Numerical tests for effects of various parameters in niching genetic algorithm applied to regional waveform inversion

In this paper,we focus on the influences of various parameters in the niching genetic algorithm inversion procedure on the results,such as various objective functions,the number of the models in each subpopulation,and the critical separation radius.The frequency-waveform integration（F-K） method is applied to synthesize three-component waveform data with noise in various epicentral distances and azimuths.Our results show that if we use a zero-th-lag cross-correlation function,then we will obtain the model with a faster convergence and a higher precision than other objective functions.The number of models in each subpopulation has a great influence on the rate of convergence and computation time,suggesting that it should be obtained through tests in practical problems.The critical separation radius should be determined carefully because it directly affects the multiextreme values in the inversion.We also compare the inverted results from full-band waveform data and surfacewave frequency-band（0.02-0.1 Hz） data,and find that the latter is relatively poorer but still has a higher precision,suggesting that surface-wave frequency-band data can also be used to invert for the crustal structure.

Using Intelligent Computational Methods for Optimizing Niching Method

Optimization implies the minimization or maximization of an objective function. Some problems have sev-eral optimum points which all, should be computed. Niching method is presented to do so. However, its efficiency can be improved via combining it with Memetic algorithm. Therefore, in this paper, Memetic method is used to improve this method in terms of convergence rate and diversity. In the proposed methods, genetic algorithm, PSO, and learning automata are used as a local search algorithm of Memetic method. The result of simulations demonstrates that proposed methods are more effective compared with Niching in terms of convergence and diversity.

Niching method using clustering crowding

This study analyzes drift phenomena of deterministic crowding and probabilistic crowding by using equivalence class model and expectation proportion equations. It is proved that the replacement errors of deterministic crowding cause the population converging to a single individual, thus resulting in premature stagnation or losing optional optima. And probabilistic crowding can maintain equilibrium multiple subpopulations as the population size is adequate large. An improved niching method using clustering crowding is proposed. By analyzing topology of fitness landscape using hill valley function and extending the search space for similarity analysis, clustering crowding determines the locality of search space more accurately, thus greatly decreasing replacement errors of crowding. The integration of deterministic and probabilistic replacement increases the capacity of both parallel local hill climbing and maintaining multiple subpopulations. The experimental results optimizing various multimodal functions show that,the performances of clustering crowding, such as the number of effective peaks maintained, average peak ratio and global optimum ratio are uniformly superior to those of the evolutionary algorithms using fitness sharing, simple deterministic crowding and probabilistic crowding.

Optimal design of hydraulic manifold blocks based on niching genetic simulated annealing algorithm

To solve the combinatorial optimization problem of outer layout and inner connection integrated schemes in the design of hydraulic manifold blocks （ HMB）, a hybrid genetic simulated annealing algo- rithm based on niche technology is presented. This hybrid algorithm, which combines genetic algorithm, simulated annealing algorithm and niche technology, has a strong capability in global and local search, and all extrema can be found in a short time without strict requests for preferences. For the complex restricted solid spatial layout problems in HMB, the optimizing mathematical model is presented. The key technologies in the integrated layout and connection design of HMB, including the realization of coding, annealing operation and genetic operation, are discussed. The framework of HMB optimal design system based on hybrid optimization strategy is proposed. An example is given to testify the effectiveness and feasibility of the algorithm.

An Opposition-Based Learning-Based Search Mechanism for Flying Foxes Optimization Algorithm

The flying foxes optimization(FFO)algorithm,as a newly introduced metaheuristic algorithm,is inspired by the survival tactics of flying foxes in heat wave environments.FFO preferentially selects the best-performing individuals.This tendency will cause the newly generated solution to remain closely tied to the candidate optimal in the search area.To address this issue,the paper introduces an opposition-based learning-based search mechanism for FFO algorithm(IFFO).Firstly,this paper introduces niching techniques to improve the survival list method,which not only focuses on the adaptability of individuals but also considers the population’s crowding degree to enhance the global search capability.Secondly,an initialization strategy of opposition-based learning is used to perturb the initial population and elevate its quality.Finally,to verify the superiority of the improved search mechanism,IFFO,FFO and the cutting-edge metaheuristic algorithms are compared and analyzed using a set of test functions.The results prove that compared with other algorithms,IFFO is characterized by its rapid convergence,precise results and robust stability.

