Single-cell and spatial omics:exploring hypothalamic heterogeneity

Elucidating the complex dynamic cellular organization in the hypothalamus is critical for understanding its role in coordinating fundamental body functions. Over the past decade, single-cell and spatial omics technologies have significantly evolved, overcoming initial technical challenges in capturing and analyzing individual cells. These high-throughput omics technologies now offer a remarkable opportunity to comprehend the complex spatiotemporal patterns of transcriptional diversity and cell-type characteristics across the entire hypothalamus. Current single-cell and single-nucleus RNA sequencing methods comprehensively quantify gene expression by exploring distinct phenotypes across various subregions of the hypothalamus. However, single-cell/single-nucleus RNA sequencing requires isolating the cell/nuclei from the tissue, potentially resulting in the loss of spatial information concerning neuronal networks. Spatial transcriptomics methods, by bypassing the cell dissociation, can elucidate the intricate spatial organization of neural networks through their imaging and sequencing technologies. In this review, we highlight the applicative value of single-cell and spatial transcriptomics in exploring the complex molecular-genetic diversity of hypothalamic cell types, driven by recent high-throughput achievements.

Spatial transcriptomics combined with single-nucleus RNA sequencing reveals glial cell heterogeneity in the human spinal cord

Glial cells play crucial roles in regulating physiological and pathological functions,including sensation,the response to infection and acute injury,and chronic neurodegenerative disorders.Glial cells include astrocytes,microglia,and oligodendrocytes in the central nervous system,and satellite glial cells and Schwann cells in the peripheral nervous system.Despite the greater understanding of glial cell types and functional heterogeneity achieved through single-cell and single-nucleus RNA sequencing in animal models,few studies have investigated the transcriptomic profiles of glial cells in the human spinal cord.Here,we used high-throughput single-nucleus RNA sequencing and spatial transcriptomics to map the cellular and molecular heterogeneity of astrocytes,microglia,and oligodendrocytes in the human spinal cord.To explore the conservation and divergence across species,we compared these findings with those from mice.In the human spinal cord,astrocytes,microglia,and oligodendrocytes were each divided into six distinct transcriptomic subclusters.In the mouse spinal cord,astrocytes,microglia,and oligodendrocytes were divided into five,four,and five distinct transcriptomic subclusters,respectively.The comparative results revealed substantial heterogeneity in all glial cell types between humans and mice.Additionally,we detected sex differences in gene expression in human spinal cord glial cells.Specifically,in all astrocyte subtypes,the levels of NEAT1 and CHI3L1 were higher in males than in females,whereas the levels of CST3 were lower in males than in females.In all microglial subtypes,all differentially expressed genes were located on the sex chromosomes.In addition to sex-specific gene differences,the levels of MT-ND4,MT2A,MT-ATP6,MT-CO3,MT-ND2,MT-ND3,and MT-CO_(2) in all spinal cord oligodendrocyte subtypes were higher in females than in males.Collectively,the present dataset extensively characterizes glial cell heterogeneity and offers a valuable resource for exploring the cellular basis of spinal cordrelated illnesses,including chronic pain,amyotrophic lateral sclerosis,and multiple sclerosis.

Locally varying geostatistical machine learning for spatial prediction

Machine learning methods dealing with the spatial auto-correlation of the response variable have garnered significant attention in the context of spatial prediction.Nonetheless,under these methods,the relationship between the response variable and explanatory variables is assumed to be homogeneous throughout the entire study area.This assumption,known as spatial stationarity,is very questionable in real-world situations due to the influence of contextual factors.Therefore,allowing the relationship between the target variable and predictor variables to vary spatially within the study region is more reasonable.However,existing machine learning techniques accounting for the spatially varying relationship between the dependent variable and the predictor variables do not capture the spatial auto-correlation of the dependent variable itself.Moreover,under these techniques,local machine learning models are effectively built using only fewer observations,which can lead to well-known issues such as over-fitting and the curse of dimensionality.This paper introduces a novel geostatistical machine learning approach where both the spatial auto-correlation of the response variable and the spatial non-stationarity of the regression relationship between the response and predictor variables are explicitly considered.The basic idea consists of relying on the local stationarity assumption to build a collection of local machine learning models while leveraging on the local spatial auto-correlation of the response variable to locally augment the training dataset.The proposed method’s effectiveness is showcased via experiments conducted on synthetic spatial data with known characteristics as well as real-world spatial data.In the synthetic(resp.real)case study,the proposed method’s predictive accuracy,as indicated by the Root Mean Square Error(RMSE)on the test set,is 17%(resp.7%)better than that of popular machine learning methods dealing with the response variable’s spatial auto-correlation.Additionally,this method is not only valuable for spatial prediction but also offers a deeper understanding of how the relationship between the target and predictor variables varies across space,and it can even be used to investigate the local significance of predictor variables.

