Limited Morphological Information Research Articles

Unroughing the cat’s tongue mushrooms: Four new species of Pseudohydnum from Brazil based on morphological and molecular phylogenetic evidence

ABSTRACT Pseudohydnum, commonly known as cat’s tongue mushrooms, is a monophyletic assemblage within Auriculariales, which encompasses species with gelatinous basidiomata, spathulate, flabellate, or shell-shaped pileus, hydnoid hymenophore, globose to ellipsoidal basidiospores, and longitudinally cruciate-septate basidia. According to the available literature, 16 species have been described in Pseudohydnum, mostly represented in temperate-boreal forests of the Northern Hemisphere. However, the limited morphological, molecular, and ecological information, especially from the Southern Hemisphere ecosystems, does not presently allow a reliable assessment of its taxonomic boundaries nor provide a complete picture of the species diversity in the genus. In an ongoing effort to examine specimens collected in dense and mixed ombrophilous forest fragments (Atlantic Rainforest domain) from Southeastern and Southern Brazil, additional taxa assigned to Pseudohydnum were identified. Four new species are recognized based mostly on characters of the pileus surface, stipe, hymenium, and basidiospores. Molecular phylogenetic analyses based on nuc rDNA internal transcribed spacer region ITS1-5.8S-ITS2 (ITS barcode), partial nuc rDNA 28S, and partial RNA polymerase II largest subunit (RPB1) sequences supported the description of these new taxa. Here, we propose Pseudohydnum brasiliense, P. brunneovelutinum, P. cupulisnymphae, and P. viridimontanum as new species. Morphological descriptions, line drawings, habitat photos, and comparisons with closely related taxa are provided. A dichotomous key for identification of currently known Southern Hemisphere Pseudohydnum species is presented.

Metastatic germ cell tumors in serous cavities and cerebrospinal fluid: A single-center experience.

Metastatic germ cell tumors (GCTs) involving body cavity effusions and cerebrospinal fluid (CSF) are rare. Diagnosis is challenging because of limited morphological and clinicopathological information in the literature. A database search of our institution from 1990 to 2024 identified 27 cases of metastatic GCTs, comprising five pediatric and 22 adolescent and adult patients, in serous cavities or the CSF, including peritoneal (15), pleural (nine), CSF (two), and pericardial (one) fluid. The most common primary site was the testis (n=10), followed by the ovaries (n=7), mediastinum (n=4), retroperitoneum (n=3), pineal gland (n=2), and sacrum/coccyx (n=1). The primary tumors in 14 patients were mixed GCTs (six with a seminoma component), followed by immature teratomas (six), yolk sac tumors (three), embryonal carcinomas (two), pure seminomas (one), and postpubertal teratomas (one). The median interval between primary tumor diagnosis and diagnosis of fluid positivity was 7 months (range: 0-134 months). In nine cases, the malignant fluid was diagnosed simultaneously with or within 1 month of the primary tumor. GCT subtyping was performed on 23 of the 27 cytological specimens. Twenty-four patients (89%) also had metastases to other sites. Thirteen patients died of the disease (48%), with a median survival time of 4 months. Metastatic GCTs in serous effusions and CSF are often associated with disseminated disease and poor prognosis. Subtyping can be performed by cytomorphology combined with immunohistochemistry.

A phylogenomic approach to a taxonomic revision: a combination, new synonymies, and a description of two new species within the camel spider genus Chanbria Muma, 1951 (Solifugae: Eremobatidae)

Abstract This study summarizes the taxonomic treatment of the camel spider genus Chanbria Muma, 1951. Taking an integrative taxonomic approach incorporating phylogenomic, morphological, and geographical information, the genus is herein revised. Of the four species currently placed in the genus, two are retained: Chanbria regalis Muma, 1951 and Chanbria serpentinus Muma, 1951. Eremochelis plicatus (Muma, 1962) is transferred to this genus because it is consistently recovered in a clade with Chanbria based on several phylogenetic analyses using hundreds of loci recovered from ultraconserved element data. In this study, we re-analyse previously acquired genomic data to assess former species hypotheses and identify new morphological synapomorphies that support the monophyly of Chanbria. The genetic data support the synonymization of Chanbria rectus Muma, 1962 syn. nov. with C. regalis. Furthermore, we synonymize Chanbria tehachapianus Muma, 1962 syn. nov. with C. regalis because C. tehachapianus was erected based on limited morphological information and lack of geographical separation between other populations of C. regalis. Two new species, Chanbria brookharti sp. nov. and Chanbria mapemes sp. nov., are described. This brings the total number of species of Chanbria described to five recognized species: C. regalis, C. serpentinus, C. plicatus com. nov., C. brookharti sp. nov., and C. mapemes sp. nov.

