scholarly journals Efficiency of eDNA and iDNA in assessing vertebrate diversity and its abundance

2021 ◽  
Author(s):  
Carolina Carvalho ◽  
Marina Oliveira ◽  
Karen Rodriguez-Castro ◽  
Bruno Saranholi ◽  
Pedro Galetti Jr
Keyword(s):  
Conventional Method ◽  
Relative Abundance ◽  
Conservation Management ◽  
Species Abundance ◽  
Environmental Dna ◽  
Biodiversity Assessment ◽  
Target Species ◽  
Efficient Tool ◽  
Water Sampler ◽  
Conventional Methods

Environmental DNA (eDNA) and invertebrate-derived DNA (iDNA) have been increasingly recognized as a powerful tool for biodiversity assessment and conservation management. However, because of uncertainties on the efficiency of eDNA/iDNA approach in comparison to conventional methods, its use to assess the vertebrate diversity is still rare. Here we assessed the efficiency of eDNA/iDNA in comparison to conventional methods to survey vertebrate diversity across several type of samplers, vertebrate groups, and location (tropical vs temperate zones), as well as its efficiency to be used as a proxy for relative abundance or biomass across different molecular methods (qPCR and metabarcoding) and types of experiments (in the lab or in the field). The metanalysis showed that, in general, there is no difference in the number of species detected or number of sites that a target species was detected when using eDNA/iDNA or conventional methods, suggesting that eDNA/iDNA and conventional methods were equally efficient in characterizing the biodiversity. However, for water sampler and fish, separately, the risk of not finding a species was greater using conventional method than eDNA, suggesting that eDNA/iDNA was more efficient in finding the target species. Abundance and biomass showed similar correlation patterns, and there was a positive correlation between eDNA/iDNA and abundance/biomass data, suggesting that eDNA/iDNA can be used as a proxy for abundance and biomass. Therefore, eDNA/iDNA has proved to be an efficient tool to assess vertebrate diversity in terms of both diversity of species and abundance or biomass.

scholarly journals Environmental DNA preserved in marine sediment for detecting jellyfish blooms after a tsunami

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Mizuki Ogata ◽  
Reiji Masuda ