Comprehensive integration of single-cell transcriptomic data illuminates the regulatory network architecture of plant cell fate specification

Plant morphogenesis relies on precise gene expression programs at the proper time and position which is orchestrated by transcription factors(TFs)in intricate regulatory networks in a cell-type specific manner.Here we introduced a comprehensive single-cell transcriptomic atlas of Arabidopsis seedlings.This atlas is the result of meticulous integration of 63 previously published scRNA-seq datasets,addressing batch effects and conserving biological variance.This integration spans a broad spectrum of tissues,including both below-and above-ground parts.Utilizing a rigorous approach for cell type annotation,we identified 47 distinct cell types or states,largely expanding our current view of plant cell compositions.We systematically constructed cell-type specific gene regulatory networks and uncovered key regulators that act in a coordinated manner to control cell-type specific gene expression.Taken together,our study not only offers extensive plant cell atlas exploration that serves as a valuable resource,but also provides molecular insights into gene-regulatory programs that varies from different cell types.

Two-dimensional particle-in-cell modeling of blow-off impulse by X-ray irradiation

Space objects such as spacecraft or missiles may be exposed to intense X-rays in outer space,leading to severe damage.The reinforcement of these objects to reduce the damage caused by X-ray irradiation is a significant concern.The blow-off impulse(BOI)is a crucial physical quantity for investigating material damage induced by X-ray irradiation.However,the accurate calculation of BOI is challenging,particularly for large deformations of materials with complex configurations.In this study,we develop a novel two-dimensional particle-in-cell code,Xablation2D,to calculate BOIs under far-field X-ray irradiation.This significantly reduces the dependence of the numerical simulation on the grid shape.The reliability of this code is verified by simulation results from open-source codes,and the calculated BOIs are consistent with the experimental and analytical results.

Data augmentation of ultrasound imaging for non-invasive white blood cell in vitro peritoneal dialysis

The limited amount of data in the healthcare domain and the necessity of training samples for increased performance of deep learning models is a recurrent challenge,especially in medical imaging.Newborn Solutions aims to enhance its non-invasive white blood cell counting device,Neosonics,by creating synthetic in vitro ultrasound images to facilitate a more efficient image generation process.This study addresses the data scarcity issue by designing and evaluating a continuous scalar conditional Generative Adversarial Network(GAN)to augment in vitro peritoneal dialysis ultrasound images,increasing both the volume and variability of training samples.The developed GAN architecture incorporates novel design features:varying kernel sizes in the generator’s transposed convolutional layers and a latent intermediate space,projecting noise and condition values for enhanced image resolution and specificity.The experimental results show that the GAN successfully generated diverse images of high visual quality,closely resembling real ultrasound samples.While visual results were promising,the use of GAN-based data augmentation did not consistently improve the performance of an image regressor in distinguishing features specific to varied white blood cell concentrations.Ultimately,while this continuous scalar conditional GAN model made strides in generating realistic images,further work is needed to achieve consistent gains in regression tasks,aiming for robust model generalization.

Comparative study of microarray and experimental data on Schwann cells in peripheral nerve degeneration and regeneration: big data analysis

A Schwann cell has regenerative capabilities and is an important cell in the peripheral nervous system.This microarray study is part of a bioinformatics study that focuses mainly on Schwann cells. Microarray data provide information on differences between microarray-based and experiment-based gene expression analyses. According to microarray data, several genes exhibit increased expression(fold change) but they are weakly expressed in experimental studies(based on morphology, protein and mRNA levels). In contrast, some genes are weakly expressed in microarray data and highly expressed in experimental studies;such genes may represent future target genes in Schwann cell studies. These studies allow us to learn about additional genes that could be used to achieve targeted results from experimental studies. In the current big data study by retrieving more than 5000 scientific articles from PubMed or NCBI, Google Scholar, and Google, 1016(up-and downregulated) genes were determined to be related to Schwann cells. However,no experiment was performed in the laboratory; rather, the present study is part of a big data analysis. Our study will contribute to our understanding of Schwann cell biology by aiding in the identification of genes.Based on a comparative analysis of all microarray data, we conclude that the microarray could be a good tool for predicting the expression and intensity of different genes of interest in actual experiments.

Unraveling Shuttle Effect and Suppression Strategy in Lithium/Sulfur Cells by In Situ/Operando X-ray Absorption Spectroscopic Characterization

The polysulfides shuttle effect represents a great challenge in achieving high capacity and long lifespan of lithium/sulfur(Li/S)cells.A comprehensive understanding of the shuttle-related sulfur speciation and diffusion process is vital for addressing this issue.Herein,we employed in situ/operando X-ray absorption spectroscopy(XAS)to trace the migration of polysulfides across the Li/S cells by precisely monitoring the sulfur chemical speciation at the cathodic electrolyte-separator and electrolyte-anode interfaces,respectively,in a real-time condition.After we adopted a shuttle-suppressing strategy by introducing an electrocatalytic layer of twinborn bismuth sulfide/bismuth oxide nanoclusters in a carbon matrix(BSOC),we found the Li/S cell showed greatly improved sulfur utilization and longer life span.The operando S Kedge XAS results revealed that the BSOC modification was bi-functional:trapping polysulfides and catalyzing conversion of sulfur species simultaneously.We elucidated that the polysulfide trapping-and-catalyzing effect of the BSOC electrocatalytic layer resulted in an effective lithium anode protection.Our results could offer potential stratagem for designing more advanced Li/S cells.

CRYSTAL STRUCTURE AND X-RAY POWDER DIFFRACTION DATA FOR RE COMPOUND HoNiSb

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SOFT X-RAY IMAGES OF CHROMOSOMES WITHIN INTACT TUMOR CELLS TREATED WITH COLCHICINE

In order to avoid any possible effect of separating procedures from intact cell on morphologic structure of the chromosomes, cultivated Hep-2 tumor cells were treated with colchicine and observed by soft X-ray contact microscopy for the first time. The fine structures of chromosomes are more clear with stereo features. The thread-like and coarse granular structures twine and tangle up together within chromosome masses which can not easily be revealed in Wright’s stained sample by light microscope or osmium stained sample by transmission electron

Rietveld Refinement and X-ray Powder Diffraction Data of GdAlSi

The X-ray powder diffraction data of the compound GdAlSi was studied by means of X-ray diffraction technique and refined by Rietveld method. The compound GdAlSi has tetragonal α-ThSi_2-type structure, space group I4_1/amd (No.141), Z=4, the lattice parameters a=041234 (1) nm, c=1.44202(1) nm. The Smith and Snyder figure of merit [5] F_N is F_ 30=2521(36). The R-factors of Rietveld refinement are R_p=0.098 and R_ wp=0.128. The X-ray powder diffraction data are given. The field dependence of the magnetization measured at room temperature and the temperature variation of the inverse magnetic susceptibility of the compound GdAlSi were also presented.

Carbon-Ion Beams Efficiently Induce Cell Killing in X-Ray Resistant Human Squamous Tongue Cancer Cells

In order to see whether carbon ion (C-ion) beams have a biological advantage over X-rays, studies were designed to examine the effects of C-ion beams on radiosensitivity in X-ray resistant cells. Clinically relevant X-ray resistant SAS-R cells derived from human tongue cancer SAS cells were used. The cells were exposed to X-rays or Spread-Out Bragg peak (SOBP) beam C-ions. Cell survival was measured using a modified high-density survival assay. Cell survival signaling and cell death signaling were analyzed using flow cytometry. The cells were labeled with putative cancer stem cell markers such as CD44 and CD326. SAS-R cells were 1.6 times more radioresistant than SAS cells after exposure to X-rays. Cell survival was similar in each cell line after exposure to C-ion beams. SAS-R cells displayed enhanced cell survival signaling when compared to SAS cells under normal conditions. On the other hand, the phosphorylation of AKT-related proteins decreased and polycaspase activities were enhanced when cells were irradiated with C-ion beams in both cell lines. More CD44 and CD326 positive cells were seen in SAS-R cells than in SAS cells. Moreover, the marker positive cell numbers significantly decreased after exposure to C-ion beams when compared to X-rays at iso-survival doses in SAS-R cells. C-ion beams efficiently induced cell killing in X-ray resistant cells which displayed activated cell survival signaling and contained more numerous cancer stem-like cells.