Versatile strategies for adult neurogenesis:avenues to repair the injured brain

Brain injuries due to trauma or stroke are major causes of adult death and disability.Unfortunately,few interventions are effective for post-injury repair of brain tissue.After a long debate on whether endogenous neurogenesis actually happens in the adult human brain,there is now substantial evidence to support its occurrence.Although neurogenesis is usually significantly stimulated by injury,the reparative potential of endogenous differentiation from neural stem/progenitor cells is usually insufficient.Alternatively,exogenous stem cell transplantation has shown promising results in animal models,but limitations such as poor long-term survival and inefficient neuronal differentiation make it still challenging for clinical use.Recently,a high focus was placed on glia-to-neuron conversion under single-factor regulation.Despite some inspiring results,the validity of this strategy is still controversial.In this review,we summarize historical findings and recent advances on neurogenesis strategies for neurorepair after brain injury.We also discuss their advantages and drawbacks,as to provide a comprehensive account of their potentials for further studies.

The role of exosomes in adult neurogenesis:implications for neurodegenerative diseases

Exosomes are cup-shaped extracellular vesicles with a lipid bilayer that is approximately 30 to 200 nm in thickness.Exosomes are widely distributed in a range of body fluids,including urine,blood,milk,and saliva.Exosomes exert biological function by transporting factors between different cells and by regulating biological pathways in recipient cells.As an important form of intercellular communication,exosomes are increasingly being investigated due to their ability to transfer bioactive molecules such as lipids,proteins,mRNAs,and microRNAs between cells,and because they can regulate physiological and pathological processes in the central nervous system.Adult neurogenesis is a multistage process by which new neurons are generated and migrate to be integrated into existing neuronal circuits.In the adult brain,neurogenesis is mainly localized in two specialized niches:the subventricular zone adjacent to the lateral ventricles and the subgranular zone of the dentate gyrus.An increasing body of evidence indicates that adult neurogenesis is tightly controlled by environmental conditions with the niches.In recent studies,exosomes released from different sources of cells were shown to play an active role in regulating neurogenesis both in vitro and in vivo,thereby participating in the progression of neurodegenerative disorders in patients and in various disease models.Here,we provide a state-of-the-art synopsis of existing research that aimed to identify the diverse components of exosome cargoes and elucidate the therapeutic potential of exosomal contents in the regulation of neurogenesis in several neurodegenerative diseases.We emphasize that exosomal cargoes could serve as a potential biomarker to monitor functional neurogenesis in adults.In addition,exosomes can also be considered as a novel therapeutic approach to treat various neurodegenerative disorders by improving endogenous neurogenesis to mitigate neuronal loss in the central nervous system.

Metabolic and proteostatic differences in quiescent and active neural stem cells

Adult neural stem cells are neurogenesis progenitor cells that play an important role in neurogenesis.Therefore,neural regeneration may be a promising target for treatment of many neurological illnesses.The regenerative capacity of adult neural stem cells can be chara cterized by two states:quiescent and active.Quiescent adult neural stem cells are more stable and guarantee the quantity and quality of the adult neural stem cell pool.Active adult neural stem cells are chara cterized by rapid proliferation and differentiation into neurons which allow for integration into neural circuits.This review focuses on diffe rences between quiescent and active adult neural stem cells in nutrition metabolism and protein homeostasis.Furthermore,we discuss the physiological significance and underlying advantages of these diffe rences.Due to the limited number of adult neural stem cells studies,we refe rred to studies of embryonic adult neural stem cells or non-mammalian adult neural stem cells to evaluate specific mechanisms.

