Efficient simulation of spatially correlated non-stationary ground motions by wavelet-packet algorithm and spectral representation method

Although the classical spectral representation method(SRM)has been widely used in the generation of spatially varying ground motions,there are still challenges in efficient simulation of the non-stationary stochastic vector process in practice.The first problem is the inherent limitation and inflexibility of the deterministic time/frequency modulation function.Another difficulty is the estimation of evolutionary power spectral density(EPSD)with quite a few samples.To tackle these problems,the wavelet packet transform(WPT)algorithm is utilized to build a time-varying spectrum of seed recording which describes the energy distribution in the time-frequency domain.The time-varying spectrum is proven to preserve the time and frequency marginal property as theoretical EPSD will do for the stationary process.For the simulation of spatially varying ground motions,the auto-EPSD for all locations is directly estimated using the time-varying spectrum of seed recording rather than matching predefined EPSD models.Then the constructed spectral matrix is incorporated in SRM to simulate spatially varying non-stationary ground motions using efficient Cholesky decomposition techniques.In addition to a good match with the target coherency model,two numerical examples indicate that the generated time histories retain the physical properties of the prescribed seed recording,including waveform,temporal/spectral non-stationarity,normalized energy buildup,and significant duration.

Spatially resolved transcriptomic profiling of placental development in dairy cow

The placenta plays a crucial role in successful mammalian reproduction.Ruminant animals possess a semi-invasive placenta characterized by a highly vascularized structure formed by maternal endometrial caruncles and fetal placental cotyledons,essential for full-term fetal development.The cow placenta harbors at least two trophoblast cell populations:uninucleate(UNC)and binucleate(BNC)cells.However,the limited capacity to elucidate the transcriptomic dynamics of the placental natural environment has resulted in a poor understanding of both the molecular and cellular interactions between trophoblast cells and niches,and the molecular mechanisms governing trophoblast differentiation and functionalization.To fill this knowledge gap,we employed Stereo-seq to map spatial gene expression patterns at near single-cell resolution in the cow placenta at 90 and 130 days of gestation,attaining high-resolution,spatially resolved gene expression profiles.Based on clustering and cell marker gene expression analyses,key transcription factors,including YBX1 and NPAS2,were shown to regulate the heterogeneity of trophoblast cell subpopulations.Cell communication and trajectory analysis provided a framework for understanding cell-cell interactions and the differentiation of trophoblasts into BNCs in the placental microenvironment.Differential analysis of cell trajectories identified a set of genes involved in regulation of trophoblast differentiation.Additionally,spatial modules and co-variant genes that help shape specific tissue structures were identified.Together,these findings provide foundational insights into important biological pathways critical to the placental development and function in cows.

Promise of spatially resolved omics for tumor research

Tumors are spatially heterogeneous tissues that comprise numerous cell types with intricate structures.By interacting with the microenvironment,tumor cells undergo dynamic changes in gene expression and metabolism,resulting in spatiotemporal variations in their capacity for proliferation and metastasis.In recent years,the rapid development of histological techniques has enabled efficient and high-throughput biomolecule analysis.By preserving location information while obtaining a large number of gene and molecular data,spatially resolved metabolomics(SRM)and spatially resolved transcriptomics(SRT)approaches can offer new ideas and reliable tools for the in-depth study of tumors.This review provides a comprehensive introduction and summary of the fundamental principles and research methods used for SRM and SRT techniques,as well as a review of their applications in cancer-related fields.

Preface for Special Issue:Single-Cell and Spatially Resolved Omics

We are delighted to present you this special issue,which consists of a collection of articles focusing on the novel and rapidly evolving field of single-cell and spatially resolved omics.This encompasses epigenomics,transcriptomics,proteomics,and metabolomics.Recent technological advances,coupled with computational techniques,have advanced the scope of this discipline to allow the investigation of individual cells down to an unprecedented level of detail.Researchers can now explore the cellular heterogeneity and the intricate interplay among its multiple molecular elements comprehensively.

Preface for Special Issue: Single-Cell and Spatially Resolved Omics

In this special issue,we are excited to present a collection of articles focusing on the emerging and rapidly evolving field of singlecell and spatially resolved omics,including epigenomics,transcriptomics,proteomics,and metabolomics.In recent years,the developmentofadvanced,high-throughput technologiessand computational methods has enabled researchers to study individual cells at an unprecedented resolution,shedding light on their heterogeneity and the complex interplay between their various molecular components.The detailed exploration of these aspects is crucial not only for a better understanding of the fundamental biology underlying cell function and organization but also for identifying novel therapeutic targets and strategies in various disease contexts.

