NEUROBIOLOGY:How the Brain Sees in Three Dimensions

The eye-brain complex allows those of us with normal vision to perceive and evaluate our surroundings in three-dimensions (3-D). The principle factor that makes this possible is parallax - the horizontal displacement of objects that results from the independent views that the left and right eyes detect and simultaneously transmit to the brain for superimposition. The common SEM micrograph is a 2-D representation of a 3-D specimen. Depriving the brain of the 3-D view can lead to erroneous conclusions about the relative sizes, positions and convergence of structures within a specimen. In addition, Walter has suggested that the stereo image contains information equivalent to a two-fold increase in magnification over that found in a 2-D image. Because of these factors, stereo pair analysis should be routinely employed when studying specimens.Imaging complementary faces of a fractured specimen is a second method by which the topography of a specimen can be more accurately evaluated.

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Differences in the brain stem terminations of large- and small-diameter vestibular primary afferents

Journal of Neurophysiology ◽

10.1152/jn.1995.74.3.1362 ◽

1995 ◽

Vol 74 (3) ◽

pp. 1362-1366 ◽

Cited By ~ 9

Author(s):

J. A. Huwe ◽

E. H. Peterson

Keyword(s):

Brain Stem ◽

Large Diameter ◽

Small Diameter ◽

Movement Control ◽

Three Dimensions ◽

Significant Shift ◽

Axon Diameter ◽

Vestibular Complex ◽

The Brain ◽

Adjacent Brain

1. We visualized the central axons of 32 vestibular afferents from the posterior canal by extracellular application of horseradish peroxidase, reconstructed them in three dimensions, and quantified their morphology. Here we compare the descending limbs of central axons that differ in parent axon diameter. 2. The brain stem distribution of descending limb terminals (collaterals and associated varicosities) varies systematically with parent axon diameter. Large-diameter afferents concentrate their terminals in rostral regions of the medial/descending nuclei. As axon diameter decreases, there is a significant shift of terminal concentration toward the caudal vestibular complex and adjacent brain stem. 3. Rostral and caudal regions of the medial/descending nuclei have different labyrinthine, cerebellar, intrinsic, commissural, and spinal connections; they are believed to play different roles in head movement control. Our data help clarify the functions of large- and small-diameter afferents by showing that they contribute differentially to rostral and caudal vestibular complex.

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Comparing Glioblastoma Surgery Decisions Between Teams Using Brain Maps of Tumor Locations, Biopsies, and Resections

JCO Clinical Cancer Informatics ◽

10.1200/cci.18.00089 ◽

2019 ◽

pp. 1-12 ◽

Cited By ~ 8

Author(s):

Domenique M.J. Müller ◽

Pierre A.J.T. Robe ◽

Roelant S. Eijgelaar ◽

Marnix G. Witte ◽

Martin Visser ◽

...

Keyword(s):

Tumor Location ◽

Three Dimensions ◽

Multidisciplinary Teams ◽

Surgical Removal ◽

Treatment Variation ◽

Probability Maps ◽

Resected Patient ◽

The Right ◽

Referral Bias ◽

The Brain

Purpose The aim of glioblastoma surgery is to maximize the extent of resection while preserving functional integrity, which depends on the location within the brain. A standard to compare these decisions is lacking. We present a volumetric voxel-wise method for direct comparison between two multidisciplinary teams of glioblastoma surgery decisions throughout the brain. Methods Adults undergoing first-time glioblastoma surgery from 2012 to 2013 performed by two neuro-oncologic teams were included. Patients had had a diagnostic biopsy or resection. Preoperative tumors and postoperative residues were segmented on magnetic resonance imaging in three dimensions and registered to standard brain space. Voxel-wise probability maps of tumor location, biopsy, and resection were constructed for each team to compare patient referral bias, indication variation, and treatment variation. To evaluate the quality of care, subgroups of differentially resected brain regions were analyzed for survival and functional outcome. Results One team included 101 patients, and the other included 174; 91 tumors were biopsied, and 181 were resected. Patient characteristics were largely comparable between teams. Distributions of tumor locations were dissimilar, suggesting referral bias. Distributions of biopsies were similar, suggesting absence of indication variation. Differentially resected regions were identified in the anterior limb of the right internal capsule and the right caudate nucleus, indicating treatment variation. Patients with (n = 12) and without (n = 6) surgical removal in these regions had similar overall survival and similar permanent neurologic deficits. Conclusion Probability maps of tumor location, biopsy, and resection provide additional information that can inform surgical decision making across multidisciplinary teams for patients with glioblastoma.

