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The promyelocytic leukemia (PML) body is a phase-separated nuclear structure physically associated with chromatin, implying its crucial roles in genome functions. However, its role in transcriptional regulation is largely unknown. We developed APEX-mediated chromatin labeling and purification (ALaP) to identify the genomic regions proximal to PML bodies. We found that PML bodies associate with active regulatory regions across the genome and with an ~300 kb of the short arm of the Y chromosome (YS300) in mouse embryonic stem cells. The PML body-association with YS300 is essential for the transcriptional activity of the neighboring Y-linked clustered genes. Mechanistically, PML bodies provide specific nuclear spaces that the de novo DNA methyltransferase DNMT3A cannot access, resulting in the steady maintenance of a hypomethylated state at Y-linked gene promoters. Our study underscores a new mechanism for gene regulation in the 3D-nuclear space and provides insights into the functional properties of nuclear structures for genome function.
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A diazirine-containing unnatural amino acid was site-specifically incorporated into IFITM3, an antiviral protein. After photo-irradiation, the interacting proteins were crosslinked with IFITM3, isolated by immunoprecipitation, and identified by quantitative SILAC proteomics.
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Data from a behavioral pilot study including the factors 'distractor number' (0,1,or n), cue-target SOA (0 va 300 ms), and presentation mode (separated vs superimposed streams). Data from an ERP experiment including the factors 'cue-alone vs cue+target', 'hit vs miss', and electrode position.
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In this work we present ZEFR, a GPU accelerated flow solver based around the high-order accurate flux reconstruction (FR) approach. Written in a combination of C++ and CUDA, ZEFR is designed to perform scale resolving simulations within the vicinity of complex geometrical configurations. A unique feature of ZEFR is its support for overset grids; a feature which greatly expands the addressable problem space compared with existing high-order codes. The C++ implementation of FR in a manner which is suitable for modern hardware platforms is described in detail. Additionally, an overview of the input deck used by ZEFR is included. Validation results are presented for a range of steady and unsteady flow problems including Couette flow, the Taylor–Green vortex, and flow around an SD7003 aerofoil. Single node performance on a NVIDIA V100 GPU is analysed where it is shown that all of the kernels in ZEFR attain a high proportion of peak memory bandwidth. Moreover, multi-node performance is also assessed with strong scalability being demonstrated from 60 to 3840 NVIDIA V100 GPUs.
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Modelling and simulation of a Flexible Manufacturing System with AGV transport
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Different human linker histone (H1) variants are expected to have distinct binding modes to the nucleosome. The position and orientation of a number of different H1 globular domains on the nucleosome were investigated through molecular docking using MGLTools and HADDOCK. The nucleosome core and linker DNA in the GH5-chromatosome structure (PDB: 4QLC) were used as a docking template. GH5 (in PDB: 4QLC) was re-docked to this template to test the docking algorithm. Docked and re-docked GH5 compared well. The docking algorithm was further tested by docking the NMR solution structure of the globular domain of chicken H1 (GH1, PDB: 1GHC) to the nucleosome template. The position of docked GH1 on the nucleosome agreed with literature. 
The N-terminal - and globular domain H1x hybrid (NGH1x) was studied using solution NMR in both low (20 mM sodium phosphate, pH 7.0) and high (20 mM sodium phosphate, 1 M sodium perchlorate, pH 7.0) ionic strength conditions (de Wit, H., Vallet, A., Brutscher, B. et al. Biomol NMR Assign (2019) 13: 249. https://doi.org/10.1007/s12104-019-09886-x). These low and high ionic strength structures were docked to the nucleosome template. 
Homology (MODELLER) and ab initio modeling (CS-ROSETTA) were employed to model structures for other human H1 globular domains: GH1.0, GH1.4, GH1oo, and GH1t. The modeled structures were also docked to the nucleosome template.
 All the docking procedures listed above produced 100 models of different energies. In each case, the lowest energy docked model was chosen. The structures of all the H1 globular domains that were docked to the template are given as PDB files (1GHC_lowest_energy.pdb; 2LSO_lowest_energy.pdb; GH5_re-docked_position.pdb; NGH1x_high_salt_NTD.pdb; NGH1x_low_salt_NTD.pdb; modeled_GH1_0_lowest_energy.pdb; modeled_GH1_4_lowest_energy.pdb; modeled_GH1oo_lowest_energy.pdb; modelled_GH1t_lowest_energy.pdb) in the data file. The nucleosome template structure is also given in PDB file format (4QLC_nucleosome_without_GH5.pdb). Finally, the docked models are also given (GH5-chromatosome.pdb; 1GHC-chromatosome.pdb; 2LSO-chromatosome.pdb; GH1_0-chromatosome.pdb; GH1_4-chromatosome.pdb; GH1oo-chromatosome.pdb; GH1t-chromatosome.pdb; NGH1x_no_salt-chromatosome.pdb; NGH1x_salt-chromatosome.pdb). The files are compatible with most molecular graphics software.
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Integrated thermodynamic-volume database for the Ni-Al γ/γ′ binary phases
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RRDE results from KOH activated char
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A dataset for human counting in a room. The data consists of images that captured using a CCTV in a room where the outside of the room is visible. It poses a challenge to discriminate between in-room and out-room humans for the model that is developed using this dataset.
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