Evolutionary Patterns Research Articles

Comparative anatomy and evolution of the atlantoaxial complex in the fossorial lineage Amphisbaenia (Squamata: Lacertoidea).

The atlas and axis are the first two vertebrae from the cervical series; these two vertebrae are responsible for neck flexion, extension, and rotation movements, while providing insertion points for muscles and tendons. Amphisbaenia is a group of fossorial squamates known for having four distinctive head shapes, which are related to different excavation methods. However, little is known about the relationship between these different digging patterns and the anatomy and evolution of the atlantoaxial complex. In this study, we used computed microtomography data to describe in detail of the atlantoaxial complex for 15 species, belonging to all six current families of Amphisbaenia. Furthermore, we evaluate evolutionary scenarios of selected characters related to the atlantoaxial complex in the most recent phylogeny for Amphisbaenia, using the criteria of parsimony and maximum likelihood. Our results indicate that the evolutionary pattern of the atlantoaxial complex presents a diversification in its morphology that is not always correlated with the shape of the head. This analysis reinforces the hypothesis of remarkable morphological convergences in the evolutionary history of Amphisbaenia. Additionally, some of the characters studied may represent independent evolution through convergence in some cases (e.g., horizontal axis of the neural column) and parallelism in others (e.g., present or absent from the transverse process).

Draft Genome Sequence of Candida saopaulonensis from a Very Premature Infant with Sepsis.

The rare fungus Candida saopaulonensis has never been reported to be associated with human infection. We report the draft genome sequence of the first clinical isolate of C. saopaulonensis, which was isolated from a very premature infant with sepsis. This is the first genome assembly reaching the near-complete chromosomal level with structural annotation for this species, opening up avenues for exploring evolutionary patterns and genetic mechanisms of pathogenesis.

Multi-Scenario Simulation and Eco-Environmental Effects Analysis of Land Use/Cover Change in China by an Integrated Cellular Automata and Markov Model

Land use transitions play a critical role in ecological environmental restoration, but they are also plagued by ecological environmental problems caused by excessive land resource development. In this study, we propose a methodological framework for unveiling the nexus profile of land use/cover change (LUCC) and eco-environmental effects. This study explored the spatiotemporal evolution patterns of LUCC over a long time series based on high-precision land use data from 1990 to 2020. Then, the ecological values (EVs) of various cities were calculated to obtain the ecological contribution rate of different land use types in the process of change. Finally, the future development trends of land use and ecological environmental quality were predicted under multiple scenarios using the cellular automata–Markov model, and scientific policy recommendations were proposed. The results showed that the expansion trajectory of the construction land in the urban agglomeration mainly expanded inwards along the mouth of the Pearl River, and the conversion of cultivated land to construction land was the most significant type of land use change. The overall ecological environmental quality of the study area showed a downwards trend, with Shenzhen exhibiting the largest decrease in EVs. Cultivated land contributed significantly to improving regional ecological environmental quality, while the land use transition types with relatively large contributions to environmental quality deterioration were conversions to construction land. Under the scenario of coordinated protection, the degree of cultivated land area reduction was significantly reduced, and the area of forestland showed a positive growth trend, with the expansion trend of construction land being reversed. These research findings can enrich the theoretical research on the sustainable development of urban agglomerations and provide reliable data support for policy-making.

Molecular phylogeny and biogeography of the aquatic dance fly subfamily Clinocerinae (Diptera: Empididae)