A biased fossil record can preserve reliable phylogenetic signal

AbstractThe fossil record is notoriously imperfect and biased in representation, hindering our ability to place fossil specimens into an evolutionary context. For groups with fossil records mostly consisting of disarticulated parts (e.g., vertebrates, echinoderms, plants), the limited morphological information preserved sparks concerns about whether fossils retain reliable evidence of phylogenetic relationships and lends uncertainty to analyses of diversification, paleobiogeography, and biostratigraphy in Earth's history. To address whether a fragmentary past can be trusted, we need to assess whether incompleteness affects the quality of phylogenetic information contained in fossil data. Herein, we characterize skeletal incompleteness bias in a large dataset (6585 specimens; 14,417 skeletal elements) of fossil squamates (lizards, snakes, amphisbaenians, and mosasaurs). We show that jaws + palatal bones, vertebrae, and ribs appear more frequently in the fossil record than other parts of the skeleton. This incomplete anatomical representation in the fossil record is biased against regions of the skeleton that contain the majority of morphological phylogenetic characters used to assess squamate evolutionary relationships. Despite this bias, parsimony- and model-based comparative analyses indicate that the most frequently occurring parts of the skeleton in the fossil record retain similar levels of phylogenetic signal as parts of the skeleton that are rarer. These results demonstrate that the biased squamate fossil record contains reliable phylogenetic information and support our ability to place incomplete fossils in the tree of life.

Stochastic reconstruction of 3D microstructures from 2D cross-sectional images using machine learning-based characterization

The availability of high-quality three-dimensional (3D) microstructures is an essential prerequisite to understanding the macroscopic behaviours of heterogeneous media. Considering the high cost of 3D microscopy imaging, it is an economical way to derive large numbers of virtual 3D microstructures from limited morphological information of 2D cross-sectional images. This paper presents an efficient method that incorporates machine learning-based characterization of 2D images to statistically reconstruct 3D microstructures. The latent stochasticity of 2D images is mastered by fitting supervised machine learning models, which essentially characterize the local morphological statistics. A morphology integration scheme is developed to project the 2D morphological statistics into the 3D space, and new equivalent 3D microstructures can then be synthesized by sequentially generating voxel values from probability sampling. The new method is tested on a series of heterogeneous media with distinct morphologies, and it is also compared with two classical methods (i.e. stochastic optimization-based reconstruction and Gaussian random field transformation) in terms of reconstruction accuracy and efficiency. Besides, various microstructural descriptors are used to quantify the discrepancies between the reconstructed and target microstructures. The results confirm that the proposed method provides a highly cost-effective and widely applicable way to reproduce 3D realizations that precisely preserve the statistical characteristics, geometrical irregularities, long-distance connectivity and anisotropy that exist in 2D cross-sectional images.

A possible brachiosaurid (Dinosauria, Sauropoda) from the mid-Cretaceous of northeastern China.