DATA PROCESSING OF UNIVERSAL QUANTITATIVE METHOD IN STANDARDLESS X-RAY PHASE ANALYSIS

Accuracy of coeffcient A_(isp) is related to the reference phase chosen during analysis. The cri- terion of choosing reference phase which may minimize the error of A_(isp) was deduced. The optimum results could be obtained by using the method of least squares if the number of sam- pies for analysis is more than the phase in samples. The procedure presented here is satisfacto- ryfor ordinary phase analysis.

Alpha-actinin expression at different differentiating time points from temporal lobe cerebral cortex neural stem cells to neuron-like cells using energy dispersive X-ray analysis

BACKGROUND： Alpha-actinin （ a -actinin） plays a key role in neuronal growth cone migration during directional differentiation from neural stem cells （NSCs） to neurons. OBJECTIVE： To detect in situ microdistribution and quantitative expression of a -actinin during directional differentiation of NSCs to neurons in the temporal lobe cerebral cortex of neonatal rats. DESIGN, TIME AND SETTING： Between January 2006 and December 2008, culture and directional differentiation of NSCs were performed at Department of Histology and Embryology, Preclinical Medical College, China Medical University. Immune electron microscopy was performed at Department of Histology and Embryology and Department of Electron Micrology, Preclinical Medical College, China Medical University. Spectrum analysis was performed at Laboratory of Electron Microscopy, Mental Research Institute, Chinese Academy of Sciences. MATERIALS： Basic fibroblast growth factor, epidermal growth factor, brain-derived nerve growth factor, type-1 insulin like growth factor, and a -actinin antibody were provided by Gibco BRL, USA; rabbit-anti-rat nestin monoclonal antibody, rabbit-anti-rat neuron specific enolase polyclonal antibody, and EDAX-9100 energy dispersive X-ray analysis were provided by PHILIPS Company, Netherlands. METHODS： NSCs, following primary and passage culture, were differentiated with serum culture medium （DMEM/F12 ＋ 10% fetal bovine serum ＋ 2 ng/mL brain-derived nerve growth factor ＋ 2 ng/mL type-1 insulin like growth factor）. MAIN OUTCOME MEASURES： Expression of a -actinin in neuron-like cells was quantitatively and qualitatively detected with immunocytochemistry using energy dispersive X-ray analysis. RESULTS： Immunocytochemistry, combined with electron microscopy, indicated that positive α -actinin expression was like a spheroid particle with high electron density. In addition, the expression was gradually concentrated from the nuclear edge to the cytoplasm and expanded into developing neurites, during differentiation of neural stem cells to neurons. Conversely, energy dispersive X-ray analysis indicated that the more mature the neural differentiation was, and the greater the expression of α -actinin. CONCLUSION： The gradual increase of α -actinin expression is related to growth, development, and maturity of differentiated neuron-like cells, in neonatal rat frontal lobe cortex, at different differentiating time points of NSCs to neurons.

Extended X-ray absorption fine structure (EXAFS) of FAPbI_(3) for understanding local structure-stability relation in perovskite solar cells

Perovskite solar cells (PSCs) employing formamidinium lead iodide (FAPbI_(3)) have shown high efficiency.However,operational stability has been issued due to phase instability of α phase FAPbI_(3) at ambient temperature.Excess precursors in the perovskite precursor solution has been proposed to improve not only power conversion efficiency (PCE) but also device stability.Nevertheless,there is a controversial issue on the beneficial effect on PCE and/or stability between excess FAI and excess PbI_(2).We report here extended X-ray absorption fine structure (EXAFS) of FAPbI_(3) to study local structural change and explain the effect of excess precursors on photovoltaic performance and stability.Perovskite films prepared from the precursor solution with excess PbI_(2)shows better stability than those from the one with excess FAI,despite similar PCE.A rapid phase transition from α phase to non-perovskite δ phase is observed from the perovskite film formed by excess FAI.Furthermore,the (Pb-I) bond distance evaluated by the Pb L_(III)-edge EXAFS study is increased by excess FAI,which is responsible for the phase transition and poor device stability.This work can provide important insight into local structure-stability relation in the FAPbI_(3)-based PSCs.

