scholarly journals Fig. S1 & Tables S1-S4

2021 ◽  
Author(s):  
E. De Crop
Keyword(s):  
Sequence Data ◽  
Western Palearctic ◽  
Biogeographical Regions ◽  
Biogeographic Regions ◽  
Preliminary Study ◽  
Taxonomical Classification ◽  
Taxonomical Position ◽  
Environmental Sequences ◽  
Australasian Region

Figure S1. Overview map of the biogeographical regions used for Table 1. Biogeographic regions are based on biogeographic realms (https://ecoregions2017.appspot.com/), with three major differences: Western Palearctic (Western part of the Palearctic realm), Asia (Eastern part of the Palearctic realm combined with the Indo-Malay realm), and Australasia (Australasian realm combined with the Oceanian realm). The Palearctic realm was spilt into Western Palearctic and Eastern Palearctic, Eastern Palearctic and the Indo-Malay realm form together the Asia region, and the Australasian realm is combined with the Oceania realm to form the Australasian region.Table S1. List of described Lactifluus species, together with the year of description, taxonomical classification (subgenus, section), the indication of how this taxonomical position was defined, the source(s) of this classification, and notes.Table S2. Extra information on the preliminary study of metabarcoding data of the genus Lactifluus, retrieved from the GlobalFungi website.Table S3. Overview of the results of the preliminary study of metabarcoding data of the genus Lactifluus, retrieved from the GlobalFungi website. Due to the generally shorter length and lower quality of environmental sequence data, the numbers in the table are to be considered an estimate.Table S4. List of the putative new species found in the environmental sequences. References of studies cited are given in S3.

scholarly journals EukRef: phylogenetic curation of ribosomal RNA to enhance understanding of eukaryotic diversity and distribution

2018 ◽  
Author(s):  
Javier del Campo ◽  
Martin Kolisko ◽  
Vittorio Boscaro ◽  
Luciana F. Santoferrara ◽  
Ramon Massana ◽  
...  
Keyword(s):  
Sequence Data ◽  
Sequencing Data ◽  
Environmental Sequencing ◽  
Eukaryotic Diversity ◽  
Microbial Eukaryotes ◽  
Reference Databases ◽  
Environmental Sequences ◽  
Lineage Diversity

AbstractEnvironmental sequencing has greatly expanded our knowledge of micro-eukaryotic diversity and ecology by revealing previously unknown lineages and their distribution. However, the value of these data is critically dependent on the quality of the reference databases used to assign an identity to environmental sequences. Existing databases contain errors, and struggle to keep pace with rapidly changing eukaryotic taxonomy, the influx of novel diversity, and computational challenges related to assembling the high-quality alignments and trees needed for accurate characterization of lineage diversity. EukRef (eukref.org) is a community driven initiative that addresses these challenges by bringing together taxonomists with expertise spanning the complete eukaryotic tree of life and microbial ecologists that actively use environmental sequencing data for the purpose of developing reliable reference databases across the diversity of microbial eukaryotes. EukRef organizes and facilitates rigorous sequence data mining and annotation by providing protocols, guidelines and tools to do so.

scholarly journals Impact of a Smart-Ring-Based Feedback System on the Quality of Chest Compressions in Adult Cardiac Arrest: A Randomized Preliminary Study

2021 ◽  
Vol 18 (10) ◽  
pp. 5408
Author(s):  
Chiwon Ahn ◽  
Seungjae Lee ◽  
Jongshill Lee ◽  
Jaehoon Oh ◽  
Yeongtak Song ◽  
...  
Keyword(s):  
Primary Outcome ◽  
Feedback System ◽  
Controlled Study ◽  
Feedback Group ◽  
Compression Depth ◽  
System Usability Scale ◽  
The Mean ◽  
Preliminary Study ◽  
The Ideal

