•Integration of CNN and gated RNN over multiple scales•Introduction of normalized focal loss for momentum based optimizers.•Provision of insights on how our extensions affect training and ...inference.•Quantitative evaluation using a wide spectrum of 2D and 3D real microscopy image data.
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Cell segmentation in microscopy images is a common and challenging task. In recent years, deep neural networks achieved remarkable improvements in the field of computer vision. The dominant paradigm in segmentation is using convolutional neural networks, less common are recurrent neural networks. In this work, we propose a new deep learning method for cell segmentation, which integrates convolutional neural networks and gated recurrent neural networks over multiple image scales to exploit the strength of both types of networks. To increase the robustness of the training and improve segmentation, we introduce a novel focal loss function. We also present a distributed scheme for optimized training of the integrated neural network. We applied our proposed method to challenging data of glioblastoma cell nuclei and performed a quantitative comparison with state-of-the-art methods. Insights on how our extensions affect training and inference are also provided. Moreover, we benchmarked our method using a wide spectrum of all 22 real microscopy datasets of the Cell Tracking Challenge.
Neomorphic mutations in isocitrate dehydrogenase 1 (IDH1) are frequently found in several human cancer types including acute myeloid leukemia (AML) and lead to the production of high levels of the ...oncometabolite (R)-2-hydroxyglutarate (R-2HG). Here we report the characterization of BAY1436032, a novel pan-mutant IDH1 inhibitor, both in vitro and in vivo. BAY1436032 specifically inhibits R-2HG production and colony growth, and induces myeloid differentiation of AML cells carrying IDH1R132H, IDH1R132C, IDH1R132G, IDH1R132L and IDH1R132S mutations. In addition, the compound impacts on DNA methylation and attenuates histone hypermethylation. Oral administration of BAY1436032 led to leukemic blast clearance, myeloid differentiation, depletion of leukemic stem cells and prolonged survival in two independent patient-derived xenograft IDH1 mutant AML mouse models. Together, BAY1436032 is highly effective against all major types of IDH1 mutant AML.
The interaction of proteins bound at distant sites on a nucleic acid chain plays an important role in many molecular biological processes. Contact between the proteins is established by looping of ...the intervening polymer, which can comprise either double- or single-stranded DNA or RNA, or interphase or metaphase chromatin. The effectiveness of this process, as well as the optimal separation distance, is highly dependent on the flexibility and conformation of the linker. This article reviews how the probability of looping-mediated interactions is calculated for different nucleic acid polymers. In addition, the application of the equations to the analysis of experimental data is illustrated.
This article describes how the probability of looping-mediated interactions is calculated for different nucleic acid polymers such as double- or single-stranded DNA or RNA, or interphase or metaphase chromatin.
The article discusses two ethical aspects of the fluoridation of water, salt, and milk. First, it considers whether fluoridation contradicts the right of self-determination. Second, it discusses the ...chances and risks of fluoridation. The answer to the first question depends on whether people can choose other options. Freedom of choice is not simply the right to choose between different options. It is a right which defends the moral integrity of persons. Nobody should be coerced to eat or drink something which he or she rejects morally. In the political sphere, personal rights of persons can be restricted if and only if it is necessary, if there is a public interest, and if the restriction of the right is reasonable. Regarding fluoridation, even in the best risk-chance scenario, some persons have to expect a net harm. Therefore, the reasoning in favor of fluoridation has to have a specific purpose. The proclaimed reasoning is that fluoridation will benefit the worst off and is therefore a demand of justice. But this argument fails as there are other options to benefit the worst off. Even in the best risk-chance scenario, only one option is morally permissible: the fluoridation of salt, which respects the freedom of choice.
Capturing Chromosome Conformation Dekker, Job; Rippe, Karsten; Dekker, Martijn ...
