Vindmcclellan9390

The mean percentages of correct predictions of the CDS and the non-CDS test sets at the genus level were 71% and 50% for bacteria, 65% and 73% for fungi (excluding AMF), and 49% and 72% for AMF (Rhizophagus irregularis), respectively. SeSaMe provides a means for estimating not only taxonomic diversity and abundance but also the gene reservoir of the reference taxonomic groups associated with AMF. Therefore, it enables users to study the symbiotic roles of associated microorganisms. It can also be applicable to other microorganisms as well as soil metagenomes. SeSaMe is freely available at www.fungalsesame.org.In this article, we introduce a novel bioinformatics program, Spore-associated Symbiotic Microbes Position-Specific Function (SeSaMe PS Function), for position-specific functional analysis of short sequences derived from metagenome sequencing data of the arbuscular mycorrhizal fungi. The unique advantage of the program lies in databases created based on genus-specific sequence properties derived from protein secondary structure, namely amino acid usages, codon usages, and codon contexts of 3-codon DNA 9-mers. SeSaMe PS Function searches a query sequence against reference sequence database, identifies 3-codon DNA 9-mers with structural roles, and creates comparative dataset containing the codon usage biases of the 3-codon DNA 9-mers from 54 bacterial and fungal genera. The program applies correlation principal component analysis in conjunction with K-means clustering method to the comparative dataset. 3-codon DNA 9-mers clustered as a sole member or with only a few members are often structurally and functionally distinctive sites that provide useful insights into important molecular interactions. The program provides a versatile means for studying functions of short sequences from metagenome sequencing and has a wide spectrum of applications. SeSaMe PS Function is available for free downloading at www.fungalsesame.org.Chinese mitten crab (Eriocheir sinensis) is an important aquaculture species in Crustacea. Functional analysis, although essential, has been hindered due to the lack of sufficient genomic or transcriptomic resources. In this study, transcriptome sequencing was conducted on 59 samples representing diverse developmental stages (fertilized eggs, zoea, megalopa, three sub-stages of larvae, juvenile crabs, and adult crabs) and different tissues (eyestalk, hepatopancreas, and muscle from juvenile crabs, and eyestalk, hepatopancreas, muscle, heart, stomach, gill, thoracic ganglia, intestine, ovary, and testis from adult crabs) of E. sinensis. A comprehensive reference transcriptome was assembled, including 19,023 protein-coding genes. Hierarchical clustering based on 128 differentially expressed cuticle-related genes revealed two distinct expression patterns during the early larval developmental stages, demonstrating the distinct roles of these genes in "crab-like" cuticle formation during metamorphosis and cuticle calcification after molting. Phylogenetic analysis of 1406 one-to-one orthologous gene families identified from seven arthropod species and Caenorhabditis elegans strongly supported the hypothesis that Malacostraca and Branchiopoda do not form a monophyletic group. Furthermore, Branchiopoda is more phylogenetically closely related to Hexapoda, and the clade of Hexapoda and Branchiopoda and the clade of Malacostraca belong to the Pancrustacea. This study offers a high-quality transcriptome resource for E. sinensis and demonstrates the evolutionary relationships of major arthropod groups. The differentially expressed genes identified in this study facilitate further investigation of the cuticle-related gene expression networks which are likely associated with "crab-like" cuticle formation during metamorphosis and cuticle calcification after molting.Previous studies reported that some important loci are missed in single-locus genome-wide association studies (GWAS), especially because of the large phenotypic error in field experiments. To solve this issue, multi-locus GWAS methods have been recommended. However, only a few software packages for multi-locus GWAS are available. Therefore, we developed an R software named mrMLM v4.0. This software integrates mrMLM, FASTmrMLM, FASTmrEMMA, pLARmEB, pKWmEB, and ISIS EM-BLASSO methods developed by our lab. There are three components in mrMLM v4.0, including dataset input, parameter setting, and result output. The fread function in data.table is used to quickly read datasets, especially big datasets, and the doParallel package is used to conduct parallel computation using multiple CPUs. In addition, the graphical user interface software mrMLM.GUI v4.0, built upon Shiny, is also available. To confirm the correctness of the aforementioned programs, all the methods in mrMLM v4.0 and three widely-used methods were used to analyze real and simulated datasets. The results confirm the superior performance of mrMLM v4.0 to other methods currently available. False positive rates are effectively controlled, albeit with a less stringent significance threshold. RGD(ArgGlyAsp)Peptides mrMLM v4.0 is publicly available at BioCode (https//bigd.big.ac.cn/biocode/tools/BT007077) or R (https//cran.r-project.org/web/packages/mrMLM.GUI/index.html) as an open-source software.

Transoral incisionless fundoplication (TIF) is an endoscopic alternative for the treatment of GERD. However, TIF does not address the hiatal hernia (HH). We present a novel approach with a laparoscopic HH repair followed by same-session TIF, coined concomitant transoral incisionless fundoplication (cTIF). The aim of this study was to assess the efficacy, safety, and feasibility of cTIF in a collaborative approach between Gastroenterology and surgery.

Patients with confirmed GERD and >2 cm HH who underwent cTIF between 2018 and 2020 were included. Symptoms were assessed using the Reflux Disease Questionnaire, GERD Health-Related Quality of Life Index, and the Reflux Symptom Index pre and post cTIF. One-way ANOVA and paired samples t-test were used for statistical analysis.

Sixty patients underwent cTIF (53% were men, mean age was 59.3 years) with 100% technical success. Mean ± SD HH measurement on endoscopy was 2.9 ± 1.5 cm. Scores on Reflux Disease Questionnaire for symptom frequency and symptom severity improved significantly from before to 6 months after cTIF (17.