Comprehensive Tree Research Articles

Tracing the evolutionary and genetic footprints of atmospheric tillandsioids transition from land to air.

Plant evolution is driven by key innovations of functional traits that enables their survivals in diverse ecological environments. However, plant adaptive evolution from land to atmospheric niches remains poorly understood. In this study, we use the epiphytic Tillandsioideae subfamily of Bromeliaceae as model plants to explore their origin, evolution and diversification. We provide a comprehensive phylogenetic tree based on nuclear transcriptomic sequences, indicating that core tillandsioids originated approximately 11.3 million years ago in the Andes. The geological uplift of the Andes drives the divergence of tillandsioids into tank-forming and atmospheric types. Our genomic and transcriptomic analyses reveal gene variations and losses associated with adaptive traits such as impounding tanks and absorptive trichomes. Furthermore, we uncover specific nitrogen-fixing bacterial communities in the phyllosphere of tillandsioids as potential source of nitrogen acquisition. Collectively, our study provides integrative multi-omics insights into the adaptive evolution of tillandsioids in response to elevated aerial habitats.

Evolution of left–right asymmetry in side-resting (pleurothetic) bivalves: a test of genes as leaders or followers

ABSTRACT Side-resting (pleurothetic) lifestyles evolved independently many times across the Bivalvia in free-lying, byssally attached and cementing lineages. Within some species individuals lie indifferently on either their right or left side (randomly pleurothetic), whereas in others they lie consistently on one side (left-pleurothetic or right-pleurothetic). Morphological differences between valves (asymmetries) typically accompany this behaviour, so it can be studied widely across living and fossil bivalves. Because direction of asymmetry is rarely inherited in cases of random asymmetry, any evolutionary transition from randomly pleurothetic to fixed (left or right) qualifies as a case of ‘genes as followers’. Origins of left-pleurothetic or right-pleurothetic taxa directly from upright (orthothetic) ancestors would represent examples of ‘genes as leaders’. I therefore surveyed pleurothetic lifestyles across the Bivalvia. By mapping pleurothetic states onto a comprehensive phylogenetic tree that included both living and fossil families, I assessed the prevalence of these alternate modes of evolution. Various lines of evidence were also used to hypothesize phylogenetic relations within the Chamidae—the only living bivalve family exhibiting all three pleurothetic states. Randomly pleurothetic forms (direction not inherited) arose from orthothetic ancestors about half as often as fixed pleurothetic forms (direction is inherited). Unlike many other animal groups, fixed pleurothetic forms rarely arose from randomly pleurothetic ancestors, suggesting a ‘genes as leaders’ mode of evolution was most prevalent. However, many fascinating examples of randomly pleurothetic forms among Upper Ordovician and Silurian bivalves suggest that evolutionary transitions from random to fixed may have been more common. Also, randomly pleurothetic forms were short-lived in some fossil lineages, which would reduce the likelihood of them being detected. Hopefully, this preliminary analysis will motivate further study of (1) phylogenetic relations of key groups like the Chamidae, and basal Limida, Ostreida and Pterioidea, and (2) morphological variation among early members of other pleurothetic bivalve groups.

Cost-effectiveness of multigene sequencing test and treatment for metastatic non-small cell lung cancer: A unique setting in the initial adoption phase in Japan allowing testing only after standard treatment

