MediLite3DNet: A lightweight network for segmentation of nasopharyngeal airways.

The precise segmentation and three-dimensional reconstruction of the nasopharyngeal airway are crucial for the diagnosis and treatment of adenoid hypertrophy in children. However, traditional methods face challenges such as information loss and low computational efficiency when addressing this task. To overcome these issues, this paper introduces an innovative lightweight 3D medical image segmentation network-MediLite3DNet.

New insights and investigation: Morphomolecular notes on the infraciliature, taxonomy, and systematics of pleurostomatid ciliates (Protozoa, Ciliophora), with establishment of a new suborder, two new genera, and three new species.

Pleurostomatid ciliates, as a highly diverse and widely distributed unicellular eukaryote group, play a crucial role in the cycling of nutrients and energy in microbial food webs. However, research on pleurostomatids remains insufficient, resulting in a paucity of molecular information and substantial gaps in knowledge of their phylogenetic relationships. In recent years, we investigated pleurostomatid diversity in various Chinese habitats, including their systematic relationships and taxonomic circumscriptions, which were comprehensively analyzed using an integrative morphomolecular approach.

Findings on three endocommensal scuticociliates (Protista, Ciliophora) from freshwater mollusks, including their morphology and molecular phylogeny with descriptions of two new species.

Unlabelled: Species of the ciliate genera and are found as endocommensals of terrestrial and freshwater mollusks, respectively. So far, there have been few studies of these genera and morphological data for most members are often incomplete. In the present work, two new species, sp.

New evidence of consistency between phylogeny and morphology for two taxa in ciliated protists, the subclasses Oligotrichia and Choreotrichia (Protista, Ciliophora).

Marine planktonic ciliates are largely oligotrichs and choreotrichs, which are two subclasses of the class Spirotrichea. The current phylogenetic assignments of oligotrichs and choreotrichs are inconsistent with previous results based on morphological features, probably hindered by the limited information from a single gene locus. Here we provide 53 new sequences from small subunit ribosomal RNA (SSU rDNA), ITS1-5.

Biodiversity of freshwater ciliates (Protista, Ciliophora) in the Lake Weishan Wetland, China: the state of the art.

Unlabelled: Ciliates are core components of the structure of and function of aquatic microbial food webs. They play an essential role in the energy flow and material circulation within aquatic ecosystems. However, studies on the taxonomy and biodiversity of freshwater ciliates, especially those in wetlands in China are limited.

Integrative studies on the taxonomy and molecular phylogeny of four new species (Protozoa, Ciliophora, Scuticociliatia).

Unlabelled: The ciliate genus comprises approximately 30 nominal species and has been reported in freshwater, brackish water, and marine habitats. Nevertheless, recent studies have indicated that there might be a large undiscovered species diversity. In the present work, four new species, namely sp.

From oral structure to molecular evidence: new insights into the evolutionary phylogeny of the ciliate order Sessilida (Protista, Ciliophora), with the establishment of two new families and new contributions to the poorly studied family Vaginicolidae.

Ciliated protists represent one of the most primitive and diverse lineages of eukaryotes, with nuclear dimorphism, a distinctive sexual process (conjugation), and extensive genome rearrangements. Among divergent ciliate lineages, the peritrich order Sessilida includes members with a colonial lifestyle, which may hint to an independent evolutionary attempt for multicellularity, although they are still single-celled organisms. To date, the evolution and phylogeny of this group are still far from clear, in part due to the paucity of molecular and/or morphological data for many taxa.

Insights into the phylogeny of the family Deviatidae (Protozoa, Ciliophora, Hypotrichia) based on multi-gene, morphological and ontogenetic information, with the establishment of a new species Deviata multilineae n. sp.

Hitherto, the phylogeny of ciliated protists, an important group of model organisms in many fields, has been mainly based on a single marker gene (SSU rDNA, nuclear small subunit ribosomal RNA gene). However, there is increasing evidence showing this is insufficient to provide robust phylogenies and has resulted in confusing systematics in many ciliates groups. Among these, the phylogenies within family Deviatidae (Spirotrichea, Hypotrichia) are ambiguous due to the dependence on SSU rDNA and undersampling.

Molecular phylogeny and taxonomy of four species (Protozoa, Ciliophora): A flagship genus of karyorelictean ciliates, with descriptions of two new species.

During faunal studies of psammophilic ciliates along the coast of Qingdao, China, several marine karyorelictean species were isolated. Among them, four species within the genus were investigated, including two species new to science: i.e.

Taxonomy and molecular phylogeny of two poorly known ciliate genera, Balantidion and Acropisthium (Protista: Ciliophora: Litostomatea), including a new species of Balantidion.

The class Litostomatea Small & Lynn, 1981 is a morphologically diverse ciliate group including hundreds of free-living and endocommensal species. The genera Acropisthium Perty, 1852 and Balantidion Eberhard, 1862 previously consisted of one free-living freshwater species each. Here, we not only highlight additional morphological features of the two type species, but also investigate a new species, Balantidion foissneri sp.

The Effects of DNA Extraction Kits and Primers on Prokaryotic and Eukaryotic Microbial Community in Freshwater Sediments.

DNA based sequencing technology has revolutionized the field of microbial ecology and environmental studies. However, biases can be introduced at all experimental steps and, thus, affect the interpretation of microbial community. So far, previous studies on the biases introduced from the key steps of DNA extraction and primer sets mainly focused on the bacterial communities in soil or sediment samples, while little is known about the effect on the eukaryotic microbial communities.

Changes of the Freshwater Microbial Community Structure and Assembly Processes during Different Sample Storage Conditions.

A long-standing dilemma for microbial analyses is how to handle and store samples, as it is widely assumed that the microbial diversity and community patterns would be affected by sample storage conditions. However, it is quite challenging to maintain consistency in field sampling, especially for water sample collection and storage. To obtain a comprehensive understanding of how sample storage conditions impact microbial community analyses and the magnitude of the potential storage effects, freshwater samples were collected and stored in bottles with lid closed and without lid at room temperature for up to 6 days.

Comparative Genome Analysis Reveals -Regulatory Elements on Gene-Sized Chromosomes of Ciliated Protists.

Gene-sized chromosomes are a distinct feature of the macronuclear genome in ciliated protists known as spirotrichs. These nanochromosomes are often only several kilobase pairs long and contain a coding region for a single gene. However, the ways in which transcription is regulated on nanochromosomes is still largely unknown.

Multi-Gene Phylogeny of the Ciliate Genus (Ciliophora, Hypotrichia), With Integrative Description of Two Species, Spec. nov. and (Cohn, 1866).

Many hypotrich genera, including , are taxonomically challenging and in a need of integrative revision. Using morphological data, molecular phylogenetic analyses, and internal transcribed spacer 2 (ITS2) secondary structures, we attempt to cast more light on species relationships within the genus . The present multifaceted approach reveals that (1) a large-sized species with numerous macronuclear nodules, isolated from sandy littoral sediments in southern China, is new to science and is endowed here with a name, spec.

Gut Mycobiota Dysbiosis in Pulmonary Tuberculosis Patients Undergoing Anti-Tuberculosis Treatment.

Patients with pulmonary tuberculosis (TB) undergoing anti-tuberculosis (anti-TB) treatment were previously reported to present gut bacterial microbiota dysbiosis, but the role of the mycobiota has not been reported. Here, we conducted a follow-up study of 29 naive TB patients who received first-line anti-TB drug treatment; we collected their fecal samples at different time points, as well as 22 fecal samples from healthy subjects. Fungal ITS2 and bacterial 16S rRNA amplicon sequencing were used to analyze the effects of active TB and anti-TB treatment on the gut microbiota.

Notes on Homalogastra similis nom. nov. (Ciliophora, Scuticociliatia), a replacement name for the junior homonym Homalogastra binucleata Liu et al., 2020.

