Morphology-based Classification Research Articles

Nephrotic Syndrome Throughout Childhood: Diagnosing Podocytopathies From the Womb to the Dorm.

The etiologies of podocyte dysfunction that lead to pediatric nephrotic syndrome (NS) are vast and vary with age at presentation. The discovery of numerous novel genetic podocytopathies and the evolution of diagnostic technologies has transformed the investigation of steroid-resistant NS while simultaneously promoting the replacement of traditional morphology-based disease classifications with a mechanistic approach. Podocytopathies associated with primary and secondary steroid-resistant NS manifest as diffuse mesangial sclerosis, minimal change disease, focal segmental glomerulosclerosis, and collapsing glomerulopathy. Molecular testing, once an ancillary option, has become a vital component of the clinical investigation and when paired with kidney biopsy findings, provides data that can optimize treatment and prognosis. This review focuses on the causes including selected monogenic defects, clinical phenotypes, histopathologic findings, and age-appropriate differential diagnoses of nephrotic syndrome in the pediatric population with an emphasis on podocytopathies.

Classification and counting of cells in brightfield microscopy images: an application of convolutional neural networks

Microscopy is integral to medical research, facilitating the exploration of various biological questions, notably cell quantification. However, this process's time-consuming and error-prone nature, attributed to human intervention or automated methods usually applied to fluorescent images, presents challenges. In response, machine learning algorithms have been integrated into microscopy, automating tasks and constructing predictive models from vast datasets. These models adeptly learn representations for object detection, image segmentation, and target classification. An advantageous strategy involves utilizing unstained images, preserving cell integrity and enabling morphology-based classification—something hindered when fluorescent markers are used. The aim is to introduce a model proficient in classifying distinct cell lineages in digital contrast microscopy images. Additionally, the goal is to create a predictive model identifying lineage and determining optimal quantification of cell numbers. Employing a CNN machine learning algorithm, a classification model predicting cellular lineage achieved a remarkable accuracy of 93%, with ROC curve results nearing 1.0, showcasing robust performance. However, some lineages, namely SH-SY5Y (78%), HUH7_mayv (85%), and A549 (88%), exhibited slightly lower accuracies. These outcomes not only underscore the model's quality but also emphasize CNNs' potential in addressing the inherent complexities of microscopic images.

Two chloroplast genomes with reduced inverted repeat regions in Mammillaria series Stylothelae (Cactaceae)

Background: The chloroplast genomes of Cactaceae exhibit boundary modifications in the inverted repeat regions (IRs), gene inversions, and deletions. Among nine Mammillaria species, three distinct chloroplast structures have been identified, although not all of these correspond to the morphology-based classification of the genus.
 Question: Is there a distinct chloroplast genome structure in the species of Mammillaria series Stylothelae?
 Studied species: Mammillaria bocasana and M. erythrosperma.
 Study site and dates: Mexico from 2019 to 2023.
 Methods: Chloroplast DNA was sequenced, and chloroplast genomes were de novo assembled using the Fast-Plast program. Complete plastome sequences were annotated and verified. The sequences were aligned in MAUVE program to detect possible structural changes. A maximum likelihood phylogeny was executed to evaluate the relationships of the studied species.
 Results: The plastomes ranged from 107,368 bp in Mammillaria bocasana to 108,069 bp in M. erythrosperma. Both presented a quadripartite structure and contained 108 genes. The IRs were ~ 1,600 bp long and included the genes rpl2, rpl23 (pseudo), and trnI-CAU. MAUVE identified a ~ 21 kb inversion in the large single copy containing a block of genes related to photosynthesis. The phylogenetic analysis placed both species in a single clade separated from the other species within Mammillaria subg. Mammillaria.
 Conclusions: The studied species of Mammillaria series Stylothelae exhibited a different and synapomorphic chloroplast genome structure. Other Mammillaria chloroplast genome structures have evolved independently in different lineages.

