708 research outputs found
Joint registration and synthesis using a probabilistic model for alignment of MRI and histological sections
Nonlinear registration of 2D histological sections with corresponding slices
of MRI data is a critical step of 3D histology reconstruction. This task is
difficult due to the large differences in image contrast and resolution, as
well as the complex nonrigid distortions produced when sectioning the sample
and mounting it on the glass slide. It has been shown in brain MRI registration
that better spatial alignment across modalities can be obtained by synthesizing
one modality from the other and then using intra-modality registration metrics,
rather than by using mutual information (MI) as metric. However, such an
approach typically requires a database of aligned images from the two
modalities, which is very difficult to obtain for histology/MRI.
Here, we overcome this limitation with a probabilistic method that
simultaneously solves for registration and synthesis directly on the target
images, without any training data. In our model, the MRI slice is assumed to be
a contrast-warped, spatially deformed version of the histological section. We
use approximate Bayesian inference to iteratively refine the probabilistic
estimate of the synthesis and the registration, while accounting for each
other's uncertainty. Moreover, manually placed landmarks can be seamlessly
integrated in the framework for increased performance.
Experiments on a synthetic dataset show that, compared with MI, the proposed
method makes it possible to use a much more flexible deformation model in the
registration to improve its accuracy, without compromising robustness.
Moreover, our framework also exploits information in manually placed landmarks
more efficiently than MI, since landmarks inform both synthesis and
registration - as opposed to registration alone. Finally, we show qualitative
results on the public Allen atlas, in which the proposed method provides a
clear improvement over MI based registration
Initial-state dependence in time-dependent density functional theory
Time-dependent density functionals in principle depend on the initial state
of the system, but this is ignored in functional approximations presently in
use. For one electron it is shown there is no initial-state dependence: for any
density, only one initial state produces a well-behaved potential. For two
non-interacting electrons with the same spin in one-dimension, an initial
potential that makes an alternative initial wavefunction evolve with the same
density and current as a ground state is calculated. This potential is
well-behaved and can be made arbitrarily different from the original potential
Why are Prices Sticky? Evidence from Business Survey Data
This paper offers new insights on the price setting behaviour of German retail firms using a novel dataset that
consists of a large panel of monthly business surveys from 1991-2006. The firm-level data allows matching changes
in firms' prices to several other firm-characteristics. Moreover, information on price expectations allow analyzing
the determinants of price updating. Using univariate and bivariate ordered probit specifications, empirical menu
cost models are estimated relating the probability of price adjustment and price updating, respectively, to both
time- and state- dependent variables. First, results suggest an important role for state-dependence; changes in
the macroeconomic and institutional environment as well as firm-specific factors are significantly related to the
timing of price adjustment. These findings imply that price setting models should endogenize the timing of price
adjustment in order to generate realistic predictions concerning the transmission of monetary policy. Second, an
analysis of price expectations yields similar results providing evidence in favour of state-dependent sticky plan
models. Third, intermediate input cost changes are among the most important determinants of price adjustment
suggesting that pricing models should explicitly incorporate price setting at different production stages. However, the results show that adjustment to input cost changes takes time indicating "additional stickiness" at the last stage of processing
Exchange-correlation kernels for excited states in solids
The performance of several common approximations for the exchange-correlation
kernel within time-dependent density-functional theory is tested for elementary
excitations in the homogeneous electron gas. Although the adiabatic
local-density approximation gives a reasonably good account of the plasmon
dispersion, systematic errors are pointed out and traced to the neglect of the
wavevector dependence. Kernels optimized for atoms are found to perform poorly
in extended systems due to an incorrect behavior in the long-wavelength limit,
leading to quantitative deviations that significantly exceed the experimental
error bars for the plasmon dispersion in the alkali metals.Comment: 7 pages including 5 figures, RevTe
A machine learning method for the discovery of minimum marker gene combinations for cell type identification from single-cell RNA sequencing
Single-cell genomics is rapidly advancing our knowledge of the diversity of cell phenotypes, including both cell types and cell states. Driven by single-cell/-nucleus RNA sequencing (scRNA-seq), comprehensive cell atlas projects characterizing a wide range of organisms and tissues are currently underway. As a result, it is critical that the transcriptional phenotypes discovered are defined and disseminated in a consistent and concise manner. Molecular biomarkers have historically played an important role in biological research, from defining immune cell types by surface protein expression to defining diseases by their molecular drivers. Here, we describe a machine learning-based marker gene selection algorithm, NS-Forest version 2.0, which leverages the nonlinear attributes of random forest feature selection and a binary expression scoring approach to discover the minimal marker gene expression combinations that optimally capture the cell type identity represented in complete scRNA-seq transcriptional profiles. The marker genes selected provide an expression barcode that serves as both a useful tool for downstream biological investigation and the necessary and sufficient characteristics for semantic cell type definition. The use of NS-Forest to identify marker genes for human brain middle temporal gyrus cell types reveals the importance of cell signaling and noncoding RNAs in neuronal cell type identity.Neuro Imaging Researc
Correlation energy of a two-dimensional electron gas from static and dynamic exchange-correlation kernels
We calculate the correlation energy of a two-dimensional homogeneous electron
gas using several available approximations for the exchange-correlation kernel
entering the linear dielectric response of the system.
As in the previous work of Lein {\it et al.} [Phys. Rev. B {\bf 67}, 13431
(2000)] on the three-dimensional electron gas, we give attention to the
relative roles of the wave number and frequency dependence of the kernel and
analyze the correlation energy in terms of contributions from the plane. We find that consistency of the kernel with the electron-pair
distribution function is important and in this case the nonlocality of the
kernel in time is of minor importance, as far as the correlation energy is
concerned. We also show that, and explain why, the popular Adiabatic Local
Density Approximation performs much better in the two-dimensional case than in
the three-dimensional one.Comment: 9 Pages, 4 Figure
Unique reporter-based sensor platforms to monitor signalling in cells
Introduction: In recent years much progress has been made in the development of tools for systems biology to study the levels of mRNA and protein, and their interactions within cells. However, few multiplexed methodologies are available to study cell signalling directly at the transcription factor level.
<p/>Methods: Here we describe a sensitive, plasmid-based RNA reporter methodology to study transcription factor activation in mammalian cells, and apply this technology to profiling 60 transcription factors in parallel. The methodology uses two robust and easily accessible detection platforms; quantitative real-time PCR for quantitative analysis and DNA microarrays for parallel, higher throughput analysis.
<p/>Findings: We test the specificity of the detection platforms with ten inducers and independently validate the transcription factor activation.
<p/>Conclusions: We report a methodology for the multiplexed study of transcription factor activation in mammalian cells that is direct and not theoretically limited by the number of available reporters
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