Study of protein-DNA interaction using new generation data

Ph.DDOCTOR OF PHILOSOPH

Knolling bot 2.0: Enhancing Object Organization with Self-supervised Graspability Estimation

Building on recent advancements in transformer based approaches for domestic robots performing knolling, the art of organizing scattered items into neat arrangements. This paper introduces Knolling bot 2.0. Recognizing the challenges posed by piles of objects or items situated closely together, this upgraded system incorporates a self-supervised graspability estimation model. If objects are deemed ungraspable, an additional behavior will be executed to separate the objects before knolling the table. By integrating this grasp prediction mechanism with existing visual perception and transformer based knolling models, an advanced system capable of decluttering and organizing even more complex and densely populated table settings is demonstrated. Experimental evaluations demonstrate the effectiveness of this module, yielding a graspability prediction accuracy of 95.7%.Comment: This paper has been accepted by the NeurIPS 2023 Robot Learning Worksho

Integrative construction of regulatory region networks in 127 human reference epigenomes by matrix factorization

© The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research. Despite large experimental and computational efforts aiming to dissect the mechanisms underlying disease risk, mapping cis-regulatory elements to target genes remains a challenge. Here, we introduce a matrix factorization framework to integrate physical and functional interaction data of genomic segments. The framework was used to predict a regulatory network of chromatin interaction edges linking more than 20 000 promoters and 1.8 million enhancers across 127 human reference epigenomes, including edges that are present in any of the input datasets. Our network integrates functional evidence of correlated activity patterns from epigenomic data and physical evidence of chromatin interactions. An important contribution of this work is the representation of heterogeneous data with different qualities as networks. We show that the unbiased integration of independent data sources suggestive of regulatory interactions produces meaningful associations supported by existing functional and physical evidence, correlating with expected independent biological features

Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation

Higher-order chromosomal organization for transcription regulation is poorly understood in eukaryotes. Using genome-wide Chromatin Interaction Analysis with Paired-End-Tag sequencing (ChIAPET), we mapped long-range chromatin interactions associated with RNA polymerase II in human cells and uncovered widespread promoter-centered intragenic, extragenic, and intergenic interactions. These interactions further aggregated into higher-order clusters, wherein proximal and distal genes were engaged through promoter-promoter interactions. Most genes with promoter-promoter interactions were active and transcribed cooperatively, and some interacting promoters could influence each other implying combinatorial complexity of transcriptional controls. Comparative analyses of different cell lines showed that cell-specific chromatin interactions could provide structural frameworks for cell-specific transcription, and suggested significant enrichment of enhancer-promoter interactions for cell-specific functions. Furthermore, genetically-identified disease-associated noncoding elements were found to be spatially engaged with corresponding genes through long-range interactions. Overall, our study provides insights into transcription regulation by three-dimensional chromatin interactions for both housekeeping and cell-specific genes in human cells

Hardware optimization for photonic time-delay reservoir computer dynamics

Reservoir computing (RC) is one kind of neuromorphic computing mainly applied to process sequential data such as time-dependent signals. In this paper, the bifurcation diagram of a photonic time-delay RC system is thoroughly studied, and a method of bifurcation dynamics guided hardware hyperparameter optimization is presented. The time-evolution equation expressed by the photonic hardware parameters is established while the intrinsic dynamics of the photonic RC system is quantitively studied. Bifurcation dynamics based hyperparameter optimization offers a simple yet effective approach in hardware setting optimization that aims to reduce the complexity and time in hardware adjustment. Three benchmark tasks, nonlinear channel equalization (NCE), nonlinear auto regressive moving average with 10th order time lag (NARMA10) and Santa Fe laser time-series prediction tasks are implemented on the photonic delay-line RC using bifurcation dynamics guided hardware optimization. The experimental results of these benchmark tasks achieved overall good agreement with the simulated bifurcation dynamics modeling results

Assessment of the Happy River Index as an Integrated Index of River Health and Human Well-Being: A Case Study of the Yellow River, China

Acceleration urbanization and industrialization has resulted in challenges such as river ecosystem degradation and water scarcity that have hindered sustainable development in China. Healthy rivers provide ecosystem services that improve human well-being. The Happy River Index (HRI) integrates trends in river health and human well-being. This study aimed to establish an HRI assessment framework. The assessment framework was applied to the Yellow River, China at three spatial scales in which the analytic hierarchy process (AHP)-entropy weight and single index quantification-multiple indices syntheses-poly-criteria integration (SMI-P) methods were utilized. Limiting factors were diagnosed by the obstacle degree model and approaches to improve the HRI in regions along the Yellow River are suggested. The results showed that: (1) the overall HRI of the Yellow River was relatively low, with some differences among different regions; (2) the HRI for the upper, middle, and lower reaches of the Yellow River showed a decreasing trend from 0.77 to 0.65; (3) Sichuan had the highest HRI at the regional scale, followed by Gansu and Qinghai, whereas Inner Mongolia had the lowest; (4) scarcity of water resources and the fragility of the ecological environment were the two dominant factors restricting the improvement of the HRI in regions along the Yellow River. The results of this study can provide a valuable reference for protection of river health and improvement of human well-being in China

