Morphological Classification Scheme Research Articles

Phylogenetic synthesis of morphological and molecular data reveals insights on the classification of diogenid hermit crabs (Crustacea: Decapoda: Anomura).

The family Diogenidae Ortmann, 1892 is a diverse and abundance group of hermit crabs, but their systematics and phylogenetic relationships are highly complex and unresolved. Herein, we gathered nucleotide sequence data from two mitochondrial (16S rRNA and COI) and two nuclear (NaK and PEPCK) genes for a total of 2,308 bp in length across 38 species from six extant diogenid genera. Molecular data were combined with 41 morphological characters to estimate the largest phylogeny of diogenid hermit crabs to date with the aim of testing the proposed taxonomic scheme of Diogenidae and addressing intergeneric relationships within this family. Despite conflicts between mitochondrial and nuclear DNA trees, the combined-data tree reflects the contributions of each dataset, and improves tree resolution and support for internal nodes. Contrary to traditional classification, our total evidence revealed a paraphyletic Diogenidae based on internally nested representatives of Coenobitidae Dana, 1851. Within Diogenidae, the studied diogenid hermit crabs were split between two clades with high support, which contradicts recent morphological classification scheme for Diogenidae sensu lato based on fossil records. The genus Diogenes Dana, 1851 was found nested inside Paguristes Dana, 1851, which formed a clade being separated from the remainder, pointing towards paraphyly in Paguristes. In another clade, Dardanus Paulson, 1875 occupied a basal position relative to the other diogenids, while Calcinus Dana, 1851 and Clibanarius Dana, 1852 showed sister relationships and formed a cluster with Ciliopagurus Forest, 1995. Among the morphological characters examined, carapace shield and telson were identified as phylogenetically significant for grouping diogenid genera, while phylogenetic insignificance of gill number was evidenced by its mosaic pattern in diogenid phylogeny. The present study sheds light on the controversial generic phylogeny of Diogenidae and highlights the necessity for thorough taxonomic revisions of this family as well as some genera (e.g., Paguristes) to reconcile current classifications with phylogenetic relationships.

A comprehensive morphological classification scheme for local ventilation performance zones in spatially heterogeneous urban areas

Modifying urban-built structures is a promising strategy for ventilation enhancement when designing sustainable communities. However, incorporating ventilation considerations into planning processes can be challenging because of tradeoffs and synergy among effects of various urban forms on local ventilation efficiency. This study aims to comprehensively integrate morphological parameters from aerodynamic perspective to distinguish local ventilation efficiency within heterogeneous urban areas. By synthesizing influences of spatial factors on airflow, “wind permeability, wind reinforcing, and wind accessibility” were resolved to form the local ventilation performance zone (LVPZ) characterization framework and its parameterization system. Accordingly, a spatial division standard and typical types of LVPZ classification scheme were developed. With an LVPZ-map generated in Wuhan, stable wind speed sequences were observed and their ventilation performance differences were interpreted among LVPZs using wind monitoring and CFD simulation. This scheme helps planners to evaluate local ventilation performance and provide a decision support tool for wind-sensitive urban development.

A remote sensing-based classification approach for river mouths of the Amazon-influenced Guianas coast

The mouths of the rivers on the 1500-km-long Guianas coast, South America, are strongly influenced by large mud banks migrating alongshore from the Amazon River. To probe this influence, a river-mouth morphological classification scheme was carried out from satellite images, complemented by data from rare previous studies of estuarine hydrodynamics. The classification highlights a variety of morphological and dynamic river-mouth types that are further influenced by both fluvial water discharge and fluvial catchment rock type. Three basic types are identified: (1) river mouths diverted westward by capes and spits built from multi-decadal to multi-millennial accumulation of mud supplied by the Amazon; among these, mouths close to the Amazon are fixed by bedrock surrounded by mud; (2) small river mouths in French Guiana fixed by outcrops of Precambrian rocks that form headlands devoid of Amazon mud; and (3) large river mouths characterized by high water discharge that imparts an orientation normal to the coast; the largest two belonging to this type (the Essequibo in Guyana and the Maroni on the border between French Guiana and Suriname) exhibit infilled mouths that are transitioning towards deltas. These river mouths show a tropical seasonal estuarine circulation regime strongly influenced by Amazon mud. The influence of mud from the distant Amazon constitutes a unique aspect of the river mouths on the Guianas coast. Field and modelling studies in the future will be needed in order to achieve better characterization of the influence of Amazon mud on the estuarine circulation systems and of the distribution of sediment types within these river mouths, including sand supplied by the rivers.

Forthcoming Issues

Recent advances in molecular diagnostics have led to better understanding of glioma tumorigenesis and biology. Numerous glioma biomarkers with diagnostic, prognostic, and predictive value have been identified. Although some of these markers are already part of the routine clinical management of glioma patients, data regarding others are limited and difficult to apply routinely. In addition, multiple methods for molecular subclassification have been proposed either together with or as an alternative to the current morphologic classification and grading scheme. This article reviews the literature regarding glioma biomarkers and offers a few practical suggestions.

A Comprehensive Morphological Classification Scheme for Local Ventilation Performance Zones in Highly Spatially Heterogeneous Urban Areas

A Comprehensive Morphological Classification Scheme for Local Ventilation Performance Zones in Highly Spatially Heterogeneous Urban Areas

Viewing Classical Radio Galaxies with the Upgraded GMRT and MeerKAT—A Progress Report

We present a progress report of a study of FR I and FR II radio galaxies. Several new morphological features in the radio emission are now revealed using the high (μJy) sensitivity reached in the range 550–1712 MHz, more than a factor of three, at the high (∼4″−7″) angular resolution with the upgraded Giant Metrewave Radio Telescope (uGMRT) and MeerKAT. Therefore, the aim of this study is to understand if we need to revise our current classification scheme for classical radio galaxies. In order to address our goals, we have carefully constructed a sample of 14 (6 FR I, 6 FR II and 2 FR 0) radio galaxies. The uGMRT and MeerKAT images of our four target sources revealed a wealth of morphological details, e.g., filamentary structure in the emission from the lobes, misalignments, radio emission beyond the hot-spots in three sources, etc.; see Fanaroff et al. (2021). Here, we present preliminary results for two more radio galaxies from our sample using uGMRT, in the light of the local environment. Finally, we are awaiting uGMRT and MeerKAT observations of remaining sample sources. Our results show that for the radio galaxies in this study, the morphological classification scheme for the classical FR I/FR II radio galaxies still holds, even with the improved imaging capabilities of the uGMRT and MeerKAT. Furthermore, we need to be cautious when using automated procedures for classification schemes, e.g., in surveys (with poorer sensitivities and angular resolutions) because of the rich morphological details that are shown in our uGMRT and MeerKAT images.

“A prospective study on the clinical course and proposed morphological classification scheme of microsporidial keratoconjunctivitis.”

ABSTRACT Background and objective: To describe the clinical course and propose a morphological classification scheme of microsporidial keratoconjunctivitis. Methods: This is a prospective study at L V Prasad Eye Institute, Odisha, between August–January (2017–19). Patients of any age or sex, microbiologically proven as microsporidial keratoconjunctivitis were included. Demographic parameters, history, clinical course, and visual outcome were analysed. All received artificial tear substitutes till resolution and topical immunosuppressants used in cases of persisting sub-epithelial infiltrates (SEI) beyond 2 weeks. Results: Fifty-three eyes of 47 cases were included with males, 72.3%. Corneal lesions were classified into 3 morphological types- coarse, ring, and flat-topped (Type1, 2 & 3). Depending upon the location, Type 1 was further sub-divided into peripheral, paracentral, central, and diffuse (Type 1a, b, c & d). The mean age was highest in Type 3(p = .026). Risk factors and prior steroid use were most common in Type 1d. The mean duration of symptom before presentation was longest in Type 3(11.6 ± 3.65) days. Severe conjunctival congestion at presentation in more than half of the eyes were seen in Type 1a, 1b and 1d, with moderate congestion at Day14 persisting in 66.7% and 40% of eyes belonging to Type 1c and 1d, respectively. Keratic precipitates were most common in Type 2. The mean duration of resolution was longest in Type 1d (38 ± 15.87) days and shortest in type 1b (7.88 ± 2.47) days (p = .022). Persistent SEIs beyond Day 90 were seen in total of 6 (11.3%) (Type 1c & 1d- 3 each) eyes and recurrent SEIs in 7(13.2%) (Type 1c-2 & 1d- 5) eyes. The mean duration of topical steroids use was longest in Type 1d (49.3 ± 22.3) days, followed by Type 1c (28 ± 0) days. Conclusion: Microsporidial keratoconjunctivitis can have a variable clinical presentation, the course of each being different depending on the host and ocular surface factors. Though considered as a self-limiting disease, central and diffuse coarse variety (Type1c&1d) required long-term topical immunosuppressants and follow-up.

AstroVaDEr: astronomical variational deep embedder for unsupervised morphological classification of galaxies and synthetic image generation

ABSTRACT We present AstroVaDEr (Astronomical Variational Deep Embedder), a variational autoencoder designed to perform unsupervised clustering and synthetic image generation using astronomical imaging catalogues. The model is a convolutional neural network that learns to embed images into a low-dimensional latent space, and simultaneously optimizes a Gaussian Mixture Model (GMM) on the embedded vectors to cluster the training data. By utilizing variational inference, we are able to use the learned GMM as a statistical prior on the latent space to facilitate random sampling and generation of synthetic images. We demonstrate AstroVaDEr’s capabilities by training it on grey-scaled gri images from the Sloan Digital Sky Survey, using a sample of galaxies that are classified by Galaxy Zoo 2. An unsupervised clustering model is found that separates galaxies based on learned morphological features such as axial ratio, surface brightness profile, orientation, and the presence of companions. We use the learned mixture model to generate synthetic images of galaxies based on the morphological profiles of the Gaussian components. AstroVaDEr succeeds in producing a morphological classification scheme from unlabelled data, but unexpectedly places high importance on the presence of companion objects – demonstrating the importance of human interpretation. The network is scalable and flexible, allowing for larger data sets to be classified, or different kinds of imaging data. We also demonstrate the generative properties of the model, which allow for realistic synthetic images of galaxies to be sampled from the learned classification scheme. These can be used to create synthetic image catalogues or to perform image processing tasks such as deblending.

The 2018 Banff Working Group classification of definitive polyomavirus nephropathy: A multicenter validation study in the modern era.

Polyomavirus nephropathy (PVN) remained inadequately classified until 2018 when the Banff Working Group published a new 3‐tier morphologic classification scheme derived from in‐depth statistical analysis of a large multinational patient cohort. Here we report a multicenter “modern‐era” validation study that included 99 patients with definitive PVN transplanted post January 1, 2009 and followed the original 2018 study design. Results validate the PVN classification, that is, the 3 PVN disease classes predicted clinical presentation, allograft function, and outcome independent of therapeutic intervention. PVN class 1 compared to classes 2 and 3 was diagnosed earlier (16.9 weeks posttransplant [median], P = .004), and showed significantly better function at 24 months postindex biopsy (serum creatinine 1.75 mg/dl, geometric mean, vs class 2: P = .037, vs class 3: P = .013). Class 1 presented during long‐term follow‐up with a low graft failure rate: 5% class 1, vs 30% class 2, vs 50% class 3 (P = .009). Persistent PVN was associated with an increased risk for graft failure (and functional decline in class 2 at 24 months postdiagnosis; serum creatinine with persistence: 2.48 mg/dL vs 1.65 with clearance, geometric means, P = .018). In conclusion, we validate the 2018 Banff Working Group PVN classification that provides significant clinical information and enhances comparative data analysis.

Multiband Galaxy Morphologies for CLASH: A Convolutional Neural Network Transferred from CANDELS

We present visual-like morphologies over 16 photometric bands, from ultraviolet to near-infrared, for 8412 galaxies in the Cluster Lensing And Supernova survey with Hubble (CLASH) obtained using a convolutional neural network (ConvNet) model. Our model follows the Cosmic Assembly Near-IR Deep Extragalactic Legacy Survey (CANDELS) main morphological classification scheme, obtaining the probability for each galaxy at each CLASH band of being spheroid, disk, irregular, point source, or unclassifiable. Our catalog contains morphologies for each galaxy with Hmag < 24.5 in every filter where the galaxy is observed. We trained an initial ConvNet model using approximately 7500 expert eyeball labels from CANDELS. We created eyeball labels for 100 randomly selected galaxies per each of the 16-filter set of CLASH (1600 galaxy images in total), where each image was classified by at least five of us. We use these labels to fine-tune the network to accurately predict labels for the CLASH data and to evaluate the performance of our model. We achieve a root-mean-square error of 0.0991 on the test set. We show that our proposed fine-tuning technique reduces the number of labeled images needed for training, as compared to directly training over the CLASH data, and achieves a better performance. This approach is very useful to minimize eyeball labeling efforts when classifying unlabeled data from new surveys. This will become particularly useful for massive data sets such as those coming from near-future surveys such as EUCLID or the LSST. Our catalog consists of prediction of probabilities for each galaxy by morphology in their different bands and is made publicly available at http://www.inf.udec.cl/~guille/data/Deep-CLASH.csv.

Molecular phylogeny of the genus Clibanarius (Decapoda: Anomura: Diogenidae) based on mitochondrial and nuclear DNA sequences

Clibanarius, a genus of hermit crabs, is one of the most diverse genera within Diogenidae. However, studies on the phylogeny within Clibanarius is very limited. We reconstruct the molecular phylogeny of the genus Clibanarius based on two mitochondrial (16S rRNA and COI) and two nuclear protein-coding (NaK and PEPCK) genes using a multigene phylogenetic approach. Eleven selected Clibanarius species from the Indo-West Pacific are analyzed and the Bayesian and maximum likelihood analyses produced identical results in topology. Results suggest that C. rutilus and C. infraspinatus are more closely related to each other than to C. snelliusi, and C. striolatus shows a close relationship to C. longitarsus. The close association of C. merguiensis with C. englaucus and C. humilis is strongly supported by the divergence of C. virescens from them. Our phylogenetic results contradict the morphological classification scheme proposed for Clibanarius and indicate that the relative length of dactyls and propodi is not phylogenetically significant in Clibanarius. In addition, we speculate that the morphological characteristic of the median cleft of the telson might be phylogenetically important for Clibanarius.

A simplified morphological classification scheme for pyramidal cells in six layers of primary somatosensory cortex of juvenile rats

The majority of neurons in the neocortex are excitatory pyramidal cells (PCs). Many systematic classification schemes have been proposed based the neuronal morphology, the chemical composition, and the synaptic connectivity, etc. Recently, a cortical column of primary somatosensory cortex (SSC) has been reconstruction and functionally simulated (Markram et al., 2015). Putting forward from this study, here we proposed a simplified classification scheme for PCs in all layers of the SSC by mainly identifying apical dendritic morphology based on a large data set of 3D neuron reconstructions. We used this scheme to classify three types in layer 2, two in layer 3, three in layer 4, four in layer 5, and six types in layer 6. These PC types were visually distinguished and confirmed by quantitative differences in their morphometric properties. The classes yielded using this scheme largely corresponded with PC classes that were defined previously based on other neuronal and synaptic properties such as long-range projects and synaptic innervations, further validating its applicability. Therefore, the morphology information of apical dendrites is sufficient for a simple scheme to classify a spectrum of anatomical types of PCs in the SSC.

Galaxies image classification using artificial bee colony based on orthogonal Gegenbauer moments

The development of automated morphological classification schemes for galaxies is important to study the formation and subsequent evolution of galaxies in our universe. This paper proposed a new machine learning method for classifying three types of galaxies image (Hubble types) namely elliptical, lenticulars, and spirals. The proposed approach consists of three stages: In the first stage, the features are extracted from the galaxies image by using Gegenbauer moments that have several properties like scale, rotation, and invariant. However, not all these extract features are relevant; therefore, in the second stage, a swarm algorithm called artificial bee colony (ABC) is used as feature selection method, where ABC has a small number of parameters and its fast convergence to the global solution. The third stage is used to evaluate the performance of the selected features in the classification of galaxies image through using the support vector machine as a classifier. The experimental results are performed based on a sample from EFIGI catalog, and the results show the high performance of the proposed method.

The Banff Working Group Classification of Definitive Polyomavirus Nephropathy: Morphologic Definitions and Clinical Correlations

Polyomavirus nephropathy (PVN) is a common viral infection of renal allografts, with biopsy-proven incidence of approximately 5%. A generally accepted morphologic classification of definitive PVN that groups histologic changes, reflects clinical presentation, and facilitates comparative outcome analyses is lacking. Here, we report a morphologic classification scheme for definitive PVN from the Banff Working Group on Polyomavirus Nephropathy, comprising nine transplant centers in the United States and Europe. This study represents the largest systematic analysis of definitive PVN undertaken thus far. In a retrospective fashion, clinical data were collected from 192 patients and correlated with morphologic findings from index biopsies at the time of initial PVN diagnosis. Histologic features were centrally scored according to Banff guidelines, including additional semiquantitative histologic assessment of intrarenal polyomavirus replication/load levels. In-depth statistical analyses, including mixed effects repeated measures models and logistic regression, revealed two independent histologic variables to be most significantly associated with clinical presentation: intrarenal polyomavirus load levels and Banff interstitial fibrosis ci scores. These two statistically determined histologic variables formed the basis for the definition of three PVN classes that correlated strongest with three clinical parameters: presentation at time of index biopsy, serum creatinine levels/renal function over 24 months of follow-up, and graft failure. The PVN classes 1-3 as described here can easily be recognized in routine renal biopsy specimens. We recommend using this morphologic PVN classification scheme for diagnostic communication, especially at the time of index diagnosis, and in scientific studies to improve comparative data analysis.

Automated morphological classification of galaxies based on projection gradient nonnegative matrix factorization algorithm

The development of automated morphological classification schemes can successfully distinguish between morphological types of galaxies and can be used for studies of the formation and subsequent evolution of galaxies in our universe. In this paper, we present a new automated machine supervised learning astronomical classification scheme based on the Nonnegative Matrix Factorization algorithm. This scheme is making distinctions between all types roughly corresponding to Hubble types such as elliptical, lenticulars, spiral, and irregular galaxies. The proposed algorithm is performed on two examples with different number of image (small dataset contains 110 image and large dataset contains 700 images). The experimental results show that galaxy images from EFIGI catalog can be classified automatically with an accuracy of ∼93% for small and ∼92% for large number. These results are in good agreement when compared with the visual classifications.

Morphological characterization via light and electron microscopy of atlantic jackknife clam (Ensis directus) hemocytes

The Atlantic jackknife clam, Ensis directus, is currently being researched as a potential species for aquaculture operations in Maine. The goal of this study was to describe the hemocytes of this species for the first time and provide a morphological classification scheme. We viewed hemocytes under light microscopy (using Hemacolor, neutral red, and Pappenheim's stains) as well as transmission electron microscopy (TEM). The 2 main types of hemocytes found were granulocytes and hyalinocytes (agranular cells). The granulocytes were subdivided into large and small granulocytes while the hyalinocytes were subdivided into large and small hyalinocytes. The large hemocytes had both a larger diameter and smaller nucleus to cell diameter ratio than their smaller counterparts. A rare cell type, the vesicular cell, was also observed and it possessed many vesicles but few or no granules. Using TEM, granulocytes were found to contain both electron-lucent and electron-dense granules of various sizes. These numerous granules were the only structures that took up the neutral red stain. Hyalinocytes had few of these granules relative to granulocytes. Large hyalinocytes had both various organelles and large vesicles in their abundant cytoplasm while small hyalinocytes had little room for organelles in their scant cytoplasm. Total hemocyte counts averaged 1.96×10(6) cells mL(-1) while differential hemocyte counts averaged 11% for small hyalinocytes, 12% for large hyalinocytes, 59% for small granulocytes, and 18% for large granulocytes. The results of this study provide a starting point for future studies on E. directus immune function.