ObjectiveTo clarify the cost-effectiveness of comprehensive diagnosis and treatment of metastatic non-small cell lung cancer in Japan, from initial diagnosis to post-standard treatment, using three different strategies. MethodsA decision tree was created using three diagnostic and treatment strategies, assuming that Foundation One CDx (F1CDx), a comprehensive genome panel, was introduced in Japan in June 2019. This comprehensive decision tree includes Markov models, cost-effectiveness analyses (CEA), and cost-utility analyses (CUA) of the three strategies from the perspective of Japanese payers. Specifically, Strategy1 involves single-gene testing at the initial diagnosis and F1CDx after standard treatment; Strategy2 involves only single-gene testing at the initial diagnosis; Strategy3 involves F1CDx at the initial diagnosis. The incremental cost-effectiveness ratios (ICERs) of the three strategies are estimated. Sensitivity analyses were performed to assess the uncertainty of the parameter settings. ResultsStrategy3 was dominated for both CUA and CEA. The ICER/quality-adjusted life year (QALY) for Strategy2 versus Strategy1 was USD 13,734 (JPY 2,080,923, USD 1 = JPY 151.39 on April 1st, 2024), which is less than the willingness to pay of USD 45,900 (JPY 7,500,000), and Strategy2 was more cost-effective than Strategy1. F1CDx was not cost-effective compared to multiple simultaneous single tests at the initial diagnosis, either after standard treatment or at the initial diagnosis. Sensitivity analysis also showed that the most influential factor on the ICER for both CEA and CUA was treatment cost. ConclusionsFrom both patient benefit and health economic perspectives, introducing F1CDx after standard treatment in June 2019 was not as cost-effective as multiple simultaneous single tests at the initial diagnosis but was more realistic from a health economic perspective than introducing F1CDx at the time of initial diagnosis. Therefore, the policy at the time of F1CDx introduction in Japan was appropriate from a short-term health-economic perspective.

Palatal groove associated with periodontal lesions: a systematic review illustrated by a decisional tree for management

BackgroundPalatal groove represents a relatively uncommon developmental root anomaly, usually found on the palatal aspect of maxillary incisors. While its origin is controversial, its presence predisposes to severe periodontal defects.AimThis study aimed to provide a systematic review of the literature focusing on the varied diagnostic techniques and treatment modalities for periodontal lesions arising from the presence of palatal groove. Based on the existing evidence and knowledge, the study also provides a comprehensive decisional tree, guiding clinicians in the challenging decision-making process face to a palatal groove.MethodsThe literature search was conducted on Medline and Cochrane databases by two independent reviewers, who also performed the screening and selection process, looking for English written articles reporting on diagnosis and management (all treatment approaches) of periodontal lesion(s) associated with a palatal groove. Based on this literature, a comprehensive decisional tree, including a standardized palatal groove evaluation and tailored treatment approaches, is proposed. Moreover, a clinical case is described to demonstrate the practical application of the developed decisional tree.ResultsOver a total of 451 articles initially identified, 34 were selected, describing 40 patients with 40 periodontal lesions associated with palatal grooves. The case report illustrates a deep, large, circumferential intra-bony defect on the palatal side of the tooth #22 associated with a shallow, moderately long palatal groove in an 18-year-old male patient. Following reevaluation, a single flap surgery was deemed necessary, combined with a regenerative procedure. At 2 years post-treatment, the tooth #22 is healthy, in a functional and esthetic position. The decision-making process, based on local and systemic patient’s conditions, should allow an early and precise diagnosis to prevent further complications and undertake an adequate treatment.ConclusionPalatal grooves are relatively rare; however, they are frequently associated with severe periodontal defects. The identification, diagnosis, prompt, and tailored management of the associated lesion is essential to mitigate potential periodontal and endodontic complications related to the presence of palatal groove.Systematic Review Registration[https://www.crd.york.ac.uk/prospero/], identifier [C CRD42022363194].

Meeting Linnean, Wallacean, and Darwinian shortfalls in global biodiversity hotspots: A model study from the Indian Himalayan Region

AbstractDespite recent efforts to make large‐scale biodiversity datasets available, several data shortfalls still exist that preclude our progress in achieving global conservation and sustainability goals. In this study, we present a comprehensive native tree dataset (1689 species) from the Indian Himalayan Region (IHR)—home to two global biodiversity hotspots—assembled from an extensive data synthesis. Based on this database, we investigate the geographic patterns and drivers of α‐ and β‐taxonomic and phylogenetic diversity of the native trees among 13 different provinces of IHR. Our results revealed a considerable variation in the α‐ and β‐taxonomic and phylogenetic diversity among the provinces of IHR, with the highest values in eastern provinces. We found phylogenetic clustering mostly in the western provinces, and phylogenetic dispersion in the eastern provinces. We found a positive correlation between the taxonomic and phylogenetic dissimilarity across the IHR. Also, the different sets of explanatory variables explained the variation of tree species richness, standardized effect size of phylogenetic diversity, net relatedness index, and nearest taxon index, with maximum contribution by temperature seasonality (Bio4). Furthermore, temperature‐related climatic distance individually explained most of the variation in the taxonomic and phylogenetic dissimilarity between the provinces of IHR. Overall, our findings unveil the patterns of taxonomic, biogeographic, and phylogenetic dimensions of tree flora in the IHR, which in turn can help in formulating scientific data‐based regional policy and conservation strategies. Looking forward, we presented a model study for bridging the Linnean, Wallacean, and Darwinian shortfalls in the globally data‐deficient biodiversity‐rich regions.