Deer antler stem cell niche: An interesting perspective

In recent years,there has been considerable exploration into methods aimed at enhancing the regenerative capacity of transplanted and/or tissue-resident cells.Biomaterials,in particular,have garnered significant interest for their potential to serve as natural scaffolds for cells.In this editorial,we provide commentary on the study by Wang et al,in a recently published issue of World J Stem Cells,which investigates the use of a decellularized xenogeneic extracellular matrix(ECM)derived from antler stem cells for repairing osteochondral defects in rat knee joints.Our focus lies specifically on the crucial role of biological scaffolds as a strategy for augmenting stem cell potential and regenerative capabilities,thanks to the establishment of a favorable microenvironment(niche).Stem cell differen-tiation heavily depends on exposure to intrinsic properties of the ECM,including its chemical and protein composition,as well as the mechanical forces it can generate.Collectively,these physicochemical cues contribute to a bio-instructive signaling environment that offers tissue-specific guidance for achieving effective repair and regeneration.The interest in mechanobiology,often conceptualized as a form of“structural memory”,is steadily gaining more validation and momen-tum,especially in light of findings such as these.

One-step cell biomanufacturing platform:porous gelatin microcarrier beads promote human embryonic stem cell-derived midbrain dopaminergic progenitor cell differentiation in vitro and survival after transplantation in vivo

Numerous studies have shown that cell replacement therapy can replenish lost cells and rebuild neural circuitry in animal models of Parkinson’s disease.Transplantation of midbrain dopaminergic progenitor cells is a promising treatment for Parkinson’s disease.However,transplanted cells can be injured by mechanical damage during handling and by changes in the transplantation niche.Here,we developed a one-step biomanufacturing platform that uses small-aperture gelatin microcarriers to produce beads carrying midbrain dopaminergic progenitor cells.These beads allow midbrain dopaminergic progenitor cell differentiation and cryopreservation without digestion,effectively maintaining axonal integrity in vitro.Importantly,midbrain dopaminergic progenitor cell bead grafts showed increased survival and only mild immunoreactivity in vivo compared with suspended midbrain dopaminergic progenitor cell grafts.Overall,our findings show that these midbrain dopaminergic progenitor cell beads enhance the effectiveness of neuronal cell transplantation.

Distribution and dynamics of niche and interspecific association of dominant phytoplankton species in the Feiyun River basin,Zhejiang,China

To investigate the dominant species and interspecific association in the phytoplankton community of the Feiyun River basin in Zhejiang Province,East China,the main stream and the Shanxi Zhaoshandu Reservoir in the downstream were chosen as the study area,for which 22 sampling sites were designated.Sampling was conducted in September 2021,January,May,and July 2022.Phytoplankton species were identified from both quantitative samples and in-vivo observations.Phytoplankton was quantified by direct counting.Results show that there were 98 species belonging to 6 phyla and 78 genera.In addition,to clarify the niches of the dominant phytoplankton species and their interspecific association,the dominance index was calculated,and a comprehensive analysis was conducted including niche width,niche overlap value,ecological response rate,overall association,chi-square test,and the stability.The phytoplankton community exhibited characteristics of a Cyanobacteria-Chlorophyta-Diatom type community,showing higher diversity in spring and lower diversity in summer.Among 11 dominants phytoplankton species from 3 phyla,both frequency and dominance degree varied seasonally,of which Microcystis sp.was the dominant species in Spring,Autumn,and Winter.The niche widths of the dominant species ranged from 0.234 to 0.933,and were categorized into three groups.The niche overlap values of the 11 dominant species ranged from 0.359 to 0.959,exhibiting significant seasonal differences-highest in winter followed by autumn,spring,and summer in turn.The overall correlation among dominant species in all four seasons revealed a non-significant negative association,resulting in an unstable community structure.A significant portion(84.2%)of species pairs displayed positive associations,suggesting a successional pattern where Diatoms dominated while other dominant species shared resources and space.Despite this pattern,stability measurements indicated that the dominant species community remained unstable.Therefore,careful monitoring is recommended for potential water environment issues arising from abnormal proliferation of dominant species in the watershed during winter.This research built a theoretical foundation with a data support to the early warning of eutrophication and provided a reference for water resources management in similar watersheds along the eastern coast of China.

In situ forming injectable MSC-loaded GelMA hydrogels combined with PD for vascularized sweat gland regeneration

Dear Editor,Three dimensional(3D)bioprinted extracellular matrix(ECM)can be used to provide both biochemical and biophysical cues to direct mesenchymal stem cells(MSCs)differentiation,and then differentiated cells were isolated for implantation in vivo using surgical procedures.However,the reduced cell activity after cell isolation from 3D constructs and low cell retention in injured sites limit its application[1].Methacrylated gelatin(GelMA)hydrogel has the advantage of fast crosslinking,which could resemble complex architectures of tissue construct in vivo[2].Here,we adopted a noninvasive bioprinting procedure to imitate the regenerative microenvironment that could simultaneously direct the sweat gland(SG)and vascular differentiation from MSCs and ultimately promote the replacement of glandular tissue in situ(Fig.1a).