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Nervous Activity of the Brain in Five Dimensions

Biophysica ◽

10.3390/biophysica1010004 ◽

2021 ◽

Vol 1 (1) ◽

pp. 38-47

Author(s):

Arturo Tozzi ◽

James F. Peters ◽

Norbert Jausovec ◽

Arjuna P. H. Don ◽

Sheela Ramanna ◽

...

Keyword(s):

Fourier Analysis ◽

Nervous Activity ◽

Three Dimensional ◽

Three Dimensions ◽

Data Sets ◽

Spatial And Temporal Patterns ◽

Five Dimensions ◽

Four Dimensions ◽

Scale Free ◽

The Brain

The nervous activity of the brain takes place in higher-dimensional functional spaces. It has been proposed that the brain might be equipped with phase spaces characterized by four spatial dimensions plus time, instead of the classical three plus time. This suggests that global visualization methods for exploiting four-dimensional maps of three-dimensional experimental data sets might be used in neuroscience. We asked whether it is feasible to describe the four-dimensional trajectories (plus time) of two-dimensional (plus time) electroencephalographic traces (EEG). We made use of quaternion orthographic projections to map to the surface of four-dimensional hyperspheres EEG signal patches treated with Fourier analysis. Once achieved the proper quaternion maps, we show that this multi-dimensional procedure brings undoubted benefits. The treatment of EEG traces with Fourier analysis allows the investigation the scale-free activity of the brain in terms of trajectories on hyperspheres and quaternionic networks. Repetitive spatial and temporal patterns undetectable in three dimensions (plus time) are easily enlightened in four dimensions (plus time). Further, a quaternionic approach makes it feasible to identify spatially far apart and temporally distant periodic trajectories with the same features, such as, e.g., the same oscillatory frequency or amplitude. This leads to an incisive operational assessment of global or broken symmetries, domains of attraction inside three-dimensional projections and matching descriptions between the apparently random paths hidden in the very structure of nervous fractal signals.

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The Brain Stem Saccadic Burst Generator Encodes Gaze in Three-Dimensional Space

Journal of Neurophysiology ◽

10.1152/jn.01379.2007 ◽

2008 ◽

Vol 99 (5) ◽

pp. 2602-2616 ◽

Cited By ~ 27

Author(s):

Marion R. Van Horn ◽

Pierre A. Sylvestre ◽

Kathleen E. Cullen

Keyword(s):

Eye Movements ◽

Brain Stem ◽

Dimensional Space ◽

Three Dimensional ◽

Saccadic Eye Movements ◽

Three Dimensions ◽

Related Information ◽

Computer Based ◽

Different Depths ◽

The Brain

When we look between objects located at different depths the horizontal movement of each eye is different from that of the other, yet temporally synchronized. Traditionally, a vergence-specific neuronal subsystem, independent from other oculomotor subsystems, has been thought to generate all eye movements in depth. However, recent studies have challenged this view by unmasking interactions between vergence and saccadic eye movements during disconjugate saccades. Here, we combined experimental and modeling approaches to address whether the premotor command to generate disconjugate saccades originates exclusively in “vergence centers.” We found that the brain stem burst generator, which is commonly assumed to drive only the conjugate component of eye movements, carries substantial vergence-related information during disconjugate saccades. Notably, facilitated vergence velocities during disconjugate saccades were synchronized with the burst onset of excitatory and inhibitory brain stem saccadic burst neurons (SBNs). Furthermore, the time-varying discharge properties of the majority of SBNs (>70%) preferentially encoded the dynamics of an individual eye during disconjugate saccades. When these experimental results were implemented into a computer-based simulation, to further evaluate the contribution of the saccadic burst generator in generating disconjugate saccades, we found that it carries all the vergence drive that is necessary to shape the activity of the abducens motoneurons to which it projects. Taken together, our results provide evidence that the premotor commands from the brain stem saccadic circuitry, to the target motoneurons, are sufficient to ensure the accurate control shifts of gaze in three dimensions.