DNA polymerase swapping in Caudoviricetes bacteriophages

BackgroundViruses with double-stranded (ds) DNA genomes in the realm Duplodnaviria share a conserved structural gene module but show a broad range of variation in their repertoires of DNA replication proteins. Some of the duplodnaviruses encode (nearly) complete replication systems whereas others lack (almost) all genes required for replication, relying on the host replication machinery. DNA polymerases (DNAPs) comprise the centerpiece of the DNA replication apparatus. The replicative DNAPs are classified into 4 unrelated or distantly related families (A-D), with the protein structures and sequences within each family being, generally, highly conserved. More than half of the duplodnaviruses encode a DNAP of family A, B or C. We showed previously that multiple pairs of closely related viruses in the order Crassvirales encode DNAPs of different families.MethodsGroups of phages in which DNAP swapping likely occurred were identified as subtrees of a defined depth in a comprehensive evolutionary tree of tailed bacteriophages that included phages with DNAPs of different families. The DNAP swaps were validated by constrained tree analysis that was performed on phylogenetic tree of large terminase subunits, and the phage genomes encoding swapped DNAPs were aligned using Mauve. The structures of the discovered unusual DNAPs were predicted using AlphaFold2.ResultsWe identified four additional groups of tailed phages in the class Caudoviricetes in which the DNAPs apparently were swapped on multiple occasions, with replacements occurring both between families A and B, or A and C, or between distinct subfamilies within the same family. The DNAP swapping always occurs “in situ”, without changes in the organization of the surrounding genes. In several cases, the DNAP gene is the only region of substantial divergence between closely related phage genomes, whereas in others, the swap apparently involved neighboring genes encoding other proteins involved in phage genome replication. In addition, we identified two previously undetected, highly divergent groups of family A DNAPs that are encoded in some phage genomes along with the main DNAP implicated in genome replication.ConclusionsReplacement of the DNAP gene by one encoding a DNAP of a different family occurred on many independent occasions during the evolution of different families of tailed phages, in some cases, resulting in very closely related phages encoding unrelated DNAPs. DNAP swapping was likely driven by selection for avoidance of host antiphage mechanisms targeting the phage DNAP that remain to be identified, and/or by selection against replicon incompatibility.

Estimation of biogenic volatile organic compound (BVOC) emissions in forest ecosystems using drone-based lidar, photogrammetry, and image recognition technologies

Abstract. Biogenic volatile organic compounds (BVOCs), as a crucial component that impacts atmospheric chemistry and ecological interactions with various organisms, play a significant role in the atmosphere–ecosystem relationship. However, traditional field observation methods are challenging for accurately estimating BVOC emissions in forest ecosystems with high biodiversity, leading to significant uncertainty in quantifying these compounds. To address this issue, this research proposes a workflow utilizing drone-mounted lidar and photogrammetry technologies for identifying plant species to obtain accurate BVOC emission data. By applying this workflow to a typical subtropical forest plot, the following findings were made: the drone-mounted lidar and photogrammetry modules effectively segmented trees and acquired single wood structures and images of each tree. Image recognition technology enabled relatively accurate identification of tree species, with the highest-frequency family being Euphorbiaceae. The largest cumulative isoprene emissions in the study plot were from the Myrtaceae family, while those of monoterpenes were from the Rubiaceae family. To fully leverage the estimation results of BVOC emissions directly from individual tree levels, it may be necessary for communities to establish more comprehensive tree species emission databases and models.

