bioRxiv (Cold Spring Harbor Laboratory),
Journal Year:
2020,
Volume and Issue:
unknown
Published: Sept. 24, 2020
Abstract
Single
cell
genomics
is
rapidly
advancing
our
knowledge
of
phenotypic
types
and
states.
Driven
by
single
cell/nucleus
RNA
sequencing
(scRNA-seq)
data,
comprehensive
atlas
projects
covering
a
wide
range
organisms
tissues
are
currently
underway.
As
result,
it
critical
that
the
transcriptional
phenotypes
discovered
defined
disseminated
in
consistent
concise
manner.
Molecular
biomarkers
have
historically
played
an
important
role
biological
research,
from
defining
immune
cell-types
surface
protein
expression
to
diseases
molecular
drivers.
Here
we
describe
machine
learning-based
marker
gene
selection
algorithm,
NS-Forest
version
2.0,
which
leverages
non-linear
attributes
random
forest
feature
binary
scoring
approach
discover
minimal
combinations
precisely
captures
type
identity
represented
complete
scRNA-seq
profiles.
The
genes
selected
provide
barcode
necessary
sufficient
characteristics
for
semantic
definition
serve
as
useful
tools
downstream
investigation.
use
identify
human
brain
middle
temporal
gyrus
reveals
importance
signaling
non-coding
RNAs
neuronal
identity.
IEEE Access,
Journal Year:
2020,
Volume and Issue:
8, P. 133295 - 133320
Published: Jan. 1, 2020
Implantable
neural
interface
devices
are
an
emerging
technology
for
continuous
brain
monitoring
and
brain-computer
(BCI).
Recording
of
electrical
signals
from
neurons
interest
has
led
to
more
efficient
personalized
diagnosis,
treatment,
prognosis
neurological
disorders.
It
facilitates
the
dynamic
mapping
whole
brain,
improving
our
understanding
links
between
functions
behaviors.
Stimulation
targeted
nerves
been
utilized
as
effective
therapy
Parkinson's
disease,
essential
tremor,
dystonia,
etc.
also
developed
motor
neuroprosthetic
devices,
quality
life
many.
Although
initial
designs
were
bulky,
recent
advances
in
semiconductor
nano-,
micro-technology
enabled
miniaturization
such
millimeter
scale.
Free-floating
implants
miniature
size
highly
scalable
be
distributed
around
region
extensively.
They
clinically
viable
they
cause
less
disturbance
body
induce
tissue
immune
response.
However,
these
research
efforts
scaling
down
have
faced
challenges
resulted
decreasing
implants,
including
issues
pertaining
wireless
powering,
data
communication,
signal
recording,
stimulation.
Through
extensive
literature
simulations,
limits
trade-offs
regarding
implant
investigated
analyzed
each
aspect
challenges.
State-of-the-art
development
future
trends
advanced
interfaces
explored.
Biomedical Optics Express,
Journal Year:
2020,
Volume and Issue:
12(1), P. 162 - 162
Published: Nov. 19, 2020
Studying
neural
connections
and
activities
in
vivo
is
fundamental
to
understanding
brain
functions.
Given
the
cm-size
three-dimensional
circuit
dynamics,
deep-tissue,
high-speed
volumetric
imaging
highly
desirable
for
study.
With
sub-micrometer
spatial
resolution,
intrinsic
optical
sectioning,
deep-tissue
penetration
capability,
two-photon
microscopy
(2PM)
has
found
a
niche
neuroscience.
However,
current
2PM
typically
relies
on
slow
axial
scan
imaging,
maximal
depth
only
about
1
mm.
Here,
we
demonstrate
that
by
integrating
gradient-index
(GRIN)
lens
tunable
acoustic
GRIN
(TAG)
into
2PM,
both
volume-imaging
rate
can
be
significantly
improved.
Specifically,
an
∼
1-cm
long
allows
relay
from
any
target
region
of
mouse
brain,
while
TAG
provides
sub-second
volume
via
100
kHz
MHz
scan.
This
technique
enables
study
calcium
dynamics
cm-deep
regions
with
sub-cellular
spatiotemporal
paving
way
interrogating
deep-brain
functional
connectome.
