Article
Computer Science, Software Engineering
Bosheng Li, Jacek Kaluzny, Jonathan Klein, Dominik L. Michels, Wojtek Palubicki, Bedrich Benes, Soren Pirk
Summary: A novel method for reconstructing the 3D geometry of botanical trees from single photographs is introduced, addressing the challenges of faithfully reconstructing a tree from single-view sensor data. The method defines a reconstruction pipeline based on three neural networks, using radial bounding volumes to grow realistic branching for the tree crown and evaluating reconstructed geometries with several metrics.
ACM TRANSACTIONS ON GRAPHICS
(2021)
Article
Multidisciplinary Sciences
Elise Parey, Alexandra Louis, Jerome Montfort, Olivier Bouchez, Celine Roques, Carole Iampietro, Jerome Lluch, Adrien Castinel, Cecile Donnadieu, Thomas Desvignes, Christabel Floi Bucao, Elodie Jouanno, Ming Wen, Sahar Mejri, Ron Dirks, Hans Jansen, Christiaan Henkel, Wei-Jen Chen, Margot Zahm, Cedric Cabau, Christophe Klopp, Andrew Thompson, Marc Robinson-Rechavi, Ingo Braasch, Guillaume Lecointre, Julien Bobe, John H. Postlethwait, Camille Berthelot, Hugues Roest Crollius, Yann Guiguen
Summary: Through the study of gene sequence and chromosomal rearrangement in teleosts, it was found that Elopomorpha and Osteoglossomorpha are sister groups to all other teleosts, resolving over 50 years of controversy on their evolutionary relationships.
Article
Computer Science, Information Systems
Bilal Ahmad, Pal Anders Floor, Ivar Farup, Oistein Hovde
Summary: Capsule endoscopy is emerging as an alternative to traditional colonoscopy, utilizing a wireless camera to examine the gastrointestinal tract. The study focuses on reconstructing 3D shapes from wireless capsule endoscopy (WCE) images to provide enhanced viewing for gastroenterologists. Different methods, such as shape from shading (SFS) and shape from focus (SFF), are evaluated and compared. The results show that both methods successfully reconstruct the 3D shapes of colon images, but SFF performs better in retaining details. Additionally, the subjective experiments indicate that contrast enhanced images and 3D models are preferred and considered useful by gastroenterologists.
Article
Automation & Control Systems
Leonard Bruns, Patric Jensfelt
Summary: This paper provides an overview of methods, datasets, and evaluation protocols for 6D pose and shape estimation of objects at a per-category level. It presents the commonalities and differences of existing works, critiques the prevailing evaluation protocol, and proposes new metrics and annotations. The study finds that existing methods struggle with unconstrained orientations and have a bias towards upright objects. The authors also provide an easy-to-use evaluation toolbox.
ROBOTICS AND AUTONOMOUS SYSTEMS
(2023)
Article
Computer Science, Information Systems
Mingrui Dai, Guohua Li
Summary: In this paper, a novel soft segmentation algorithm is introduced to automatically segment tree crowns in point clouds and reconstruct the tree crown surface. The experimental results showed that the segmented crown was accurate, and the reconstructed crown looked natural. With the reconstructed crown geometry, various crown attributes can be estimated.
Article
Computer Science, Artificial Intelligence
Wei Dong, Yixing Lao, Michael Kaess, Vladlen Koltun
Summary: We present ASH, a modern and high-performance framework for parallel spatial hashing on GPU, which achieves higher performance, supports richer functionality, and requires fewer lines of code (LoC) compared to existing GPU hash map implementations. ASH provides a versatile tensor interface and enables direct access to spatially varying data via indices, allowing seamless integration with modern libraries such as PyTorch.
IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE
(2023)
Article
Optics
Lei Huang, Tianyi Wang, Oleg Chubar, Guillaume Dovillaire, An He, Maksim Rakitin, Mourad Idir
Summary: X-ray wavefront measurement is an important tool for beam diagnostics, and Hartmann wavefront sensing is a promising technique for in situ measurements. In this study, a simulation tool for X-ray Hartmann Wavefront Sensor (HWS) is developed under the SRW framework. This tool can optimize wavefront sensor parameters and predict measurement results under different beamline configurations.