Phylogeny and evolutionary timescales of the tribes Tagiadini and Celaenorrhinini (Hesperiidae, Pyrginae) inferred from mitochondrial genome and nuclear genes

AbstractTagiadini and Celaenorrhinini, two closely related groups of skippers in the subfamily Pyrginae, are mainly distributed across the Oriental, Palaearctic and African regions. While some efforts have been made to explore the phylogenetic relationships within Tagiadini and Celaenorrhinini, several unresolved issues still persist. In this study, we sequenced 13 complete mitochondrial genomes from Tagiadini and Celaenorrhinini. Additionally, we extracted nuclear genes CAD, EF‐1α, IDH, MDH, RPS5 and Wingless from the public database. Through comparative analysis, we gained insights into the structure of these newly sequenced mitogenomes. Furthermore, we constructed a comprehensive phylogenetic tree for Tagiadini and Celaenorrhinini, integrating the newly obtained mitochondrial genomes and nuclear genes with previously published mitogenomes and data from the sequence read archive (SRA). The total length of the mitochondrial genomes of the 13 skipper species ranged from 15,228 bp (Seseria sambara indosinica) to 15,431 bp (Pseudocoladenia festa). The newly sequenced genomes featured the standard set of 13 protein‐coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs) and a non‐coding A + T‐rich region implicated in replication initiation. The phylogenetic analysis encompassing all mitochondrial and nuclear gene data consistently upheld the monophyly of genera within the tribes Tagiadini and Celaenorrhinini. Most of the intergeneric relationships identified in our study agreed with recent genomic discoveries, showing enhanced nodal support values in some cases. Lastly, we estimated the divergence of the Tagiadini + Celaenorrhinini branch at approximately 44.06 million years ago (Ma) during the middle Eocene epoch. The crown ages of Tagiadini and Celaenorrhinini were estimated at approximately 41.69 Ma and 38.49 Ma, respectively.

Delving into the diversity of genus Ironus Bastian, 1865 with special reference to Ironus dentifurcatus Argo & Heyns, 1972 (Ironidae: Enoplida), collected from coal mines

Summary In the exploration of nematode diversity within the coal mine spoil of Sonebhadra district, an isolate of Ironus dentifurcatus Argo & Heyns, 1972 was collected from the soil surrounding the roots of Prosopis juliflora. This study aims to unravel taxonomic intricacies of I. dentifurcatus through analysis of morphometric data, morphological characteristics utilising both light and scanning electron microscopy, and genetic scrutiny employing the SSU 18s rDNA gene marker. The study adds valuable information to the evolutionary history of I. dentifurcatus by constructing a comprehensive phylogenetic tree. This analysis is further augmented by an exploration of phylogeography and genetic divergence within the genus Ironus Bastian, 1865. The results reveal the genetic variability within the species of Ironus and the possible adaptative radiations in the group.

Phylogeny and historical biogeography of the swallow family (Hirundinidae) inferred from comparisons of thousands of UCE loci

Swallows (Hirundinidae) are a globally distributed family of passerine birds that exhibit remarkable similarity in body shape but tremendous variation in plumage, sociality, nesting behavior, and migratory strategies. As a result, swallow species have become models for empirical behavioral ecology and evolutionary studies, and variation across the Hirundinidae presents an excellent opportunity for comparative analyses of trait evolution. Exploiting this potential requires a comprehensive and well-resolved phylogenetic tree of the family. To address this need, we estimated swallow phylogeny using genetic data from thousands of ultraconserved element (UCE) loci sampled from nearly all recognized swallow species. Maximum likelihood, coalescent-based, and Bayesian approaches yielded a well-resolved phylogenetic tree to the generic level, with minor disagreement among inferences at the species level, which likely reflect ongoing population genetic processes. The UCE data were particularly useful in helping to resolve deep nodes, which previously confounded phylogenetic reconstruction efforts. Divergence time estimates from the improved swallow tree support a Miocene origin of the family, roughly 13 million years ago, with subsequent diversification of major groups in the late Miocene and Pliocene. Our estimates of historical biogeography support the hypothesis that swallows originated in the Afrotropics and have subsequently expanded across the globe, with major in situ diversification in Africa and a secondary major radiation following colonization of the Neotropics. Initial examination of nesting and sociality indicates that the origin of mud nesting – a relatively rare nest construction phenotype in birds – was a major innovation coincident with the origin of a clade giving rise to over 40% of extant swallow diversity. In contrast, transitions between social and solitary nesting appear less important for explaining patterns of diversification among swallows.

