972 research outputs found
Reorganization of columnar architecture in the growing visual cortex
Many cortical areas increase in size considerably during postnatal
development, progressively displacing neuronal cell bodies from each other. At
present, little is known about how cortical growth affects the development of
neuronal circuits. Here, in acute and chronic experiments, we study the layout
of ocular dominance (OD) columns in cat primary visual cortex (V1) during a
period of substantial postnatal growth. We find that despite a considerable
size increase of V1, the spacing between columns is largely preserved. In
contrast, their spatial arrangement changes systematically over this period.
While in young animals columns are more band-like, layouts become more
isotropic in mature animals. We propose a novel mechanism of growth-induced
reorganization that is based on the `zigzag instability', a dynamical
instability observed in several inanimate pattern forming systems. We argue
that this mechanism is inherent to a wide class of models for the
activity-dependent formation of OD columns. Analyzing one member of this class,
the Elastic Network model, we show that this mechanism can account for the
preservation of column spacing and the specific mode of reorganization of OD
columns that we observe. We conclude that neurons systematically shift their
selectivities during normal development and that this reorganization is induced
by the cortical expansion during growth. Our work suggests that cortical
circuits remain plastic for an extended period in development in order to
facilitate the modification of neuronal circuits to adjust for cortical growth.Comment: 8+13 pages, 4+8 figures, paper + supplementary materia
Coverage, Continuity and Visual Cortical Architecture
The primary visual cortex of many mammals contains a continuous
representation of visual space, with a roughly repetitive aperiodic map of
orientation preferences superimposed. It was recently found that orientation
preference maps (OPMs) obey statistical laws which are apparently invariant
among species widely separated in eutherian evolution. Here, we examine whether
one of the most prominent models for the optimization of cortical maps, the
elastic net (EN) model, can reproduce this common design. The EN model
generates representations which optimally trade of stimulus space coverage and
map continuity. While this model has been used in numerous studies, no
analytical results about the precise layout of the predicted OPMs have been
obtained so far. We present a mathematical approach to analytically calculate
the cortical representations predicted by the EN model for the joint mapping of
stimulus position and orientation. We find that in all previously studied
regimes, predicted OPM layouts are perfectly periodic. An unbiased search
through the EN parameter space identifies a novel regime of aperiodic OPMs with
pinwheel densities lower than found in experiments. In an extreme limit,
aperiodic OPMs quantitatively resembling experimental observations emerge.
Stabilization of these layouts results from strong nonlocal interactions rather
than from a coverage-continuity-compromise. Our results demonstrate that
optimization models for stimulus representations dominated by nonlocal
suppressive interactions are in principle capable of correctly predicting the
common OPM design. They question that visual cortical feature representations
can be explained by a coverage-continuity-compromise.Comment: 100 pages, including an Appendix, 21 + 7 figure
Machine Learning-based Brokers for Real-time Classification of the LSST Alert Stream
The unprecedented volume and rate of transient events that will be discovered
by the Large Synoptic Survey Telescope (LSST) demands that the astronomical
community update its followup paradigm. Alert-brokers -- automated software
system to sift through, characterize, annotate and prioritize events for
followup -- will be critical tools for managing alert streams in the LSST era.
The Arizona-NOAO Temporal Analysis and Response to Events System (ANTARES) is
one such broker. In this work, we develop a machine learning pipeline to
characterize and classify variable and transient sources only using the
available multiband optical photometry. We describe three illustrative stages
of the pipeline, serving the three goals of early, intermediate and
retrospective classification of alerts. The first takes the form of variable vs
transient categorization, the second, a multi-class typing of the combined
variable and transient dataset, and the third, a purity-driven subtyping of a
transient class. While several similar algorithms have proven themselves in
simulations, we validate their performance on real observations for the first
time. We quantitatively evaluate our pipeline on sparse, unevenly sampled,
heteroskedastic data from various existing observational campaigns, and
demonstrate very competitive classification performance. We describe our
progress towards adapting the pipeline developed in this work into a real-time
broker working on live alert streams from time-domain surveys.Comment: 33 pages, 14 figures, submitted to ApJ
Successful object encoding induces increased directed connectivity in presymptomatic early-onset Alzheimer's disease
Background: Recent studies report increases in neural activity in brain regions critical to episodic memory at preclinical stages of Alzheimerâs disease (AD). Although electroencephalography (EEG) is widely used in AD studies, given its non-invasiveness and low cost, there is a need to translate the findings in other neuroimaging methods to EEG.
Objective: To examine how the previous findings using functional magnetic resonance imaging (fMRI) at preclinical stage in presenilin-1 E280A mutation carriers could be assessed and extended, using EEG and a connectivity approach.
Methods: EEG signals were acquired during resting and encoding in 30 normal cognitive young subjects, from an autosomal dominant early-onset AD kindred from Antioquia, Colombia. Regions of the brain previously reported as hyperactive were used for connectivity analysis.