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Intrinsic Functional Connectivity is Organized as Three Interdependent Gradients

Scientific Reports ◽

10.1038/s41598-019-51793-7 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 2

Author(s):

Jiahe Zhang ◽

Olamide Abiose ◽

Yuta Katsumi ◽

Alexandra Touroutoglou ◽

Bradford C. Dickerson ◽

...

Keyword(s):

Functional Connectivity ◽

Three Dimensions ◽

Coordinate Space ◽

Similarity Matrix ◽

Sources Of Information ◽

Dimensional Solution ◽

Intrinsic Functional Connectivity ◽

Two Samples ◽

Functional Features ◽

The Brain

Abstract The intrinsic functional architecture of the brain supports moment-to-moment maintenance of an internal model of the world. We hypothesized and found three interdependent architectural gradients underlying the organization of intrinsic functional connectivity within the human cerebral cortex. We used resting state fMRI data from two samples of healthy young adults (N’s = 280 and 270) to generate functional connectivity maps of 109 seeds culled from published research, estimated their pairwise similarities, and multidimensionally scaled the resulting similarity matrix. We discovered an optimal three-dimensional solution, accounting for 98% of the variance within the similarity matrix. The three dimensions corresponded to three gradients, which spatially correlate with two functional features (external vs. internal sources of information; content representation vs. attentional modulation) and one structural feature (anatomically central vs. peripheral) of the brain. Remapping the three dimensions into coordinate space revealed that the connectivity maps were organized in a circumplex structure, indicating that the organization of intrinsic connectivity is jointly guided by graded changes along all three dimensions. Our findings emphasize coordination between multiple, continuous functional and anatomical gradients, and are consistent with the emerging predictive coding perspective.

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Using a new three-dimensional CUBIC tissue-clearing method to examine the brain during experimental cerebral malaria

International Immunology ◽

10.1093/intimm/dxab060 ◽

2021 ◽

Author(s):

Julia Matsuo-Dapaah ◽

Michelle Sue Jann Lee ◽

Ken J Ishii ◽

Kazuki Tainaka ◽

Cevayir Coban

Keyword(s):

Olfactory Bulb ◽

Cerebral Malaria ◽

Fluorescent Microscopy ◽

Three Dimensions ◽

Whole Brain ◽

Cerebral Microvessels ◽

Experimental Cerebral Malaria ◽

Tissue Clearing ◽

The Brain ◽

Clearing Method

Abstract Cerebral malaria (CM) is a life-threatening complication of the malaria disease caused by Plasmodium falciparum infection and is responsible for the death of half a million people annually. The molecular pathogenesis underlying CM in humans is not completely understood, although sequestration of infected erythrocytes in cerebral microvessels is thought to play a major role. In contrast, experimental cerebral malaria (ECM) models in mice have been thought to be distinct from human CM, and are mainly caused by inflammatory mediators. Here, to understand the spatial distribution and the potential sequestration of parasites in the whole-brain microvessels during a mouse model of ECM, we utilized the new tissue-clearing method CUBIC (Clear, Unobstructed, Brain/Body Imaging Cocktails and Computational analysis) with light sheet fluorescent microscopy (LSFM), and reconstructed images in three-dimensions (3D). We demonstrated significantly greater accumulation of Plasmodium berghei ANKA (PbANKA) parasites in the olfactory bulb of mice, compared with the other parts of the brain, including the cerebral cortex, cerebellum, and brainstem. Furthermore, we show that PbANKA parasites preferentially accumulate in the brainstem when the olfactory bulb is surgically removed. This study therefore not only highlights a successful application of CUBIC tissue-clearing technology to visualize the whole brain and its microvessels during ECM, but it also shows CUBIC’s future potential for visualizing pathological events in the whole ECM brain at the cellular level, an achievement that would greatly advance our understanding of human cerebral malaria.

