MLSpatial: A machine-learning method to reconstruct the spatial distribution of cells from scRNA-seq by extracting spatial features.

MOTIVATION: Single-cell RNA sequencing (scRNA-seq) technologies allow us to interrogate the state of an individual cell within its microenvironment. However, prior to sequencing, cells should be dissociated first, making it difficult to obtain their spatial information. Since the spatial distribution of cells is critical in a few circumstances such as cancer immunotherapy, we present MLSpatial, a novel computational method to learn the relationship between gene expression patterns and spatial locations of cells, and then predict cell-to-cell distance distribution based on scRNA-seq data alone. RESULTS: We collected the drosophila embryo dataset, which contains both the fluorescence in situ hybridization (FISH) data and single cell RNA-seq (scRNA-seq) data of drosophila embryo. The FISH data provided the spatial position of 3039 cells and the expression of 84 genes for each cell. The scRNA-seq data contains the expressions of 8924 genes in 1297 high-quality cells with cell location unknown. For a comparison, we also collected the MERFISH data of 645 osteosarcoma cells with cell location and the expression status of 10,050 genes known. For each data, the cells were randomly divided into a training set and a test set, in the ratio of 7:3. The cell-to-cell distances our model extracted had a higher correspondence (i.e., correlation coefficient 0.99) with those of the real situation than those of existing methods in the FISH data of drosophila embryo. However, in the osteosarcoma data, our model captured the spatial relationship between cells, with a correlation of 0.514 to that of the real situation. We also applied the model trained using the FISH data of drosophila embryo into the single cell data of drosophila embryo, for which the real location of cells are unknown. The reconstructed pseudo drosophila embryo and the real embryo (as shown by the FISH data) had a high similarity in the spatial distribution of gene expression. CONCLUSION: MLSpatial can accurately restore the relative position of cells from scRNA-seq data; however, the performance depends on the type of cells. The trained model might be useful in reconstructing the spatial distributions of single cells with only scRNA-seq data, provided that the scRNA-seq data and the FISH data are under similar background (i.e., the same tissue with similar disease background).

Application of desulfurization gypsum as activator for modified magnesium slag-fly ash cemented paste backfill material.

Recycling industrial solid waste for mine backfill is one of the best ways to achieve green production in multiple industries. In this paper, the desulfurization gypsum (DG) as an activator is combined with the modified magnesium slag-fly ash cementitious paste backfill (MFPB) technology for the co-disposal of solid waste and goaf treatment, and the influence of DG on the performance of MFPB was comprehensively analyzed through rheological properties, mechanical properties, durability, microscopic analysis and environmental characteristics experiments. The results show that the fresh MFPB mortar conforms to the Herschel-Bulkley model at different maximum shear rate (γ̇max) conditions. When the γ̇max is 100 s-1, the mortar exhibits shear-thickening properties. The apparent viscosity, yield stress and static yield stress of mortar decreased first and then increased with the increase of DG content, and all had the minimum value when DG was 2.5 %. The thixotropy of the mortar was significantly increased with the addition of DG, and the change in thixotropy was significantly correlated with the difference between the two yield stresses. Both the rheological and mini-slump results demonstrate that DG can improve the flowability of MFPB mortars. In addition, the UCS of D0 under steam curing and standard water curing conditions for 28 d were 4.342 MPa and 2.827 MPa, and the sample containing DG were 6.109-8.241 MPa and 6.669-9.492 MPa, respectively. The addition of DG not only improves the strength of MFPB, but also improves the durability of MFPB. Microscopic analysis (XRD, SEM, and TG-DTG) indicated that this was mainly because DG promoted the hydration reaction of the MMS-FA system and accelerated the generation of C-S(A)-H and AFt. Finally, in the results of in situ leaching based on durability and leaching based on standard HJ 557, all the indexes of MFPB meet the standard of class III groundwater in GB/T 14848-2017, and it has an effective stabilization/solidification effect on heavy metals (As, Cu, Ni, Ba, Zn and Mo, etc.). To sum up, the collaboration of DG and MFPB technology can not only efficiently clean and utilize a variety of solid wastes (MMS, FA and DG), but also greatly improve the performance of MFPB to promote its application.