Morphological characterization via light and electron microscopy of Atlantic jackknife clam (Ensis directus) hemocytes

The Atlantic jackknife clam, Ensis directus, is currently being researched as a potential species for aquaculture operations in Maine. The goal of this study was to describe the hemocytes of this species for the first time and provide a morphological classification scheme. We viewed hemocytes under light microscopy (using Hemacolor, neutral red, and Pappenheim’s stains) as well as transmission electron microscopy (TEM). The 2 main types of hemocytes found were granulocytes and hyalinocytes (agranular cells). The granulocytes were subdivided into large and small granulocytes while the hyalinocytes were subdivided into large and small hyalinocytes. The large hemocytes had both a larger diameter and smaller nucleus to cell diameter ratio than their smaller counterparts. A rare cell type, the vesicular cell, was also observed and it possessed many vesicles but few or no granules. Using TEM, granulocytes were found to contain both electron-lucent and electron-dense granules of various sizes. These numerous granules were the only structures that took up the neutral red stain. Hyalinocytes had few of these granules relative to granulocytes. Large hyalinocytes had both various organelles and large vesicles in their abundant cytoplasm while small hyalinocytes had little room for organelles in their scant cytoplasm. Total hemocyte counts averaged 1.96×106 cells mL−1 while differential hemocyte counts averaged 11% for small hyalinocytes, 12% for large hyalinocytes, 59% for small granulocytes, and 18% for large granulocytes. The results of this study provide a starting point for future studies on E. directus immune function.

DNA barcoding of genus Metapenaeopsis (Decapoda: Penaeidae) and molecular phylogeny inferred from mitochondrial and nuclear DNA sequences

Metapenaeopsis Bouvier, 1905 is the most diverse genus within Penaeidae. Metapenaeopsis shrimps exhibited subtle morphological differences, which make identification a difficult task based on taxonomic keys alone. In this study, we carried out DNA barcoding and phylogenetic analyses to examine taxonomy and phylogeny of genus Metapenaeopsis based on mitochondrial (COI) and nuclear (PEPCK and NaK) genes. Despite limited performance of DNA barcoding in delineating Metapenaeopsis shrimps, it questioned the taxonomic status of the two subspecies, Metapenaeopsis mogiensis intermedia and Metapenaeopsis mogiensis mogiensis, as well as three separate species: Metapenaeopsis provocatoria longirostris, Metapenaeopsis quinquedentata and Metapenaeopsis velutina. The major pattern of relationships between all studied taxa of Metapenaeopsis was similar across all analytical methods in which species with one-valved petasma were genetically distinct from those with two-valved petasma. As expected from morphology, the remaining species with stridulating organ constituted a strongly supported clade. In contrast, a paraphyletic clade was resolved for species without stridulating organ which contradicts Crosnier's morphological classification scheme for Metapenaeopsis. Overall, the present molecular data indicated that the shape of petasma and stridulating organ were both phylogenetically significant morphological characters for this genus, adding further evidence for the Crosnier's proposal.

A unified nomenclature for tectonic structures on the surface of Enceladus

Enceladus has experienced widespread and diverse tectonic deformation. The diversity and nonuniform distribution of structures visible on the surface attests to a complicated and perhaps long-lived tectonic history. Currently, no fundamental classification scheme based on morphology exists for the tectonic structures on Enceladus, which limits analysis and discussion of tectonic structures and regional and global tectonic histories. Characterization and classification of structures on Enceladus is an important first step in understanding its tectonic history. Here, we propose a global morphologic (i.e., nongenetic) classification scheme for tectonic structures on Enceladus. Five classes of tectonic structures on Enceladus have been identified based on images and limited topographic data: troughs, scarps, chasmata, ridges, and bands. Morphological variation of structures exists within these classes, reinforcing the complicated tectonic history of this small body.

Correlations Between the Morphological Type and Concentration Indices in Different Photometric Bands

In this work, we continue to examine whether the u-, g-, i- and z-band concentration indices are a good morphological classification tool. Our statistical results demonstrate that compared with the r-band concentration index, the g-band concentration index may be a better choice for use as a parameter in automated morphological classification schemes. The u-band concentration index is the worst choice of the five photometric band concentration indices.