Discovering metabolic vulnerability using spatially resolved metabolomics for antitumor small molecule-drug conjugates development as a precise cancer therapy strategy

Against tumor-dependent metabolic vulnerability is an attractive strategy for tumor-targeted therapy.However,metabolic inhibitors are limited by the drug resistance of cancerous cells due to their metabolic plasticity and heterogeneity.Herein,choline metabolism was discovered by spatially resolved metabolomics analysis as metabolic vulnerability which is highly active in different cancer types,and a choline-modified strategy for small molecule-drug conjugates(SMDCs)design was developed to fool tumor cells into indiscriminately taking in choline-modified chemotherapy drugs for targeted cancer therapy,instead of directly inhibiting choline metabolism.As a proof-of-concept,choline-modified SMDCs were designed,screened,and investigated for their druggability in vitro and in vivo.This strategy improved tumor targeting,preserved tumor inhibition and reduced toxicity of paclitaxel,through targeted drug delivery to tumor by highly expressed choline transporters,and site-specific release by carboxylesterase.This study expands the strategy of targeting metabolic vulnerability and provides new ideas of developing SMDCs for precise cancer therapy.

Single-cell and spatially resolved omics:Advances and limitations

Recent advances in experimental and computational single-cell and spatially resolved omics have opened new avenues for research in biology and medicine.These technologies allow for the study of individual cells in unprecedented detail,providing insights into the heterogeneity within tissues and organs,and how different cells interact with each other.Humans and other eukaryotes are composed of billions of cells,each with vastly heterogeneous cell types and functional cell states determined by intrinsic and extrinsic factors.

Delayed response to the photovoltaic performance in a double quantum dots photocell with spatially correlated fluctuation

A viable strategy for enhancing photovoltaic performance is to comprehend the underlying quantum physical regime of charge transfer in a double quantum dots(DQD) photocell. This work explored the photovoltaic performance dependent spatially correlated fluctuation in a DQD photocell. The effects of spatially correlated fluctuation on charge transfer and output photovoltaic efficiency were explored in a proposed DQD photocell model. The results revealed that the charge transport process and the time to peak photovoltaic efficiency were both significantly delayed by the spatially correlated fluctuation, while the anti-spatially correlated fluctuation reduced the output peak photovoltaic efficiency. Further results revealed that the delayed response could be suppressed by gap difference and tunneling coefficient within two dots. Subsequent investigation demonstrated that the delayed response was caused by the spatial correlation fluctuation slowing the generative process of noise-induced coherence, which had previously been proven to improve the quantum photovoltaic performance in quantum photocells. And the reduced photovoltaic properties were verified by the damaged noise-induced coherence owing to the anti-spatial correlation fluctuation and a hotter thermal ambient environment. The discovery of delayed response generated by the spatially correlated fluctuations will deepen the understanding of quantum features of electron transfer, as well as promises to take our understanding even further concerning quantum techniques for high efficiency DQD solar cells.

Reconstructing in vivo spatially offset Raman spectroscopy of human skin tissue using a GPU-accelerated Monte Carlo platform

As one type of spatially offset Raman spectroscopy(SORS), inverse SORS is particularly suited to in vivo biomedical measurements due to its ring-shaped illumination scheme. To explain inhomogeneous Raman scattering during in vivo inverse SORS measurements, the light–tissue interactions when excitation and regenerated Raman photons propagate in skin tissue were studied using Monte Carlo simulation. An eight-layered skin model was first built based on the latest transmission parameters. Then, an open-source platform, Monte Carlo e Xtreme(MCX), was adapted to study the distribution of 785 nm excitation photons inside the model with an inverse spatially shifted annular beam. The excitation photons were converted to emission photons by an inverse distribution method based on excitation flux with spatial offsets Δs of 1 mm, 2 mm, 3 mm and 5 mm. The intrinsic Raman spectra from separated skin layers were measured by continuous linear scanning to improve the simulation accuracy. The obtained results explain why the spectral detection depth gradually increases with increasing spatial offset, and address how the intrinsic Raman spectrum from deep skin layers is distorted by the reabsorption and scattering of the superficial tissue constituents. Meanwhile, it is demonstrated that the spectral contribution from subcutaneous fat will be improved when the offset increases to 5 mm, and the highest detection efficiency for dermal layer spectral detection could be achieved when Δs = 2 mm. Reasonably good matching between the calculated spectrum and the measured in vivo inverse SORS was achieved, thus demonstrating great utility of our modeling method and an approach to help understand the clinical measurements.