Walsh Spectral Characteristics and the Auto-Correlation Function Characteristics of Forming Orthomorphic Permutations of Multi-Output Functions

Orthomorphic permutations have good characteristics in cryptosystems. In this paper, by using of knowledge about relation between orthomorphic permutations and multi-output functions, and conceptions of the generalized Walsh spectrum of multi-output functions and the auto-correlation function of multi-output functions to investigate the Walsh spectral characteristics and the auto-correlation function characteristics of orthormophic permutations, several results are obtained.

Biometric feature extraction using local fractal auto-correlation

Image texture feature extraction is a classical means for biometric recognition. To extract effective texture feature for matching, we utilize local fractal auto-correlation to construct an effective image texture descriptor. Three main steps are involved in the proposed scheme： （i） using two-dimensional Gabor filter to extract the texture features of biometric images; （ii） calculating the local fractal dimension of Gabor feature under different orientations and scales using fractal auto-correlation algorithm; and （iii） linking the local fractal dimension of Gabor feature under different orientations and scales into a big vector for matching. Experiments and analyses show our proposed scheme is an efficient biometric feature extraction approach.

Spatial analysis of the osteoarthritis microenvironment: techniques, insights, and applications

Osteoarthritis(OA)is a debilitating degenerative disease affecting multiple joint tissues,including cartilage,bone,synovium,and adipose tissues.OA presents diverse clinical phenotypes and distinct molecular endotypes,including inflammatory,metabolic,mechanical,genetic,and synovial variants.Consequently,innovative technologies are needed to support the development of effective diagnostic and precision therapeutic approaches.Traditional analysis of bulk OA tissue extracts has limitations due to technical constraints,causing challenges in the differentiation between various physiological and pathological phenotypes in joint tissues.This issue has led to standardization difficulties and hindered the success of clinical trials.Gaining insights into the spatial variations of the cellular and molecular structures in OA tissues,encompassing DNA,RNA,metabolites,and proteins,as well as their chemical properties,elemental composition,and mechanical attributes,can contribute to a more comprehensive understanding of the disease subtypes.Spatially resolved biology enables biologists to investigate cells within the context of their tissue microenvironment,providing a more holistic view of cellular function.Recent advances in innovative spatial biology techniques now allow intact tissue sections to be examined using various-omics lenses,such as genomics,transcriptomics,proteomics,and metabolomics,with spatial data.This fusion of approaches provides researchers with critical insights into the molecular composition and functions of the cells and tissues at precise spatial coordinates.Furthermore,advanced imaging techniques,including high-resolution microscopy,hyperspectral imaging,and mass spectrometry imaging,enable the visualization and analysis of the spatial distribution of biomolecules,cells,and tissues.Linking these molecular imaging outputs to conventional tissue histology can facilitate a more comprehensive characterization of disease phenotypes.This review summarizes the recent advancements in the molecular imaging modalities and methodologies for in-depth spatial analysis.It explores their applications,challenges,and potential opportunities in the field of OA.Additionally,this review provides a perspective on the potential research directions for these contemporary approaches that can meet the requirements of clinical diagnoses and the establishment of therapeutic targets for OA.

SPEECH ENHANCEMENT BASED ON DYNAMIC NOISE ESTIMATION WITHIN AUTO-CORRELATION DOMAIN

Most noise suppression algorithms of single channel use the mean of noisy segments to estimate the characteristics of noise spectrum, ignoring the estimation of noise in speech segments. Therefore, when the energy level of noise varies with the time, the performance of removing noise will be degraded. To solve this problem, a speech enhancement approach based on dynamic noise estimation within correlation domain was proposed. This method exploits the characteristics that noise energy mainly concentrates on 0 th order correlation coefficients, signal is auto correlated but signal and noise, noise and noise are uncorrelated, then estimates and decomposes the noise, thus helps to solve the above mentioned problem. The results of recognition experiments on speech signals of 15 Chinese cities’ names corrupted by noise of exhibition hall shows, this approach is better than SS (Spectral Subtraction) method, adapts better to the variances of energy levels of speech signal corrupted by noise, has some practicability to improve the robustness of recognition systems under noisy environment.

