455 research outputs found
Scalable Multiresolution Image Segmentation and Its Application in Video Object Extraction Algorithm
This paper presents a novel multiresolution image segmentation method based on the discrete wavelet transform and Markov Random Field (MRF) modelling. A major contribution of this work is to add spatial scalability to the segmentation algorithm producing the same segmentation pattern at different resolutions. This property makes it suitable for the scalable object-based wavelet coding. The correlation between different resolutions of pyramid is considered by a multiresolution analysis which is incorporated into the objective function of the MRF segmentation algorithm. Allowing for smoothness terms in the objective function at different resolutions improves border smoothness and creates visually more pleasing objects/regions, particularly at lower resolutions where downsampling distortions are more visible. Application of the spatial segmentation in video segmentation, compared to traditional image/video object extraction algorithms, produces more visually pleasing shape masks at different resolutions which is applicable for object-based video wavelet coding. Moreover it allows for larger motion, better noise tolerance and less computational complexity. In addition to spatial scalability, the proposed algorithm outperforms the standard image/video segmentation algorithms, in both objective and subjective tests
Robust co-immunoprecipitation with mass spectrometry for Caenorhabditis elegans using solid-phase enhanced sample preparation
Studying protein interactions in vivo can reveal key molecular mechanisms of biological processes. Co-immunoprecipitation with mass spectrometry detects protein–protein interactions with high throughput. The nematode Caenorhabditis elegans is a powerful genetic model organism for in vivo studies. Yet its rigid and complex tissues require optimization for biochemistry applications to ensure reproducibility. The authors optimized co-immunoprecipitation with mass spectrometry by combining a native co-immunoprecipitation procedure with single-pot, solid-phase enhanced sample preparation. The authors' results for the highly conserved chromatin regulator FACT subunits HMG-3 and HMG-4 demonstrated that single-pot, solid-phase enhanced sample preparation-integrated co-immunoprecipitation with mass spectrometry procedures for C. elegans samples are highly robust. Moreover, in an accompanying study about the chromodomain factor MRG-1 (MRG15 in humans), the authors demonstrated remarkably high reproducibility for ten replicate experiments
X-ray magneto-optics of lanthanide materials: principles and applications
Lanthanide metals are a particular class of magnetic materials in which the
magnetic moments are carried mainly by the localized electrons of the 4f shell.
They are frequently found in technically relevant systems, to achieve, e.g.,
high magnetic anisotropy. Magneto-optical methods in the x-ray range are well
suited to study complex magnetic materials in an element-specific way. In this
work, we report on recent progress on the quantitative determination of
magneto-optical constants of several lanthanides in the soft x-ray region and
we show some examples of applications of magneto-optics to hard-magnetic
interfaces and exchange-coupled layered structures containing lanthanide
elements.Comment: 7 pages, 6 figures, invited contribution to the Symposium "X-ray
magneto-optics" of the Spring Meeting of the German Physical Society held in
Regensburg, Germany, 8-12 March 2004. Revised version, minor change
H3.3K27M mutation is not a suitable target for immunotherapy in HLA-A2(+) patients with diffuse midline glioma
Diffuse midline glioma is the leading cause of solid cancer-related deaths in children with very limited treatment options. A majority of the tumors carry a point mutation in the histone 3 variant (H3.3) creating a potential HLA-A*02:01 binding epitope (H3.3K27M(26-35)). Here, we isolated an H3.3K27M-specific T cell receptor (TCR) from transgenic mice expressing a diverse human TCR repertoire. Despite a high functional avidity of H3.3K27M-specific T cells, we were not able to achieve recognition of cells naturally expressing the H3.3K27M mutation, even when overexpressed as a transgene. Similar results were obtained with T cells expressing the published TCR 1H5 against the same epitope. CRISPR/Cas9 editing was used to exclude interference by endogenous TCRs in donor T cells. Overall, our data provide strong evidence that the H3.3K27M mutation is not a suitable target for cancer immunotherapy, most likely due to insufficient epitope processing and/or amount to be recognized by HLA-A*02:01 restricted CD8(+) T cells
Review of biorthogonal coupled cluster representations for electronic excitation
Single reference coupled-cluster (CC) methods for electronic excitation are
based on a biorthogonal representation (bCC) of the (shifted) Hamiltonian in
terms of excited CC states, also referred to as correlated excited (CE) states,
and an associated set of states biorthogonal to the CE states, the latter being
essentially configuration interaction (CI) configurations. The bCC
representation generates a non-hermitian secular matrix, the eigenvalues
representing excitation energies, while the corresponding spectral intensities
are to be derived from both the left and right eigenvectors. Using the
perspective of the bCC representation, a systematic and comprehensive analysis
of the excited-state CC methods is given, extending and generalizing previous
such studies. Here, the essential topics are the truncation error
characteristics and the separability properties, the latter being crucial for
designing size-consistent approximation schemes. Based on the general order
relations for the bCC secular matrix and the (left and right) eigenvector
matrices, formulas for the perturbation-theoretical (PT) order of the
truncation errors (TEO) are derived for energies, transition moments, and
property matrix elements of arbitrary excitation classes and truncation levels.