Distribution,abundance,and realized niches of meroplankton by two different mesh size nets during spring 2017 in the Southern Yellow Sea,China

Meroplankton play a crucial role in both benthic and pelagic ecosystems.Existing quantitative research on estimating the quantities of meroplankton groups is both underrepresented and inaccurate.To investigate and evaluate the influence of varying mesh sizes(505 and 160μm)on the sampling efficiency of meroplankton,we conducted an examination using two commonly used plankton nets during the spring season in the Southern Yellow Sea(SYS).Our study revealed a total of 12 meroplankton groups,with 9 groups identified in the 505-μm mesh nets and 11 groups in the 160-μm mesh nets.The results demonstrated the superior collection efficiency of the 160-μm net compared to the 505-μm net across the majority of meroplankton groups.Furthermore,we focused on exploring the abundance,distribution patterns,and realized niches of meroplankton collected by the two mesh size nets,and observed that the distribution of meroplankton closely resembled the distribution of possible benthic adults in the SYS.Correlation analysis of the six dominant groups collected in the 160-μm mesh nets revealed that seawater temperature and salinity emerged as the key environmental factors driving variations in meroplankton abundance within the SYS.This study also found that a smaller mesh size net does not necessarily capture meroplankton more comprehensively.A comprehensive understanding of the ecological characteristics of meroplankton requires the combination of two types of nets for research.Our research significantly advances our understanding of the quantification,abundance,and distribution of meroplankton,serving as a valuable contribution to the broader landscape of detailed quantitative meroplankton studies.

Elevation transition of aquatic insects closely matches a thermal feature in the Yungas of Northwestern Argentina

Temperature is a key factor that shapes the distribution of organisms.Having knowledge about how species respond to temperature is relevant to devise strategies for addressing the impacts of climate change.Aquatic insects are particularly vulnerable to climate change,yet there is still much to learn about their ecology and distribution.In the Yungas ecoregion of Northwestern Argentina,cold-and warm-adapted species of the orders Ephemeroptera,Plecoptera,and Trichoptera(EPT)are segregated by elevation.We modeled the ecological niche of South American EPT species in this region using available data and projected their potential distribution in geographic space.Species were grouped based on their ecogeographic similarity,and we analyzed their replacement pattern along elevation gradients,focusing on the ecotone where opposing thermal preferences converge.Along this interface,we identified critical points where the combined incidence of cold and warm assemblages maximizes,indicating a significant transition zone.We found that the Montane Cloud Forest holds the interface,with a particularly greater suitability at its lower boundary.The main axis of the interface runs in a N-S direction and falls between 14°C-16°C mean annual isotherms.The probability of a particular location within a basin being classified as part of the interface increases as Kira’s warmth index approaches a score around 150.Understanding the interface is critical for defining the thermal limits of species distribution and designing biomonitoring programs.Changes in the location of thermal constants related to mountainous ecotones may cause vertical displacement of aquatic insects and vegetation communities.We have recognized significant temperature thresholds that serve as indicators of suitability for the interface.As global warming is anticipated to shift these indicators,we suggest using them to monitor the imprints of climate change on mountain ecosystems.

Post-disaster spatial reconstruction from the perspective of a rural settlement niche in the upper reaches of the Minjiang River