Spatial distribution of shallow landslides caused by Typhoon Lekima in 2019 in Zhejiang Province, China

In recent years, the coastal region of Southeast China has witnessed a significant increase in the frequency and intensity of extreme rainfall events associated with landfalling typhoons. The hilly and mountainous terrain of this area, combined with rapid rainfall accumulation, has led to a surge in flash floods and severe geological hazards. On August 10, 2019, Typhoon Lekima made landfall in Zhejiang Province, China, and its torrential rainfall triggered extensive landslides, resulting in substantial damage and economic losses. Utilizing high-resolution satellite images, we compiled a landslide inventory of the affected area, which comprises a total of 2,774 rainfallinduced landslides over an area of 2965 km2. The majority of these landslides were small to mediumsized and exhibited elongated, clustered patterns. Some landslides displayed characteristics of high-level initiation, obstructing or partially blocking rivers, leading to the formation of debris dams. We used the inventory to analyze the distribution pattern of the landslides and their relationship with topographical, geological, and hydrological factors. The results showed that landslide abundance was closely related to elevation, slope angle, faults, and road density. The landslides were predominantly located in hilly and low mountainous areas, with elevations ranging from 150 to 300 m, slopes of 20 to 30 degrees, and a NE-SE aspect. Notably, we observed the highest Landslide Number Density(LND) and Landslide Area Percentage(LAP) in the rhyolite region. Landslides were concentrated within approximately 4 km on either side of fault zones, with their size and frequency negatively correlated with distances to faults, roads, and river systems. Furthermore, under the influence of typhoons, regions with denser vegetation cover exhibited higher landslide density, reaching maximum values in shrubland areas. In areas experiencing significantly increased concentrated rainfall, landslide density also showed a corresponding rise. In terms of spatial distribution, the rainfall-triggered landslides primarily occurred in the northeastern part of the study area, particularly in regions characterized by complex topography such as Shanzao Village in Yantan Town, Xixia Township, and Shangzhang Township. The research findings offer crucial data on the rainfallinduced landslides triggered by Typhoon Lekima, shedding light on their spatial distribution patterns. These findings provide valuable references for mitigating risks and planning reconstruction in typhoon-affected area.

Chrestenson Spectrum and Auto-Correlation Function of Inverse Permutations of Quick Trickle Permutations

In this paper, a sufficient and necessary condition of quick trickle permutations is given from the point of inverse permutations. The bridge is built between quick trickle permutations and m-value logic functions. By the methods of the Chrestenson spectrum of m-value logic functions and the auto-correlation function of m-value logic functions to investigate the Chrestenson spectral characteristics and the auto-correlation function charac- teristics of inverse permutations of quick trickle permutations, a determinant arithmetic of quick trickle permutations is given. Using the results, it becomes easy to judge that a permutation is a quick trickle permutation or not by using computer. This gives a new pathway to study constructions and enumerations of quick trickle permutations.

Cyclic-Auto-Correlation Based Timing Estimation Algorithm for Time-Frequency Overlapping Multi-Carrier Signals

In recent years,the time-frequency overlapping multi-carrier signal has been a novel and valuable topic in blind signal processing,especially in the non-cooperative receiving field.But there is little related research in public published papers.This paper proposes two timing estimation algorithms,which are non-data-aided and based on the cyclic auto-correlation function.In order to evaluate the performance of the proposed algorithms,the theoretical bound of the timing estimation is derived.According to the analyses and simulation results,the effectiveness of the proposed algorithms has been demonstrated.It shows that MethodⅠhas better performance than MethodⅡ.However,MethodⅡdoes not need prior information,so it has a wider range of applications.