AbstractThis study presents the first molecular phylogenetic analysis of the Clinocerinae, challenging the traditionally accepted monophyly of this subfamily. DNA was extracted from fresh and museum specimens representing all biogeographical regions. Maximum likelihood (ML) and Bayesian inference (BI) phylogenetic analyses were performed based on sequences from two mitochondrial genes, cytochrome c oxidase subunit I (COI) and cytochrome β, and three nuclear genes, carbomoylphosphate synthase domain of rudimentary, elongation factor‐1α and isocitrate dehydrogenase. Through molecular data and morphological examination, our results reveal a division within Clinocerinae, distinguishing ‘typical’ or Clinocerinae (s.s.) from several genera, specifically Afroclinocera Sinclair, Asymphyloptera Collin and Proagomyia Collin, possibly lending support for a reclassification of these genera outside Clinocerinae. Bergenstammia Mik is proposed as a junior synonym of Phaeobalia Mik, syn. n., and the following new combinations are recognized: Phaeobalia albanica (Wagner) comb. n., Phaeobalia aurinae (Pusch & Wagner) comb. n., Phaeobalia carniolica (Horvat) comb. n., Phaeobalia frigida (Vaillant) comb. n., Phaeobalia glacialis (Palaczyk & Słowińska) comb. n., Phaeobalia multiseta (Strobl) comb. n., Phaeobalia nudimana (Vaillant) comb. n., Phaeobalia nudipes (Loew) comb. n., Phaeobalia pulla (Vaillant & Wagner) comb. n., Phaeobalia pyrenaica (Vaillant & Vinçon) comb. n., Phaeobalia slovaca (Wagner) comb. n. and Phaeobalia thomasi (Vaillant & Vinçon) comb. n. Re‐evaluation of the genus Roederiodes resulted in the following new combinations: Clinocerella macedonicus (Wagner & Horvat) comb. n. and Clinocerella montenegrinus (Wagner & Horvat) comb. n. The origins of Clinocerinae (s.s.) are traced back to the Holarctic region, Laurasian origin, with a likely complex history of dispersal events into the Southern Hemisphere. Based on current knowledge, the greatest generic and species richness is confined to the Palaearctic Region. These findings provide valuable insights into the evolutionary relationships and distribution patterns of Clinocerinae (s.s.), challenging existing taxonomic classifications and shedding light on their historical biogeography.

Novelties and Perspectives of Intestinal Ultrasound in the Personalised Management of Patients with Inflammatory Bowel Diseases—A Systematic Review

Inflammatory bowel diseases (IBDs) affect over 4.9 million individuals worldwide. Colonoscopy (CS) is the gold-standard technique for diagnosis. The remissive–recurrent pattern of evolution raises the need for non-invasive techniques to monitor disease activity. This review aims to present the advantages of intestinal ultrasound (IUS) in managing IBDs. Our search was conducted on the PubMed, Embase, and Cochrane (CENTRAL) databases, selecting original studies comparing IUS with other imaging and invasive monitoring methods. Our search yielded 8654 results, of which 107 met the inclusion criteria. Increased bowel wall thickness (BWT) and colour Doppler signal (CDS) are discriminative for disease activity. IUS can predict disease outcomes and detect response to treatment or postoperative recurrence. Contrast-enhanced ultrasound (CEUS) and elastography help differentiate fibrotic from inflammatory stenoses. The difficult rectal assessment limits the use of IUS in ulcerative colitis (UC). Transmural healing may develop as a therapeutic target as it is associated with better outcomes. Patients are compliant with this technique, and its results correlate well with CS and other imaging methods. In conclusion, IUS proves to be essential in assessing IBD activity and treatment response, predicting outcomes and detecting complications. CEUS and elastography are researched to improve the diagnostic values of IUS.

Transcriptome-wide expression landscape and starch synthesis pathway co-expression network in sorghum.

The gene expression landscape across different tissues and developmental stages reflects their biological functions and evolutionary patterns. Integrative and comprehensive analyses of all transcriptomic data in an organism are instrumental to obtaining a comprehensive picture of gene expression landscape. Such studies are still very limited in sorghum, which limits the discovery of the genetic basis underlying complex agricultural traits in sorghum. We characterized the genome-wide expression landscape for sorghum using 873 RNA-sequencing (RNA-seq) datasets representing 19 tissues. Our integrative analysis of these RNA-seq data provides the most comprehensive transcriptomic atlas for sorghum, which will be valuable for the sorghum research community for functional characterizations of sorghum genes. Based on the transcriptome atlas, we identified 595 housekeeping genes (HKGs) and 2080 tissue-specific expression genes (TEGs) for the 19 tissues. We identified different gene features between HKGs and TEGs, and we found that HKGs have experienced stronger selective constraints than TEGs. Furthermore, we built a transcriptome-wide co-expression network (TW-CEN) comprising 35 modules with each module enriched in specific Gene Ontology terms. High-connectivity genes in TW-CEN tend to express at high levels while undergoing intensive selective pressure. We also built global and seed-preferential co-expression networks of starch synthesis pathways, which indicated that photosynthesis and microtubule-based movement play important roles in starch synthesis. The global transcriptome atlas of sorghum generated by this study provides an important functional genomics resource for trait discovery and insight into starch synthesis regulation in sorghum.

