Inferring Single-Cell 3D Chromosomal Structures Based On the Lennard-Jones Potential

Reconstructing three‐dimensional (3D) chromosomal structures based on single‐cell Hi‐C data is a challenging scientific problem due to the extreme sparseness of the single‐cell Hi‐C data. In this research, we used the Lennard‐Jones potential to reconstruct both 500 kb and high‐resolution 50 kb chromosomal structures based on single‐cell Hi‐C data. A chromosome was represented by a string of 500 kb or 50 kb DNA beads and put into a 3D cubic lattice for simulations. A 2D Gaussian function was used to impute the sparse single‐cell Hi‐C contact matrices. We designed a novel loss function based on the Lennard‐Jones potential, in which the ε value, i.e., the well depth, was used to indicate how stable the binding of every pair of beads is. For the bead pairs that have single‐cell Hi‐C contacts and their neighboring bead pairs, the loss function assigns them stronger binding stability. The Metropolis–Hastings algorithm was used to try different locations for the DNA beads, and simulated annealing was used to optimize the loss function. We proved the correctness and validness of the reconstructed 3D structures by evaluating the models according to multiple criteria and comparing the models with 3D‐FISH data

Control of astrocyte progenitor specification, migration and maturation by Nkx6.1 homeodomain transcription factor.

Although astrocytes are the most abundant cell type in the central nervous system (CNS), little is known about their molecular specification and differentiation. It has previously been reported that transcription factor Nkx6.1 is expressed in neuroepithelial cells that give rise to astrocyte precursors in the ventral spinal cord. In the present study, we systematically investigated the function of Nkx6.1 in astrocyte development using both conventional and conditional Nkx6.1 mutant mice. At early postnatal stages, Nkx6.1 was expressed in a subpopulation of astrocytes in the ventral spinal cord. In the conventional Nkx6.1KO spinal cord, the initial specification of astrocyte progenitors was affected by the mutation, and subsequent migration and differentiation were disrupted in newborn mice. In addition, the development of VA2 subtype astrocytes was also inhibited in the white matter. Further studies with Nkx6.1 conditional mutants revealed significantly delayed differentiation and disorganized arrangement of fibrous astrocytes in the ventral white matter. Together, our studies indicate that Nkx6.1 plays a vital role in astrocyte specification and differentiation in the ventral spinal cord

Forward modeling of P- and S-waves response of fractures intersected with horizontal wells in tight reservoirs

Horizontal wells play an important role in expanding the drilling volume of reservoirs and oil production area, and are widely used in unconventional reservoirs. Fractures have a positive effect on reservoir permeability, but fractures can also cause accidents such as casing deformation and inter-well frac-hit. It is of great significance to identify and evaluate fractures intersected with horizontal wells in tight reservoirs. In this paper, a three-dimensional numerical model of horizontal wells and fractures in tight reservoirs is designed. The responses of monopole P-wave and dipole S-wave to fractures with different width, dip angle and filling medium are systematically studied, by using three-dimensional finite difference algorithm. The results show that when the fracture is filled with calcite, the amplitude attenuation of monopole P-wave and dipole S-wave has a monotonic exponential increase with the increase of fracture width and the decrease of fracture dip angle. In the real data processing, the amplitude attenuation of P- and S-waves can be used to jointly evaluate the fracture filled with calcite. When the fracture is filled with water, both P- and S-waves have prominent amplitude attenuation. P wave amplitude attenuation does not have a monotonic variation with the increase of fracture width but it has a monotonic increase with the decrease of fracture dip angle. S wave amplitude attenuation has a monotonic increase with the increase of fracture width and the decrease of fracture dip angle. The amplitude attenuation of P- and S- waves rises significantly when the fracture is filled with natural gas. This study is crucial for better understanding the response of P- and S-waves to fractures intersected with borehole in tight reservoirs, and it provides useful information for the inversion of fracture parameters by using P- and S-waves

Impact of climate change on "evaporation paradox" in province of Jiangsu in southeastern China.

Contrary to the common expectation that the reference evapotranspiration (ETo), which is an indicator of the atmospheric evaporation capability, increases in warming climate, the decline of the ETo has been reported worldwide, and this contradiction between the expected increasing ETo and the observed decreasing one is now termed the "evaporation paradox". Based on the updated meteorological data (1960-2019), we separately detected the spatiotemporal characteristics and the causes of the "evaporation paradox" in three subregions, namely Huaibei, Jianghuai, and Sunan, and throughout the entire province of Jiangsu in southeastern China. Different from the reported continuous unidirectional variations in the ETo, in the province of Jiangsu, it generally showed a decreasing trend before 1990 but followed an increasing trend from 1990 to 2019, which led to the different characteristics of the "evaporation paradox" in the periods from 1960 to 1989, from 1990 to 2019, and from 1960 to 2019. In the first 30 years, the reduction of the wind speed (WS) was the main reason for the decreased ETo, which consequently gave rise to the "evaporation paradox" in spring and winter in the Huaibei region and only in winter in the two other subregions and throughout the entire province. We noticed that the "evaporation paradox" in spring in the Sunan region was expressed by the decreased daily mean air temperature (Tmean) and the increased ETo which was chiefly induced by the decreased relative humidity (RH) and the increased vapor pressure deficit (VPD). After 1990, the decreased WS also dominated the decreased ETo and resulted in the "evaporation paradox" in winter in the Jianghuai region. Furthermore, the decreased sunshine hour (SH) was the main factor influencing the decreased ETo, thereby inducing the "evaporation paradox" in summer and autumn in the Jianghuai region and only in autumn in the Huaibei region and throughout the whole province from 1990 to 2019. In the whole study period from 1960 to 2019, the decreased SH was also found to be responsible for the decreased ETo and for the "evaporation paradox" in summer in all the subregions and throughout the whole province. However, regarding the "evaporation paradox" in autumn, in winter, and in the entire year in the Huaibei region and throughout the whole province, the observed decreased ETo was largely due to the reduced WS from 1960 to 2019. In summary, in addition to the air temperature, the ETo has shifted due to the other meteorological variables (especially the WS, the SH, and the VPD) and shaped the unique spatiotemporal characteristics of the "evaporation paradox" in the province of Jiangsu in southeastern China. Moreover, future studies and simulations addressing the regional climate change and hydrological cycles should take account of the changeable key meteorological variables in different subregions and seasons of the province of Jiangsu