Accurate design of spatially separated double active site in Bi_(4)NbO_(8)Cl single crystal to promote Z-Scheme photocatalytic overall water splitting

The efficiency of photocatalytic overall water splitting was mainly limited by the slow reaction kinetics of water oxidation.How to design effective surface active site to overcome the slow water oxidation reaction was a major challenge.Here,we propose a strategy to accelerate surface water oxidation through the fabrication spatially separated double active sites.FeCoPi/Bi_(4)NbO_(8)Cl-OVs photocatalyst with spatially separated double active site was prepared by hydrogen reduction photoanode deposition method.Due to the high matching of the spatial loading positions of FeCoPi and OVs with the photogenerated charge distribution of Bi_(4)NbO_(8)Cl and corresponding reaction mechanisms of substrate,the FeCoPi and OVs on the(001)and(010)crystal planes of Bi_(4)NbO_(8)Cl photocatalyst provided surface active site for water oxidation reaction and electron shuttle reaction(Fe^(3+)/Fe^(2+)),respectively.Under visible light irradiation,the evolution O_(2)rate of FeCoPi/Bi_(4)NbO_(8)Cl OVs was 16.8μmol h^(-1),as 32.9 times as Bi_(4)NbO_(8)Cl.Furthermore,a hydrogen evolution co-catalyst PtRu@Cr_(2)O_(3)was prepared by sequential photodeposition method.Due to the introduction of Ru,the Schottky barrier between PbTiO_(3)and Pt was effectively reduced,which promoted the transfer of photogenerated electrons to PtRu@Cr_(2)O_(3)thermodynamically,the evolution H_(2)rate on PtRu@Cr_(2)O_(3)/PbTiO_(3)increased to 664.8 times.On based of the synchronous enhancement of the water oxidation performance on FeCoPi/Bi_(4)NbO_(8)Cl-OVs and water reduction performance on PtRu@Cr_(2)O_(3)/PbTiO_(3),a novel Z-Scheme photocatalytic overall water splitting system(FeCoPi/Bi_(4)NbO_(8)Cl-OVs)mediated by Fe^(3+)/Fe^(2+)had successfully constructed.Under visible light irradiation,the evolution rates of H_(2)and O_(2)were 2.5 and 1.3μmol h^(-1),respectively.This work can provide some reference for the design of active site and the controllable synthesis of OVs spatial position.On the other hand,the hydrogen evolution co catalyst(PtRu@Cr_(2)O_(3))and the co catalyst FeCoPi for oxygen evolution contributed to the construction of an overall water splitting system.

Dissecting the brain with spatially resolved multi-omics

Recent studies have highlighted spatially resolved multi-omics technologies,including spatial genomics,transcriptomics,proteomics,and metabolomics,as powerful tools to decipher the spatial heterogeneity of the brain.Here,we focus on two major approaches in spatial transcriptomics(next-generation sequencing-based technologies and image-based technologies),and mass spectrometry imaging technologies used in spatial proteomics and spatial metabolomics.Furthermore,we discuss their applications in neuroscience,including building the brain atlas,uncovering gene expression patterns of neurons for special behaviors,deciphering the molecular basis of neuronal communication,and providing a more comprehensive explanation of the molecular mechanisms underlying central nervous system disorders.However,further efforts are still needed toward the integrative application of multi-omics technologies,including the real-time spatial multi-omics analysis in living cells,the detailed gene profile in a whole-brain view,and the combination of functional verification.

Enhanced THz Radiation from Spatially Inhomogeneous Fields

Nonlinear terahertz(THz)radiation from gas media usually relies on the asymmetric laser-induced current produced by ultra-intense two-color laser fields with a specific phase delay.Here a new scheme is proposed and theoretically investigated,in which the radiation is generated by spatially inhomogeneous fields induced by relatively low-intensity monochromatic lasers and an array of single triangular metallic nanostructures.Our simulations are based on the classical photocurrent model and the time-dependent Schrodinger equations separately.It is found that the collective motion of the ionized electrons can be efficiently controlled by the inhomogeneous field,resulting in strong residual currents.The intensity of the THz radiation could be enhanced by about two orders of magnitude by increasing the spatial inhomogeneity of the field.