Chloroplast genome structure analysis of Equisetum unveils phylogenetic relationships to ferns and mutational hotspot region

Equisetum is one of the oldest extant group vascular plants and is considered to be the key to understanding vascular plant evolution. Equisetum is distributed almost all over the world and has a high degree of adaptability to different environments. Despite the fossil record of horsetails (Equisetum, Equisetaceae) dating back to the Carboniferous, the phylogenetic relationship of this genus is not well, and the chloroplast evolution in Equisetum remains poorly understood. In order to fill this gap, we sequenced, assembled, and annotated the chloroplast genomes of 12 species of Equisetum, and compared them to 13 previously published vascular plants chloroplast genomes to deeply examine the plastome evolutionary dynamics of Equisetum. The chloroplast genomes have a highly conserved quadripartite structure across the genus, but these chloroplast genomes have a lower GC content than other ferns. The size of Equisetum plastomes ranges from 130,773 bp to 133,684 bp and they encode 130 genes. Contraction/expansion of IR regions and the number of simple sequences repeat regions underlie large genomic variations in size among them. Comparative analysis revealed we also identified 13 divergence hotspot regions. Additionally, the genes accD and ycf1 can be used as potential DNA barcodes for the identification and phylogeny of the genus Equisetum. Twelve photosynthesis-related genes were specifically selected in Equisetum. Comparative genomic analyses implied divergent evolutionary patterns between Equisetum and other ferns. Phylogenomic analyses and molecular dating revealed a relatively distant phylogenetic relationship between Equisetum and other ferns, supporting the division of pteridophyte into Lycophytes, Equisetaceae and ferns. The results show that the chloroplast genome can be used to solve phylogenetic problems within or between Equisetum species, and also provide genomic resources for the study of Equisetum systematics and evolution.

Inventory, Dynamic Evolution, and Scenario Projections of Agricultural Carbon Emissions in Shandong Province, China

The reduction in agricultural carbon emissions (ACEs) in Shandong Province is essential to China’s carbon peak and carbon neutrality objectives. In this regard, we constructed an ACE inventory for Shandong Province at a resolution of 1 km × 1 km, integrating the emission factor method with geographic information system (GIS) technology. Building upon this, we explored the dynamic evolution patterns of ACEs using kernel density estimation and conditional probability density estimation. Additionally, long short-term memory networks were trained to predict ACEs under various scenarios. The results showed that: (1) ACEs in Shandong Province exhibited two stages of change, i.e., “rise and decline”. Notably, 64.39% of emissions originated from the planting industry. The distribution of emissions was closely correlated with regional agricultural production modes. Specifically, CO2 emissions were predominantly distributed in crop cultivation areas, while CH4 and N2O emissions were primarily distributed in livestock breeding areas. The uncertainty of the emission inventory ranged from −12.04% to 10.74%, mainly caused by emission factors. (2) The ACE intensity of various cities in Shandong Province is decreasing, indicating a decoupling between ACEs and agricultural economic growth. Furthermore, the emission disparities among different cities are diminishing, although significant spatial non-equilibrium still persists. (3) From 2022 to 2030, the ACEs in Shandong Province will show a continuous downward trend. By 2030, the projected values under the baseline scenario, low-carbon scenario I, and low-carbon scenario II will be 6301.74 × 104 tons, 5980.67 × 104 tons, and 5850.56 × 104 tons. The low-carbon scenario reveals greater potential for ACE reduction while achieving efficient rural economic development and urbanization simultaneously. This study not only advances the methodology of the ACE inventory but also provides quantitative references and scientific bases for promoting low-carbon, efficient, and sustainable regional agriculture.