In the analysis of the separability properties of the transition moments, the
decisive role of the so-called dual ground state is revealed. Due to the use of
CE states the bCC approach can be compared to so-called intermediate state
representation (ISR) methods based exclusively on suitably orthonormalized CE
states. As the present analysis shows, the bCC approach has decisive advantages
over the conventional CI treatment, but also distinctly weaker TEO and
separability properties in comparison with a full (and hermitian) ISR method
Self-consistent Green's function approaches
We present the fundamental techniques and working equations of many-body
Green's function theory for calculating ground state properties and the
spectral strength. Green's function methods closely relate to other polynomial
scaling approaches discussed in chapters 8 and 10. However, here we aim
directly at a global view of the many-fermion structure. We derive the working
equations for calculating many-body propagators, using both the Algebraic
Diagrammatic Construction technique and the self-consistent formalism at finite
temperature. Their implementation is discussed, as well as the inclusion of
three-nucleon interactions. The self-consistency feature is essential to
guarantee thermodynamic consistency. The pairing and neutron matter models
introduced in previous chapters are solved and compared with the other methods
in this book.Comment: 58 pages, 14 figures, Submitted to Lect. Notes Phys., "An advanced
course in computational nuclear physics: Bridging the scales from quarks to
neutron stars", M. Hjorth-Jensen, M. P. Lombardo, U. van Kolck, Editor
Comparison of Zn_{1-x}Mn_xTe/ZnTe multiple-quantum wells and quantum dots by below-bandgap photomodulated reflectivity
Large-area high density patterns of quantum dots with a diameter of 200 nm
have been prepared from a series of four Zn_{0.93}Mn_{0.07}Te/ZnTe multiple
quantum well structures of different well width (4 nm, 6 nm, 8 nm and 10 nm) by
electron beam lithography followed by Ar+ ion beam etching. Below-bandgap
photomodulated reflectivity spectra of the quantum dot samples and the parent
heterostructures were then recorded at 10 K and the spectra were fitted to
extract the linewidths and the energy positions of the excitonic transitions in
each sample. The fitted results are compared to calculations of the transition
energies in which the different strain states in the samples are taken into
account. We show that the main effect of the nanofabrication process is a
change in the strain state of the quantum dot samples compared to the parent
heterostructures. The quantum dot pillars turn out to be freestanding, whereas
the heterostructures are in a good approximation strained to the ZnTe lattice
constant. The lateral size of the dots is such that extra confinement effects
are not expected or observed.Comment: 23 pages, LaTeX2e (amsmath, epsfig), 7 EPS figure
SUMOylation of the chromodomain factor MRG-1 in C. elegans affects chromatin-regulatory dynamics
Epigenetic mechanisms to control chromatin accessibility and structure is important for gene expression in eukaryotic cells. Chromatin regulation ensures proper development and cell fate specification but is also essential later in life. Modifications of histone proteins as an integral component of chromatin can promote either gene expression or repression, respectively. Proteins containing specific domains such as the chromodomain recognize mono-, di- or tri-methylated lysine residues on histone H3. The chromodomain protein MRG-1 in Caenorhabditis elegans is the ortholog of mammalian MRG15, which belongs to the MORF4 Related Gene (MRG) family in humans. In C. elegans MRG-1 predominantly binds methylated histone H3 lysine residues at position 36 (H3K36me3). MRG-1 is important during germline maturation and for safeguarding the germ cell identity. However, it lacks enzymatic activity and depends on protein-protein interaction to cooperate with other factors to regulate chromatin. To elucidate the variety of MRG-1 interaction partners we performed in-depth protein-protein interaction analysis using immunoprecipitations coupled with mass-spectrometry. Besides previously described and novel interactions with other proteins, we also detected a strong association with the Small Ubiquitin-like Modifier (SUMO). Since SUMO is known to be attached to proteins in order to modulate the target proteins activity we assessed whether MRG-1 is post-translationally modified by SUMOylation. Notably, we provide evidence that MRG-1 is indeed SUMOylated and that this post-translational modification influences the chromatin-binding profile of MRG-1 in the C. elegans genome. Our presented study hints towards an important role of SUMOylation in the context of epigenetic regulation via the chromodomain protein MRG-1, which may be a conserved phenomenon also in mammalian species
Prediction of huge X-ray Faraday rotation at the Gd N_4,5 threshold
X-ray absorption spectra in a wide energy range around the 4d-4f excitation
threshold of Gd were recorded by total electron yield from in-plane magnetized
Gd metal films. Matching the experimental spectra to tabulated absorption data
reveals unprecedented short light absorption lengths down to 3 nm. The
associated real parts of the refractive index for circularly polarized light
propagating parallel or antiparallel to the Gd magnetization, determined
through the Kramers-Kronig transformation, correspond to a magneto-optical
Faraday rotation of 0.7 degrees per atomic layer. This finding shall allow the
study of magnetic structure and magnetization dynamics of lanthanide elements
in nanosize systems and dilute alloys.Comment: 4 pages, 2 figures, final version resubmitted to Phys. Rev. B, Brief
Reports. Minor change
- …