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.

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.

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.

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).

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.

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.

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.

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.

Colorectal cancer and dormant metastases:Put to sleep or destroy?

After reading the review by An et al“Biological factors driving colorectal cancer metastasis”,which covers the problem of the metastasis of colorectal cancer(CRC),I had a desire to discuss with readers one of the exciting problems associated with dormant metastases.Most deaths from CRCs are caused by metastases,which can be detected both at diagnosis of the primary tumor and several years or even decades after treatment.This is because tumor cells that enter the bloodstream can be destroyed by the immune system,cause metastatic growth,or remain dormant for a long time.Dormant tumor cells may not manifest themselves throughout a person’s life or,after some time and under appropriate conditions,may give rise to the growth of metastases.In this editorial,we will discuss the most important features of dormant metastases and the mechanisms of premetastatic niche formation,as well as factors that contribute to the activation of dormant metastases in CRCs.We will pay special attention to the possible mechanisms involved in the formation of circulating tumor cell complexes and the choice of therapeutic strategies that promote the dormancy or destruction of tumor cells in CRCs.

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.

Unveiling the role of hypoxia-inducible factor 2alpha in osteoporosis:Implications for bone health

BACKGROUND Osteoporosis(OP)has become a major public health problem worldwide.Most OP treatments are based on the inhibition of bone resorption,and it is necessary to identify additional treatments aimed at enhancing osteogenesis.In the bone marrow(BM)niche,bone mesenchymal stem cells(BMSCs)are exposed to a hypoxic environment.Recently,a few studies have demonstrated that hypoxiainducible factor 2alpha(HIF-2α)is involved in BMSC osteogenic differentiation,but the molecular mechanism involved has not been determined.AIM To investigate the effect of HIF-2αon the osteogenic and adipogenic differentiation of BMSCs and the hematopoietic function of hematopoietic stem cells(HSCs)in the BM niche on the progression of OP.METHODS Mice with BMSC-specific HIF-2αknockout(Prx1-Cre;Hif-2αfl/fl mice)were used for in vivo experiments.Bone quantification was performed on mice of two genotypes with three interventions:Bilateral ovariectomy,semilethal irradiation,and dexamethasone treatment.Moreover,the hematopoietic function of HSCs in the BM niche was compared between the two mouse genotypes.In vitro,the HIF-2αagonist roxadustat and the HIF-2αinhibitor PT2399 were used to investigate the function of HIF-2αin BMSC osteogenic and adipogenic differentiation.Finally,we investigated the effect of HIF-2αon BMSCs via treatment with the mechanistic target of rapamycin(mTOR)agonist MHY1485 and the mTOR inhibitor rapamycin.RESULTS The quantitative index determined by microcomputed tomography indicated that the femoral bone density of Prx1-Cre;Hif-2αfl/fl mice was lower than that of Hif-2αfl/fl mice under the three intervention conditions.In vitro,Hif-2αfl/fl mouse BMSCs were cultured and treated with the HIF-2αagonist roxadustat,and after 7 d of BMSC adipogenic differentiation,the oil red O staining intensity and mRNA expression levels of adipogenesis-related genes in BMSCs treated with roxadustat were decreased;in addition,after 14 d of osteogenic differentiation,BMSCs treated with roxadustat exhibited increased expression of osteogenesis-related genes.The opposite effects were shown for mouse BMSCs treated with the HIF-2αinhibitor PT2399.The mTOR inhibitor rapamycin was used to confirm that HIF-2αregulated BMSC osteogenic and adipogenic differentiation by inhibiting the mTOR pathway.Consequently,there was no significant difference in the hematopoietic function of HSCs between Prx1-Cre;Hif-2αfl/fl and Hif-2αfl/fl mice.CONCLUSION Our study showed that inhibition of HIF-2αdecreases bone mass by inhibiting the osteogenic differentiation and increasing the adipogenic differentiation of BMSCs through inhibition of mTOR signaling in the BM niche.

A Reference Vector-Assisted Many-Objective Optimization Algorithm with Adaptive Niche Dominance Relation

It is still a huge challenge for traditional Pareto-dominatedmany-objective optimization algorithms to solve manyobjective optimization problems because these algorithms hardly maintain the balance between convergence and diversity and can only find a group of solutions focused on a small area on the Pareto front,resulting in poor performance of those algorithms.For this reason,we propose a reference vector-assisted algorithmwith an adaptive niche dominance relation,for short MaOEA-AR.The new dominance relation forms a niche based on the angle between candidate solutions.By comparing these solutions,the solutionwith the best convergence is found to be the non-dominated solution to improve the selection pressure.In reproduction,a mutation strategy of k-bit crossover and hybrid mutation is used to generate high-quality offspring.On 23 test problems with up to 15-objective,we compared the proposed algorithm with five state-of-the-art algorithms.The experimental results verified that the proposed algorithm is competitive.