Review
Forestry
Serajis Salekin, Cristian Higuera Catalan, Daniel Boczniewicz, Darius Phiri, Justin Morgenroth, Dean F. Meason, Euan G. Mason
Summary: Taper functions are crucial tools for forest management, with a growing number of studies focusing on their development and application. Most studies have been conducted in Europe and the Americas, and modern machine learning methods are increasingly being utilized for the establishment of taper functions.
Article
Engineering, Civil
Nagavciuc Viorica, Roibu Catalin-Constantin, Mursa Andrei, Stirbu Marian-Ionut, Popa Ionel, Ionita Monica
Summary: This study used tree-ring width to reconstruct streamflow of the Lower Danube River and found a significant correlation between tree-ring width and river streamflow. The analysis of the past 250 years showed 14 extremely high flow years and 14 extremely low flow years for the Danube River. The reconstruction of river streamflow based on tree-ring width has important scientific and practical implications for water resource management and environmental-hydrological protection.
JOURNAL OF HYDROLOGY
(2023)
Article
Mathematics, Applied
Samuel Bignardi, Anthony Joseph Yezzi, Alper Yildirim, Christopher F. Barnes, Romeil Sandhu
Summary: This paper discusses the potential of using remote sensing radar techniques for shape reconstruction by inverting pulse-compressed radar signals. The study highlights the challenges encountered and proposes solutions to overcome them, showcasing the success of the variational approach through simulations and the possibility of further expansion into active surfaces and level set applications.
Article
Environmental Sciences
M. C. A. Torbenson, J. H. Stagge
Summary: This study compares three different approaches for reconstructing flow, showing that baseflow separation can improve the accuracy of reconstruction. The relationship between tree growth and baseflow is stronger than that with streamflow, supporting the feasibility of using baseflow as the predictor variable.
WATER RESOURCES RESEARCH
(2021)
Review
Forestry
Tongwen Zhang, Jinghui Song, Yuting Fan, Yan Liu, Shulong Yu, Dong Guo, Tianhao Hou, Kailong Guo
Summary: This paper compiles and analyzes the literature on vegetation index research based on tree-ring information in the past 20 years. It provides an overview of the relationship between tree-ring parameters and NDVI, as well as NDVI reconstruction. The research shows a strong correlation between tree-ring parameters and NDVI in summer. In addition, combining tree rings with NDVI is useful for assessing forest decline, quantifying the forest response to drought, and monitoring forest productivity. Future research should consider multiple environmental factors and conduct large-scale studies on the climate response of forest tree growth and the reconstruction of historical vegetation index sequences.
Article
Multidisciplinary Sciences
Wenjie Hou, Ang Li, Weimin Song
Summary: This study investigates the direct shear behaviors of ballast with different morphological parameters using the discrete element method. The initial packing states and shear results are analyzed, and one-way ANOVA tests are conducted to explore the impact of ballast shape. The results show that the four parameters significantly affect the internal friction and porosities. Additionally, the ballast shape affects the coordination number during the direct shear process.
SCIENTIFIC REPORTS
(2023)
Review
Mathematics
Dalibor Martisek, Karel Mikulasek
Summary: Shape-from-Focus methods have been developed for about twenty years, which can obtain the shape of 3D objects from a series of partially focused images. By identifying focused parts and composing a fully focused 2D image, these methods reconstruct a 3D profile of the surface to be observed.
Article
Multidisciplinary Sciences
Alae-Eddine Sahbou, Driss Iraqi, Rachid Mentag, Slimane Khayi
Summary: BuscoPhylo is an easy-to-use tool that allows students and scientists to perform Busco-based phylogenomic analysis using a set of genome sequences. It is a user-friendly web server that can be accessed freely at https://buscophylo.inra.org.ma/. The source code and documentation are available for free under an MIT license at https://github.com/alaesahbou/BuscoPhylo.
SCIENTIFIC REPORTS
(2022)
Article
Paleontology
Jodie L. Murphy, Mark N. Puttick, Joseph E. O'Reilly, Davide Pisani, Philip C. J. Donoghue
Summary: The study investigated 486 tetrapod morphological cladistic datasets to establish an empirical distribution of consistency among characters and datasets. It was found that the consistency between phylogenetic history and individual character histories has a bearing on the evolutionary process, with the most significant decreases resulting from the addition of taxa rather than characters. This research challenges the conjecture that high quality phylogenetic characters are quickly exhausted in the search for phylogenetic resolution.