This study aimed to assess the effectiveness of a novel chest compression (CC) smart-ring-based feedback system in a manikin simulation. In this randomized, crossover, controlled study, we evaluated the effect of smart-ring CC feedback on cardiopulmonary resuscitation (CPR). The learnability and usability of the tool were evaluated with the System Usability Scale (SUS). Participants were divided into two groups and each performed CCs with and without feedback 2 weeks apart, using different orders. The primary outcome was compression depth; the proportion of accurate-depth (5–6 cm) CCs, CC rate, and the proportion of complete CCs (≤1 cm of residual leaning) were assessed additionally. The feedback group and the non-feedback group showed significant differences in compression depth (52.1 (46.3–54.8) vs. 47.1 (40.5–49.9) mm, p = 0.021). The proportion of accurate-depth CCs was significantly higher in the interventional than in the control condition (88.7 (30.0–99.1) vs. 22.6 (0.0–58.5%), p = 0.033). The mean SUS score was 83.9 ± 8.7 points. The acceptability ranges were ‘acceptable’, and the adjective rating was ‘excellent’. CCs with smart-ring feedback could help achieve the ideal range of depth during CPR. The smart-ring may be a valuable source of CPR feedback.

scholarly journals Quality of Life, Depression, Anxiety Symptoms and Mood State of Wheelchair Athletes and Non-athletes: A Preliminary Study

2019 ◽  
Vol 10 ◽  
Author(s):  
Rodrigo Luiz Vancini ◽  
Andressa Amato Gomes ◽  
Hudson de Paula-Oliveira ◽  
Claudio de Lira ◽  
Weverton Rufo-Tavares ◽  
...  
Keyword(s):  
Quality Of Life ◽  
Mood State ◽  
Anxiety Symptoms ◽  
Wheelchair Athletes ◽  
Preliminary Study

scholarly journals A new Plasmodium vivax reference sequence with improved assembly of the subtelomeres reveals an abundance of pir genes

2016 ◽  
Vol 1 ◽  
pp. 4 ◽  
Author(s):  
Sarah Auburn ◽  
Ulrike Böhme ◽  
Sascha Steinbiss ◽  
Hidayat Trimarsanto ◽  
Jessica Hostetler ◽  
...  
Keyword(s):  
South America ◽  
Plasmodium Vivax ◽  
Sequence Data ◽  
Ex Vivo ◽  
Vital Role ◽  
Asia Pacific ◽  
Reference Sequence ◽  
Manual Curation ◽  
Illumina Sequence

Plasmodium vivax is now the predominant cause of malaria in the Asia-Pacific, South America and Horn of Africa. Laboratory studies of this species are constrained by the inability to maintain the parasite in continuous ex vivo culture, but genomic approaches provide an alternative and complementary avenue to investigate the parasite’s biology and epidemiology. To date, molecular studies of P. vivax have relied on the Salvador-I reference genome sequence, derived from a monkey-adapted strain from South America. However, the Salvador-I reference remains highly fragmented with over 2500 unassembled scaffolds.  Using high-depth Illumina sequence data, we assembled and annotated a new reference sequence, PvP01, sourced directly from a patient from Papua Indonesia. Draft assemblies of isolates from China (PvC01) and Thailand (PvT01) were also prepared for comparative purposes. The quality of the PvP01 assembly is improved greatly over Salvador-I, with fragmentation reduced to 226 scaffolds. Detailed manual curation has ensured highly comprehensive annotation, with functions attributed to 58% core genes in PvP01 versus 38% in Salvador-I. The assemblies of PvP01, PvC01 and PvT01 are larger than that of Salvador-I (28-30 versus 27 Mb), owing to improved assembly of the subtelomeres.  An extensive repertoire of over 1200 Plasmodium interspersed repeat (pir) genes were identified in PvP01 compared to 346 in Salvador-I, suggesting a vital role in parasite survival or development. The manually curated PvP01 reference and PvC01 and PvT01 draft assemblies are important new resources to study vivax malaria. PvP01 is maintained at GeneDB and ongoing curation will ensure continual improvements in assembly and annotation quality.

scholarly journals Soil quality of the tea and apple-growing sites in Mindat District, Chin state, Myanmar: A preliminary study

2021 ◽  
Vol 70 (1) ◽  
pp. 27-40
Author(s):  
Yaung Kwee ◽  
Khin Soe
Keyword(s):  
Physicochemical Properties ◽  
Silty Clay ◽  
Subtropical Climate ◽  
Clay Loam ◽  
Silty Clay Loam ◽  
Preliminary Study ◽  
Phosphorus And Potassium ◽  
Very High ◽  
Physicochemical Properties Of Soils