Human Brain Mapping,
Journal Year:
2021,
Volume and Issue:
42(17), P. 5523 - 5534
Published: Sept. 14, 2021
Abstract
Deidentifying
MRIs
constitutes
an
imperative
challenge,
as
it
aims
at
precluding
the
possibility
of
re‐identification
a
research
subject
or
patient,
but
same
time
should
preserve
much
geometrical
information
possible,
in
order
to
maximize
data
reusability
and
facilitate
interoperability.
Although
several
deidentification
methods
exist,
no
comprehensive
comparative
evaluation
performance
has
been
carried
out
across
them.
Moreover,
possible
ways
these
can
compromise
subsequent
analysis
not
exhaustively
tested.
To
tackle
issues,
we
developed
AnonyMI,
novel
MRI
method,
implemented
user‐friendly
3D
Slicer
plugin‐in,
which
providing
balance
between
identity
protection
preservation.
test
features,
performed
two
series
analyses
on
compared
AnonyMI
other
state‐of‐the‐art
methods,
evaluate,
time,
how
efficient
they
are
deidentifying
affect
analyses,
with
particular
emphasis
source
localization
procedures.
Our
results
show
that
all
three
significantly
reduce
risk
provides
best
conservation.
Notably,
also
offers
technical
advantages
such
interface,
multiple
input–output
capabilities,
being
tailored
specific
needs,
batch
processing
visualization
for
quality
assurance.
Nucleic Acids Research,
Journal Year:
2021,
Volume and Issue:
50(D1), P. D1131 - D1138
Published: Oct. 8, 2021
Brain
is
the
central
organ
of
nervous
system
and
any
brain
disease
can
seriously
affect
human
health.
Here
we
present
BrainBase
(https://ngdc.cncb.ac.cn/brainbase),
a
curated
knowledgebase
for
diseases
that
aims
to
provide
whole
picture
associated
genes.
Specifically,
based
on
manual
curation
2768
published
articles
along
with
information
retrieval
from
several
public
databases,
features
comprehensive
collection
7175
disease-gene
associations
spanning
total
123
linking
5662
genes,
16
591
drug-target
interactions
covering
2118
drugs/chemicals
623
five
types
specific
genes
in
light
expression
specificity
tissue/regions/cerebrospinal
fluid/cells.
In
addition,
considering
severity
glioma
among
tumors,
current
version
incorporates
21
multi-omics
datasets,
presents
molecular
profiles
across
various
samples/conditions
identifies
four
groups
featured
potential
clinical
significance.
Collectively,
integrates
not
only
valuable
but
also
through
data
analysis,
accordingly
bearing
great
promise
serve
as
diseases.
Advanced Photonics Research,
Journal Year:
2021,
Volume and Issue:
3(3)
Published: Dec. 22, 2021
Optogenetics
is
proved
to
be
a
powerful
tool
for
exploring
the
connection
between
behavior
and
neural
circuits.
The
progress
greatly
benefits
from
advances
of
optical
techniques
that
enable
high
spatiotemporal
resolution
selective
single‐neuron
stimulation
through
modulating
light.
Efficient
propagation
modulated
light,
however,
handicapped
by
strong
scattering
in
biological
tissues,
which
results
inherent
tradeoff
penetration
depth
resolution.
Schemes
like
graded
index
(GRIN)
lens‐based
microendoscopes
are
developed
yield
more
confined
delivery
but
tissue
damage
caused
insertion
bulky
components
cannot
ignored.
Herein,
an
optically
precise
neuron
using
ultrathin
multimode
fiber
(MMF)
demonstrated,
empowered
wavefront
shaping
achieve
light
focusing
rapid
raster
scanning
without
mechanical
movement
at
distal
end
MMF
even
mouse
skull.
With
this
method,
primary
neurons
expressing
Chr2
can
regulated
spatiotemporally
experiment.
Although
lot
shall
further
improved,
work
may
open
up
new
venues
noninvasive
or
minimally
invasive
all‐optical
investigation
circuits
used‐to‐be
inaccessible
brain
regions.
Journal of Alzheimer s Disease,
Journal Year:
2022,
Volume and Issue:
86(1), P. 21 - 42
Published: Jan. 11, 2022
The
COVID-19
pandemic
has
accelerated
neurological,
mental
health
disorders,
and
neurocognitive
issues.
However,
there
is
a
lack
of
inexpensive
efficient
brain
evaluation
screening
systems.
