75 research outputs found
Multi-Modal Neuroimaging Analysis and Visualization Tool (MMVT)
Sophisticated visualization tools are essential for the presentation and
exploration of human neuroimaging data. While two-dimensional orthogonal views
of neuroimaging data are conventionally used to display activity and
statistical analysis, three-dimensional (3D) representation is useful for
showing the spatial distribution of a functional network, as well as its
temporal evolution. For these purposes, there is currently no open-source, 3D
neuroimaging tool that can simultaneously visualize desired combinations of
MRI, CT, EEG, MEG, fMRI, PET, and intracranial EEG (i.e., ECoG, depth
electrodes, and DBS). Here we present the Multi-Modal Visualization Tool
(MMVT), which is designed for researchers to interact with their neuroimaging
functional and anatomical data through simultaneous visualization of these
existing imaging modalities. MMVT contains two separate modules: The first is
an add-on to the open-source, 3D-rendering program Blender. It is an
interactive graphical interface that enables users to simultaneously visualize
multi-modality functional and statistical data on cortical and subcortical
surfaces as well as MEEG sensors and intracranial electrodes. This tool also
enables highly accurate 3D visualization of neuroanatomy, including the
location of invasive electrodes relative to brain structures. The second module
includes complete stand-alone pre-processing pipelines, from raw data to
statistical maps. Each of the modules and module features can be integrated,
separate from the tool, into existing data pipelines. This gives the tool a
distinct advantage in both clinical and research domains as each has highly
specialized visual and processing needs. MMVT leverages open-source software to
build a comprehensive tool for data visualization and exploration.Comment: 29 pages, 10 figure
Canalization of Gene Expression and Domain Shifts in the Drosophila Blastoderm by Dynamical Attractors
The variation in the expression patterns of the gap genes in the blastoderm of
the fruit fly Drosophila melanogaster reduces over time as a
result of cross regulation between these genes, a fact that we have demonstrated
in an accompanying article in PLoS Biology (see Manu et al.,
doi:10.1371/journal.pbio.1000049). This biologically essential process is an
example of the phenomenon known as canalization. It has been suggested that the
developmental trajectory of a wild-type organism is inherently stable, and that
canalization is a manifestation of this property. Although the role of gap genes
in the canalization process was established by correctly predicting the response
of the system to particular perturbations, the stability of the developmental
trajectory remains to be investigated. For many years, it has been speculated
that stability against perturbations during development can be described by
dynamical systems having attracting sets that drive reductions of volume in
phase space. In this paper, we show that both the reduction in variability of
gap gene expression as well as shifts in the position of posterior gap gene
domains are the result of the actions of attractors in the gap gene dynamical
system. Two biologically distinct dynamical regions exist in the early embryo,
separated by a bifurcation at 53% egg length. In the anterior region,
reduction in variation occurs because of stability induced by point attractors,
while in the posterior, the stability of the developmental trajectory arises
from a one-dimensional attracting manifold. This manifold also controls a
previously characterized anterior shift of posterior region gap domains. Our
analysis shows that the complex phenomena of canalization and pattern formation
in the Drosophila blastoderm can be understood in terms of the
qualitative features of the dynamical system. The result confirms the idea that
attractors are important for developmental stability and shows a richer variety
of dynamical attractors in developmental systems than has been previously
recognized
Reactive oxygen species and male reproductive hormones
Reports of the increasing incidence of male infertility paired with decreasing semen quality have triggered studies
on the effects of lifestyle and environmental factors on the male reproductive potential. There are numerous exogenous
and endogenous factors that are able to induce excessive production of reactive oxygen species (ROS) beyond that of
cellular antioxidant capacity, thus causing oxidative stress. In turn, oxidative stress negatively affects male reproductive
functions and may induce infertility either directly or indirectly by affecting the hypothalamus-pituitary-gonadal (HPG)
axis and/or disrupting its crosstalk with other hormonal axes. This review discusses the important exogenous and
endogenous factors leading to the generation of ROS in different parts of the male reproductive tract. It also highlights
the negative impact of oxidative stress on the regulation and cross-talk between the reproductive hormones. It further
describes the mechanism of ROS-induced derangement of male reproductive hormonal profiles that could ultimately
lead to male infertility. An understanding of the disruptive effects of ROS on male reproductive hormones would
encourage further investigations directed towards the prevention of ROS-mediated hormonal imbalances, which in turn
could help in the management of male infertility
Reflections on the Narrative Approach : Dilemmas of Power, Emotions and Social Location While Constructing Life-Stories
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