In this study, two sites from tea and apple growing sites were collected from Pyay village and Nine Mile village, Mindat district, Chin state of West Myanmar under a humid subtropical climate. The results of physicochemical properties of observed soils were neutral pH, favorable moisture, silty clay loam texture, very high content of organic carbon, organic matter and total nitrogen. However, the tea growing soil was very poor in phosphorus and potassium content. Moreover, both soils lack of available potassium. The content of heavy metals in both soils was not varied from each other and followed the order: Fe (iron) > Cu (copper) >Zn (zinc) > Pb (lead) > Cr (chromium) and was below the maximum allowed concentrations (MAC). Therefore, the studied soils are generally favorable for cultivation under the condition of application of phosphorus and potassium fertilizers. However, due to the regular application of fertilizers and pesticides, it is necessary to monitor these soils for PTE levels. Further research is recommended, which must include analyses of the physicochemical properties of soils to a two depths of 0-30 and 30-60 cm, especially for the area where fruit plants are grown. In addition, higher density of soil samples and sub-samples are necessary to produce a reliable dataset that will allow proper statistical analysis.

scholarly journals VGEA: an RNA viral assembly toolkit

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12129
Author(s):  
Paul E. Oluniyi ◽  
Fehintola Ajogbasile ◽  
Judith Oguzie ◽  
Jessica Uwanibe ◽  
Adeyemi Kayode ◽  
...  
Keyword(s):  
De Novo ◽  
Sequence Data ◽  
Workflow Management ◽  
Viral Population ◽  
Lassa Virus ◽  
Viral Genomes ◽  
Bioinformatics Tools ◽  
Reference Sequences ◽  
Genome Assemblies

Next generation sequencing (NGS)-based studies have vastly increased our understanding of viral diversity. Viral sequence data obtained from NGS experiments are a rich source of information, these data can be used to study their epidemiology, evolution, transmission patterns, and can also inform drug and vaccine design. Viral genomes, however, represent a great challenge to bioinformatics due to their high mutation rate and forming quasispecies in the same infected host, bringing about the need to implement advanced bioinformatics tools to assemble consensus genomes well-representative of the viral population circulating in individual patients. Many tools have been developed to preprocess sequencing reads, carry-out de novo or reference-assisted assembly of viral genomes and assess the quality of the genomes obtained. Most of these tools however exist as standalone workflows and usually require huge computational resources. Here we present (Viral Genomes Easily Analyzed), a Snakemake workflow for analyzing RNA viral genomes. VGEA enables users to map sequencing reads to the human genome to remove human contaminants, split bam files into forward and reverse reads, carry out de novo assembly of forward and reverse reads to generate contigs, pre-process reads for quality and contamination, map reads to a reference tailored to the sample using corrected contigs supplemented by the user’s choice of reference sequences and evaluate/compare genome assemblies. We designed a project with the aim of creating a flexible, easy-to-use and all-in-one pipeline from existing/stand-alone bioinformatics tools for viral genome analysis that can be deployed on a personal computer. VGEA was built on the Snakemake workflow management system and utilizes existing tools for each step: fastp (Chen et al., 2018) for read trimming and read-level quality control, BWA (Li & Durbin, 2009) for mapping sequencing reads to the human reference genome, SAMtools (Li et al., 2009) for extracting unmapped reads and also for splitting bam files into fastq files, IVA (Hunt et al., 2015) for de novo assembly to generate contigs, shiver (Wymant et al., 2018) to pre-process reads for quality and contamination, then map to a reference tailored to the sample using corrected contigs supplemented with the user’s choice of existing reference sequences, SeqKit (Shen et al., 2016) for cleaning shiver assembly for QUAST, QUAST (Gurevich et al., 2013) to evaluate/assess the quality of genome assemblies and MultiQC (Ewels et al., 2016) for aggregation of the results from fastp, BWA and QUAST. Our pipeline was successfully tested and validated with SARS-CoV-2 (n = 20), HIV-1 (n = 20) and Lassa Virus (n = 20) datasets all of which have been made publicly available. VGEA is freely available on GitHub at: https://github.com/pauloluniyi/VGEA under the GNU General Public License.

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