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Primary Evidence of a Donut-Like, Fourth Spatial Dimension in the Brain

10.1101/072397 ◽

2016 ◽

Author(s):

James F. Peters ◽

Ebubekir İnan ◽

Arturo Tozzi ◽

Sheela Ramanna

Keyword(s):

Brain Activity ◽

Functional Space ◽

Temporal Patterns ◽

Spatial Dimension ◽

Blood Oxygen Level Dependent ◽

Three Dimensions ◽

Renyi Entropy ◽

Rényi Entropy ◽

Objective Detection ◽

The Brain

ABSTRACTWe introduce a novel method for the measurement of information in fMRI neuroimages, i.e., nucleus clustering’s Rényi entropy derived from strong proximities in feature-based Voronoï tessellations, e.g., maximal nucleus clustering (MNC). We show how MNC is a novel, fast and inexpensive image-analysis technique, independent from the standard blood-oxygen-level dependent signals, which facilitates the objective detection of hidden temporal patterns of entropy/information in zones of fMRI images generally not taken into account by the subjective standpoint of the observer. In order to evaluate the potential applications of MNC, we looked for the presence of a fourth dimension’s distinctive hallmarks in a temporal sequence of 2D images taken during spontaneous brain activity. Indeed, recent findings suggest that several brain activities, such as mind-wandering and memory retrieval, might take place in the functional space of a four dimensional hypersphere, which is a double donut-like structure undetectable in the usual three dimensions. We found that the Rényi entropy is higher in MNC areas than in the surrounding ones, and that these temporal patterns closely resemble the trajectories predicted by the possible presence of a hypersphere in the brain.

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Survey Based Study: Classification of Patients with Alzheimer’s Disease

Iraqi Journal of Science ◽

10.24996/ijs.2020.61.11.31 ◽

2020 ◽

pp. 3093-3115

Author(s):

Shaimaa A. Al-Majeed ◽

Mohammed S. H. Al- Tamimi

Keyword(s):

Alzheimer’S Disease ◽

Alzheimer's Disease ◽

Sensory System ◽

Two Dimensions ◽

Three Dimensions ◽

Accurate Identification ◽

Previous Decade ◽

Neuroimaging Data ◽

The Brain

Neuroimaging is a description, whether in two-dimensions (2D) or three-dimensions (3D), of the structure and functions of the brain. Neuroimaging provides a valuable diagnostic tool, in which a limited approach is used to create images of the focal sensory system by medicine professionals. For the clinical diagnosis of patients with Alzheimer's Disease (AD) or Mild Cognitive Impairs (MCI), the accurate identification of patients from normal control persons (NCs) is critical. Recently, numerous researches have been undertaken on the identification of AD based on neuroimaging data, including images with radiographs and algorithms for master learning. In the previous decade, these techniques were also used slowly to differentiate AD and MCI symptoms from structure classification methods. This review focuses on neuroimaging studies conducted to detect and classify AD, through a survey based on Google Scholar content. We explore the challenges of this field and evaluate the performance of these studies along with their negative aspects.

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A principle of economy predicts the functional architecture of grid cells

eLife ◽

10.7554/elife.08362 ◽

2015 ◽

Vol 4 ◽

Cited By ~ 30

Author(s):

Xue-Xin Wei ◽

Jason Prentice ◽

Vijay Balasubramanian

Keyword(s):

Three Dimensions ◽

Periodic Lattice ◽

Grid System ◽

Grid Cells ◽

Grid Structure ◽

Functional Architecture ◽

Optimal Organization ◽

Scale Ratio ◽

Hierarchical Code ◽

The Brain

Grid cells in the brain respond when an animal occupies a periodic lattice of ‘grid fields’ during navigation. Grids are organized in modules with different periodicity. We propose that the grid system implements a hierarchical code for space that economizes the number of neurons required to encode location with a given resolution across a range equal to the largest period. This theory predicts that (i) grid fields should lie on a triangular lattice, (ii) grid scales should follow a geometric progression, (iii) the ratio between adjacent grid scales should be √e for idealized neurons, and lie between 1.4 and 1.7 for realistic neurons, (iv) the scale ratio should vary modestly within and between animals. These results explain the measured grid structure in rodents. We also predict optimal organization in one and three dimensions, the number of modules, and, with added assumptions, the ratio between grid periods and field widths.

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