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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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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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The dataset is a set of network traffic traces in pcap/csv format captured from a single user. The traffic is classified in 5 different activities (Video, Bulk, Idle, Web, and Interactive) and the label is shown in the filename. There is also a file (mapping.csv) with the mapping of the host's IP address, the csv/pcap filename and the activity label. Activities: Interactive: applications that perform real-time interactions in order to provide a suitable user experience, such as editing a file in google docs and remote CLI's sessions by SSH. Bulk data transfer: applications that perform a transfer of large data volume files over the network. Some examples are SCP/FTP applications and direct downloads of large files from web servers like Mediafire, Dropbox or the university repository among others. Web browsing: contains all the generated traffic while searching and consuming different web pages. Examples of those pages are several blogs and new sites and the moodle of the university. Vídeo playback: contains traffic from applications that consume video in streaming or pseudo-streaming. The most known server used are Twitch and Youtube but the university online classroom has also been used. Idle behaviour: is composed by the background traffic generated by the user computer when the user is idle. This traffic has been captured with every application closed and with some opened pages like google docs, YouTube and several web pages, but always without user interaction. The capture is performed in a network probe, attached to the router that forwards the user network traffic, using a SPAN port. The traffic is stored in pcap format with all the packet payload. In the csv file, every non TCP/UDP packet is filtered out, as well as every packet with no payload. The fields in the csv files are the following (one line per packet): Timestamp, protocol, payload size, IP address source and destination, UDP/TCP port source and destination. The fields are also included as a header in every csv file. The amount of data is stated as follows: Bulk : 19 traces, 3599 s of total duration, 8704 MBytes of pcap files Video : 23 traces, 4496 s, 1405 MBytes Web : 23 traces, 4203 s, 148 MBytes Interactive : 42 traces, 8934 s, 30.5 MBytes Idle : 52 traces, 6341 s, 0.69 MBytes The code of our machine learning approach is also included. There is a README.txt file with the documentation of how to use the code.
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