Suitability evaluation on marine ranching in Guangdong,South China

The ecological suitability of marine resources and environmental conditions for marine ranching in Guangdong,South China was evaluated.Niche theory was used to establish an ecological suitability evaluation model for marine ranching site selection,and suitability evaluation of marine ranching was conducted in.Results show that the ecological suitability index of marine ranching site selection was greater than 64.0 in 20 sites,including offshore Shantou Bay,offshore Zhanjiang Port,and Longdou Bay etc.,which are the priority areas for marine ranching.In other 13 sites,the ecological suitability index ranged between 8.0 and 32.0,including Houjiang Bay,Haimen Bay,and Jieshi Bay etc.,indicating the suitability for marine ranching.However,the ecological suitability index was 0 in Shantou Bay,Zhujiang(Pearl)River estuary,Huangmao Sea,Guanghai Bay,Zhanjiang Port,Qiongzhou Strait,and Anpu Port.These sites are thus unsuitable for marine ranching.This study provides a theoretical basis for site selection and planning of marine ranching in Guangdong Province.

Leaf nitrogen resorption is more important than litter nitrogen mineralization in mediating the diversity–productivity relationship along a nitrogen-limited temperate forest succession chronosequence

The resorption of nutrients by plants before litter fall and the mineralization of nutrients from plant litter by soil processes are both important pathways supporting primary productivity. While the positive relationship between plant biodiversity and primary productivity is widely accepted for natural ecosystems, the roles of nutrient resorption and mineralization in mediating that relationship remains largely unknown. Here, we quantified the relative importance of nitrogen(N) resorption and N mineralization in driving plant community N investment and the correlation between species diversity and community productivity along an N-limited successional chronosequence of the mixed broadleaved–Korean pine(Pinus koraiensis) forest in northeastern China. Leaf N resorption efficiency(NRE) at the community level increased significantly along the successional chronosequence,whereas litter N mineralization rate decreased significantly. Leaf NRE was more important than litter N mineralization rate in driving the diversity–productivity relationship. However, higher leaf NRE led to less N mineralization as succession progressed along the chronosequence. Our results highlight the importance of the N resorption pathway rather than the N mineralization pathway for forest N acquisition with community succession,and they provide mechanistic insights into the positive effects of biodiversity on ecosystem functioning. In future forest management practices, we recommend appropriate application of N fertilizer to mitigate the adverse effects of N-poor soil on seedling regeneration during late succession and thus maintain the sustainable development of temperate forest ecosystems.

Effects of functional phylogeny of light-response-related orthologous genes on seedling survival in a subtropical forest

Background: Light is an important environmental factor affecting the growth and survival of plants in forest communities. The competition for light resources and divergent responses to light may affect plant species coexistence in natural forests through niche partitioning and environmental filtering, respectively.Methods: In the present study, sequences of light-response-related functional genes were extracted from transcriptomic data of 99 tree species in a subtropical forest and average and nearest taxon phylogenetic diversity of adult(A_Apd’, A_NTpd’) and seedling neighbors(S_Apd’, S_NTpd’) around each focal seedling were calculated to evaluate effects of differentiation in light-response-related genes on community assembly processes.Results: The results showed that seedling survival was related to S_NTpd’, S_Apd’and A_Apd’of two chlorophyll ab-binding proteins involved in the assembly of photosystem Ⅱ and two genes responsive to light intensity,indicating seedlings surrounded by neighbors with distinct light responses tended to have high survival rates.Conclusions: Our results indicated that niche partitioning due to competition for light resources between plants may act as the key mechanism in determining seedling dynamics in subtropical forests.

Cellular and molecular characteristics of the premetastatic niches

The premetastatic niches(PMN)formed by primary tumor-derived molecules regulate distant organs and tissues to further favor tumor colonization.Targeted PMN therapy may prevent tumor metastasis in the early stages,which is becoming increasingly important.At present,there is a lack of in-depth understanding of the cellular and molecular characteristics of the PMN.Here,we summarize current research advances on the cellular and molecular characteristics of the PMN.We emphasize that PMN intervention is a potential therapeutic strategy for early prevention of tumor metastasis,which provides a promising basis for future research and clinical application.

Single-cell RNA sequencing in cornea research:Insights into limbal stem cells and their niche regulation

The corneal epithelium is composed of stratified squamous epithelial cells on the outer surface of the eye,which acts as a protective barrier and is critical for clear and stable vision.Its continuous renewal or wound healing depends on the proliferation and differentiation of limbal stem cells(LSCs),a cell population that resides at the limbus in a highly regulated niche.Dysfunction of LSCs or their niche can cause limbal stem cell deficiency,a disease that is manifested by failed epithelial wound healing or even blindness.Nevertheless,compared to stem cells in other tissues,little is known about the LSCs and their niche.With the advent of single-cell RNA sequencing,our understanding of LSC characteristics and their microenvironment has grown considerably.In this review,we summarized the current findings from single-cell studies in the field of cornea research and focused on important advancements driven by this technology,including the heterogeneity of the LSC population,novel LSC markers and regulation of the LSC niche,which will provide a reference for clinical issues such as corneal epithelial wound healing,ocular surface reconstruction and interventions for related diseases.