Time series prediction of reservoir bank landslide failure probability considering the spatial variability of soil properties

Historically,landslides have been the primary type of geological disaster worldwide.Generally,the stability of reservoir banks is primarily affected by rainfall and reservoir water level fluctuations.Moreover,the stability of reservoir banks changes with the long-term dynamics of external disastercausing factors.Thus,assessing the time-varying reliability of reservoir landslides remains a challenge.In this paper,a machine learning(ML)based approach is proposed to analyze the long-term reliability of reservoir bank landslides in spatially variable soils through time series prediction.This study systematically investigated the prediction performances of three ML algorithms,i.e.multilayer perceptron(MLP),convolutional neural network(CNN),and long short-term memory(LSTM).Additionally,the effects of the data quantity and data ratio on the predictive power of deep learning models are considered.The results show that all three ML models can accurately depict the changes in the time-varying failure probability of reservoir landslides.The CNN model outperforms both the MLP and LSTM models in predicting the failure probability.Furthermore,selecting the right data ratio can improve the prediction accuracy of the failure probability obtained by ML models.

FPGA-based position reconstruction method for neutron beam flux spatial distribution measurement in BNCT

A new measurement method for the spatial distribution of neutron beam flux in boron neutron capture therapy(BNCT)is being developed based on the two-dimensional Micromegas detector.To address the issue of long processing times in traditional offline position reconstruction methods,this paper proposes a field programmable gate array based online position reconstruction method utilizing the micro-time projection chamber principle.This method encapsulates key technical aspects:a self-adaptive serial link technique built upon the dynamical adjustment of the delay chain length,fast sorting,a coordinate-matching technique based on the mapping between signal timestamps and random access memory(RAM)addresses,and a precise start point-merging technique utilizing a circular combined RAM.The performance test of the selfadaptive serial link shows that the bit error rate of the link is better than 10-12 at a confidence level of 99%,ensuring reliable data transmission.The experiment utilizing the readout electronics and Micromegas detector shows a spatial resolution of approximately 1.4 mm,surpassing the current method’s resolution level of 5 mm.The beam experiment confirms that the readout electronics system can obtain the flux spatial distribution of neutron beams online,thus validating the feasibility of the position reconstruction method.The online position reconstruction method avoids traditional methods,such as bubble sorting and traversal searching,simplifies the design of the logic firmware,and reduces the time complexity from O(n2)to O(n).This study contributes to the advancement in measuring neutron beam flux for BNCT.

Characterization and spatial analysis of coseismic landslides triggered by the Luding Ms 6.8 earthquake in the Xianshuihe fault zone, Southwest China

On September 5, 2022, a magnitude Ms 6.8 earthquake occurred along the Moxi fault in the southern part of the Xianshuihe fault zone located in the southeastern margin of the Tibetan Plateau,resulting in severe damage and substantial economic loss. In this study, we established a coseismic landslide database triggered by Luding Ms 6.8 earthquake, which includes 4794 landslides with a total area of 46.79 km^(2). The coseismic landslides primarily consisted of medium and small-sized landslides, characterized by shallow surface sliding. Some exhibited characteristics of high-position initiation resulted in the obstruction or partial obstruction of rivers, leading to the formation of dammed lakes. Our research found that the coseismic landslides were predominantly observed on slopes ranging from 30° to 50°, occurring at between 1000 m and 2500 m, with slope aspects varying from 90° to 180°. Landslides were also highly developed in granitic bodies that had experienced structural fracturing and strong-tomoderate weathering. Coseismic landslides concentrated within a 6 km range on both sides of the Xianshuihe and Daduhe fault zones. The area and number of coseismic landslides exhibited a negative correlation with the distance to fault lines, road networks, and river systems, as they were influenced by fault activity, road excavation, and river erosion. The coseismic landslides were mainly distributed in the southeastern region of the epicenter, exhibiting relatively concentrated patterns within the IX-degree zones such as Moxi Town, Wandong River basin, Detuo Town to Wanggangping Township. Our research findings provide important data on the coseismic landslides triggered by the Luding Ms 6.8 earthquake and reveal the spatial distribution patterns of these landslides. These findings can serve as important references for risk mitigation, reconstruction planning, and regional earthquake disaster research in the earthquake-affected area.

Estimation-free spatial-domain image reconstruction of structured illumination microscopy

Structured illumination microscopy(SIM)achieves super-resolution(SR)by modulating the high-frequency information of the sample into the passband of the optical system and subsequent image reconstruction.The traditional Wiener-filtering-based reconstruction algorithm operates in the Fourier domain,it requires prior knowledge of the sinusoidal illumination patterns which makes the time-consuming procedure of parameter estimation to raw datasets necessary,besides,the parameter estimation is sensitive to noise or aberration-induced pattern distortion which leads to reconstruction artifacts.Here,we propose a spatial-domain image reconstruction method that does not require parameter estimation but calculates patterns from raw datasets,and a reconstructed image can be obtained just by calculating the spatial covariance of differential calculated patterns and differential filtered datasets(the notch filtering operation is performed to the raw datasets for attenuating and compensating the optical transfer function(OTF)).Experiments on reconstructing raw datasets including nonbiological,biological,and simulated samples demonstrate that our method has SR capability,high reconstruction speed,and high robustness to aberration and noise.

Monitoring Bridge Deformation Using Auto-Correlation Adjustment Technique for Total Station Observations

Bridges are omnipresent in every society and they affect its human, social, ecological, economical and cultural aspects. This is why a durable and safe usage of bridges is an imperative goal of structural management. Measurement and monitoring have an essential role in structural management. The benefits of the information obtained by monitoring are apparent in several domains. In deformation analysis, the functional relationship between the acting forces and the resulting deformations should be established. If time depending observations are given, a regression could be used as a functional model. In case of stochastic model uncorrelated observations with identical variance are assumed. Due to the high sampling rate, a small time difference arises between two observations. Thus the assumed stochastic model is not suitable. The calculation has to be effected by means of auto-correlated observations. This paper investigates an integrated monitoring system for the estimation of the deformation (i.e., static, quasi-static) behavior of bridges from total station observations and studies the effect of autocorrelation technique on the accuracy of the estimated parameters and variances. The results have shown that autocorrelation technique is reduced the standard deviation of X&Y-direction about 6.7% to 29.4% and 6.5% to 15.5% of the original value, respectively, but the situation was differ in Z direction;the standard deviation in vertical component Z was increased.

Spatially resolved metabolomics visualizes heterogeneous distribution of metabolites in lung tissue and the anti-pulmonary fibrosis effect of Prismatomeris connate extract

Pulmonary fibrosis (PF) is a chronic progressive end-stage lung disease. However, the mechanisms underlying the progression of this disease remain elusive. Presently, clinically employed drugs are scarce for the treatment of PF. Hence, there is an urgent need for developing novel drugs to address such diseases. Our study found for the first time that a natural source of Prismatomeris connata Y. Z. Ruan (Huang Gen, HG) ethyl acetate extract (HG-2) had a significant anti-PF effect by inhibiting the expression of the transforming growth factor beta 1/suppressor of mothers against decapentaplegic (TGF-β1/Smad) pathway. Network pharmacological analysis suggested that HG-2 had effects on tyrosine kinase phosphorylation, cellular response to reactive oxygen species, and extracellular matrix (ECM) disassembly. Moreover, mass spectrometry imaging (MSI) was used to visualize the heterogeneous distribution of endogenous metabolites in lung tissue and reveal the anti-PF metabolic mechanism of HG-2, which was related to arginine biosynthesis and alanine, asparate and glutamate metabolism, the downregulation of arachidonic acid metabolism, and the upregulation of glycerophospholipid metabolism. In conclusion, we elaborated on the relationship between metabolite distribution and the progression of PF, constructed the regulatory metabolic network of HG-2, and discovered the multi-target therapeutic effect of HG-2, which might be conducive to the development of new drugs for PF.

Design of Protograph LDPC-Coded MIMO-VLC Systems with Generalized Spatial Modulation