We recently established a new species, Homalogastra binucleata, with a morphological description and phylogenetic analyses based on SSU rRNA gene sequence data (Liu et al., 2020). Helmut Berger (Salzburg, Austria) commented that Homalogastra binucleata Liu et al.

Overview of the Diversity, Phylogeny and Biogeography of Strombidiid Oligotrich Ciliates (Protista, Ciliophora), With a Brief Revision and a Key to the Known Genera.

Strombidiids are common free-living ciliates that have colonized coastal and open oceanic waters across the world. In recent years, numerous new taxa and gene sequences of strombidiids have been reported, revealing a large diversity of both their morphologic and genetic features. Here, we compare the taxonomic characters of all genera in the family Strombidiidae, provide a key to their identification, and investigate their molecular phylogeny.

Chromosome organization and gene expansion in the highly fragmented genome of the ciliate Strombidium stylifer.

Chromosomes are well-organized carriers of genetic information in eukaryotes and are usually quite long, carrying hundreds and thousands of genes. Intriguingly, a clade of single-celled ciliates, Spirotrichea, feature nanochromosomes-also called "gene-sized chromosomes". These chromosomes predominantly carry only one gene, flanked by short telomere sequences.

New Contributions to the Diversity of Hypotrichous Ciliates: Description of a New Genus and Two New Species (Protozoa, Ciliophora).

Ciliated protists (ciliates) are extremely diverse and play important ecological roles in almost all kinds of habitats. In this study, two new hypotrichs, n. g.

Integrative Studies on a New Ciliate n. sp. (Protista, Ciliophora, Peritrichia) Based on the Morphological and Molecular Data, With Notes on the Phylogeny and Systematics of the Family Epistylididae.

During an investigation on freshwater peritrichs, a new colonial sessilid ciliate, n. sp., was isolated from aquatic plants in an artificial freshwater pond in Qingdao, China.

New contributions to the taxonomy of urostylid ciliates (Ciliophora, Hypotrichia), with establishment of a new genus and new species.

Hypotrichia, one of the most complex and highly differentiated groups in Ciliophora, has been the object of extensive studies, especially in recent years. Nevertheless, methodological difficulties and insufficient faunistic studies have limited our understanding of their biodiversity and phylogeny. In this study, one novel urostylid ciliate, Pseudoholosticha zhaoi nov.

Biodiversity-based development and evolution: the emerging research systems in model and non-model organisms.

Evolutionary developmental biology, or Evo-Devo for short, has become an established field that, broadly speaking, seeks to understand how changes in development drive major transitions and innovation in organismal evolution. It does so via integrating the principles and methods of many subdisciplines of biology. Although we have gained unprecedented knowledge from the studies on model organisms in the past decades, many fundamental and crucially essential processes remain a mystery.

Large-scale phylogenomic analysis provides new insights into the phylogeny of the class Oligohymenophorea (Protista, Ciliophora) with establishment of a new subclass Urocentria nov. subcl.

The class Oligohymenophorea is one of the most diverse assemblage of ciliated protists, which are particularly important in fundamental biological studies including understanding the evolutionary relationships among the lineages. Phylogenetic relationships within the class remain largely elusive, especially within the subclass Peniculia, which contains the long-standing problematic taxa Urocentrum and Paranassula. In the present study, we sequenced the genomes and/or transcriptomes of six non-culturable oligohymenophoreans using single-cell sequencing techniques.

Taxonomy, Ontogenesis and Evolutionary Relationships of the Algae-Bearing Ciliate () comb. nov., With Establishment of a New Genus and New Family (Protista, Ciliophora, Hypotrichia).

Hypotrichs are the most complex and highly differentiated ciliate lineages and have great potential for evolutionary novelties. Problems in hypotrich systematics are mainly due to discordance between the morphological and genetic data (mainly small subunit rRNA gene). Species with morphologies that are characteristic of two or more higher rank taxa are probably a major contributing factor to these conflicts.