Machine Learning based Sorting of Somatic Embryos for In-Line processing in Automated SE Fluidics System

Somatic embryogenesis (SE) can be a viable method for the clonal propagation of many economically significant forest trees, particularly coniferous trees like pines and spruces. However, large-scale production of SE plants requires automation to reduce manual labor and attain cost-efficiency. The most labor-intensive step of the SE process for SE plant production is selecting and harvesting mature embryos. Embryo maturation is not a synchronized process; selecting the most developed embryos capable of continuous development is necessary. However, there needs to be more research conducted on mapping morphological features to germination-competent mature somatic embryos. This paper lays down the preliminary work of employing machine learning techniques for classifying large volumes of images of mature somatic embryos processed using an automated SE processing system based on fluidics processing referred to as SE Fluidics system. The results show that machine learning could be an alternative classification methodology instead of the traditional manual morphology-based classification process based on image analysis. The paper discusses two popular image classification techniques, namely Convolution Neural Network (CNN) and Support Vector Machine (SVM), applying them to both binary (black and white) and grayscale images. It is observed that grayscale images provide better accuracy with the SVM technique and outperform morphology-based classification in terms of processing speed (17.6% faster) across the test envelope. On the other hand, CNN-based classification shows better processing speeds only at a lower number of convolution layers. Hence, the data scientist can optimally select the number of convolution layers to get the desired accuracy-processing speed combination.

Structural and Functional Disparities within the Human Gut Virome in Terms of Genome Topology and Representative Genome Selection.

Circularity confers protection to viral genomes where linearity falls short, thereby fulfilling the form follows function aphorism. However, a shift away from morphology-based classification toward the molecular and ecological classification of viruses is currently underway within the field of virology. Recent years have seen drastic changes in the International Committee on Taxonomy of Viruses' operational definitions of viruses, particularly for the tailed phages that inhabit the human gut. After the abolition of the order Caudovirales, these tailed phages are best defined as members of the class Caudoviricetes. To determine the epistemological value of genome topology in the context of the human gut virome, we designed a set of seven experiments to assay the impact of genome topology and representative viral selection on biological interpretation. Using Oxford Nanopore long reads for viral genome assembly coupled with Illumina short-read polishing, we showed that circular and linear virus genomes differ remarkably in terms of genome quality, GC skew, transfer RNA gene frequency, structural variant frequency, cross-reference functional annotation (COG, KEGG, Pfam, and TIGRfam), state-of-the-art marker-based classification, and phage-host interaction. Furthermore, the disparity profile changes during dereplication. In particular, our phage-host interaction results demonstrated that proportional abundances cannot be meaningfully compared without due regard for genome topology and dereplication threshold, which necessitates the need for standardized reporting. As a best practice guideline, we recommend that comparative studies of the human gut virome always report the ratio of circular to linear viral genomes along with the dereplication threshold so that structural and functional metrics can be placed into context when assessing biologically relevant metagenomic properties such as proportional abundance.

Morphology-based molecular classification of spinal cord ependymomas using deep neural networks.

Based on DNA-methylation, ependymomas growing in the spinal cord comprise two major molecular types termed spinal (SP-EPN) and myxopapillary ependymomas (MPE(-A/B)), which differ with respect to their clinical features and prognosis. Due to the existing discrepancy between histomorphogical diagnoses and classification using methylation data, we asked whether deep neural networks can predict the DNA methylation class of spinal cord ependymomas from hematoxylin and eosin stained whole-slide images. Using explainable AI, we further aimed to prospectively improve the consistency of histology-based diagnoses with DNA methylation profiling by identifying and quantifying distinct morphological patterns of these molecular ependymoma types. We assembled a case series of 139 molecularly characterized spinal cord ependymomas (nMPE = 84, nSP-EPN = 55). Self-supervised and weakly-supervised neural networks were used for classification. We employed attention analysis and supervised machine-learning methods for the discovery and quantification of morphological features and their correlation to the diagnoses of experienced neuropathologists. Our best performing model predicted the DNA methylation class with 98% test accuracy and used self-supervised learning to outperform pretrained encoder-networks (86% test accuracy). In contrast, the diagnoses of neuropathologists matched the DNA methylation class in only 83% of cases. Domain-adaptation techniques improved model generalization to an external validation cohort by up to 22%. Statistically significant morphological features were identified per molecular type and quantitatively correlated to human diagnoses. The approach was extended to recently defined subtypes of myxopapillary ependymomas (MPE-(A/B), 80% test accuracy). In summary, we demonstrated the accurate prediction of the DNA methylation class of spinal cord ependymomas (SP-EPN, MPE(-A/B)) using hematoxylin and eosin stained whole-slide images. Our approach may prospectively serve as a supplementary resource for integrated diagnostics and may even help to establish a standardized, high-quality level of histology-based diagnostics across institutions-in particular in low-income countries, where expensive DNA-methylation analyses may not be readily available.