Post-disaster recovery and reconstruction provide an effective way to reduce the disaster vulnerability of, and promote leapfrog development in, an affected area. To date, studies that have used administrative boundaries to investigate the reconstruction of settlement space have not been able to clearly define the real boundaries of land use changes or quantify the degree of response to the ‘Build-Back-Better’ initiative, and have lacked any consideration of the fourth reconstruction stage–development period(10 years). This study constructed a mountain settlement niche and analyzed the characteristics, spatial reconstruction, and drivers of rural settlements during 2009–2019 in the upper reaches of the Minjiang River, southwest China. The results showed the following:(1) Natural factors were the basis for the formation and development of mountain settlement niches. The scale of the settlement niche and its land use structure depended on the physical geography features and the ethnic farming and grazing traditions. The settlement niche provided a realistic boundary for the spatial reconstruction.(2) The layout of residential land around cropland was the common feature of the mountain settlement niche. Of all the land use types, the roads and rural residential lands showed the most change over the 10 years;13,860 residential patches increased in size and 4,742 patches were abandoned.(3) The area of orchards, planted to reconstruct the economy in the mountains, increased by nearly 2.5 times.(4) Collapses, landslides, and debris flow disasters and the ecological red line influenced the spatial reconstruction. While the main focus of post-disaster recovery is spatial reconstruction, initiatives should include economic and spiritual recovery, and should also achieve sustainable development of the region.

A Single-Cell Landscape of Human Liver Transplantation Reveals a Pathogenic Immune Niche Associated with Early Allograft Dysfunction

Liver transplantation(LT)is the standard therapy for individuals afflicted with end-stage liver disease.Despite notable advancements in LT technology,the incidence of early allograft dysfunction(EAD)remains a critical concern,exacerbating the current organ shortage and detrimentally affecting the prognosis of recipients.Unfortunately,the perplexing hepatic heterogeneity has impeded characterization of the cellular traits and molecular events that contribute to EAD.Herein,we constructed a pioneering single-cell transcriptomic landscape of human transplanted livers derived from non-EAD and EAD patients,with 12 liver samples collected from 7 donors during the cold perfusion and portal reperfusion stages.Comparison of the 75231 cells of non-EAD and EAD patients revealed an EAD-associated immune niche comprising mucosal-associated invariant T cells,granzyme B^(+)(GZMB^(+))granzyme K^(+)(GZMK^(+))natural killer cells,and S100 calcium binding protein A12^(+)(S100A12^(+))neutrophils.Moreover,we verified this immune niche and its association with EAD occurrence in two independent cohorts.Our findings elucidate the cellular characteristics of transplanted livers and the EAD-associated pathogenic immune niche at the single-cell level,thus,offering valuable insights into EAD onset.

Genetically-and environmentally-dependent processes drive interspecific and intraspecific divergence in the Chinese relict endemic genus Dipteronia

China is a hotspot of relict plant species that were once widespread throughout the Northern Hemisphere.Recent research has demonstrated that the occurrence of long-term stable refugia in the mountainous regions of central and south-western China allowed their persistence through the late Neogene climate fluctuations.One of these relict lineages is Dipteronia,an oligotypic tree genus with a fossil record extending to the Paleocene.Here,we investigated the genetic variability,demographic dynamics and diversification patterns of the two currently recognized Dipteronia species(Dipteronia sinensis and D.dyeriana).Molecular data were obtained from 45 populations of Dipteronia by genotyping three cpDNA regions,two single copy nuclear genes and 15 simple sequence repeat loci.The genetic study was combined with niche comparison analyses on the environmental space,ecological niche modeling,and landscape connectivity analysis.We found that the two Dipteronia species have highly diverged both in genetic and ecological terms.Despite the incipient speciation processes that can be observed in D.sinensis,the occurrence of long-term stable refugia and,particularly,a dispersal corridor along Daba Shan-west Qinling,likely ensured its genetic and ecological integrity to date.Our study will not only help us to understand how populations of Dipteronia species responded to the tectonic and climatic changes of the Cenozoic,but also provide insight into how Arcto-Tertiary relict plants in East Asia survived,evolved,and diversified.