Unveiling kiwifruit TCP genes: evolution, functions, and expression insights

ABSTRACT The TEOSINTE-BRANCHED1/CYCLOIDEA/PROLEFERATING-CELL-FACTORS (TCP) gene family is a plant-specific transcriptional factor family involved in leaf morphogenesis and senescence, lateral branching, hormone crosstalk, and stress responses. To date, a systematic study on the identification and characterization of the TCP gene family in kiwifruit has not been reported. Additionally, the function of kiwifruit TCPs in regulating kiwifruit responses to the ethylene treatment and bacterial canker disease pathogen (Pseudomonas syringae pv. actinidiae, Psa) has not been investigated. Here, we identified 40 and 26 TCP genes in Actinidia chinensis (Ac) and A. eriantha (Ae) genomes, respectively. The synteny analysis of AcTCPs illustrated that whole-genome duplication accounted for the expansion of the TCP family in Ac. Phylogenetic, conserved domain, and selection pressure analysis indicated that TCP family genes in Ac and Ae had undergone different evolutionary patterns after whole-genome duplication (WGD) events, causing differences in TCP gene number and distribution. Our results also suggested that protein structure and cis-element architecture in promoter regions of TCP genes have driven the function divergence of duplicated gene pairs. Three and four AcTCP genes significantly affected kiwifruit responses to the ethylene treatment and Psa invasion, respectively. Our results provided insight into general characters, evolutionary patterns, and functional diversity of kiwifruit TCPs.

Evolution of Pore Spaces in Marine Organic-Rich Shale: Insights from Multi-Scale Analysis of a Permian–Pennsylvanian Sample

The quantitative evolution pattern of pore space and genetic pore types along the maturation process in organic-rich shale reservoirs is unclear, which affects the assessment of shale storage capacity and petroleum production. A black shale outcrop sample from Kansas that is of Permian–Pennsylvanian age was collected and subjected to thermal simulation experiments at 10 different maturity stages to understand the pore sizes and pore types. Scanning electron microscopy (SEM) and image processing were used to characterize the full-scale pore-size distribution and volume evolution of this shale sample by combining low-temperature gas (CO2 and N2) physisorption and mercury intrusion porosimetry (MIP) in order to discuss the effects of hydrocarbon generation and diagenesis (HG&D) on pore development at different pore sizes. The study showed that the original shale sample is dominated by slit-like pores, with mainly organic matter (OM) pores distributed in 0–100 nm, intraparticle pores (Intra-P) of clays distributed in 30–100 nm, and interparticle pores (Inter-P) distributed in 100–1000 nm. With the increase in maturity or Ro, the OM pores increased gradually, and the OM pore-size distribution diverged to the two poles. In the oil generation stage, the OM pores were distributed in the range of 30–100 nm, while in the gas generation stage, the OM-hosted pores were mainly distributed in the range of 10–20 nm and 100–500 nm. Further into the over-maturity stage, the OM pores were mainly distributed in the range of 0–10 nm and >100 nm. The pore volume distribution across the whole pore sizes showed that the pore volume of low-maturity shale samples was mainly provided by 100–1000 nm (macropores), and the pore volumes of 0–2 nm, 30–100 nm and 1000+ nm pores gradually increase with increasing thermal maturity, with the final pore-size distribution having four peaks at 0–2, 30–100, 500–1000 nm, and 10–100 µm. Hydrocarbon generation mainly affects the pore volume in the 0–2 nm and 100–1000 nm intervals, with a positive correlation. The 2–30 nm and 30–100 nm pores were likely controlled by diagenesis, such as mineral transformation, illitization, and cementation during the maturation process.

Evolution of H6N6 viruses in China between 2014 and 2019 involves multiple reassortment events

H6N6 avian influenza viruses (AIVs) have been widely detected in wild birds, poultry, and even mammals. Recently, H6N6 viruses were reported to be involved in the generation of H5 and H7 subtype viruses. To investigate the emergence, evolutionary pattern, and potential for an epidemic of H6N6 viruses, the complete genomes of 198 H6N6 viruses were analyzed, including 168 H6N6 viruses deposited in the NCBI and GISAID databases from inception to January 2019 and 30 isolates collected from China between November 2014 and January 2019. Using phylogenetic analysis, the 198 strains of H6N6 viruses were identified as 98 genotypes. Molecular clock analysis indicated that the evolution of H6N6 viruses in China was constant and not interrupted by selective pressure. Notably, the laboratory isolates reassorted with six subtype viruses: H6N2, H5N6, H7N9, H5N2, H4N2, and H6N8, resulting in nine novel H6N6 reassortment events. These results suggested that H6N6 viruses can act as an intermediary in the evolution of H5N6, H6N6, and H7N9 viruses. Animal experiments demonstrated that the 10 representative H6N6 viruses showed low pathogenicity in chickens and were capable of infecting mice without prior adaptation. Our findings suggest that H6N6 viruses play an important role in the evolution of AIVs, and it is necessary to continuously monitor and evaluate the potential epidemic of the H6N6 subtype viruses.