Results: Mutation carriers exhibited increasing connectivity at analyzed regions. Among them, the right precuneus exhibited the highest changes in connectivity.
Conclusion: Increased connectivity in hyperactive cerebral regions is seen in individuals, genetically-determined to develop AD, at preclinical stage. The use of a connectivity approach and a widely available neuroimaging technique opens the possibility to increase the use of EEG in early detection of preclinical AD.Postprint (author's final draft
Computing Interpretable Representations of Cell Morphodynamics
Shape changes (morphodynamics) are one of the principal ways cells interact with their environments and perform key intrinsic behaviours like division. These dynamics arise from a myriad of complex signalling pathways that often organise with emergent simplicity to carry out critical functions including predation, collaboration and migration. A powerful method for analysis can therefore be to quantify this emergent structure, bypassing the low-level complexity. Enormous image datasets are now available to mine. However, it can be difficult to uncover interpretable representations of the global organisation of these heterogeneous dynamic processes. Here, such representations were developed for interpreting morphodynamics in two key areas: mode of action (MoA) comparison for drug discovery (developed using the economically devastating Asian soybean rust crop pathogen) and 3D migration of immune system T cells through extracellular matrices (ECMs). For MoA comparison, population development over a 2D space of shapes (morphospace) was described using two models with condition-dependent parameters: a top-down model of diffusive development over Waddington-type landscapes, and a bottom-up model of tip growth. A variety of landscapes were discovered, describing phenotype transitions during growth, and possible perturbations in the tip growth machinery that cause this variation were identified. For interpreting T cell migration, a new 3D shape descriptor that incorporates key polarisation information was developed, revealing low-dimensionality of shape, and the distinct morphodynamics of run-and-stop modes that emerge at minute timescales were mapped. Periodically oscillating morphodynamics that include retrograde deformation flows were found to underlie active translocation (run mode). Overall, it was found that highly interpretable representations could be uncovered while still leveraging the enormous discovery power of deep learning algorithms. The results show that whole-cell morphodynamics can be a convenient and powerful place to search for structure, with potentially life-saving applications in medicine and biocide discovery as well as immunotherapeutics.Open Acces
The shocklet transform: a decomposition method for the identification of local, mechanism-driven dynamics in sociotechnical time series
We introduce a qualitative, shape-based, timescale-independent time-domain transform used to extract local dynamics from sociotechnical time seriesâtermed the Discrete Shocklet Transform (DST)âand an associated similarity search routine, the Shocklet Transform And Ranking (STAR) algorithm, that indicates time windows during which panels of time series display qualitatively-similar anomalous behavior. After distinguishing our algorithms from other methods used in anomaly detection and time series similarity search, such as the matrix profile, seasonal-hybrid ESD, and discrete wavelet transform-based procedures, we demonstrate the DSTâs ability to identify mechanism-driven dynamics at a wide range of timescales and its relative insensitivity to functional parameterization. As an application, we analyze a sociotechnical data source (usage frequencies for a subset of words on Twitter) and highlight our algorithmsâ utility by using them to extract both a typology of mechanistic local dynamics and a data-driven narrative of socially-important events as perceived by English-language Twitter
Rhythmic constant pitch time stretching for digital audio
Constant pitch time stretching is not uncommon in audio editing software, however several issues arise when it is used on musical recordings, most notably the doubling and skipping of rhythmic transients. This paper examines three signal processing algorithms which are commonly used to provide constant pitch time stretching: these are SOLA (Synchronous Overlap and Add), TD-PSOLA (Time Domain Pitch Synchronous Overlap and Add), and Phase Vocoder. Enhancements to the SOLA and TD-PSOLA algorithms are provided which may make them more suited to rhythmic music. It is found that each of these three algorithms introduce audible artifacts in the time stretched waveform, the severity of these side effects and what causes them is also discussed
A framework for studying behavioral evolution by reconstructing ancestral repertoires
Although extensive behavioral changes often exist between closely related
animal species, our understanding of the genetic basis underlying the evolution
of behavior has remained limited. Here, we propose a new framework to study
behavioral evolution by computational estimation of ancestral behavioral
repertoires. We measured the behaviors of individuals from six species of fruit
flies using unsupervised techniques and identified suites of stereotyped
movements exhibited by each species. We then fit a Generalized Linear Mixed
Model to estimate the suites of behaviors exhibited by ancestral species, as
well as the intra- and inter-species behavioral covariances. We found that much
of intraspecific behavioral variation is explained by differences between
individuals in the status of their behavioral hidden states, what might be
called their "mood." Lastly, we propose a method to identify groups of
behaviors that appear to have evolved together, illustrating how sets of
behaviors, rather than individual behaviors, likely evolved. Our approach
provides a new framework for identifying co-evolving behaviors and may provide
new opportunities to study the genetic basis of behavioral evolution
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