Dynamics and timing of diversification events of ciliated eukaryotes from a large phylogenomic perspective

Ciliophora, an exceptionally diverse lineage of unicellular eukaryotes, exhibits a remarkable range of species richness across classes in the ciliate Tree of Life. In this study, we have acquired transcriptome and genome data from 40 representative species in seven ciliate classes. Utilizing 247 genes and 105 taxa, we devised a comprehensive phylogenomic tree for Ciliophora, encompassing over 60 % of orders and constituting the most extensive dataset of ciliate species to date. We established a robust phylogenetic framework that encompasses ambiguous taxa and the major classes within the phylum. Our findings support the monophyly of each of two subphyla (Postciliodesmatophora and Intramacronucleata), along with three subclades (Protocruzia, CONTHREEP, and SAPML) nested within Intramacronucleata, and elucidate evolutionary positions among the major classes within the phylum. Drawing on the robust ciliate Tree of Life and three constraints, we estimated the radiation of Ciliophora around 1175 Ma during the middle of the Proterozoic Eon, and most of the ciliate classes diverged from their sister lineage during the latter half of this period. Additionally, based on the time-calibrated tree and species richness pattern, we investigated net diversification rates of Ciliophora and its classes. The global net diversification rate for Ciliophora was estimated at 0.004979 species/Ma. Heterogeneity in net diversification rates was evident at the class level, with faster rates observed in Oligohymenophorea and Spirotrichea than other classes within the subclades CONTHREEP and SAPML, respectively. Notably, our analysis suggests that variations in net diversification rates, rather than clade ages, appear to contribute to the differences in species richness in Ciliophora at the class level.

Efficient Motif Discovery in Protein Sequences Using a Branch and Bound Algorithm.

Identifying motifs within sets of protein sequences constitutes a pivotal challenge in proteomics, imparting insights into protein evolution, function prediction, and structural attributes. Motifs hold the potential to unveil crucial protein aspects like transcription factor binding sites and protein-protein interaction regions. However, prevailing techniques for identifying motif sequences in extensive protein collections often entail significant time investments. Furthermore, ensuring the accuracy of obtained results remains a persistent motif discovery challenge. This paper introduces an innovative approach-a branch and bound algorithm-for exact motif identification across diverse lengths. This algorithm exhibits superior performance in terms of reduced runtime and enhanced result accuracy, as compared to existing methods. To achieve this objective, the study constructs a comprehensive tree structure encompassing potential motif evolution pathways. Subsequently, the tree is pruned based on motif length and targeted similarity thresholds. The proposed algorithm efficiently identifies all potential motif subsequences, characterized by maximal similarity, within expansive protein sequence datasets. Experimental findings affirm the algorithm's efficacy, highlighting its superior performance in terms of runtime, motif count, and accuracy, in comparison to prevalent practical techniques.

ForestSemantic: a dataset for semantic learning of forest from close-range sensing

ABSTRACT Information about trees in forest is essential for the assessment of the quantity and the quality of forest ecosystem services. Recently, Deep Learning (DL) methods were regarded as a new cornerstone of algorithm development. Semantic annotations of 3D forest scenes are fundamental for DL algorithm developments. Its necessity has become more urgent as DL is data-driven and requires large amount of training and verification data. However, high-quality annotated forest datasets are still rare, as trees comprise of irregular structures and small components and pose significantly greater challenges even for manual recognition in comparison with artificial objects. This paper introduces a new open point cloud dataset ForestSemantic for forest semantic studies at both individual tree- and plot-levels. The dataset is based on TLS data with different forest conditions. Manual annotation was carried out to a level of detail 4, i.e., until all visible branches. Semantic information is provided at both plot- and tree-levels, as well as at both object- and point-level. Thus, the dataset supports both instance and semantic studies, such as objects detection and segmentation and classification at both tree- and plot-levels. In addition, the dataset also provides comprehensive structural tree traits as reference for further methodological development and verification. This dataset is expected to facilitate research in new dimensions and benchmarks of different systems and solutions. A few examples are demonstrated in this paper to unveil the potentials of the dataset for various applications. In future, it is also possible to simulate other types of point clouds by down-sampling and deforming, and to transfer the dataset for training and verification of other close-range sensing systems, as the dataset was generated using TLS point clouds that represent the highest spatial resolution and geometric accuracy in all close-range point clouds.