Benefits of Morphology-Based Functional Group Classification to Study Dynamic Changes in Phytoplankton in Saline-Alkali Wetlands, Taking Typical Saline-Alkali Wetlands in Northeast China as an Example

Phytoplankton are sensitive to the change in hydrological environment and can effectively reflect the health status of water, so they are often used for water quality assessment. To understand the recovery process of phytoplankton community structure characteristics and water quality conditions, two methods of phytoplankton classification functional group (FG) and morphology-based functional group (MBFG) were compared based on morphological differences and applicability. In this study, we investigated the changes in the aquatic environmental conditions and phytoplankton functional groups in the saline wetland of Dagangzipao during the restoration process of the Songnen Plain. The functional group division method suitable for saline-alkali wetlands was also determined. The results showed that there were 86 species belonging to 47 genera and seven phyla. The average phytoplankton biomass range in 2020 is 0.37 mg/L–3.59 mg/L, and the average phytoplankton biomass range in 2021 is 0.01 mg/L–1.44 mg/L. The Q-index showed that the water quality was in a good state. The redundancy analysis showed that the characteristics of phytoplankton functional groups showed a good indication of the habitat characteristics of saline-alkali wetlands, and the environmental interpretation of the MBFG was higher than that of the FG. The results provide a reference for the sustainable development of saline wetland water environment protection and ecological restoration.

Molecular phylogeny, biogeography, and species delimitation of segmented spider genus Liphistius (Araneae: Liphistiidae) in Thailand

Abstract Mesothelae, or primitively segmented trapdoor spiders, form the most basal clade among living spiders. In Southeast Asia, Liphistius is the only genus recognized in the extant family Liphistiidae. Liphistius taxonomy and species identification are based largely on characters of the genitalia; however, the female genitalia show high intraspecific variation, males are rarely collected, and the phylogenetic relationships among the 69 described Liphistius species are unresolved. Here, we focused on the Liphistius of Thailand, including 37 described and numerous undescribed species in four species groups. We generated sequences from five loci (COI, 16S, H3, 28S, and ITS2) for 162 specimens from 52 sites in Thailand and Myanmar to reconstruct phylogenetic relationships, infer historical biogeography, and delimit species. The five-locus data set resolved nearly all species and species group relationships and was mostly congruent with morphology-based classifications. Ancestral area reconstruction suggested that Liphistius originated in Sibumasu (Siam–Burma–Malaysia–Sumatra) and diversified into several species groups, four (birmanicus, bristowei, linang, and trang) of which are found in Thailand. Speciation within Liphistius occurred in the area corresponding to their current distribution. All delimitation methods tested (ASAP, GMYC, PTP, STACEY and BFD) delimited specimens from discrete locations as separate species; variation in the number of species proposed (ranging from 53 to 72) stemmed from variation in delimitation of sympatric cryptic species.

Morphology-based classification of the flying capacities of aquatic insects: A first attempt

Abstract Flight is a key feature of the reproduction and dispersal of emerging aquatic insects. However, morphological measurements of insect flight are mostly available for terrestrial taxa and dragonflies, while aquatic insects have been poorly investigated. We analyzed seven flight-related morphological parameters of 32 taxa belonging to five orders of emerging aquatic insects (Ephemeroptera, Trichoptera, Plecoptera, Diptera, and Megaloptera) with different life history traits related to flight (dispersal strategy, voltinism, adult lifespan, and swarming behavior). After correcting for allometry, we used an a priori-free approach to cluster the individuals according to their flight-related morphology. Then, we explored the levels of agreement between these clusters, taxonomy, and several life history traits of the taxa. All orders were scattered among several clusters, suggesting a large range of flight capacities, particularly for Diptera. We found swarming taxa in each cluster, showing that morphological adaptations to swarming are not identical in all aquatic insects. The clusters did not match the expected dispersal capacity of the taxa as derived from the literature or databases. Heavy wide-winged insects notably gathered taxa traditionally described as good or weak dispersers. Flight capacities based on morphology partly matched with the taxonomy and life-history traits of aquatic insect imagoes. Other parameters such as flight propensity, energy stores, and wing kinematics should help refine their flying and dispersal capacity.

