A Comparative Study of Feature Selection Methods for the Discriminative Analysis of Temporal Lobe Epilepsy

It is crucial to differentiate patients with temporal lobe epilepsy (TLE) from the healthy population and determine abnormal brain regions in TLE. The cortical features and changes can reveal the unique anatomical patterns of brain regions from structural magnetic resonance (MR) images. In this study, structural MR images from 41 patients with left TLE, 34 patients with right TLE, and 58 normal controls (NC) were acquired, and four kinds of cortical measures, namely cortical thickness, cortical surface area, gray matter volume (GMV), and mean curvature, were explored for discriminative analysis. Three feature selection methods including the independent sample t-test filtering, the sparse-constrained dimensionality reduction model (SCDRM), and the support vector machine-recursive feature elimination (SVM-RFE) were investigated to extract dominant features among the compared groups for classification using the support vector machine (SVM) classifier. The results showed that the SVM-RFE achieved the highest performance (most classifications with more than 84% accuracy), followed by the SCDRM, and the t-test. Especially, the surface area and GMV exhibited prominent discriminative ability, and the performance of the SVM was improved significantly when the four cortical measures were combined. Additionally, the dominant regions with higher classification weights were mainly located in the temporal and the frontal lobe, including the entorhinal cortex, rostral middle frontal, parahippocampal cortex, superior frontal, insula, and cuneus. This study concluded that the cortical features provided effective information for the recognition of abnormal anatomical patterns and the proposed methods had the potential to improve the clinical diagnosis of TLE

The Mitochondrial Genome of Cylicocyclus elongatus (Strongylida: Strongylidae) and Its Comparative Analysis with Other Cylicocyclus Species

Cylicocyclus elongatus (C. elongatus) is one of the species in Cylicocyclus, subfamily Cyathostominae, but its taxonomic status in Cylicocyclus is controversial. Mitochondrial (mt) genome is an excellent gene marker which could be used to address the taxonomy controversy. In the present study, the complete mt genome of C. elongatus was determined, and sequence and phylogenetic analyses were performed based on mtDNA data to determine the classification of C. elongatus. The circular complete mt genome of C.elongatus was 13875 bp in size, containing 12 protein-coding genes (12 PCGs), 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and 2 non-coding regions (NCRs). The A + T content of C. elongatus complete mt genome was 76.64%. There were 19 intergenic spacers with lengths of 2–53 bp and 2 overlaps with lengths of 1–2 bp in the impact complete mt genome. ATT and TAA were the most common start and termination codons of 12 PCGs, respectively. Comparative analyses of mt genomes nucleotide sequence and amino acid sequence showed that there were higher identities between C. elongatus and five other Cylicocyclus, rather than with P. imparidentatum. Phylogenetic analyses based on concatenated nucleotide sequences of 12 PCGs of 23 species in the family Strongylidae showed that C. elongatus was closely related to Cylicocyclus species, rather than P. imparidentatum. We concluded that C. elongatus was a member in Cylicocyclus based on comparative and phylogenetic analyses of mt genome sequences. The data of the complete mt genome sequence of C. elongatus provide a new and useful genetic marker for further research on Cyathostominae nematodes

Chromosome-Level Genome Assembly and Transcriptome Comparison Analysis of Cephalopholis sonnerati and Its Related Grouper Species

The tomato hind, Cephalopholis sonnerati, is a bottom-dwelling coral reef fish, which is widely distributed in the Indo-Pacific and Red Sea. C. sonnerati also features complex social structures and behaviour mechanisms. Here, we present a high-quality, chromosome-level genome assembly for C. sonnerati that was derived using PacBio sequencing and Hi-C technologies. A 1043.66 Mb genome with an N50 length of 2.49 Mb was assembled, produced containing 795 contigs assembled into 24 chromosomes. Overall, 97.2% of the complete BUSCOs were identified in the genome. A total of 26,130 protein-coding genes were predicted, of which 94.26% were functionally annotated. Evolutionary analysis revealed that C. sonnerati diverged from its common ancestor with E. lanceolatus and E. akaara approximately 41.7 million years ago. In addition, comparative genome analyses indicated that the expanded gene families were highly enriched in the sensory system. Finally, we found the tissue-specific expression of 8108 genes. We found that these tissue-specific genes were highly enriched in the brain. In brief, the high-quality, chromosome-level reference genome will provide a valuable genome resource for studies of the genetic conservation, resistance breeding, and evolution of C. sonnerati

Microbiota Community Structure and Interaction Networks within <i>Dermacentor silvarum</i>, <i>Ixodes persulcatus</i>, and <i>Haemaphysalis concinna</i>

Ticks carry and transmit a variety of pathogens, which are very harmful to humans and animals. To characterize the microbial interactions in ticks, we analysed the microbiota of the hard ticks, Dermacentor silvarum, Ixodes persulcatus, and Haemaphysalis concinna, using 16S rRNA, showing that microbial interactions are underappreciated in terms of shaping arthropod microbiomes. The results show that the bacterial richness and microbiota structures of these three tick species had significant differences. Interestingly, the bacterial richness (Chao1 index) of all ticks decreased significantly after they became engorged. All the operational taxonomic units (OTUs) were assigned to 26 phyla, 67 classes, 159 orders, 279 families, and 627 genera. Microbial interactions in D. silvarum demonstrated more connections than in I. persulcatus and H. concinna. Bacteria with a high abundance were not important families in microbial interactions. Positive interactions of Bacteroidaceae and F_Solibacteraceae Subgroup 3 with other bacterial families were detected in all nine groups of ticks. This study provides an overview of the microbiota structure and interactions of three tick species and improves our understanding of the role of the microbiota in tick physiology and vector capacity, thus being conducive to providing basic data for the prevention of ticks and tick-borne diseases

Controllable synthesis of monodispersed silver nanoparticles as standards for quantitative assessment of their cytotoxicity.

