Human transcriptional interactome of chromatin contribute to gene co-expression

BACKGROUND: Transcriptional interactome of chromatin is one of the important mechanisms in gene transcription regulation. By chromatin conformation capture and 3D FISH experiments, several chromatin interactions cases among sequence-distant genes or even inter-chromatin genes were reported. However, on genomics level, there is still little evidence to support these mechanisms. Recently based on Hi-C experiment, a genome-wide picture of chromatin interactions in human cells was presented. It provides a useful material for analysing whether the mechanism of transcriptional interactome is common. RESULTS: The main work here is to demonstrate whether the effects of transcriptional interactome on gene co-expression exist on genomic level. While controlling the effects of transcription factors control similarities (TCS), we tested the correlation between Hi-C interaction and the mutual ranks of gene co-expression rates (provided by COXPRESdb) of intra-chromatin gene pairs. We used 6,084 genes with both TF annotation and co-expression information, and matched them into 273,458 pairs with similar Hi-C interaction ranks in different cell types. The results illustrate that co-expression is strongly associated with chromatin interaction. Further analysis using GO annotation reveals potential correlation between gene function similarity, Hi-C interaction and their co-expression. CONCLUSIONS: According to the results in this research, the intra-chromatin interactome may have relation to gene function and associate with co-expression. This study provides evidence for illustrating the effect of transcriptional interactome on transcription regulation

TAO Conceptual Design Report: A Precision Measurement of the Reactor Antineutrino Spectrum with Sub-percent Energy Resolution

The Taishan Antineutrino Observatory (TAO, also known as JUNO-TAO) is a satellite experiment of the Jiangmen Underground Neutrino Observatory (JUNO). A ton-level liquid scintillator detector will be placed at about 30 m from a core of the Taishan Nuclear Power Plant. The reactor antineutrino spectrum will be measured with sub-percent energy resolution, to provide a reference spectrum for future reactor neutrino experiments, and to provide a benchmark measurement to test nuclear databases. A spherical acrylic vessel containing 2.8 ton gadolinium-doped liquid scintillator will be viewed by 10 m^2 Silicon Photomultipliers (SiPMs) of >50% photon detection efficiency with almost full coverage. The photoelectron yield is about 4500 per MeV, an order higher than any existing large-scale liquid scintillator detectors. The detector operates at -50 degree C to lower the dark noise of SiPMs to an acceptable level. The detector will measure about 2000 reactor antineutrinos per day, and is designed to be well shielded from cosmogenic backgrounds and ambient radioactivities to have about 10% background-to-signal ratio. The experiment is expected to start operation in 2022

Radiation Dose Calculations for a Hypothetical Accident in Xianning Nuclear Power Plant

Atmospheric dispersion modeling and radiation dose calculations have been performed for a hypothetical AP1000 SGTR accident by HotSpot code 3.03. TEDE, the respiratory time-integrated air concentration, and the ground deposition are calculated for various atmospheric stability classes, Pasquill stability categories A–F with site-specific averaged meteorological conditions. The results indicate that the maximum plume centerline ground deposition value of 1.2E+2 kBq/m2 occurred at about 1.4 km and the maximum TEDE value of 1.41E-05 Sv occurred at 1.4 km from the reactor. It is still far below the annual regulatory limits of 1 mSv for the public as set in IAEA Safety Report Series number 115. The released radionuclides might be transported to long distances but will not have any harmful effect on the public

Water quality and pollution source apportionment responses to rainfall in steppe lake estuaries: A case study of Hulun Lake in northern China

Hulun Lake, the largest inland steppe lake in China, is encountering severe water quality degradation. Estuaries play important roles in material and energetic exchange between rivers and lakes. The water quality at the estuaries of Hulun Lake directly reflects the impact of both human activities and natural factors on the lake’s overall water quality, especially during rainfall events. From July 28, 2021, to August 4, 2021, water samples from 62 sites were collected in the three estuaries of Hulun Lake before and after a moderate rainfall event. 13 water parameters, including dissolved oxygen (DO), Turbidity (Tur), Total Nitrogen (TN), Total Phosphorus (TP), Total Organic Nitrogen (TON), and Total Organic Phosphorus (TOP) were measured. The spatio-temporal distribution of water quality in the estuaries was assessed based on water quality index (WQI). Besides, an improved approach integrating stepwise linear regression (SLR) and principal component analysis (PCA) was utilized to construct a WQImin model for an effective assessment of water quality in these estuaries. Furthermore, the absolute principal component scores-multiple linear regression (APCS-MLR) model was employed to identify and quantify the environmental drivers underlying the water quality in the estuaries. The results of WQI indicated that the water quality of the sites in the estuaries of Hulun Lake was “medium” or “poor”, both before and after the rainfall, with a general deterioration in water quality in response to the rainfall. The simplified WQImin model consisted of 5 crucial parameters (i.e., TN, TP, ammonium (NH4+-N), Tur, and permanganate index (CODMn)), and it performed well without parameter weights. Spatial differences in some water parameters among the estuaries were detected, which were attributed to the natural factors and human activities upstream. The principal environmental factors affecting the water quality in the estuaries consisted of hydrodynamic processes, internal phosphorus release, external phosphorus input, external nitrogen input, nitrification in the estuaries, and external organic input and internal organic release. Therefore, we propose basin management strategies such as limiting grazing pressure, adopting enclosed pasture, wetland restoration, optimizing water renewal cycle in Hulun Lake, and transboundary water quality management to tackle water contamination in Hulun Lake.publishedVersio

PointDreamer: Zero-shot 3D Textured Mesh Reconstruction from Colored Point Cloud by 2D Inpainting

Reconstructing textured meshes from colored point clouds is an important but challenging task in 3D graphics and vision. Most existing methods predict colors as implicit functions in 3D or UV space, suffering from blurry textures or the lack of generalization capability. Addressing this, we propose PointDreamer, a novel framework for textured mesh reconstruction from colored point cloud. It produces meshes with enhanced fidelity and clarity by 2D image inpainting, taking advantage of the mature techniques and massive data of 2D vision. Specifically, we first project the input point cloud into 2D space to generate sparse multi-view images, and then inpaint empty pixels utilizing a pre-trained 2D diffusion model. Next, we design a novel Non-Border-First strategy to unproject the colors of the inpainted dense images back to 3D space, thus obtaining the final textured mesh. In this way, our PointDreamer works in a zero-shot manner, requiring no extra training. Extensive qualitative and quantitative experiments on various synthetic and real-scanned datasets show the SoTA performance of PointDreamer, by significantly outperforming baseline methods with 30\% improvement in LPIPS score (from 0.118 to 0.068). Code at: https://github.com/YuQiao0303/PointDreamer