4,735 research outputs found
Special studies of AROD system concepts and designs
Signal processing techniques for range and range rate measurements in airborne range and orbit determinatio
Decomposability of soil organic matter over time: the Soil Incubation Database (SIDb, version 1.0) and guidance for incubation procedures
Exploiting single-cell expression to characterize co-expression replicability
BACKGROUND: Co-expression networks have been a useful tool for functional genomics, providing important clues about the cellular and biochemical mechanisms that are active in normal and disease processes. However, co-expression analysis is often treated as a black box with results being hard to trace to their basis in the data. Here, we use both published and novel single-cell RNA sequencing (RNA-seq) data to understand fundamental drivers of gene-gene connectivity and replicability in co-expression networks. RESULTS: We perform the first major analysis of single-cell co-expression, sampling from 31 individual studies. Using neighbor voting in cross-validation, we find that single-cell network connectivity is less likely to overlap with known functions than co-expression derived from bulk data, with functional variation within cell types strongly resembling that also occurring across cell types. To identify features and analysis practices that contribute to this connectivity, we perform our own single-cell RNA-seq experiment of 126 cortical interneurons in an experimental design targeted to co-expression. By assessing network replicability, semantic similarity and overall functional connectivity, we identify technical factors influencing co-expression and suggest how they can be controlled for. Many of the technical effects we identify are expression-level dependent, making expression level itself highly predictive of network topology. We show this occurs generally through re-analysis of the BrainSpan RNA-seq data. CONCLUSIONS: Technical properties of single-cell RNA-seq data create confounds in co-expression networks which can be identified and explicitly controlled for in any supervised analysis. This is useful both in improving co-expression performance and in characterizing single-cell data in generally applicable terms, permitting cross-laboratory comparison within a common framework
Fixation and consensus times on a network: a unified approach
We investigate a set of stochastic models of biodiversity, population
genetics, language evolution and opinion dynamics on a network within a common
framework. Each node has a state, 0 < x_i < 1, with interactions specified by
strengths m_{ij}. For any set of m_{ij} we derive an approximate expression for
the mean time to reach fixation or consensus (all x_i=0 or 1). Remarkably in a
case relevant to language change this time is independent of the network
structure.Comment: 4+epsilon pages, two-column, RevTeX4, 3 eps figures; version accepted
by Phys. Rev. Let
Random copying in space
Random copying is a simple model for population dynamics in the absence of
selection, and has been applied to both biological and cultural evolution. In
this work, we investigate the effect that spatial structure has on the
dynamics. We focus in particular on how a measure of the diversity in the
population changes over time. We show that even when the vast majority of a
population's history may be well-described by a spatially-unstructured model,
spatial structure may nevertheless affect the expected level of diversity seen
at a local scale. We demonstrate this phenomenon explicitly by examining the
random copying process on small-world networks, and use our results to comment
on the use of simple random-copying models in an empirical context.Comment: 26 pages, 11 figures. Based on invited talk at AHRC CECD Conference
on "Cultural Evolution in Spatially Structured Populations" at UCL, September
2010. To appear in ACS - Advances in Complex System
An exactly solvable coarse-grained model for species diversity
We present novel analytical results about ecosystem species diversity that
stem from a proposed coarse grained neutral model based on birth-death
processes. The relevance of the problem lies in the urgency for understanding
and synthesizing both theoretical results of ecological neutral theory and
empirical evidence on species diversity preservation. Neutral model of
biodiversity deals with ecosystems in the same trophic level where per-capita
vital rates are assumed to be species-independent. Close-form analytical
solutions for neutral theory are obtained within a coarse-grained model, where
the only input is the species persistence time distribution. Our results
pertain: the probability distribution function of the number of species in the
ecosystem both in transient and stationary states; the n-points connected time
correlation function; and the survival probability, definned as the
distribution of time-spans to local extinction for a species randomly sampled
from the community. Analytical predictions are also tested on empirical data
from a estuarine fish ecosystem. We find that emerging properties of the
ecosystem are very robust and do not depend on specific details of the model,
with implications on biodiversity and conservation biology.Comment: 20 pages, 4 figures. To appear in Journal of Statistichal Mechanic
Charged State of a Spherical Plasma in Vacuum
The stationary state of a spherically symmetric plasma configuration is
investigated in the limit of immobile ions and weak collisions. Configurations
with small radii are positively charged as a significant fraction of the
electron population evaporates during the equilibration process, leaving behind
an electron distribution function with an energy cutoff. Such charged plasma
configurations are of interest for the study of Coulomb explosions and ion
acceleration from small clusters irradiated by ultraintense laser pulses and
for the investigation of ion bunches propagation in a plasma
Comprehensive Analysis of Coronal Mass Ejection Mass and Energy Properties Over a Full Solar Cycle
The LASCO coronagraphs, in continuous operation since 1995, have observed the
evolution of the solar corona and coronal mass ejections (CMEs) over a full
solar cycle with high quality images and regular cadence. This is the first
time that such a dataset becomes available and constitutes a unique resource
for the study of CMEs. In this paper, we present a comprehensive investigation
of the solar cycle dependence on the CME mass and energy over a full solar
cycle (1996-2009) including the first in-depth discussion of the mass and
energy analysis methods and their associated errors. Our analysis provides
several results worthy of further studies. It demonstrates the possible
existence of two event classes; 'normal' CMEs reaching constant mass for
R_{\sun} and 'pseudo' CMEs which disappear in the C3 FOV. It shows that the
mass and energy properties of CME reach constant levels, and therefore should
be measured, only above \sim 10 R_\sun. The mass density (g/R_\sun^2) of
CMEs varies relatively little ( order of magnitude) suggesting that the
majority of the mass originates from a small range in coronal heights. We find
a sudden reduction in the CME mass in mid-2003 which may be related to a change
in the electron content of the large scale corona and we uncover the presence
of a six-month periodicity in the ejected mass from 2003 onwards.Comment: 42 pages, 16 figures, To appear in Astrophysical Journa
Voter Model with Time dependent Flip-rates
We introduce time variation in the flip-rates of the Voter Model. This type
of generalisation is relevant to models of ageing in language change, allowing
the representation of changes in speakers' learning rates over their lifetime
and may be applied to any other similar model in which interaction rates at the
microscopic level change with time. The mean time taken to reach consensus
varies in a nontrivial way with the rate of change of the flip-rates, varying
between bounds given by the mean consensus times for static homogeneous (the
original Voter Model) and static heterogeneous flip-rates. By considering the
mean time between interactions for each agent, we derive excellent estimates of
the mean consensus times and exit probabilities for any time scale of flip-rate
variation. The scaling of consensus times with population size on complex
networks is correctly predicted, and is as would be expected for the ordinary
voter model. Heterogeneity in the initial distribution of opinions has a strong
effect, considerably reducing the mean time to consensus, while increasing the
probability of survival of the opinion which initially occupies the most slowly
changing agents. The mean times to reach consensus for different states are
very different. An opinion originally held by the fastest changing agents has a
smaller chance to succeed, and takes much longer to do so than an evenly
distributed opinion.Comment: 16 pages, 6 figure
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