Evaluating soil acidification risk and its effects on biodiversity–ecosystem multifunctionality relationships in the drylands of China

Background:Soil acidifcationn caused by anthropogenic activities may aft soil biochemical cydling,bidiversity,productivity,and multiple eosystem-related functions in drylands.However,to date,such information is lacking to support this hypothesis.Methods Based on a transect survey of 78 naturally assembled shrub communities,we caloulated acid deposition flux in Northwest China and evaluated its likely ecological ffets by testing three altemnative hypotheses,namely:.nidche complementarity,mass ratio,and vegetation quantity hypotheses Rao's quadratic entopy and community-weighted mean traits were employed to represent the complementary aspect of niche complementarity and mass ratio effects,respectively.Resulbs:We observed that in the past four decades,the concentrations of exchangeable base cations in soil in Northwest China have decreased significantly to the extent of having faced the risk of depletion,whereas changes in the calium carbonate content and pH of soil were not significant.Adid deposition primani ly increased the aboweground biomass and shrub density in shrublands but had no sigmificant effect on shrub richness and ecasystem multifunctionality(EMF),indicating that acid deposition had positive but weak ecological effects on dryland ecosystems.Community wd ghted mean of functional traits(representing the mass ratio hypothesis)correlated negatively with EMF,whereas both Rao's quadratic entropy(representing the niche complementarity hypothesis)and aboveground biomass(representing the vegetation quantity hypothesis)correlated positively but insignifcantly with EMF.These biodiversity-EMF relationships highlight the fragility and instability of drylands relative to forest ecasystems.Concuions:The findings from this study serve as important reference points to understand the ris of soil acidification in arid regions and its impacts on biodiversity-EMF relationships.

Woody plant taxonomic,functional,and phylogenetic diversity decrease along elevational gradients in Andean tropical montane forests:Environmental filtering and arrival of temperate taxa

Mountains are paramount for exploring biodiversity patterns due to the mosaic of topographies and climates encompassed over short distances.Biodiversity research has traditionally focused on taxonomic diversity when investigating changes along elevational gradients,but other facets should be considered.For first time,we simultaneously assessed elevational trends in taxonomic,functional,and phylogenetic diversity of woody plants in Andean tropical montane forests and explored their underlying ecological and evolutionary causes.This investigation covered four transects(traversing ca.2200 m a.s.l.) encompassing 114 plots of 0.1 ha across a broad latitudinal range(ca.10°).Using Hill numbers to quantify abundance-based diversity among 37,869 individuals we observed a consistent decrease in taxonomic,functional,and phylogenetic diversity as elevation increased,although the decrease was less pronounced for higher Hill orders.The exception was a slight increase in phylogenetic diversity when dominant species were over-weighted.The decrease in taxonomic and functional diversity might be attributed to an environmental filtering process towards highlands,where the increasingly harsher conditions exclude species and functional strategies.Besides,the differences in steepness decrease between Hill orders suggest that rare species disproportionately contribute to functional diversity.For phylogenetic diversity the shifting elevational trend between Hill orders indicates a greater than previously considered influence in central Andean highlands of tropical lowlands originated species with strong niche conservatism relative to distantly related temperate lineages.This could be explained by a decreasing presence and abundance of temperate,extratropical taxa towards the central Andes relative to northern or southern Andes,where they are more prevalent.

Projected impacts of climate change and anthropogenic effects on habitat distribution of endangered Javan Hawk-Eagle in Indonesia

Changing climate will jeopardize biodiversity,particularly the geographic distribution of endemic species.One such species is the Javan Hawk-Eagle(JHE,Nisaetus bartelsi),a charismatic raptor found only on Java Island,Indonesia.Thus,it is crucial to develop an appropriate conservation strategy to preserve the species.Ecological niche modeling is considered a valuable tool for designing conservation plans for the JHE.We provide an ecological niche modeling approach and transfer its model to future climate scenarios for the JHE.We utilize various machine learning algorithms under sustainability and business-as-usual(BAU)scenarios for 2050.Additionally,we investigate the conservation vulnerability of the JHE,capturing multifaceted pressures on the species from climate dissimilarities and human disturbance variables.Our study reveals that the ensemble model performs exceptionally well,with temperature emerging as the most critical factor affecting the JHE distribution.This finding indicates that climate change will have a significant impact on the JHE species.Our results suggest that the JHE distribution will likely decrease by 28.41%and 40.16%from the current JHE distribution under sustainability and BAU scenarios,respectively.Furthermore,our study reveals high-potential refugia for future JHE,covering 7,596 km^(2)(61%)under the sustainability scenario and only 4,403 km^(2)(35%)under the BAU scenario.Therefore,effective management and planning,including habitat restoration,refugia preservation,habitat connectivity,and local community inclusivity,should be well-managed to achieve JHE conservation targets.