Rate-compatible spatially coupled repeat-accumulate codes via successive extension

A rate-compatible spatially coupled repeat-accumulate (RC-SC-RA) code is proposed. Its protograph is obtained by extending a given (J, K, L) SC-RA coupled chain (denoted as the mother chain) with extra check nodes and parity bit nodes T times. At each time, the extension is realized via coupling the message bits in the same way as that in the mother chain. Rate-compatibility is achieved by adjusting the extension parameters and applying random puncturing technique. Density evolution analysis shows that the iterative decoding thresholds of all the member codes in the proposed RC-SC-RA code family are very close to Shannon limits over the binary erasure channel. Finite length simulation results are consistent with the thresholds well. Moreover, the proposed RC-SC-RA codes perform better than spatially coupled low density parity check (SC-LDPC) codes in decoding performance especially in lower-rate region.

Remote Sensing of Ecosystem Services:An Opportunity for Spatially Explicit Assessment

Ecosystem service is an emerging concept that grows to be a hot research area in ecology.Spatially explicit ecosystem service values are important for ecosystem service management.However,it is difficult to quantify ecosystem services.Remote sensing provides images covering Earth surface,which by nature are spatially explicit.Thus,remote sensing can be useful for quantitative assessment of ecosystem services.This paper reviews spatially explicit ecosystem service studies conducted in ecology and remote sensing in order to find out how remote sensing can be used for ecosystem service assessment.Several important areas considered include land cover,biodiversity,and carbon,water and soil related ecosystem services.We found that remote sensing can be used for ecosystem service assessment in three different ways:direct monitoring,indirect monitoring,and combined use with ecosystem models.Some plant and water related ecosystem services can be directly monitored by remote sensing.Most commonly,remote sensing can provide surrogate information on plant and soil characteristics in an ecosystem.For ecosystem process related ecosystem services,remote sensing can help measure spatially explicit parameters.We conclude that acquiring good in-situ measurements and selecting appropriate remote sensor data in terms of resolution are critical for accurate assessment of ecosystem services.

Effect of spatially nonlocal versus local optical response of a gold nanorod on modification of the spontaneous emission

The spontaneous emission rate of a two-level quantum emitter(QE)near a gold nanorod is numerically investigated.Three different optical response models for the free-electron gas are adopted,including the classical Drude local response approximation,the nonlocal hydrodynamic model,and the generalized nonlocal optical response model.Nonlocal optical response leads to a blueshift and a reduction in the enhancement of the spontaneous emission rate.Within all the three models,the resonance frequency is largely determined by the aspect ratio(the ratio of the nanorod length to the radius)and increases sharply with decreasing aspect ratio.For nanorod with a fixed length,it is found that the larger the radius is,the higher the resonance frequency is,and the smaller the enhancement is.However,if the length of the nanorod increases,the peak frequency falls sharply,while the spontaneous emission enhancement grows rapidly.For nanorod with a fixed aspect ratio,the peak frequency decreases slowly with increasing nanorod size.Larger nanorod shows smaller nonlocal effect.At a certain frequency,there is an optimal size to maximize the enhancement of the spontaneous emission rate.Higher order modes are more affected by the nonlocal smearing of the induced charges,leading to larger blueshift and greater reduction in the enhancement.These results should be significant for investigating the spontaneous emission rate of a QE around a gold nanorod.

Control of Spatially Interconnected Systems with Random Communication Losses

This paper deals with analysis and synthesis problems of spatially interconnected systems where communicated information may get lost between subsystems. Spatial shift operator and temporal forward shift operator are introduced to model the interconnected systems as discrete time-space multidimensional linear systems with Markovian jumping parameters which reflect the state of communication channels. To ensure the whole system＇s well-posedness and mean square stability for a given packet loss rate, a condition is derived through analysis. Then a procedure of designing distributed dynamic output feedback controllers is proposed. The controllers have the same structure as the plants and are solved within the linear matrix inequality （LMI） framework. Finally, we apply these results to study the effect of communication losses on the multiple vehicle platoon control system, which further illustrates the effectiveness of the proposed model and method.