Brachiosauridae is a lineage of titanosauriform sauropods that includes some of the most iconic non-avian dinosaurs. Undisputed brachiosaurid fossils are known from the Late Jurassic through the Early Cretaceous of North America, Africa, and Europe, but proposed occurrences outside this range have proven controversial. Despite occasional suggestions that brachiosaurids dispersed into Asia, to date no fossils have provided convincing evidence for a pan-Laurasian distribution for the clade, and the failure to discover brachiosaurid fossils in the well-sampled sauropod-bearing horizons of the Early Cretaceous of Asia has been taken to evidence their genuine absence from the continent. Here we report on an isolated sauropod maxilla from the middle Cretaceous (Albian–Cenomanian) Longjing Formation of the Yanji basin of northeast China. Although the specimen preserves limited morphological information, it exhibits axially twisted dentition, a shared derived trait otherwise known only in brachiosaurids. Referral of the specimen to the Brachiosauridae receives support from phylogenetic analysis under both equal and implied weights parsimony, providing the most convincing evidence to date that brachiosaurids dispersed into Asia at some point in their evolutionary history. Inclusion in our phylogenetic analyses of an isolated sauropod dentary from the same site, for which an association with the maxilla is possible but uncertain, does not substantively alter these results. We consider several paleobiogeographic scenarios that could account for the occurrence of a middle Cretaceous Asian brachiosaurid, including dispersal from either North America or Europe during the Early Cretaceous. The identification of a brachiosaurid in the Longshan fauna, and the paleobiogeographic histories that could account for its presence there, are hypotheses that can be tested with continued study and excavation of fossils from the Longjing Formation.

Realistic soil particle generation based on limited morphological information by probability-based spherical harmonics

Three-dimensional imaging techniques, such as X-ray computed tomography, have been used to scan realistic particle geometries. However, these techniques are labor intensive, time-consuming, and costly to obtain a large number of particles. Therefore, it is desirable if computers can be taught to generate realistic particles based on given morphological properties. This paper develops a particle generation technique by integrating spherical harmonics and probability functions. This technique only requires morphological information from one particle to generate a large number of particles and eliminates the need for scanning many particles for particle generation. The spherical harmonics coefficients of this particle are analog of the morphological gene. The probability function is used to add variances to spherical harmonics coefficients to simulate gene mutation. A dimensionless factor is developed to control degrees of gene mutation. The effectiveness and accuracy of the proposed technique are verified by particle shape descriptors computed by the computational geometry techniques.

Analysis of fracture properties of three-dimensional reconstructed rock model using hierarchical-fractal annealing algorithm

The irregularity and multi-scale features are the most important and intrinsic characteristics for rocks, which are caused by the variety of microstructures. In this paper, a novel reconstruction method is proposed to reconstruct a porous rock model based on limited morphological information. The configurations of the pore structures in Xingluokeng sandstone are investigated by the X-ray Micro-CT observation. Then, a triaxial compressive test is conducted to obtain necessary mechanical properties. Compared with the traditional reconstruction method, the novel reconstruction method adopts the hierarchical annealing algorithm and gains considerable computational efficiency. Moreover, considering the irregularity and multi-scale features of rocks, the fractal function variables over time, and the local histogram function are introduced to describe these characteristics. The finite element-smooth particle dynamic coupling method is employed to simulate the mechanical responses and fractures of the reconstructed model under compression. The topological verification and comparison between the simulation results and experimental data show that the novel reconstruction method can predict the large scale properties of rocks with limited experimental results, which indicate the novel reconstruction method has a important application in the prediction of geological conditions for engineering project.

Accelerating multi-point statistics reconstruction method for porous media via deep learning

Reconstruction of three-dimensional (3D) porous media from a single two-dimensional (2D) image or limited morphological information has been an outstanding problem. Specifically, multi-point statistics (MPS)-based methods have been proved to be effective and promising to address this problem. Besides, recently sampling-based MPS methods that reconstruct 3D microstructure layer by layer have attracted increasing attention, for its relatively lower computational cost and memory demand. However, due to the nature that one has to search and match multi-point information in a data structure like binary tree or list for each simulation, it is very time-consuming, especially for large template used to reconstruct geometrically complex media. In this paper, to overcome this challenge, for the first time to the best of our knowledge, an accelerating reconstruction method based on deep learning is proposed. Specially, conditional generative adversarial networks (CGAN) is leveraged to model and characterize the relation between the sampling image which contains conditioning data and the target void-solid image. Unlike conventional MPS-based method generally performing simulation point by point, our method is able to directly translate the sampling image to the target one instantaneously, thus leading to a significant speedup factor (∼760 for 2D reconstruction and ∼25 for 3D reconstruction on CPU). Meanwhile, to assess the performance of our method, we test it on sandstone samples, and two-point correlation function, lineal-path function and two-point cluster function, as well as local porosity distribution are quantitatively compared with those of the target microstructure. The comparison indicates that our method is of high efficiency while preserving good agreement of statistical functions with that of the target system. We remark that our approach opens the door to a new methodology that incorporating machine learning/deep learning techniques into conventional methods to address CPU- or memory-demanding issues in a wide range of related fields.