Article
Evolutionary Biology
Roberto Feuda, Matthew Goulty, Nicola Zadra, Tiziana Gasparetti, Ezio Rosato, Davide Pisani, Annapaola Rizzoli, Nicola Segata, Lino Ometto, Omar Rota Stabelli
Summary: This study analyzed the genomes of 61 dipteran species to reconstruct the evolutionary affinities of 528 opsin genes and found lineage-specific events in opsins, such as independent expansions in flies and mosquitoes. Molecular evolutionary studies indicated higher gene turnover rate, overall mutation rate, and site-specific selective pressure in Anopheles compared to Drosophila. The contrasting dynamics in the evolution of opsin genes between Anopheles and Drosophila provide a foundation for future studies on the dipteran visual system.
GENOME BIOLOGY AND EVOLUTION
(2021)
Article
Evolutionary Biology
James F. Fleming, Davide Pisani, Kazuharu Arakawa
Summary: Research shows that there are multiple opsins duplications within Tardigrada, however, the expression levels of these opsins change during ontogeny and most of them are not co-temporally expressed, indicating that tardigrades are unlikely to be able to distinguish color.
GENOME BIOLOGY AND EVOLUTION
(2021)
Article
Paleontology
Thomas J. Smith, Mark N. Puttick, Joseph E. O'Reilly, Davide Pisani, Philip C. J. Donoghue
Summary: Cladistic character matrices are often used in analyses of morphological disparity, but their sampling may lead to biases in morphospace occupation. Differences in tree shape can predict genuine differences in morphospace occupation, cautioning against uncritical repurposing of cladistic datasets in disparity analyses. Uniformity in lineage sampling across time and topology is important for distinguishing evolutionary phenomena from artefactual signals.
Article
Biology
Aurelien Lowie, Barbara De Kegel, Mark Wilkinson, John Measey, James C. O'Reilly, Nathan J. Kley, Philippe Gaucher, Jonathan Brecko, Thomas Kleinteich, Dominique Adriaens, Anthony Herrel
Summary: This study explored the relationships between skull shape, head musculature, and in vivo bite forces in caecilians. The results showed that there is a correlation between bite force and external head shape, but no relationship between bite force and skull shape. Skull shape is constrained by factors other than demands for bite force generation, while muscles are the principal drivers of variation in bite force. There is a covariation between the shape of the cranium and mandible, as well as with jaw muscle architecture.
JOURNAL OF EXPERIMENTAL BIOLOGY
(2022)
Article
Geosciences, Multidisciplinary
Richard J. Howard, Mattia Giacomelli, Jesus Lozano-Fernandez, Gregory D. Edgecombe, James F. Fleming, Reinhardt M. Kristensen, Xiaoya Ma, Jorgen Olesen, Martin V. Sorensen, Philip F. Thomsen, Matthew A. Wills, Philip C. J. Donoghue, Davide Pisani
Summary: This study estimates the evolutionary time-tree for Ecdysozoans using improved fossil calibrations. The results suggest that Scalidophora is the sister group to Nematoida + Panarthropoda and that the divergence of Ecdysozoa occurred at least 23 myr before the first potential ecdysozoan trace fossils.
JOURNAL OF THE GEOLOGICAL SOCIETY
(2022)
Article
Biochemistry & Molecular Biology
Kevin J. Peterson, Alan Beavan, Peter J. Chabot, Mark A. McPeek, Davide Pisani, Bastian Fromm, Oleg Simakov
Summary: WGDs do not result in the creation of miRNA novelty, nor do WGDs correlate to increases in complexity. Instead, it is the number of miRNA seed sequences in the genome itself that not only better correlate to instances in complexification, but also mechanistically explain why complexity increases when new miRNA families are established.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Multidisciplinary Sciences
Chenyang Cai, Erik Tihelka, Mattia Giacomelli, John F. Lawrence, Robin Kundrata, Shuhei Yamamoto, Margaret K. Thayer, Alfred F. Newton, Richard A. B. Leschen, Matthew L. Gimmel, Liang Lu, Michael S. Engel, Patrice Bouchard, Diying Huang, Davide Pisani, Philip C. J. Donoghue
Summary: Beetles are the most biodiverse animal order, and this study uses phylogenomic techniques to propose new classification changes and analyze the origin and divergence time of beetles, finding differences from previous hypotheses.