Ankle Radiographic Characteristics of Two Different Types of Valgus Ankle Arthritis: With or Without Progressive Collapsing Foot Deformity

Category: Ankle Arthritis; Ankle Introduction/Purpose: Establishing a surgical plan for ankle arthritis requires a thorough understanding of the deforming forces involved. While ankle morphology-based classification and application are common in the surgical treatment of varus ankle arthritis (i.e., Takakura stage), such an approach has not been described for valgus ankle arthritis. Progressive collapsing foot deformity (PCFD) has been identified as the major cause of non-traumatic valgus ankle arthritis. However, mounting evidence suggests that it can also develop without PCFD, which may mean that the etiology and possibly the outcomes of treatment are different when comparing the two groups. Therefore, this study aimed to investigate whether weightbearing ankle radiographs can be used to differentiate PCFD origin from non-PCFD origin in valgus ankle arthritis. Methods: This study retrospectively reviewed patients who were surgically treated for asymmetric valgus ankle arthritis at our institution between 2017 and 2021. Patients with valgus tibiotalar tilt (TT >4 degrees and Meary’s angle>30 degrees) were included in the PCFD group (n=24). A control group (non-PCFD group [n=24]) with valgus tibiotalar tilt>4 degrees and Meary’s angle < 4 degrees was also established. In the weightbearing ankle anteroposterior (AP) view, the TT and medial distal tibial angle (MDTA) were measured. Additionally, to assess mediolateral position of the talus, the talar center migration (TCM) and lateral talar dome-plafond distance (LTD-P) ratio was measured (Figure 1A). Other PCFD radiographic parameters were also measured. In weightbearing computed tomography (WBCT), the degree of axial plane talocalcaneal subluxation was assessed using transmalleolar axis method as previously described, and the prevalence of sinus tarsi bony impingement was assessed. All parameters were compared between groups using Student t- or chi-square tests. Results: Both groups demonstrated a similar degree of TT, with a mean and standard deviation of 11.1±7.8 degrees in the PCFD group and 12.7±5.9 degrees in the non-PCFD group (p=0.2013, Table 1). However, the PCFD group showed a significantly greater TCM and LTD-P ratio compared to those of the non-PCFD group (p < 0.0001), indicating that PCFD patients have a more medially translated talus in ankle AP radiographs (Figure 1A). WBCT showed that the PCFD group had a greater axial plane talocalcaneal subluxation (p < 0.0001) and a higher prevalence of sinus tarsi bony impingement (p=0.0077) compared to the non- PCFD group, indicating a different degree of subtalar joint subluxation between the two groups. Conclusion: This study demonstrates that weightbearing ankle radiographs reveal different morphologies based on the etiology of valgus ankle arthritis. While both groups exhibited similar degrees of valgus tibiotalar tilt, PCFD patients demonstrated medial translation of the talus compared to non-PCFD patients. We propose a morphology-based classification (Figure 1B) that may assist in differentiating between the PCFD and non-PCFD origins of valgus ankle arthritis. Also, the different morphology of the valgus tibiotalar tilt in the each group may mean that they may require different treatments, as well as potentially different outcomes of treatment for the valgus tibiotalar tilt.

Phylogeny and infrageneric classification of Clerodendrum (Lamiaceae)