Trust-region based instantaneous optimal semi-active control of long-span spatially extended structures with MRF-04K damper

In the field of civil engineering, magnetorheological fluid （MRF） damper-based semi-active control systems have received considerable attention for use in protecting structures from natural hazards such as strong earthquakes and high winds. In this paper, the MRF damper-based semi-active control system is applied to a long-span spatially extended structure and its feasibility is discussed. Meanwhile, a _trust-region method based instantaneous optimal semi-active control algorithm （TIOC） is proposed to improve the performance of the semi-active control system in a multiple damper situation. The proposed TIOC describes the control process as a bounded constraint optimization problem, in which an optimal semi- active control force vector is solved by the trust-region method in every control step to minimize the structural responses. A numerical example of a railway station roof structure installed with MRF-04K dampers is presented. First, a modified Bouc- Wen model is utilized to describe the behavior of the selected MRF-04K damper. Then, two semi-active control systems, including the well-known clipped-optimal controller and the proposed TIOC controller, are considered. Based on the characteristics of the long-span spatially extended structure, the performance of the control system is evaluated under uniform earthquake excitation and travelling-wave excitation with different apparent velocities. The simulation results indicate that the MR fluid damper-based semi-active control systems have the potential to mitigate the responses of full-scale long-span spatially extended structures under earthquake hazards. The superiority of the proposed TIOC controller is demonstrated by comparing its control effectiveness with the clipped-optimal controller for several different cases.

Approximation approach to the SRM based on root decomposition in the simulation of spatially varying ground motions

The spectral representation method （SRM） is widely used to simulate spatially varying ground motions. This study focuses on the approximation approach to the SRM based on root decomposition, which can improve the efficiency of the simulation. The accuracy of the approximation approach may be affected by three factors： matrix for decomposition, distribution of frequency interpolation nodes and elements for interpolation. The influence of these factors on the accuracy of this approach is examined and the following conclusions are drawn. The SRM based on the root decomposition of the lagged coherency matrix exhibits greater accuracy than the SRM based on the root decomposition of the cross spectral matrix. The equal energy distribution of frequency interpolation nodes proposed in this study is more effective than the counter pith with an equal spacing. Elements for interpolation do not have much of an effect on the accuracy, so interpolation of the elements of the decomposed matrix is recommended because it is less complicated from a computational efficiency perspective.

Running safety assessment of a train traversing a three-tower cable-stayed bridge under spatially varying ground motion

To explore the influence of spatially varying ground motion on the dynamic behavior of a train passing through a three-tower cable-stayed bridge,a 3D train–track–bridge coupled model is established for accurately simulating the train–bridge interaction under earthquake excitation,which is made up of a vehicle model built by multi-body dynamics,a track–bridge finite element model,and a 3D rolling wheel–rail contact model.A conditional simulation method,which takes into consideration the wave passage effect,incoherence effect,and site-response effect,is adopted to simulate the spatially varying ground motion under different soil conditions.The multi-time-step method previously proposed by the authors is also adopted to improve computational efficiency.The dynamic responses of the train running on a three-tower cablestayed bridge are calculated with differing earthquake excitations and train speeds.The results indicate that(1)the earthquake excitation significantly increases the responses of the train–bridge system,but at a design speed,all the running safety indices meet the code requirements;(2)the incoherence and site-response effects should also be considered in the seismic analysis for long-span bridges though there is no fixed pattern for determining their influences;(3)different train speeds that vary the vibration characteristics of the train–bridge system affect the vibration frequencies of the car body and bridge.

Selection of quantum path in high-order harmonics and isolated sub-100 attosecond generation in few-cycle spatially inhomogeneous laser fields

We theoretically study the selection of the quantum path in high-order harmonics（HHG） and isolated attosecond pulse generation from a one-dimensional（1D） model of a H_2~＋ molecule in few-cycle inhomogeneous laser fields.We show that the inhomogeneity of the laser fields play an important role in the HHG process.The cutoff of the harmonics can be extended remarkably,and the harmonic spectrum becomes smooth and has fewer modulations.We investigate the time-frequency profile of the time-dependent dipole,which shows that the short quantum path is enhanced and the long quantum path disappears in spatially inhomogeneous fields.The semi-classical three-step model is also applied to illustrate the physical mechanism of HHG.The influence of driving field carrier-envelop phase（CEP） on HHG is also discussed.By superposing a series of properly selected harmonics,an isolated attosecond pulse（IAP） with duration 53 as can be obtained by a 15-fs,1600-nm laser pulse with the parameter ε = 0.0013（e is the parameter that determines the order of inhomogeneity of the laser field）.