Science (American Association for the Advancement of Science),
02/2002, Letnik:
295, Številka:
5558
Journal Article
Recenzirano
We describe an approach to detect the frequency of interaction between any two genomic loci. Generation of a matrix of interaction frequencies between sites on the same or different chromosomes ...reveals their relative spatial disposition and provides information about the physical properties of the chromatin fiber. This methodology can be applied to the spatial organization of entire genomes in organisms from bacteria to human. Using the yeast Saccharomyces cerevisiae, we could confirm known qualitative features of chromosome organization within the nucleus and dynamic changes in that organization during meiosis. We also analyzed yeast chromosome III at the G1 stage of the cell cycle. We found that chromatin is highly flexible throughout. Furthermore, functionally distinct AT- and GC-rich domains were found to exhibit different conformations, and a population-average 3D model of chromosome III could be determined. Chromosome III emerges as a contorted ring.
In eukaryotes, the interaction of DNA with proteins and supramolecular complexes involved in gene expression is controlled by the dynamic organization of chromatin inasmuch as it defines the DNA ...accessibility. Here, the nuclear distribution of microinjected fluorescein-labeled dextrans of 42 kDa to 2.5 MDa molecular mass was used to characterize the chromatin accessibility in dependence on histone acetylation. Measurements of the fluorescein-dextran sizes were combined with an image correlation spectroscopy analysis, and three different interphase chromatin condensation states with apparent pore sizes of 16-20 nm, 36-56 nm and 60-100 nm were identified. A reversible change of the chromatin conformation to a uniform 60-100 nm pore size distribution was observed upon increased histone acetylation. This result identifies histone acetylation as a central factor in the dynamic regulation of chromatin accessibility during interphase. In mitotic chromosomes, the chromatin exclusion limit was 10-20 nm and independent of the histone acetylation state.
We have used scanning force microscopy (SFM) to study the conformation of a 1868 base pair plasmid (p1868) in its open circular form and at a superhelical density of σ = −0.034. The samples were ...deposited on a mica surface in the presence of MgCl2. DNA images were obtained both in air and in aqueous solutions, and the dimensions of the DNA superhelix were analysed. Evaluation of the whole plasmid yielded average superhelix dimensions of 27 ± 9 nm (outer superhelix diameter D), 107 ± 51 nm (superhelix pitch P), and 54 ± 8° (superhelix pitch angle α). We also analysed compact superhelical regions within the plasmid separately, and determined values of D = 9.2 ± 3.3 nm, P = 42 ± 13 nm and α = 63 ± 20° for samples scanned in air or rehydrated in water. These results indicate relatively large conformation changes between superhelical and more open regions of the plasmid. In addition to the analysis of the DNA superhelix dimensions, we have followed the deposition process of open circular p1868 to mica in real time. These experiments show that it is possible to image DNA samples by SFM without prior drying, and that the surface bound DNA molecules retain some ability to change their position on the surface.
The oligonucleotides d(G‐A)7G and d(G‐A)12G self‐associate under physiological conditions (10 mM MgCl2, neutral pH) into a stable double‐helical structure (psRR‐DNA) in which the two polypurine ...strands are in a parallel orientation in contrast to the antiparallel disposition of conventional B‐DNA. We have characterized psRR‐DNA by gel electrophoresis, UV absorption, vacuum UV circular dichroism, monomer‐excimer fluorescence of oligonucleotides end‐labelled with pyrene, and chemical probing with diethyl pyrocarbonate and dimethyl sulfate. The duplex is stable at pH 4–9, suggesting that the structure is compatible with, but does not require, protonation of the A residues. The data support a model derived from force‐field analysis in which the parallel‐stranded d(G‐A)n helix is right‐handed and constituted of alternating, symmetrical Gsyn.Gsyn and Aanti.Aanti base pairs with N1H…O6 and N6H…N7 hydrogen bonds, respectively. This dinucleotide structure may be the source of a negative peak observed at 190 nm in the vacuum UV CD spectrum, a feature previously reported only for left‐handed Z‐DNA. The related sequence d(GAAGGA)4G also forms a parallel‐stranded duplex but one that is less stable and probably involves a slightly different secondary structure. We discuss the potential intervention of psRR‐DNA in recombination, gene expression and the stabilization of genomic structure.
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