As
result,
considerable
fraction
patients
with
or
psychobehavioral
predicaments
either
do
not
get
timely
diagnosed
fail
to
receive
personalized
treatment
plans.
This
especially
true
in
the
elderly
populations,
wherein
only
16%
seniors
say
they
regular
cognitive
evaluations.
Therefore,
great
need
for
development
an
optimized
clinical
workflow
methodology
like
what
already
existence
prostate
breast
exams.
Such
should
be
designed
facilitate
objective
early
detection
cost-effective
such
disorders.
In
this
paper
we
have
reviewed
existing
protocols,
recent
technological
advances
suggested
reliable
workflows
screening.
protocols
range
from
questionnaires
smartphone
apps
multi-modality
mapping
advanced
imaging
where
applicable.
To
that
end,
Society
Brain
Mapping
Therapeutics
(SBMT)
proposes
Brain,
Spine
Mental
Health
Screening
(NEUROSCREEN)
as
multi-faceted
approach.
Beside
other
assessment
tools,
NEUROSCREEN
employs
guided
assessments
quantitative
electroencephalography
(qEEG)
well
potential
genetic
testing
decline
risk
effective
tools
diagnosis,
monitor
disease
progression,
guide
interventions.
Operationalizing
expected
result
reduced
healthcare
costs
improving
quality
life
at
national
later,
global
scales.
Frontiers in Psychology,
Journal Year:
2022,
Volume and Issue:
13
Published: Dec. 22, 2022
Scientific
reductionism,
the
view
that
higher
level
functions
can
be
explained
by
properties
at
some
lower-level
or
levels,
has
been
an
assumption
of
nervous
system
analyses
since
acceptance
neuron
doctrine
in
late
19th
century,
and
became
a
dominant
experimental
approach
with
development
intracellular
recording
techniques
mid-20th
century.
Subsequent
refinements
electrophysiological
approaches
continual
molecular
genetic
have
promoted
focus
on
cellular
mechanisms
explanations
sensory,
motor,
cognitive
functions.
Reductionist
assumptions
also
influenced
our
views
etiology
treatment
psychopathologies,
more
recently
led
to
claims
we
can,
even
should,
pharmacologically
enhance
normal
brain.
Reductionism
remains
area
active
debate
philosophy
science.
In
neuroscience
psychology,
typically
focuses
mind-brain
question
cognition,
how
if
they
neurobiological
terms.
However,
these
debates
are
affected
complexity
phenomena
being
considered
difficulty
obtaining
necessary
detail.
We
instead
ask
whether
features
identified
simpler
aspects
systems
support
current
explaining
behaviors.
While
my
is
do
not,
this
does
not
invite
opposing
prevalent
dichotomous
thinking
detail
irrelevant
should
computations
representations.
need
consider
address
long-standing
dilemma
ostensibly
through
discrete
cell
communication
generate
population
effects
across
multiple
spatial
temporal
scales
behavior.
Frontiers in Neuroscience,
Journal Year:
2020,
Volume and Issue:
14
Published: June 3, 2020
Sensory
stimulation
is
an
attractive
paradigm
for
studying
brain
activity
using
various
optical-,
ultrasound-
and
MRI-based
functional
neuroimaging
methods.
Optoacoustics
has
been
recently
suggested
as
a
powerful
new
tool
scalable
mapping
of
multiple
hemodynamic
parameters
with
rich
contrast
previously
unachievable
spatio-temporal
resolution.
Yet,
its
utility
the
processing
peripheral
inputs
at
whole
level
so
far
not
quantified.
We
employed
volumetric
multi-spectral
optoacoustic
tomography
(vMSOT)
to
non-invasively
monitor
HbO,
HbR
HbT
dynamics
across
mouse
somatosensory
cortex
evoked
by
electrical
paw
stimuli.
show
that
elevated
contralateral
activation
preserved
in
HbO
map
(invisible
MRI)
under
isoflurane
anesthesia.
Brain
shown
be
predominantly
confined
cortex,
strongest
hindpaw
region
sensorimotor
cortex.
Furthermore,
vMSOT
detected
presence
initial
dip
delta
channel.
Sensorimotor
cortical
was
identified
over
all
other
regions
but
HbR.
Pearson's
correlation
enabled
localizing
response
further
highlighting
ability
bridge
imaging
performance
deficiencies
modalities.