Modeling and optimization of networked evolutionary game based on incomplete information with switched topologies

AbstractIn the realm of evolutionary game theory, the majority of scenarios involve players with incomplete knowledge, specially regarding their opponents' actions and payoffs compounded by the ever‐shifting landscape of players' interactions. These dynamics present formidable challenges in both the analysis and optimization of game evolution. To address this, a novel model named the networked evolutionary game (NEG) is proposed based on incomplete information with switched topologies. This model captures situations where players possess limited insight into their opponents' benefits, yet make decisions based on their own payoffs while adapting to different networks and new players. To bridge the gap between incomplete and complete information games, R. Selten's transformation method is leveraged, a renowned approach that converts an incomplete information game into an interim agent game, thereby establishing the equivalence of pure Nash equilibria (NE) in both scenarios. Employing the semi‐tensor product (STP) of matrices, a powerful tool in logistic system, the evolution of the model is articulated through algebraic relationships. This enables to unravel the patterns of game evolution and identify the corresponding pure Nash equilibria. By introducing control players, strategically positioned within the game, optimized control is facilitated over the evolutionary trajectory, ultimately leading to convergence towards an optimal outcome. Finally, these concepts are illustrated with a practical example within the paper.

Single-Cell DNA Sequencing Reveals an Evolutionary Pattern of CHIP in Transplant Eligible Multiple Myeloma Patients

Clonal hematopoiesis of indeterminate potential (CHIP) refers to the phenomenon where a hematopoietic stem cell acquires fitness-increasing mutation(s), resulting in its clonal expansion. CHIP is frequently observed in multiple myeloma (MM) patients, and it is associated with a worse outcome. High-throughput amplicon-based single-cell DNA sequencing was performed on circulating CD34+ cells collected from twelve MM patients before autologous stem cell transplantation (ASCT). Moreover, in four MM patients, longitudinal samples either before or post-ASCT were collected. Single-cell sequencing and data analysis were assessed using the MissionBio Tapestri® platform, with a targeted panel of 20 leukemia-associated genes. We detected CHIP pathogenic mutations in 6/12 patients (50%) at the time of transplant. The most frequently mutated genes were TET2, EZH2, KIT, DNMT3A, and ASXL1. In two patients, we observed co-occurring mutations involving an epigenetic modifier (i.e., DNMT3A) and/or a gene involved in splicing machinery (i.e., SF3B1) and/or a tyrosine kinase receptor (i.e., KIT) in the same clone. Longitudinal analysis of paired samples revealed a positive selection of mutant high-fitness clones over time, regardless of their affinity with a major or minor sub-clone. Copy number analysis of the panel of all genes did not show any numerical alterations present in stem cell compartment. Moreover, we observed a tendency of CHIP-positive patients to achieve a suboptimal response to therapy compared to those without. A sub-clone dynamic of high-fitness mutations over time was confirmed.

Bears into the Niche-Space: Phylogeography and Phyloclimatic Model of the Family Ursidae

Assessing niche evolution remains an open question and an actively developing area of study. The family Ursidae consists of eight extant species for which, despite being the most studied family of carnivores, little is known about the influence of climate on their evolutionary history and diversification. We evaluated their evolutionary patterns based on a combined phylogeography and niche modeling approach. We used complete mitogenomes, estimated divergence times, generated ecological niche models and applied a phyloclimatic model to determine the species evolutionary and diversification patterns associated with their respective environmental niches. We inferred the family evolutionary path along the environmental conditions of maximum temperature and minimum precipitation, from around 20 million years ago to the present. Our findings show that the phyloclimatic niches of the bear species occupy most of the environmental space available on the planet, except for the most extreme warm conditions, in accordance with the wide geographic distribution of Ursidae. Moreover, some species exhibit broader environmental niches than others, and in some cases, they explore precipitation axes more extensively than temperature axes or vice versa, suggesting that not all species are equally adaptable to these variables. We were able to elucidate potential patterns of niche conservatism and evolution, as well as niche overlapping, suggesting interspecific competitive exclusion between some of the bear species. We present valuable insights into the ecological and evolutionary processes driving the diversification and distribution of the Ursidae. Our approach also provides essential information for guiding effective conservation strategies, particularly in terms of distribution limits in the face of climate change.