Identifying a survival-associated cell type based on multi-level transcriptome analysis in idiopathic pulmonary fibrosis

BackgroundIdiopathic pulmonary fibrosis (IPF) is a progressive disease with a five-year survival rate of less than 40%. There is significant variability in survival time among IPF patients, but the underlying mechanisms for this are not clear yet.Methods and resultsWe collected single-cell RNA sequence data of 13,223 epithelial cells taken from 32 IPF patients and bulk RNA sequence data from 456 IPF patients in GEO. Based on unsupervised clustering analysis at the single-cell level and deconvolution algorithm at bulk RNA sequence data, we discovered a special alveolar type 2 cell subtype characterized by high expression of CCL20 (referred to as ATII-CCL20), and found that IPF patients with a higher proportion of ATII-CCL20 had worse prognoses. Furthermore, we uncovered the upregulation of immune cell infiltration and metabolic functions in IPF patients with a higher proportion of ATII-CCL20. Finally, the comprehensive decision tree and nomogram were constructed to optimize the risk stratification of IPF patients and provide a reference for accurate prognosis evaluation.ConclusionsOur study by integrating single-cell and bulk RNA sequence data from IPF patients identified a special subtype of ATII cells, ATII-CCL20, which was found to be a risk cell subtype associated with poor prognosis in IPF patients. More importantly, the ATII-CCL20 cell subtype was linked with metabolic functions and immune infiltration.

Last stand: Application of a criteria-based framework to inform conservation of a critically threatened tropical lowland forest fragment

Investing resources into protecting small, isolated tropical forest fragments can require considerable justification, especially in the context of limited resources and competing development pressures. Nevertheless, fragments may be suitable targets for conservation if they offer irreplaceable biodiversity outcomes and align with conservation aspirations. This is particularly true for island systems such as Oceania, where tropical lowland forest fragments may be the last remaining representatives of critical habitat due to agriculture or urban expansion on limited flat land. Despite this urgency, the decision to invest significant resources into a permanent conservation investment should be informed by a systematic framework to evaluate relevant conservation criteria for one or multiple sites. Here we present a case study where we applied the criteria-based framework of the Forest Legacy Program of the United States Forest Service, to assess the importance, threat, and strategic benefits of the last known remnant (9.33 ha) of lowland lava flow forest in American Samoa (Polynesia). We expounded on the FLP framework by providing examples of potential evidence and corresponding datasets that could inform the conservation criteria. For the case study, we conducted a comprehensive high-precision tree census to quantify forest structure and composition and compare with other forest types in the country, which revealed high conservation importance based on unique community composition and irreplaceable tree species representations, including Pometia pinnata, Dendrocnide harveyi, and two banyan figs Ficus obliqua and F. prolixa. Analysis of historical (70-year) aerial imagery and recent land cover maps, evidence of recent small-scale incursions, documented attempts by the landowners to obtain development permits, and the need for a court-imposed injunction and a conservation lease to prevent further encroachment, all indicated a high likelihood of conversion (threat) if left unprotected. Finally, we found that protection of this fragment would strategically align with the conservation, management, and education portfolios of the American Samoa government, and provide significant cultural and well-being benefits to the public, specific to the fact that this is the last representative of lava flow forest and is easily accessible to the public. We conclude that there is strong justification for conservation of Naumati forest, which in this case would be through a land purchase. More broadly, criteria-based approaches are often broad and flexible and can be widely applied, but they require significant work to collect data and generate evidence that is meaningful to conservation practitioners working on-the-ground. Effectively linking data to evidence to criteria and ultimately to decision-making is key to justifying sound conservation investments.