This paper investigates the bit-interleaved coded generalized spatial modulation(BICGSM) with iterative decoding(BICGSM-ID) for multiple-input multiple-output(MIMO) visible light communications(VLC). In the BICGSM-ID scheme, the information bits conveyed by the signal-domain(SiD) symbols and the spatial-domain(SpD) light emitting diode(LED)-index patterns are coded by a protograph low-density parity-check(P-LDPC) code. Specifically, we propose a signal-domain symbol expanding and re-allocating(SSER) method for constructing a type of novel generalized spatial modulation(GSM) constellations, referred to as SSERGSM constellations, so as to boost the performance of the BICGSM-ID MIMO-VLC systems.Moreover, by applying a modified PEXIT(MPEXIT) algorithm, we further design a family of rate-compatible P-LDPC codes, referred to as enhanced accumulate-repeat-accumulate(EARA) codes,which possess both excellent decoding thresholds and linear-minimum-distance-growth property. Both analysis and simulation results illustrate that the proposed SSERGSM constellations and P-LDPC codes can remarkably improve the convergence and decoding performance of MIMO-VLC systems. Therefore, the proposed P-LDPC-coded SSERGSM-mapped BICGSMID configuration is envisioned as a promising transmission solution to satisfy the high-throughput requirement of MIMO-VLC applications.

Fingerspelling Recognition by Hand Shape Using Higher-Order Local Auto-Correlation Features

The fingerspelling recognition by hand shape is an important step for developing a human-computer interaction system. A method of fingerspelling recognition by hand shape using HLAC （higher-order local auto-correlation） features is proposed. Furthermore, in order to use HLAC features more effectively, the use of image processing techniques： reducing an image resolution, dividing an image, and image pre-processing techniques, is also proposed. The experimental results show that the proposed method is promising.

Spatial Variation in CO_(2) Concentration Improves the Simulated Surface Air Temperature Increase in the Northern Hemisphere

The increasing concentration of atmospheric CO_(2) since the Industrial Revolution has affected surface air temperature.However,the impact of the spatial distribution of atmospheric CO_(2) concentration on surface air temperature biases remains highly unclear.By incorporating the spatial distribution of satellite-derived atmospheric CO_(2) concentration in the Beijing Normal University Earth System Model,this study investigated the increase in surface air temperature since the Industrial Revolution in the Northern Hemisphere(NH) under historical conditions from 1976-2005.In comparison with the increase in surface temperature simulated using a uniform distribution of CO_(2),simulation with a nonuniform distribution of CO_(2)produced better agreement with the Climatic Research Unit(CRU) data in the NH under the historical condition relative to the baseline over the period 1901-30.Hemispheric June-July-August(JJA) surface air temperature increased by 1.28℃ ±0.29℃ in simulations with a uniform distribution of CO_(2),by 1.00℃±0.24℃ in simulations with a non-uniform distribution of CO_(2),and by 0.24℃ in the CRU data.The decrease in downward shortwave radiation in the non-uniform CO_(2) simulation was primarily attributable to reduced warming in Eurasia,combined with feedbacks resulting from increased leaf area index(LAI) and latent heat fluxes.These effects were more pronounced in the non-uniform CO_(2)simulation compared to the uniform CO_(2) simulation.Results indicate that consideration of the spatial distribution of CO_(2)concentration can reduce the overestimated increase in surface air temperature simulated by Earth system models.

Ultrafast dynamics of femtosecond laser-induced high spatial frequency periodic structures on silicon surfaces

Femtosecond laser-induced periodic surface structures(LIPSS)have been extensively studied over the past few decades.In particular,the period and groove width of high-spatial-frequency LIPSS(HSFL)is much smaller than the diffraction limit,making it a useful method for efficient nanomanufacturing.However,compared with the low-spatial-frequency LIPSS(LSFL),the structure size of the HSFL is smaller,and it is more easily submerged.Therefore,the formation mechanism of HSFL is complex and has always been a research hotspot in this field.In this study,regular LSFL with a period of 760 nm was fabricated in advance on a silicon surface with two-beam interference using an 800 nm,50 fs femtosecond laser.The ultrafast dynamics of HSFL formation on the silicon surface of prefabricated LSFL under single femtosecond laser pulse irradiation were observed and analyzed for the first time using collinear pump-probe imaging method.In general,the evolution of the surface structure undergoes five sequential stages:the LSFL begins to split,becomes uniform HSFL,degenerates into an irregular LSFL,undergoes secondary splitting into a weakly uniform HSFL,and evolves into an irregular LSFL or is submerged.The results indicate that the local enhancement of the submerged nanocavity,or the nanoplasma,in the prefabricated LSFL ridge led to the splitting of the LSFL,and the thermodynamic effect drove the homogenization of the splitting LSFL,which evolved into HSFL.