ROYAL SOCIETY OPEN SCIENCE
(2022)
Review
Ecology
Daniel B. Mills, Richard A. Boyle, Stuart J. Daines, Erik A. Sperling, Davide Pisani, Ip C. J. Donoghu, Timothy M. Lenton
Summary: The origin of mitochondria and the oxygenation of Earth have been found to be decoupled by recent research. The authors review the literature and conclude that eukaryogenesis and the rise of oxygen were separate events, and that obligate aerobiosis in eukaryotes only became widespread in the past 1 billion years.
NATURE ECOLOGY & EVOLUTION
(2022)
Editorial Material
Biochemistry & Molecular Biology
Davide Pisani, Maria Eleonora Rossi, Ferdinand Marletaz, Roberto Feuda
Summary: Phylogenetic studies have traditionally placed the simple Xenoacoelomorph worms as the sister group of all other animals with bilateral body symmetry. A new study suggests that misidentification of orthologous genes might have contributed to this placement.
Article
Multidisciplinary Sciences
Mattia Giacomelli, Maria Eleonora Rossi, Jesus Lozano-Fernandez, Roberto Feuda, Davide Pisani
Summary: Genomic data has helped in the understanding of the Tree of Life, but certain nodes remain unresolved. By using simulated datasets, this study found that recoding amino acid data can improve the accuracy of phylogenetic inference. The results suggest that the placement of comb jellies as sister to all other animals in phylogenies inferred from amino acid sequences is likely a tree reconstruction artifact.
Article
Multidisciplinary Sciences
Ksenia Juravel, Luis Porras, Sebastian Hoehna, Davide Pisani, Gert Woerheide
Summary: An accurate understanding of the evolution and ecology of animals relies on an accurate phylogeny. However, there are still unresolved nodes in the animal tree, including the root of animals, the root of Bilateria, and the monophyly of Deuterostomia. In this study, we utilized newly assembled genome gene content and morphological datasets to investigate these difficult nodes. Our results support the idea that sponges are the sister group of all other animals, Xenacoelomorpha is the sister group of other Bilateria, and provide tentative support for the monophyly of Deuterostomia.
Article
Paleontology
Romain Sabroux, Gregory D. Edgecombe, Davide Pisani, Russell J. Garwood
Summary: The author reexamined three Middle Jurassic sea spider species from La Voulte-sur-Rhone using X-ray microtomography and reflectance transformation imaging, and reclassified their taxonomic affiliations. They found that Palaeopycnogonides gracilis belongs to the new family Palaeopycnogonididae, Colossopantopodus boissinensis belongs to the extant family Colossendeinae, and Palaeoendeis elmii has affinities with Endeidae. The impact of these new taxonomic assignments on the use of Jurassic sea spiders as fossil calibrations is discussed.
PAPERS IN PALAEONTOLOGY
(2023)
Article
Biology
Ruolin Wu, Davide Pisani, Philip C. J. Donoghue
Summary: Panarthropoda, including Onychophora, Tardigrada, and Euarthropoda, is a clade with the majority of animal biodiversity. The relationships among these phyla are disputable, and resolving them is essential to understanding the evolutionary assembly of panarthropod bodyplans. Molecular phylogenetic analyses generally support the monophyly of Onychophora and Euarthropoda, excluding Tardigrada (Lobopodia hypothesis). However, morphological data analyses can also be interpreted to support the monophyly of Tardigrada and Euarthropoda, excluding Onychophora (Tactopoda hypothesis). Additionally, there is support for a clade of Onychophora and Tardigrada that excludes Euarthropoda (Protarthropoda hypothesis). Our study shows that morphological datasets cannot statistically distinguish between the Lobopodia, Tactopoda, and Protarthropoda hypotheses, calling into question the accuracy of morphology-based phylogenies and evolutionary hypotheses of Panarthropoda, including fossil species.
Article
Evolutionary Biology
Jiahui Xu, Mark Wilkinson, Miaoying Chen, Qi Zhang, Ran Yang, Zhenzhen Yi
Summary: By adding 857 environmental sequences to the hypotrich LSU rDNA gene sequences, this study significantly increased the resolution for hypotrich phylogenetics. The traditional hypotrich orders were found to be polyphyletic, with a monophyletic core Urostylida in the trees. The inferred ecological transitions in Hypotricha were found to be influenced by genes, methods, and taxa.