A hierarchical-fractal approach for the rock reconstruction and numerical analysis

A novel reconstruction method is proposed to reconstruct porous rock model based on limited morphological information from experiments. X-ray Micro-CT observations and triaxial compressive tests are initially conducted to obtain the raw CT images and necessary mechanical parameters. Then, a hierarchical annealing algorithm is proposed to gain large profits in computational efficiency. Moreover, the fractal system control function with time variables and local histogram system control function are introduced to characterize the irregular and multi-scale features in rocks. Finally, the comparisons between the numerical results and experimental data show that the proposed novel reconstruction method has a powerful capacity to predict the properties of rocks for engineering purposes.

3D Numerical Reconstruction of Porous Sandstone Using Improved Simulated Annealing Algorithms

In this paper, a 3D numerical reconstruction method is proposed based on improved simulated annealing algorithms and limited morphological information from experiments. Firstly, X-ray micro-CT experimental tests are applied to obtain the CT images and the mechanical parameters of Xingluokeng sandstone. Then, the voxel block exchanging algorithm is introduced to accelerate the preliminary reconstruction stage of the porous sandstone model. Two-point probability control function, lineal-path control function and fractal control function are employed to characterize complex pore morphologies. The system updating algorithm is improved to avoid wasting time on the unnecessary and unsuccessful position exchange. Finally, to verify the proposed method, the topological and mechanical properties of the reconstructed porous sandstone model are analyzed by a distance-ordered homotopic thinning algorithm as well as the numerical compression. Moreover, the numerical results of the reconstructed model are compared with the experimental data. It is found that the proposed method in this paper has a good ability to predict the properties of the rocks for engineering purposes.

Reconstruction of three-dimensional heterogeneous media from a single two-dimensional section via co-occurrence correlation function

Accurately modeling and reconstructing three-dimensional (3D) microstructure of heterogeneous media from limited morphological information obtained from a single two-dimensional (2D) section remains an outstanding problem. Specially, based on simulated annealing (SA) procedure, two-point correlation function S2 is widely used to reconstruct various 3D microstructures in many different cases. However, two-point correlation function is a lower-order statistical descriptor and is generally not sufficient to accurately characterize a microstructure. From the perspective of texture description, a co-occurrence correlation function (CCF) based on gray-level co-occurrence matrix is presented, and four feature functions are derived from it and used as objective function in SA procedure. Moreover, the CCF can be both manageably measured from a single 2D image and embody non-trivial higher-order morphological information. Furthermore, to avoid completely re-computing the CCF in the reconstruction, a fast updating method for CCF is proposed, and thus accelerating the reconstruction process. The four feature functions are utilized to reconstruct different types of media, including square array of nonoverlapping disks, anode microstructure of solid oxide fuel cell and sandstone core. Meanwhile, the two-point correlation function reconstructions are used for comparison. Unconstrained functions including lineal-path function and two-point cluster function are used to quantitatively ascertain the accuracy of the reconstructions, and the comparison of run time is also demonstrated. The results indicate that the proposed method can accurately reconstruct the microstructures with correlation functions being in good agreement with those of the target.

Analyzing fracture properties of the 3D reconstructed model of porous rocks

The non-negligible fissures, cracks or pore structures, which are contained in rocks, have significant influences on their mechanical properties. In this paper, a novel method is developed to reconstruct a three-dimensional multiple phase rock model from the limited morphological information of Chongqing sandstone. Firstly, X-ray micro-CT experimental tests are applied to Chongqing sandstone to obtain the raw CT images and the mechanical parameters. Then, the two-point correlation function, lineal-path function and fractal function are combined to generate the reconstructed model. Next, the reconstructed model subjected to compressive loads is simulated by Finite Element-Smoothed Particle Hydrodynamics (FE-SPH) coupling method with a brittle model formulation. Finally, the initiation, propagation and coalescence of cracks are investigated during the numerical simulation. The topological and mechanical properties of the reconstructed model are carefully analyzed and compared with that of the reference model. The comparison of the numerical modeling results and the experimental data shows a good consistency. This indicates that the proposed method has the ability to predict macroscopic behaviors of rocks from limited experimental information.