Origin, evolution, and diversification of inositol 1,4,5-trisphosphate 3-kinases in plants and animals.

In Eukaryotes, inositol polyphosphates (InsPs) represent a large family of secondary messengers and play crucial roes in various cellular processes. InsPs are synthesized through a series of pohophorylation reactions catalyzed by various InsP kinases in a sequential manner. Inositol 1,4,5-trisphosphate 3-kinase (IP3 3-kinase/IP3K), one member of InsP kinase, plays important regulation roles in InsPs metabolism by specifically phosphorylating inositol 1,4,5-trisphosphate (IP3) to inositol 1,3,4,5-tetrakisphosphate (IP4) in animal cells. IP3Ks were widespread in fungi, plants and animals. However, its evolutionary history and patterns have not been examined systematically. A total of 104 and 31 IP3K orthologues were identified across 57 plant genomes and 13 animal genomes, respectively. Phylogenetic analyses indicate that IP3K originated in the common ancestor before the divergence of fungi, plants and animals. In most plants and animals, IP3K maintained low-copy numbers suggesting functional conservation during plant and animal evolution. In Brassicaceae and vertebrate, IP3K underwent one and two duplication events, respectively, resulting in multiple gene copies. Whole-genome duplication (WGD) was the main mechanism for IP3K duplications, and the IP3K duplicates have experienced functional divergence. Finally, a hypothetical evolutionary model for the IP3K proteins is proposed based on phylogenetic theory. Our study reveals the evolutionary history of IP3K proteins and guides the future functions of animal, plant, and fungal IP3K proteins.

Immune cell-related prognostic risk model and tumor immune environment modulation in esophageal carcinoma based on single-cell and bulk RNA sequencing.

Immune cells play a pivotal role in the tumor microenvironment, exerting significant influence on tumor progression and patient outcomes, but the current biomarkers are insufficient to fully capture the complex and diverse tumor immune microenvironment and the impact of immunotherapy. The advent of single-cell sequencing allows us to explore the tumor microenvironment at an unprecedented resolution, enabling the identification and characterization of distinct subsets of immune cells, thereby paving the way for the development of prognostic models using immune cells. Leveraging single-cell data, our study deeply investigated the intricacies of immune microenvironment heterogeneity in esophageal carcinoma. We elucidated the composition, functionality, evolution, and intercellular communication patterns of immune cells, culminating in the construction of an independent prognostic model at the single-cell level. Furthermore, we conducted a comprehensive analysis of disparities in immune infiltration and immune checkpoint expression between patients categorized into high- and low-risk groups, which may impact patient prognosis. In summary, our study harnessed multiomics data to delineate the immune profile of esophageal carcinoma patients, provide a method for leveraging molecular signatures of immune cells to identify potential biomarkers, while concurrently providing evidence for the potential benefits of immunotherapy.

Is RNA editing truly absent in the complex thalloid liverworts (Marchantiopsida)? Evidence of extensive RNA editing from Cyathodium cavernarum.

RNA editing is a crucial modification in plants' organellar transcripts that converts cytidine to uridine (C-to-U; and sometimes uridine to cytidine) in RNA molecules. This post-transcriptional process is controlled by the PLS-class protein with a DYW domain, which belongs to the pentatricopeptide repeat (PPR) protein family. RNA editing is widespread in land plants; however, complex thalloid liverworts (Marchantiopsida) are the only group reported to lack both RNA editing and DYW-PPR protein. The liverwort Cyathodium cavernarum (Marchantiopsida, Cyathodiaceae), typically found in cave habitats, was newly found to have 129 C-to-U RNA editing sites in its chloroplast and 172 sites in its mitochondria. The Cyathodium genus, specifically C. cavernarum, has a large number of PPR editing factor genes, including 251 DYW-type PPR proteins. These DYW-type PPR proteins may be responsible for C-to-U RNA editing in C. cavernarum. Cyathodium cavernarum possesses both PPR DYW proteins and RNA editing. Our analysis suggests that the remarkable RNA editing capability of C. cavernarum may have been acquired alongside the emergence of DYW-type PPR editing factors. These findings provide insight into the evolutionary pattern of RNA editing in land plants.