Relationship Identification between Water-Energy Resource Utilization Efficiency and Ecological Risk in the Context of Assessment-Decoupling Two-Stage Framework—A Case Study of Henan Province, China

The situation of resource utilization and eco-environment protection remains critical globally. The harmony between eco-environment health and water-energy utilization efficiency is a strong support for the realization of high-quality development. In this paper, an Assessment-Decoupling two-stage framework was developed to investigate the relationship between water-energy resource utilization and ecological security. In detail, an improved input-output indicator system was constructed to assess the water-energy resource utilization efficiency (WEUE), and its influencing factors were examined from multiple system perspectives; then, we intended to evaluate the ecological risk (ER) from a raster-scale perspective based on land-use types; and finally, the decoupling idea was introduced to quantify the fitness relationship of the above two aspects. The framework was applied to Henan Province, China. The study found that: (1) the WEUE of Henan Province shows a “W” pattern of development during 2000–2020; in 2000–2010, the WEUE of South Henan declined, while in 2010–2020, the WEUE of Henan Province gradually improved, with significant increases in various districts. (2) The ecological risk index (ERI) in Henan Province generally shows a decreasing trend, and the spatial difference is more obvious, with the high-risk areas mainly concentrated in the central, east, and south Henan, and the west of Henan is mainly a low-risk area. (3) There is strong spatial variation in the decoupling states of WEUE and ERI of the 18 districts in Henan Province, and the differences become more pronounced over time. The number of districts with a strong negative decoupling state has been increasing during the entire period, and a total of 14 districts have reached the above state in 2020. The developed framework offers a new idea for clarifying the relationship between resource utilization and ecological conditions, and the obtained results can provide data support for the realization of sustainable development

Temporal and Spatial Changes in Soil Organic Carbon in a Semi-Arid Area of Aohan County, Chifeng City, China

Soil organic carbon (SOC) plays a crucial role in arid zones, while land-use change could lead to changes in the balance of SOC. Therefore, the aim of this study was to determine the impact of land-use change on the temporal and spatial variability in SOC at the county scale. A semi-arid zone (Aohan County, Northeast China) covering a surface of 3800 km2 was selected for this study. SOC data for 65 and 182 soil samples from 1985 and 2021, respectively, were collected for major land-use types (forestland, farmland, grassland, and sandy land) across Aohan County to a depth of 20 cm. The impacts of different land-use types and land-use changes on SOC were evaluated. The results showed that land-use change enhanced the spatial variability in SOC over the last 36 years. The mean SOC in 2021 (7.49 g kg−1) was significantly higher than that in 1985 (6.91 g kg−1). Converting sandy land into grassland and farmland into forest or grassland would lead to significant accumulation of SOC, while the depletion of SOC occurred after grassland afforestation. The balance between aboveground biomass inputs and SOC decomposition was the determining reason that affected the accumulation of SOC. Vegetation restoration due to land-use change could alter both soil texture and the C/N ratio and could have positive effects on ecosystem recovery

Carbon Dioxide Emission Equivalent Analysis of Water Resource Behaviors: Determination and Application of CEEA Function Table

To achieve the global temperature control target under the background of climate warming, it is necessary to establish a systematic carbon dioxide (CO2) emission accounting method system in the field of water resources as soon as possible. In this study, the carbon dioxide emission equivalent analysis (CEEA) method for different water resource behaviors (WRBs) is proposed from four dimensions of development, allocation, utilization, and protection, and a function table of CEEA (FT-CEEA) for WRBs is constructed. The FT-CEEA includes CEEA formulae for 16 aspects in four categories of water resource development, allocation, utilization, and protection. The CEEA method is applied to 31 provinces in China. The results reveal that: (1) There are significant spatial differences in the carbon dioxide emission equivalent (CEE) of WRBs in different provinces of China under the influence of various factors such as water supply structure and natural conditions. (2) Reservoir storage, tap water allocation, and wastewater treatment are the main contributors to CEE in the categories of water resource development, allocation, and protection behaviors, respectively. (3) The water resource utilization behavior category has the most significant CO2 emission and absorption effects, and industrial and domestic water utilization behaviors are the main sources of emission effects. (4) The overall CO2 emission effect of WRBs is greater than the absorption effect. Measures such as increasing the proportion of hydroelectric power generation, improving ecological water security capacity, and strengthening the level of wastewater treatment and reclaimed water reuse are effective ways to promote the goal of carbon neutrality in the field of water resources