽

The Mean ◽

The Impact

AbstractWhilst lithopanspermia depends upon massive impacts occurring at a speed above some limit, the intact delivery of organic chemicals or other volatiles to a planet requires the impact speed to be below some other limit such that a significant fraction of that material escapes destruction. Thus the two opposite ends of the impact speed distributions are the regions of interest in the bioastronomical context, whereas much modelling work on impacts delivers, or makes use of, only the mean speed. Here the probability distributions of impact speeds upon Mars are calculated for (i) the orbital distribution of known asteroids; and (ii) the expected distribution of near-parabolic cometary orbits. It is found that cometary impacts are far more likely to eject rocks from Mars (over 99 percent of the cometary impacts are at speeds above 20 km/sec, but at most 5 percent of the asteroidal impacts); paradoxically, the objects impacting at speeds low enough to make organic/volatile survival possible (the asteroids) are those which are depleted in such species.

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Recent Applications of High Resolution Electron Microscopy to Crystalline Arrays of Virus Particles

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100070199 ◽

1978 ◽

Vol 36 (3) ◽

pp. 470-482 ◽

Cited By ~ 1

Author(s):

R.W. Horne

Keyword(s):

Electron Microscopy ◽

Image Processing ◽

Analytical Techniques ◽

Staining Technique ◽

High Resolution Electron Microscopy ◽

Optical Diffraction ◽

Full Potential ◽

Virus Particles ◽

Resolution Electron ◽

Wide Range

The technique of surrounding virus particles with a neutralised electron dense stain was described at the Fourth International Congress on Electron Microscopy, Berlin 1958 (see Home & Brenner, 1960, p. 625). For many years the negative staining technique in one form or another, has been applied to a wide range of biological materials. However, the full potential of the method has only recently been explored following the development and applications of optical diffraction and computer image analytical techniques to electron micrographs (cf. De Hosier & Klug, 1968; Markham 1968; Crowther et al., 1970; Home & Markham, 1973; Klug & Berger, 1974; Crowther & Klug, 1975). These image processing procedures have allowed a more precise and quantitative approach to be made concerning the interpretation, measurement and reconstruction of repeating features in certain biological systems.

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Microfabrication research at the National Submicron Facility

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100074331 ◽

1983 ◽

Vol 41 ◽

pp. 86-89

Author(s):

E.D. Wolf

Keyword(s):

Integrated Circuits ◽

Particle Physics ◽

High Speed ◽

New Technology ◽

High Energy ◽

High Energy Particle ◽

New Science ◽

Wide Range ◽

Intermediate Domain ◽

Circuit Function

Most microelectronics devices and circuits operate faster, consume less power, execute more functions and cost less per circuit function when the feature-sizes internal to the devices and circuits are made smaller. This is part of the stimulus for the Very High-Speed Integrated Circuits (VHSIC) program. There is also a need for smaller, more sensitive sensors in a wide range of disciplines that includes electrochemistry, neurophysiology and ultra-high pressure solid state research. There is often fundamental new science (and sometimes new technology) to be revealed (and used) when a basic parameter such as size is extended to new dimensions, as is evident at the two extremes of smallness and largeness, high energy particle physics and cosmology, respectively. However, there is also a very important intermediate domain of size that spans from the diameter of a small cluster of atoms up to near one micrometer which may also have just as profound effects on society as “big” physics.

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Application of TEM to Deformation, Wear, and Fracture of Ceramics

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100052377 ◽

1974 ◽

Vol 32 ◽

pp. 472-473

Author(s):

B. J. Hockey

Keyword(s):

Wear Resistance ◽

High Temperature ◽

Mechanical Behavior ◽

Brittle Materials ◽

High Temperature Strength ◽

Wide Range ◽

Corrosive Environments ◽

Further Development

Ceramics, such as Al2O3 and SiC have numerous current and potential uses in applications where high temperature strength, hardness, and wear resistance are required often in corrosive environments. These materials are, however, highly anisotropic and brittle, so that their mechanical behavior is often unpredictable. The further development of these materials will require a better understanding of the basic mechanisms controlling deformation, wear, and fracture.The purpose of this talk is to describe applications of TEM to the study of the deformation, wear, and fracture of Al2O3. Similar studies are currently being conducted on SiC and the techniques involved should be applicable to a wide range of hard, brittle materials.

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Observation of Atom Rows in Thorium Pyromellitate Using a Field Emission STEM

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s042482010007802x ◽

1977 ◽

Vol 35 ◽

pp. 80-81

Author(s):

H. Todokoro ◽

S. Nomura ◽

T. Komoda

Keyword(s):

Field Emission ◽

Amorphous Carbon ◽

Carbon Film ◽

Dark Field Image ◽

Dark Field ◽

Amorphous Carbon Film ◽

Atomic Size ◽

Wide Range ◽

A Chain

It is interesting to observe polymers at atomic size resolution. Some works have been reported for thorium pyromellitate by using a STEM (1), or a CTEM (2,3). The results showed that this polymer forms a chain in which thorium atoms are arranged. However, the distance between adjacent thorium atoms varies over a wide range (0.4-1.3nm) according to the different authors.The present authors have also observed thorium pyromellitate specimens by means of a field emission STEM, described in reference 4. The specimen was prepared by placing a drop of thorium pyromellitate in 10-3 CH3OH solution onto an amorphous carbon film about 2nm thick. The dark field image is shown in Fig. 1A. Thorium atoms are clearly observed as regular atom rows having a spacing of 0.85nm. This lattice gradually deteriorated by successive observations. The image changed to granular structures, as shown in Fig. 1B, which was taken after four scanning frames.

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