A guide to the winged aphids (Homoptera) of Costa Rica.

This guide is a compilation of limited morphological and biological information on the winged morphs of 60 species of aphids that have been collected in Costa Rica. It should not be viewed as a definitive taxonomic treatise on the aphids of Costa Rica, rather it is a tool that can be used to assist in research on the biology, host plant relationships, taxonomy, and virus transmission capabilities of aphids. Each species is covered in an identical manner. Morphological and biological information is provided in both Spanish and English as well as photographs of slide mounted specimens. Keys are provided to help the user in identifying the species. Most of the specimens examined were taken in traps associated with epidemiological studies. Limited field collecting has generated host records and these have been added to a list of the aphids of Central America that was compiled by Pamela Anderson and appended in the guide with her permission. The authors hope that this book will be useful to entomologists in Costa Rica and Central America.

On the inverse problem of the reconstruction of food microstructure from limited statistical information. A study on bread

The possibility to reconstruct food microstructure by limited morphological information has fundamental importance for theoretical and practical applications. We implemented the simulated annealing method proposed by Yeong and Torquato (1998) for reconstructing bread structure through the information contained into the lineal-path distribution function, L(r), and two-point correlation function, S2(r). The method enabled the evolution of two-phase random image toward bread structure. When using the information of lineal-path distribution function, the generated images well captured the main morphological features of bread, although several deviations still existed. This was in accordance with the significant differences between the original and reconstructed images as measured by two-point correlation function. By hybrid reconstruction, based on both correlation functions, a better reconstruction in terms of both number and size of pores was obtained. In the future the use of more several statistical correlation functions could enable further improvement in reconstruction of bread microstructure.

A five-marker molecular phylogeny of the Styphelieae (Epacridoideae, Ericaceae) supports a broad concept of Styphelia

The Styphelieae is the largest of the seven tribes within the subfamily Epacridoideae Arn. (Ericaceae Juss.). Recent molecular phylogenetic work has resulted in the recircumscription of some genera and the erection of new ones, but several non-monophyletic genera remain. Most of them are concentrated in the well-supported Styphelia–Astroloma clade, which contains species currently assigned to Leucopogon R.Br., Styphelia Sm., Astroloma R.Br., Croninia J.M. Powell and Coleanthera Stschegl. Parsimony and Bayesian analyses of sequence data from four plastid markers (rbcL, matK, trnH–psbA, and atpB–rbcL), and the nuclear ribosomal internal transcribed spacer (ITS) for 207 taxa corroborate the polyphyly of the genera Astroloma, Leucopogon and Styphelia and resolve 12 well supported groups. Of these groups, two can be distinguished by unique morphological features and another six by different character combinations. The remaining groups are morphologically heterogeneous and inconsistent, and not readily distinguishable. A number of species remain ungrouped either because their phylogenetic relationships are not clear or because they do not show strong morphological affinities with the group to which they have a close phylogenetic relationship. Translating the results into a phylogenetic classification is a choice between accepting a single, large genus or at least 12 smaller genera. The first option would result in a heterogeneous assemblage conveying limited morphological information. The multi-generic option would be a better reflection of the morphological diversity of the clade, but would result in many genera lacking readily observable, diagnostic morphological characters. We prioritise the nomenclatural stability inherent in the former approach and advocate expanding Styphelia to include all taxa in the Styphelia–Astroloma clade.

Updating the description and taxonomic status of Brachionus sessilis Varga, 1951 (Rotifera: Brachionidae) based on detailed morphological analysis and molecular data.

Brachionus sessilis Varga, 1951 is an epizoic rotifer living exclusively on cladocerans of the genus Diaphanosoma. Current taxonomic knowledge relies solely on limited morphological information, whereas there is no type material. Here, we aim to resolve issues concerning its morphology and taxonomy using both morphological and genetic characters on material sampled from Lake Balaton (Hungary), as well as Lake Doirani (Greece) that was selected for comparison purposes. Biometrical analysis was based on extensive lorica measurements. Phylogenetic reconstruction was based on DNA sequence information of the mitochondrial cytochrome c oxidase subunit I (COI) and 16S rRNA gene regions as well as of the nuclear internal transcribed spacer 1 (ITS1). Well-supported evidence for substantial differentiation of B. sessilis from its closest phylogenetic relatives supports its species-rank status. Our phylogenetic analysis suggests a highly supported clade encompassing B. sessilis and another epizoic rotifer, namely B. rubens.