A Multiple Criteria Decision-Making Method Generated by the Space Colonization Algorithm for Automated Pruning Strategies of Trees

The rise of mechanical automation in orchards has sparked research interest in developing robots capable of autonomous tree pruning operations. To achieve accurate pruning outcomes, these robots require robust perception systems that can reconstruct three-dimensional tree characteristics and execute appropriate pruning strategies. Three-dimensional modeling plays a crucial role in enabling accurate pruning outcomes. This paper introduces a specialized tree modeling approach using the space colonization algorithm (SCA) tailored for pruning. The proposed method extends SCA to operate in three-dimensional space, generating comprehensive cherry tree models. The resulting models are exported as normalized point cloud data, serving as the input dataset. Multiple criteria decision analysis is utilized to guide pruning decisions, incorporating various factors such as tree species, tree life cycle stages, and pruning strategies during real-world implementation. The pruning task is transformed into a point cloud neural network segmentation task, identifying the trunks and branches to be pruned. This approach reduces the data acquisition time and labor costs during development. Meanwhile, pruning training in a virtual environment is an application of digital twin technology, which makes it possible to combine the meta-universe with the automated pruning of fruit trees. Experimental results demonstrate superior performance compared to other pruning systems. The overall accuracy is 85%, with mean accuracy and mean Intersection over Union (IoU) values of 0.83 and 0.75. Trunks and branches are successfully segmented with class accuracies of 0.89 and 0.81, respectively, and Intersection over Union (IoU) metrics of 0.79 and 0.72. Compared to using the open-source synthetic tree dataset, this dataset yields 80% of the overall accuracy under the same conditions, which is an improvement of 6%.

CO2 abatement feasibility for blast furnace CCUS retrofits in BF-BOF steel plants in China

As one of the energy and carbon intensive industries, the steel industry's low-carbon transition will contribute to the achievement of China's carbon neutrality goal. In this study, a comprehensive source-sink matching-trinomial tree real option evaluation model for China's steel industry was established by combining the database of carbon emissions from blast furnaces of BF-BOF process steel plants, and onshore and offshore CO2 storage potential and injection capacity rate database. By using this model, we investigate the CO2 abatement potential and investment decisions for blast furnace CCUS full-chain projects in China's BF-BOF process steel plants. The results show that a total of 420.07Mt/a of CO2 reductions can be achieved, attributed to 111 steel plants screened for source-sink matching. If no extra incentive policy was included, the current carbon market only supported immediate investment in 14 steel plant CCUS retrofit full-chain projects, which could achieve 36.47Mt/a of CO2 reductions, with a critical carbon price ranging from 6.96 to 202.98USD/t, averaged at 86.97 USD/t. Technological advances, rising carbon prices and government incentives would all contribute to the development of CCUS full-chain projects in the steel industry. The findings provide a strategy for the deployment of blast furnace CCUS retrofit in China's steel industry.

Assembling an illustrated family‐level tree of life for exploration in mobile devices

AbstractSince the concept of the tree of life was introduced about 150 years ago, a considerable fraction of the scientific community has focused its efforts on its reconstruction, with remarkable progress during the last two decades with the advent of DNA sequences. However, the assemblage of a comprehensive and explorable tree of life has been a difficult task to achieve due to two main obstacles: (i) information is scattered into several individual sources and (ii) practical visualization tools for exploring large trees are needed. To overcome both challenges, we aimed to synthesize a family‐level tree of life by compiling over 1400 published phylogenetic studies, choosing the source trees that represent the best phylogenetic hypotheses to date based on a set of objective criteria. Moreover, we dated the tree by employing over 550 secondary calibrations using publicly available sequences for more than 5000 taxa and by incorporating age ranges from the fossil record for over 2800 taxa. Additionally, we developed a mobile app for smartphones to facilitate the visualization and exploration of the resulting tree. Interactive features include exploration by the zooming and panning gestures of touch screens, collapsing branches, visualizing specific clades as subtrees, a search engine, and a timescale to determine extinction and divergence dates, among others. Small illustrations of organisms are displayed at the terminals to better visualize the morphological diversity of life. Our assembled tree currently includes over 7000 families, and its content will be expanded through regular updates to cover all life on earth at the family level.