Rapid Identification of Apple Maturity Based on Multispectral Sensor Combined with Spectral Shape Features

The rapid and convenient detection of maturity is of great significance to determine the harvest time and postharvest storage conditions of apples. In this study, a portable visible and near-infrared (VIS/NIR) analysis device prototype was developed based on a multispectral sensor and applied to ‘Fuji’ apple maturity detection. The multispectral data of apples with maturity variation was measured, and the prediction model was established by a least-square support vector machine and linear discriminant analysis. Due to the low resolution of the multispectral data, regular preprocessing methods cannot improve the prediction accuracy. Instead, the spectral shape features (spectral ratio, spectral difference, and normalized spectral intensity difference) were used for preprocessing and model establishment, and the combination of the three features effectively improved the model performance with a prediction accuracy of 88.46%. In addition, the validation accuracy of the optimal model was 84.72%, and the area under curve (AUC) value of each maturity level was higher than 0.8972. The results show that the multispectral sensor is an appliable choice for the development of the portable detection device of apple maturity, and the data processing method proposed in this study provides a potential solution to improve the detection accuracy for multispectral sensors

A novel approach for amplification and purification of mouse oligodendrocyte progenitor cells

Although transgenic and knockout mice are widely used to study the specification and differentiation of oligodendrocyte precursor cells (OPCs), mouse primary OPCs are difficult to be purified and maintained, and many in vitro studies have to resort to rat OPCs as substitutes. In this study, we reported that mouse O4 negative early-stage OPCs can be obtained by culturing cortical tissue blocks, and the simultaneous treatment of OPCs with PDGFaa, bFGF and EGF is the key for the propagation of mouse OPCs in culture. Epidermal growth factor (EGF) was found to be a potent mitogen for OPCs and cooperate with Platelet Derived Growth Factor-AA (PDGFaa) to extend cell division and inhibit their differentiation. EGF also collaborates with PDGFaa and basic fibroblast growth factor (bFGF) to convert bipolar or tripolar OPCs to more vital fibroblast-like OPCs without compromising their oligodendrocyte differentiation potential. In addition, EGF promoted the survival and proliferation of glial progenitor cells (GPCs) derived from primary OPC cultures, and a mixture of GPCs and OPCs can be obtained and propagated in the presence of EGF, bFGF and PDGFaa. Once EGF is withdrawn, GPC population decreased sharply and fibroblast-like OPCs changed into typical OPCs morphology, then homogeneous OPCs were obtained subsequently

Spontaneous Lymphatic Vessel Formation and Regression in the Murine Cornea

This study provides the first evidence that the murine cornea has a full range of lymphatic plasticity. Spontaneous lymphatic formation and regression occur in this unique tissue during a critical period after birth

A Relativistic Density-Functional Investigation of Vibrational Frequencies of CN￣- on Cu and Ag Electrodes

对ＣＮ￣－在铜和银电极上的吸附性质进行了相对论密度泛函簇模型计算。结果表明，电场微扰方法可以描述ＣＮ￣－在铜和银电极上吸附的表面现象，电极势诱导的频率移动被理解为Ｓｔａｒｋ效应所引起；内振动模式Ｍ－ＣＮ和Ｃ－Ｎ的耦合对电位诱导的Ｃ－Ｎ振动频率变化的大小起重要作用。计算所得的由Ｓｔａｒｋ效应所引起Ｃ－Ｎ振动频率变化的斜率与实验结果相符。Abstract Potential Dependence,Vibrational Frequency,copper-electrode,Silver-electrode,Relativistic density-functional calculationAcknowledgements This work was supported by the National Natural Science Foundationof China and ChinaPostdoctoral Science Foundation.作者联系地址：厦门大学化学系Author's Address: Chemistry Department,Xiamen University,Xiamen 36100

Modeling of the dynamic behaviors of heat transfer during the construction of roadway using moving mesh

Heat hazard is major challenge for the safe and efficient exploitation of deep resources. Understanding the heat transfer behaviors in roadway is the premise of temperature prediction and ventilation design. A fully coupled model incorporated with a moving mesh method was developed, which considers the convective heat transfer between surrounding rock and airflow, unsteady-state heat transfer in rock, and non-isothermal flow in roadway. The characteristics of thermal performance and its evolution law in an excavating roadway were obtained. The numerical model was validated against previous experimental data with a deviation of less than 3%. Analysis of the airflow and temperature field revealed the characteristic of convection heat transfer in the wall and local heat accumulation in roadway. The air temperature in roadway is associated with the airflow characteristics, and a local high temperature zone is presented in the vortex zone. By comparing the heat flux of the surrounding rock and excavation condition, it is found that the heat released from the working face poses a crucial effect on the airflow temperature in roadway. The present study provided a robust theoretical basis for improving cooling efficiency and thermal comfort in roadway construction