<p id="abspara0010"> Silver nanoparticles (Ag NPs) are appealing due to their excellent antibacterial/antivirus properties. At the meantime, the wide applications of Ag NPs as antibacterial/antivirus agents arise the concern of Ag NPs&rsquo; toxicity. However, quantitative understanding of the cytotoxicity of Ag NPs is minimum since that the Ag NPs in current studies have wide size distributions, in which the size effect of Ag NPs on cytotoxicity was unable to be accurately evaluated. In this work, unprecedentedly monodispersed Ag NPs with sizes of 25, 35, 45, 60 and 70&nbsp;nm were obtained, respectively, by using an optimized polyol method with poly(vinyl pyrrolidone) (PVP) as surfactant. It was found that the reaction temperature, reaction time, concentration of the surfactant and reactants are playing important roles in determining the size and size distribution of Ag NPs. With the monodispersed Ag NPs as standard samples, the size- and dose- dependent cytotoxicity of Ag NPs against Human lung fibroblast (HLF) cells was accurately accomplished in terms of cell viability, apoptosis and necrosis, reactive oxygen species, etc. We expect that the monodispersed Ag NPs will act as the standard samples for quantitatively characterizing the toxicity of Ag NPs <em>in&nbsp;vitro</em> and <em>in&nbsp;vivo</em>.</p

Genetic variability within and among Haemonchus contortus isolates from goats and sheep in China

BACKGROUND: Haemonchus contortus (order Strongylida) is a common parasitic nematode infecting small ruminants and causing significant economic losses worldwide. Knowledge of genetic variation within and among H. contortus populations can provide a foundation for understanding transmission patterns, the spread of drug resistance alleles and might assist in the control of haemonchosis. METHODS: 152 H. contortus individual adult worms were collected from seven different geographical regions in China. The second internal transcribed spacer (ITS-2) of the nuclear ribosomal DNA and mitochondrial nicotinamide dehydrogenase subunit 4 gene (nad4) were amplified by polymerase chain reaction (PCR) and sequenced directly. The sequence variations and population genetic diversities were determined. RESULTS: Nucleotide sequence analyses revealed 18 genotypes (ITS-2) and 142 haplotypes (nad4) among the 152 worms, with nucleotide diversities of 2.6% and 0.027, respectively, consistent with previous reports from other countries, including Australia, Brazil, Germany, Italy, Malaysia, Sweden, the USA and Yemen. Population genetic analyses revealed that 92.4% of nucleotide variation was partitioned within populations; there was no genetic differentiation but a high gene flow among Chinese populations; some degree of genetic differentiation was inferred between some specimens from China and those from other countries. CONCLUSIONS: This is the first study of genetic variation within H. contortus in China. The results revealed high within-population variations, low genetic differentiation and high gene flow among different populations of H. contortus in China. The present results could have implications for studying the epidemiology and ecology of H. contortus in China

Two benzimidazole resistance-associated SNPs in the isotype-1 β-tubulin gene predominate in Haemonchus contortus populations from eight regions in China

Haemonchus contortus is one of the most important parasitic nematodes of small ruminants around the world, particularly in tropical and subtropical regions. The control of haemonchosis relies mainly on anthelmintics, but the excessive and prolonged use of anthelmintics is causing serious drug resistance issues in many countries. As benzimidazole (BZ) anthelmintics have been broadly used in China, we hypothesized that resistance is widespread. Given the link between three known single nucleotide polymorphisms (SNPs, designated F167Y, E198A and F200Y) in the isotype-1 β-tubulin gene and BZ resistance, our goal here was to explore the presence of these mutations in H. contortus from small ruminants (sheep and goats) from eight provinces in China using PCR-coupled sequencing. In addition, the genetic diversity and genetic relationship of isotype-1 β-tubulin sequence haplotypes were also investigated. Among 192 H. contortus adult individuals representing the eight populations, we identified six distinct sequence types, five of which had SNP E198A (GCA) and/or F200Y (TAC). Sequence analysis showed that the frequencies of SNPs E198A and F200Y were 0–70% and 0–31%, respectively. SNP F167Y (TAC) was not detected in any population. In addition, high haplotype diversities (0.455–0.939) and nucleotide diversities (0.018–0.039) were calculated. A network analysis of the isotype-1 β-tubulin gene sequences showed that SNPs E198A and F200Y occurred in multiple distinct groupings, suggesting multiple independent origins of these SNPs. The findings of this first study of SNPs in the isotype-1 β-tubulin gene of H. contortus populations suggest that BZ resistance is prevalent in some regions of China, and that any control strategy might focus on monitoring BZ resistance in this country

Additional file 1: Figure S1. of Population structure of Haemonchus contortus from seven geographical regions in China, determined on the basis of microsatellite markers

Locations of seven populations of Haemonchus contortus in China. (TIF 2529 kb