Abstract The infrageneric classification of the genus Clerodendrum (Lamiaceae) has been highly problematic due to different concepts and subdivisions being applied to the treatment of Asian, Australian, and African species. Earlier molecular phylogenetic studies based on Sanger sequencing and limited sampling have indicated that previous morphology-based infrageneric classifications are not congruent with the phylogeny due to morphological convergence in many lineages. Advances in high-throughput DNA sequencing provide more information allowing more robust phylogenetic reconstruction at larger scale. We present the first comprehensive phylogenetic study of Clerodendrum that includes representatives of all previously recognized infrageneric taxa and using targeted sequencing data obtained from the Angiosperms353 enrichment to resolve the phylogenetic relationships. In agreement with previous phylogenetic work, our phylogeny shows that Asian and Australian species form a sister clade to an African Clade. Clerodendrum is monophyletic with the exclusion of some tropical coastal species, including some Australian species, which fall within a clade containing Volkameria and New World genera. We recognize two subgenera: subgen. Clerodendrum for Asian and Australian species and the new subgen. Afroclerodendrum for African and Malagasy species. Our findings support an infrageneric classification of Clerodendrum with a total of 13 sections based on molecular phylogenetic evidence and morphology that clearly accommodate the Asian, remaining Australian, and African species. Of these, we propose three new sections: sect. Albiflora, sect. Fortunata and sect. Megaflora for clades presenting unique morphological characters. The sectional classification and taxonomic consequences are discussed.

Marine Flora of French Polynesia: An Updated List Using DNA Barcoding and Traditional Approaches.

Located in the heart of the South Pacific Ocean, the French Polynesian islands represent a remarkable setting for biological colonization and diversification, because of their isolation. Our knowledge of this region's biodiversity is nevertheless still incomplete for many groups of organisms. In the late 1990s and 2000s, a series of publications provided the first checklists of French Polynesian marine algae, including the Chlorophyta, Rhodophyta, Ochrophyta, and Cyanobacteria, established mostly on traditional morphology-based taxonomy. We initiated a project to systematically DNA barcode the marine flora of French Polynesia. Based on a large collection of ~2452 specimens, made between 2014 and 2023, across the five French Polynesian archipelagos, we re-assessed the marine floral species diversity (Alismatales, Cyanobacteria, Rhodophyta, Ochrophyta, Chlorophyta) using DNA barcoding in concert with morphology-based classification. We provide here a major revision of French Polynesian marine flora, with an updated listing of 702 species including 119 Chlorophyta, 169 Cyanobacteria, 92 Ochrophyta, 320 Rhodophyta, and 2 seagrass species-nearly a two-fold increase from previous estimates. This study significantly improves our knowledge of French Polynesian marine diversity and provides a valuable DNA barcode reference library for identification purposes and future taxonomic and conservation studies. A significant part of the diversity uncovered from French Polynesia corresponds to unidentified lineages, which will require careful future taxonomic investigation.

From clinical variables to multiomics analysis: a margin morphology-based gross classification system for hepatocellular carcinoma stratification

ObjectiveSelecting interventions for patients with solitary hepatocellular carcinoma (HCC) remains a challenge. Despite gross classification being proposed as a potential prognostic predictor, its widespread use has been restricted due to...

Chloroplast genome evolution and phylogeny of the early-diverging charophycean green algae with a focus on the Klebsormidiophyceae and Streptofilum.

The Klebsormidiophyceae are a class of green microalgae observedglobally in both freshwater and terrestrial habitats. Morphology-based classification schemes of this class have been shown to be inadequate due to the simple morphology of these algae, the tendency of morphology to vary in culture versus field conditions, and rampant morphological homoplasy. Molecular studies revealing cryptic diversity have renewed interest in this group. We sequenced the complete chloroplast genomes of a broad series of taxa spanning the known taxonomic breadth of this class. We also sequenced the chloroplast genomes of three strains of Streptofilum, a recently discovered green algal lineage with close affinity to the Klebsormidiophyceae. Our results affirm the previously hypothesized polyphyly of the genus Klebsormidium as well as the polyphyly of the nominal species in this genus, K. flaccidum. Furthermore, plastome sequences strongly support the status of Streptofilum as a distinct, early-diverging lineage of charophytic algae sister to a clade comprising Klebsormidiophyceae plus Phragmoplastophyta. We also uncovered major structural alterations in the chloroplast genomes of species in Klebsormidium that have broad implications regarding the underlying mechanisms of chloroplast genome evolution.