The Spatiotemporal Variation Characteristics and Influencing Factors of Green Vegetation in China

Green vegetation is one of the main objects of ecological environment restoration and protection, objectively reflecting the quality of regional ecological environments. Studying its spatial distribution characteristics is of great significance to the formulation of ecological environment restoration policies. Based on data on urban green vegetation in China from 2000 to 2022, this study attempts to analyze the destruction and protection patterns of urban green vegetation in China from the perspectives of total changes in green vegetation contraction and growth and spatial evolution characteristics and trends, and it explores the driving factors affecting the change in green vegetation area. The results show the following: (1) Green vegetation growth and contraction occurred alternately in China from 2000 to 2022. Vegetation contraction showed a “point–line–plane” evolution pattern, forming a contraction stage of point-like aggregation, linear series, and planar spread. Vegetation growth has always presented a frontal pattern. (2) The growth and contraction of green vegetation in China showed a north–south differentiation phenomenon. The vegetation contraction phenomenon spread in the Central Plains urban agglomeration and its surrounding areas and showed an expanding trend. The growth trend is obviously moving northward, mainly concentrated in Inner Mongolia, Ningxia, Gansu, Xinjiang, and other northern provinces, which also coincides with the key ecological restoration policies in northern China in recent years. (3) City scale, economic level, population scale, agro-industrial structure, and water resources content have significant effects on the spatial distribution of green vegetation.

A state estimation method based on CNN-LSTM for ball screw

Ball screw is widely used in the engineering field, and accurate estimation of their state is crucial for the reliability of system operation. However, existing methods often overlook the time series characteristics and spatial correlation of vibration signals, unable to provide complete degradation information and divide the degradation process, resulting in limited prediction accuracy. Therefore, a state estimation method for ball screw based on Convolutional Neural Networks (CNN) and Long Short-Term Memory Neural Networks (LSTM) is proposed. An experiment of ball screw transmission equipment was conducted to collect vibration signals throughout the entire life cycle and verify the proposed method. Firstly, the frequency domain amplitude signal of the transformed ball screw is normalized to eliminate scale differences, which serves as the input for CNN feature extraction. Then, these deep features are input into the LSTM network to capture the fault evolution patterns that reveal the degradation of ball screw performance, and achieve accurate estimation of ball screw state. The final prediction accuracy was 97.87%, verifying the effectiveness of the proposed method.

Exploring evolutionary trajectories in ovarian cancer patients by longitudinal analysis of ctDNA.

We analysed whether temporal heterogeneity of ctDNA encodes evolutionary patterns in ovarian cancer. Targeted sequencing of 275 cancer-associated genes was performed in a primary tumor biopsy and in ctDNA of six longitudinal plasma samples from 15 patients, using the Illumina platform. While there was low overall concordance between the mutational spectrum of the primary tumor biopsies vs. ctDNA, TP53 variants were the most commonly shared somatic alterations. Up to three variant clusters were detected in each tumor biopsy, likely representing predominant clones of the primary tumor, most of them harbouring a TP53 variant. By tracing these clusters in ctDNA, we propose that liquid biopsy may allow to assess the contribution of ancestral clones of the tumor to relapsed abdominal masses, revealing two evolutionary patterns. In pattern#1, clusters detected in the primary tumor biopsy were likely relapse seeding clones, as they contributed a major share to ctDNA at relapse. In pattern#2, similar clusters were present in tumors and ctDNA; however, they were entirely cleared from liquid biopsy after chemotherapy and were undetectable at relapse. ctDNA private variants were present among both patterns, with some of them mirroring subclonal expansions after chemotherapy. We demonstrate that tracing the temporal heterogeneity of ctDNA, even below exome scale resolution, deciphers evolutionary trajectories in ovarian cancer. Furthermore, we describe two evolutionary patterns that may help to identify relapse seeding clones for targeted therapy.