Examining heterogeneity of stromal cells in tumor microenvironment based on pan-cancer single-cell RNA sequencing data

Tumor tissues contain both tumor and non-tumor cells,which include infiltrated immune cells and stromal cells,collectively called the tumor microenvironment(TME).Single-cell RNA sequencing(sc RNAseq)enables the examination of heterogeneity of tumor cells and TME.In this review,we examined sc RNAseq datasets for multiple cancer types and evaluated the heterogeneity of major cell type composition in different cancer types.We further showed that endothelial cells and fibroblasts/myofibroblasts in different cancer types can be classified into common subtypes,and the subtype composition is clearly associated with cancer characteristic and therapy response.

COVID-19 Related Research by Data Mining in Single Cell Transcriptome Profiles

The outbreak of coronavirus disease 2019(COVID-2019)has drawn public attention all over the world.As a newly emerging area,single cell sequencing also exerts its power in the battle over the epidemic.In this review,the up-to-date knowledge of COVID-19 and its receptor is summarized,followed by a collection of the mining of single cell transcriptome profiling data for the information in aspects of the vulnerable cell types in humans and the potential mechanisms of the disease.

X-Ray Induced Mutation Frequency at the <i>Hypoxanthine Phosphoribosyltransferase</i>Locus in Clinically Relevant Radioresistant Cells

To elucidate the molecular mechanisms underlying cellular radioresistance, clinically relevant radioresistant cell lines were established via long-term exposure to X-rays with stepwise dose escalation. Established cells continue to proliferate despite exposure to 2 Gy X-rays/day for more than 30 days, a standard protocol in cancer radiotherapy. DNA repair fidelity in radioresistant and the parental cells by evaluating the mutation frequency at the hypoxanthine phosphoribosyltransferase (HPRT) locus after exposure to X-rays was determined. Mutation spectrum at the HPRT locus was examined by multiplex polymerase chain reaction. Rejoining kinetics of X-ray-induced DNA double strand breaks (dsbs) was evaluated by the detection of phosphorylated histone H2AX (γH2AX) after X-irradiation. The fold increase in the HPRT mutation frequency due to acute radiation was similar between radioresistant and the parental cell lines. However, fractionated radiation (FR) consisting of 2 Gy X-rays/day increased the mutation frequency at the HPRT locus in parental but not in radioresistant cells. Analysis of the FR-induced mutations at the HPRT locus revealed a high frequency of deletion mutations (>70%) in parental but not in radioresistant cells. As assessed by γH2AX immunostaining, DNA dsbs induced by acute exposure to 10 Gy of X-rays were repaired to the control level within 7 days in radioresistant but not in the parental cells. Moreover, 2 Gy × 5 FR increased the number of γH2AX-positive cells in parental cultures but not in radioresistant cultures. DNA dsbs induced by 2 Gy/day FR are repaired with fidelity in radioresistant but not in parental cells.

Research on Enhanced Contraband Dataset ACXray Based on ETL

To address the shortage of public datasets for customs X-ray images of contraband and the difficulties in deploying trained models in engineering applications,a method has been proposed that employs the Extract-Transform-Load(ETL)approach to create an X-ray dataset of contraband items.Initially,X-ray scatter image data is collected and cleaned.Using Kafka message queues and the Elasticsearch(ES)distributed search engine,the data is transmitted in real-time to cloud servers.Subsequently,contraband data is annotated using a combination of neural networks and manual methods to improve annotation efficiency and implemented mean hash algorithm for quick image retrieval.The method of integrating targets with backgrounds has enhanced the X-ray contraband image data,increasing the number of positive samples.Finally,an Airport Customs X-ray dataset(ACXray)compatible with customs business scenarios has been constructed,featuring an increased number of positive contraband samples.Experimental tests using three datasets to train the Mask Region-based Convolutional Neural Network(Mask R-CNN)algorithm and tested on 400 real customs images revealed that the recognition accuracy of algorithms trained with Security Inspection X-ray(SIXray)and Occluded Prohibited Items X-ray(OPIXray)decreased by 16.3%and 15.1%,respectively,while the ACXray dataset trained algorithm’s accuracy was almost unaffected.This indicates that the ACXray dataset-trained algorithm possesses strong generalization capabilities and is more suitable for customs detection scenarios.