Influence of Mechanical Grinding on Particle Characteristics of Coal Gasification Slag.

Based on the test results of laser particle size analyzer, specific surface area analyzer and infrared spectrometer, the grinding kinetics of coal gasification slag (CGS) was systematically described by using Divas-Aliavden grinding kinetics, Rosin-Rammler-Bennet (RRB) distribution model and particle size fractal theory. The influence of grinding time and particle group of CGS on the strength activity index of mortar was studied by using the strength activity index of mortar and grey correlation analysis. The results show that the particles are gradually refined before mechanical grinding of CGS for 75 min. When the mechanical grinding time is greater than 75 min, the "agglomeration phenomenon" of fine CGS particles led to the decrease in various properties. Divas-Aliavden grinding kinetics, the RRB model and fractal dimension can characterize the change of CGS particle size in the grinding process quantitatively. The strength activity index of CGS at different curing ages is positively correlated with grinding time, and the influence on the later strength activity index is the most obvious. The relationship between CGS particle size distribution and strength activity index were probed using grey correlation analysis. The CGS particle groups with the particle size of 20~30 µm and 10~20 µm have the greatest impact on the early and late strength activity index, respectively. Therefore, the optimal grinding time of CGS as auxiliary cementing material is 75 min, considering factors, such as economy and performance, and the specific surface area (SSA) is 4.4874 m2·g-1.

Peiminine Suppresses RANKL-Induced Osteoclastogenesis by Inhibiting the NFATc1, ERK, and NF-κB Signaling Pathways.

Osteoclasts (OCs) play an important role in osteoporosis, a disease that is mainly characterized by bone loss. In our research, we aimed to identify novel approach for regulating osteoclastogenesis and thereby treating osteoporosis. Previous studies have set a precedent for screening traditional Chinese herbal extracts for effective inhibitors. Peiminine is an alkaloid extracted from the bulb of Fritillaria thunbergii Miq that reportedly has anticancer and anti-inflammatory effects. Thus, the potential inhibitory effect of peiminine on OC differentiation was investigated via a series of experiments. According to the results, peiminine downregulated the levels of specific genes and proteins in vitro and consequently suppressed OC differentiation and function. Based on these findings, we further investigated the underlying molecular mechanisms and identified the NF-κB and ERK1/2 signaling pathways as potential targets of peiminine. In vivo, peiminine alleviated bone loss in an ovariectomized mouse model.

Molecular Characterization of Water- and Methanol-Soluble Organic Compounds Emitted from Residential Coal Combustion Using Ultrahigh-Resolution Electrospray Ionization Fourier Transform Ion Cyclotron Resonance Mass Spectrometry.

Water-soluble organic compounds (WSOC) and methanol-soluble organic compounds (MSOC) in smoke particles emitted from residential coal combustion were characterized by ultrahigh-resolution mass spectrometry. The results showed that the molecular compositions of WSOC and MSOC are different. S-containing compounds (CHOS and CHONS) are found to be the dominant components (65-87%) of the WSOC, whereas CHO and CHON compounds make a great contribution (79-96%) to the MSOC samples. It is worth noting that greater abundance of S-containing compounds was found in smoke produced from coal combustion compared to biomass burning and atmospheric samples. The molecular compositions of WSOC and MSOC also varied significantly depending on the maturity of the coal. The WSOC and MSOC derived from the combustion of low-maturity coal contained a higher proportion of oxidized functional groups but with a lower degree of aromaticity than the compounds derived from the combustion of high-maturity coal. Our findings suggest that organic molecules with a high modified aromaticity index, low O/C ratio, and low polarity showed stronger light absorption. This study also suggests that CHO and CHON compounds significantly contributed to the light absorption of WSOC and MSOC and that the contribution of CHON may be stronger.

Influence of pyrolysis temperature and feedstock on carbon fractions of biochar produced from pyrolysis of rice straw, pine wood, pig manure and sewage sludge.