Molecular systematics of Jania species (Corallinales, Rhodophyta) from south-eastern Australia based on cox1 and psbA DNA sequence analyses

Taxonomy of the calcified marine red macroalgal genus Jania (Corallinales, Rhodophyta) is traditionally built on the comparative analyses of vegetative and reproductive morpho-anatomical characters. However, Jania species often display high levels of morphological plasticity leading to frequent homoplasies. Cryptic speciation and the occurrence of overlapping diagnostic characters between some species often compromises species identification based on the type method. Molecular methods represent powerful tools to help test morphology-based classifications, delineate morphologically challenging species, and solve taxonomic quagmires. A recent morphology-based taxonomic study of the genus Jania, using the type-method and focusing on the south-eastern Australian flora, recognized five species and two varieties. To test this morphology-based assessment we performed dual-marker (cox1 and psbA) phylogenetic and species delineation analyses of selected south-eastern Australia Jania herbarium specimens. Our results confirmed the molecular distinction of Jania crassa, J. micrarthrodia, J. pedunculata, J. rosea, and J. sagittata in Australia. The highly polymorphic J. rosea represents a species-complex. A group of specimens identified as Jania rosea are Corallina berteroi, which represents another species-complex in the genus Corallina. Several potentially new species were also resolved. Molecular phylogenetic analyses of Jania species from other localities around Australia and the world, including type and topotype specimens, are called for. Also, the development of new primers and potentially new markers specifically designed to better amplify and sequence contemporary and historically significant Jania specimens deposited in herbaria are crucial to obtain greater phylogenetic support on deeper nodes and improved taxonomic certainty.

Evolutionary history, traits, and weediness inDigitaria(Poaceae: Panicoideae)

AbstractDigitaria is a large pantropical genus, which includes a number of economically problematic agricultural weeds. Difficulties in species identification and the circumscription of the genus have previously hindered progress in understanding its evolution and developing a stable classification. We investigate the evolutionary history of Digitaria by combining two approaches: (i) phylogenetic analyses of the currently available Sanger sequence data with previously unpublished sequences mainly from South East Asia, and (ii) newly generated genomic data from low-copy nuclear genes obtained using the Angiosperms353 probe kit, with new data mainly from Madagascar. Both methods gave congruent results. The combination of these results allowed us to confirm a new clade structure within Digitaria lineages, in partial agreement with the previous morphology-based classifications. We confirm that Digitaria as traditionally circumscribed is not monophyletic, comprising Anthephora, Baptorhachis, Chaetopoa, and Chlorocalymma. We present an inference of key character evolution with morphological support for clades with spikelets arranged in binate and ternate groups, with variable trichome morphology, spikelet length, and culm length. Geographical clade structure is also observed. No phylogenetic signal of weedy function was observed.

Finding AGN remnant candidates based on radio morphology with machine learning

Context. Remnant radio galaxies represent the dying phase of radio-loud active galactic nuclei (AGN). Large samples of remnant radio galaxies are important for quantifying the radio-galaxy life cycle. The remnants of radio-loud AGN can be identified in radio sky surveys based on their spectral index, and identifications can be confirmed through visual inspection based on their radio morphology. However, this latter confirmation process is extremely time-consuming when applied to the new large and sensitive radio surveys. Aims. Here, we aim to reduce the amount of visual inspection required to find AGN remnants based on their morphology using supervised machine learning trained on an existing sample of remnant candidates. Methods. For a dataset of 4107 radio sources with angular sizes of larger than 60 arcsec from the LOw Frequency ARray (LOFAR) Two-Metre Sky Survey second data release (LoTSS-DR2), we started with 151 radio sources that were visually classified as ‘AGN remnant candidate’. We derived a wide range of morphological features for all radio sources from their corresponding Stokes-I images: from simple source-catalogue-derived properties to clustered Haralick-features and self-organising-map(SOM)-derived morphological features. We trained a random forest classifier to separate the AGN remnant candidates from the yet-to-be inspected sources. Results. The SOM-derived features and the total-to-peak flux ratio of a source are shown to have the greatest influence on the classifier. For each source, our classifier outputs a positive prediction, if it believes the source to be a likely AGN remnant candidate, or a negative prediction. The positive predictions of our model include all initially inspected AGN remnant candidates, plus a number of yet-to-be inspected sources. We estimate that 31 ± 5% of sources with positive predictions from our classifier will be labelled AGN remnant candidates upon visual inspection, while we estimate the upper bound of the 95% confidence interval for AGN remnant candidates in the negative predictions to be 8%. Visual inspection of just the positive predictions reduces the number of radio sources requiring visual inspection by 73%. Conclusions. This work shows the usefulness of SOM-derived morphological features and source-catalogue-derived properties in capturing the morphology of AGN remnant candidates. The dataset and method outlined in this work bring us closer to the automatic identification of AGN remnant candidates based on radio morphology alone and the method can be used in similar projects that require automatic morphology-based classification in conjunction with small labelled sample sizes.