Three-Dimensional Heterogeneous Material Microstructure Reconstruction from Limited Morphological Information via Stochastic Optimization

We present a general computational framework that enables one to generate realistic 3D microstructure models of heterogeneous materials from limited morphological information via stochastic optimization. In our framework, the 3D material microstructure is represented as a 3D array, whose entries indicate the local state of that voxel. The limited structural data obtained in various experiments correspond to different mathematical transformations of the 3D array. Reconstructing the 3D material structure from such limited data is formulated as an inverse problem, originally proposed by Yeong and Torquato [Phys. Rev. E 57, 495 (1998)], which is solved using the simulated annealing procedure. The utility, versatility and robustness of our general framework are illustrated by reconstructing a polycrystalline microstructure from 2D EBSD micrographs and a binary metallic alloy from limited angle projections. Our framework can be also applied in the reconstructions based on small-angle x-ray scattering (SAXS) data and has ramifications in 4D materials science (e.g., charactering structural evolution over time).

Accurate modeling and reconstruction of three-dimensional percolating filamentary microstructures from two-dimensional micrographs via dilation-erosion method

Heterogeneous materials are ubiquitous in nature and synthetic situations and have a wide range of important engineering applications. Accurate modeling and reconstructing three-dimensional (3D) microstructure of topologically complex materials from limited morphological information such as a two-dimensional (2D) micrograph is crucial to the assessment and prediction of effective material properties and performance under extreme conditions. Here, we extend a recently developed dilation–erosion method and employ the Yeong–Torquato stochastic reconstruction procedure to model and generate 3D austenitic–ferritic cast duplex stainless steel microstructure containing percolating filamentary ferrite phase from 2D optical micrographs of the material sample. Specifically, the ferrite phase is dilated to produce a modified target 2D microstructure and the resulting 3D reconstruction is eroded to recover the percolating ferrite filaments. The dilation–erosion reconstruction is compared with the actual 3D microstructure, obtained from serial sectioning (polishing), as well as the standard stochastic reconstructions incorporating topological connectedness information. The fact that the former can achieve the same level of accuracy as the latter suggests that the dilation–erosion procedure is tantamount to incorporating appreciably more topological and geometrical information into the reconstruction while being much more computationally efficient.

A Bayesian approach to star-galaxy classification

Star-galaxy classification is one of the most fundamental data-processing tasks in survey astronomy, and a critical starting point for the scientific exploitation of survey data. For bright sources this classification can be done with almost complete reliability, but for the numerous sources close to a survey's detection limit each image encodes only limited morphological information. In this regime, from which many of the new scientific discoveries are likely to come, it is vital to utilise all the available information about a source, both from multiple measurements and also prior knowledge about the star and galaxy populations. It is also more useful and realistic to provide classification probabilities than decisive classifications. All these desiderata can be met by adopting a Bayesian approach to star-galaxy classification, and we develop a very general formalism for doing so. An immediate implication of applying Bayes's theorem to this problem is that it is formally impossible to combine morphological measurements in different bands without using colour information as well; however we develop several approximations that disregard colour information as much as possible. The resultant scheme is applied to data from the UKIRT Infrared Deep Sky Survey (UKIDSS), and tested by comparing the results to deep Sloan Digital Sky Survey (SDSS) Stripe 82 measurements of the same sources. The Bayesian classification probabilities obtained from the UKIDSS data agree well with the deep SDSS classifications both overall (a mismatch rate of 0.022, compared to 0.044 for the UKIDSS pipeline classifier) and close to the UKIDSS detection limit (a mismatch rate of 0.068 compared to 0.075 for the UKIDSS pipeline classifier). The Bayesian formalism developed here can be applied to improve the reliability of any star-galaxy classification schemes based on the measured values of morphology statistics alone.