In this study, the influences of feedstock and pyrolysis temperature on carbon fractions of biochar were investigated. Four types of organic wastes (rice straw (RS), pine wood (PW), pig manure (PM) and sewage sludge (SS)) were pyrolyzed at different temperatures (300 °C, 400 °C, 500 °C, 600 °C and 700 °C). Biochar produced at low temperature exhibited high yields, high dissolved organic carbon (DOC) content and unstable organic carbon content. In contrast, biochar formed at high temperature showed high C content and C stability with a low O/C and H/C ratios. In addition, the biochar pyrolyzed from PW contained the lowest DOC of the four biochar types. The properties of DOC fractions (F1, F2 and F3) released from biochar differed depending on feedstock, pyrolysis temperatures, and extraction procedures. The highest specific ultraviolet absorbance at 254 nm of the F1 and F2 fractions were observed for RS biochar, suggesting that more aromatic organic matter was present in sequentially extracted fractions of RS biochar than in extracts from the other biochars. In addition, the hot water extracts (F2) mostly showed higher aromaticity than cold water extracts (F1). The stability of biochars was greatly enhanced at pyrolysis temperatures >500 °C. If the biochars produced in this study were to be used for carbon sequestration in soil, the first priority should be PW, followed in order by RS and PM.

Abundance and Light Absorption Properties of Brown Carbon Emitted from Residential Coal Combustion in China.

Brown carbon (BrC) fractions, including water-soluble organic carbon (WSOC), water-soluble humic-like substances (HULISw), alkaline soluble organic carbon (ASOC), and methanol soluble organic carbon (MSOC) were extracted from particles emitted from the residential combustion of coal with different geological maturities. The abundances and light absorption properties of these BrC fractions were comprehensively studied. The results showed that the abundances of the different constituents of the BrC fraction varied greatly with the extraction solvent, accounting for 4.3%-46%, 2.3%-23%, 3.2%-14%, and 76%-98% of the total carbon content in particles. The specific UV-vis absorbance (SUVA254) of BrC fractions followed the order of MSOC > ASOC > HULISw > WSOC. The WSOC and MSOC fractions from the combustion of low maturity coal had relatively low SUVA254 and high SR values. The mass absorption efficiencies (MAE365) for ASOC and MSOC were higher than for WSOC, and WSOC and MSOC from low maturity coal combustion had relatively low levels of light absorption. These findings indicated that coal combustion is a potential source of atmospheric BrC and the abundance and light absorption of the coal combustion-derived BrC fractions were strongly dependent on the extraction methods used and the coal maturity rather than the coal shapes.

Fractional amplitude of low-frequency fluctuation changes in functional dyspepsia: a resting-state fMRI study.

Recently, there is an increasing interest in the study of the role of brain dysfunction in the pathogenesis of symptoms of functional dyspepsia (FD). More specifically, abnormal brain activities in patients with FD during the resting state have been proven by several positron emission tomography (PET) studies. Resting-state functional magnetic resonance imaging (fMRI) is also a valuable tool in investigating spontaneous brain activity abnormalities in pathological conditions. In the present study, we examined the amplitude of low-frequency fluctuations (ALFF) and fractional (f)ALFF changes in patients with FD by using fMRI. Twenty-nine patients with FD and sixteen healthy controls participated in this study. Between-group differences in ALFF/fALFF were examined using a permutation-based nonparametric test after accounting for the gender and age effects. The results revealed a significant between-group difference in fALFF but not in ALFF in multiple brain regions including the right insula, brainstem and cerebellum. Seed-based resting-state functional connectivity analysis revealed that FD patients have increased correlations between the right cerebellum and multiple brain regions including the bilateral brainstem, bilateral cerebellum, bilateral thalamus, left para-/hippocampus, left pallidum and left putamen. Furthermore, fLAFF values in the right insula were positively correlated with the severity of the disease. These findings have provided further evidence of spontaneous brain activity abnormalities in FD patients which might contribute to our understanding of the pathophysiology of the disease.