Intrusion Detection Model Using Chaotic MAP for Network Coding Enabled Mobile Small Cells

Wireless Network security management is difficult because of the ever-increasing number of wireless network malfunctions,vulnerabilities,and assaults.Complex security systems,such as Intrusion Detection Systems(IDS),are essential due to the limitations of simpler security measures,such as cryptography and firewalls.Due to their compact nature and low energy reserves,wireless networks present a significant challenge for security procedures.The features of small cells can cause threats to the network.Network Coding(NC)enabled small cells are vulnerable to various types of attacks.Avoiding attacks and performing secure“peer”to“peer”data transmission is a challenging task in small cells.Due to the low power and memory requirements of the proposed model,it is well suited to use with constrained small cells.An attacker cannot change the contents of data and generate a new Hashed Homomorphic Message Authentication Code(HHMAC)hash between transmissions since the HMAC function is generated using the shared secret.In this research,a chaotic sequence mapping based low overhead 1D Improved Logistic Map is used to secure“peer”to“peer”data transmission model using lightweight H-MAC(1D-LM-P2P-LHHMAC)is proposed with accurate intrusion detection.The proposed model is evaluated with the traditional models by considering various evaluation metrics like Vector Set Generation Accuracy Levels,Key Pair Generation Time Levels,Chaotic Map Accuracy Levels,Intrusion Detection Accuracy Levels,and the results represent that the proposed model performance in chaotic map accuracy level is 98%and intrusion detection is 98.2%.The proposed model is compared with the traditional models and the results represent that the proposed model secure data transmission levels are high.

GEO公共数据库中4例多指畸形患者细胞间质和上皮细胞的单细胞转录组分析

背景:多指畸形患者中参与Heghog信号通路的一些转录因子发生异常表达,这些转录因子调控大量靶基因的表达,从而影响细胞的功能。目的:通过单细胞转录组分析多指畸形患者的转录组特征。方法:从GEO公共数据库中下载4例多指畸形患者细胞间质和上皮细胞的单细胞转录组数据,将成纤维细胞和角质细胞划分为细胞亚群,并分析不同亚群的转录因子,构建转录因子及其靶基因的调控网络,分析调控因子的功能。结果与结论:对单细胞的转录谱数据进行分析发现,与多指畸形中细胞功能高度相关的调控因子有HOXD13、MSX2、LHX2、EMX2、LEF1、CREB3L2以及LHX2等HOX家族成员和GLI2转录因子。成纤维细胞中的HOXD13、MSX2和LHX2在多指畸形过程中发挥作用,而HES2和GLIS1在角质细胞的形成和发育过程中起重要作用。结果表明:HOXD13、MSX2和LHX2等转录因子的高表达可能与多指畸形的发育密切相关。通过靶向特定的转录因子或调节其活性,可能为纠正或预防多指畸形提供潜在的治疗策略。

Cell-Portal技术在数码城市GIS室内场景管理中的应用

借鉴游戏中的方法,提出了基于Cell-Portal的室内模型管理与调度策略,从而实现了数码城市GIS室内、外场景的一体调度策略和场景管理。试验证明,该方法不会增加数据生产中的工作量,适应数码城市GIS深入发展的需要。

基于CELL宽带引擎架构的MPI研究与实现

研究了在CBEA上移植MPI消息传递编程模型和标准接口的可行性,并利用IBM CELL SDK 3.0实现了一组常用的MPI编程接口。实验结果表明,该组MPI接口可满足CBEA上应用开发的数据传输性能要求,并且其性能已接近现有DMA数据传输模式。该组MPI接口为CELL应用开发人员提供了一种通用编程接口解决方案。