Brief Insight on Nanovesicular Liposomes as Drug-delivery Carriers for Medical Applications

Nanotechnology has revolutionized and improved the potential of drug-delivery systems. Lipidic nanovesicles, termed liposomes, offer several benefits as drug-delivery carriers due to their compositional similarity with human biological membranes. Some of the advantages offered by liposomes include targeted drug delivery and improved pharmacokinetics of an entrapped drug substance, leading to enhanced bioavailability. Additionally, the reduction in the drug dose or dosing frequency, reduced drug toxicity or side effects, longer and controlled therapeutic response of a drug essential for the treatment of chronic diseases, and improved patient acceptance margins are some other benefits offered by liposomes. The easily modifiable surface of liposomes makes it an ideal vehicle for targeting a drug to the desired site. The current review provides insight on liposomes as drug-delivery carriers. This review summarizes the classification of compositional constituents of liposomes based on their chemical nature and structure. Morphology-based classification of liposomes along with methods of preparation and characterization for liposomes are also summarized. The current review emphasizes the medical applications of liposomes, specifically as delivery carriers for therapeutic and diagnostic agents. The article features detailed therapeutic applications of liposomes based on routes of administration and specific disease conditions. Diagnostic applications of liposomes for improving the efficiency of available techniques to treat diseases such as cancer are also discussed. Liposomes are thus reviewed as multifaceted nanovesicular carriers with potential therapeutic and diagnostic medical applications. The prospective multifunctional application of combining imaging functionality with therapeutic agents in a single liposome for diagnosis and real-time treatment is anticipated to be the future of liposomal formulations.

Microcystis pangenome reveals cryptic diversity within and across morphospecies.

Microcystis, a common harmful algal bloom (HAB) taxon, threatens water supplies and human health, yet species delimitation is contentious in this taxon, leading to challenges in research and management of this threat. Historical and common morphology-based classifications recognize multiple morphospecies, most with variable and diverse ecologies, while DNA sequence-based classifications indicate a single species with multiple ecotypes. To better delimit Microcystis species, we conducted a pangenome analysis of 122 genomes. Core- and non-core gene phylogenetic analyses placed 113 genomes into 23 monophyletic clusters containing at least two genomes. Overall, genome-related indices revealed that Microcystis contains at least 16 putative genospecies. Fifteen genospecies included at least one Microcystis aeruginosa morphospecies, and 10 genospecies included two or more morphospecies. This classification system will enable consistent taxonomic identification of Microcystis and thereby aid in resolving some of the complexities and controversies that have long characterized eco-evolutionary research and management of this important HAB taxon.

Metabolism-associated molecular classification of gastric adenocarcinoma.

Most gastric cancers (GC) are adenocarcinomas, whereas GC is a highly heterogeneous disease due to its molecular heterogeneity. However, traditional morphology-based classification systems, including the WHO classification and Lauren's classification, have limited utility in guiding clinical treatment. We performed nonnegative matrix factorization (NMF) clustering based on 2752 metabolism-associated genes. We characterized each of the subclasses from multiple angles, including subclass-associated metabolism signatures, immune cell infiltration, clinic10al characteristics, drug sensitivity, and pathway enrichment. As a result, four subtypes were identified: immune suppressed, metabolic, mesenchymal/immune exhausted and hypermutated. The subtypes exhibited significant prognostic differences, which suggests that the metabolism-related classification has clinical significance. Metabolic and hypermutated subtypes have better overall survival, and the hypermutated subtype is likely to be sensitive to anti-PD-1 immunotherapy. In addition, our work showed a strong connection with previously established classifications, especially Lei's subtype, to which we provided an interpretation based on the immune cell infiltration perspective, deepening the understanding of GC heterogeneity. Finally, a 120-gene classifier was generated to determine the GC classification, and a 10-gene prognostic model was developed for survival time prediction.