Development and evaluation of INT2GRATE: a platform for comprehensive assessment of the role of germline variants informed by tumor signature profile in Lynch syndrome.

The presence of variants of uncertain significance (VUS) in DNA mismatch repair (MMR) genes leads to uncertainty in the clinical management of patients being evaluated for Lynch syndrome (LS). Currently, there is no platform to systematically use tumor-derived evidence alongside germline data for the assessment of VUS in relation to LS. We developed INT2GRATE (INTegrated INTerpretation of GeRmline And Tumor gEnomes) to leverage information from the tumor genome to inform the potential role of constitutional VUS in MMR genes. INT2GRATE platform has two components: a comprehensive evidence-based decision tree that integrates well-established clinico-genomic data from both the tumor and constitutional genomes to help inform the potential relevance of germline VUS in LS; and a web-based user interface (UI). With the INT2GRATE decision tree operating in the backend, INT2GRATE UI enables the front-end collection of comprehensive clinical genetics and tumor-derived evidence for each VUS to facilitate INT2GRATE assessment and data sharing in the publicly accessible ClinVar database. The performance of the INT2GRATE decision tree was assessed by qualitative retrospective analysis of genomic data from 5057 cancer patients with MMR alterations which included 52 positive control cases. Of 52 positive control cases with LS and pathogenic MMR alterations, 23 had all the testing parameters for the evaluation by INT2GRATE. All these variants were correctly categorized as INT2GRATE POSITIVE. The stringent INT2GRATE decision tree flagged 29 of positive cases by identifying the absence or unusual presentation of specific evidence, highlighting the conservative INT2GRATE logic in favor of a higher degree of confidence in the results. The remaining 99% of cases were correctly categorized as INCONCLUSIVE due to the absence of LS criteria and ≥1 tumor parameters. INT2GRATE is an effective platform for clinical and genetics professionals to collect and assess clinical genetics and complimentary tumor-derived information for each germline VUS in suspected LS patients. Furthermore, INT2GRATE enables the collation of integrated tumor-derived evidence relevant to germline VUS in LS, and sharing them with a large community, a practice that is needed in precision oncology.

Multifiltering Algorithm for Enhancing the Accuracy of Individual Tree Parameter Extraction at Eucalyptus Plantations Using LiDAR Data

Accurately quantifying individual tree parameters is a critical step for assessing carbon sequestration in forest ecosystems. However, it is challenging to gather comprehensive tree point cloud data when using either unmanned aerial vehicle light detection and ranging (UAV-LiDAR) or terrestrial laser scanning (TLS) alone. Moreover, there is still limited research on the effect of point cloud filtering algorithms on the extraction of individual tree parameters from multiplatform LiDAR data. Here, we employed a multifiltering algorithm to increase the accuracy of individual tree parameter (tree height and diameter at breast height (DBH)) extraction with the fusion of TLS and UAV-LiDAR (TLS-UAV-LiDAR) data. The results showed that compared to a single filtering algorithm (improved progressive triangulated irregular network densification, IPTD, or a cloth simulation filter, CSF), the multifiltering algorithm (IPTD + CSF) improves the accuracy of tree height extraction with TLS, UAV-LiDAR, and TLS-UAV-LiDAR data (with R2 improvements from 1% to 7%). IPTD + CSF also enhances the accuracy of DBH extraction with TLS and TLS-UAV-LiDAR. In comparison to single-platform LiDAR (TLS or UAV-LiDAR), TLS-UAV-LiDAR can compensate for the missing crown and stem information, enabling a more detailed depiction of the tree structure. The highest accuracy of individual tree parameter extraction was achieved using the multifiltering algorithm combined with TLS-UAV-LiDAR data. The multifiltering algorithm can facilitate the application of multiplatform LiDAR data and offers an accurate way to quantify individual tree parameters.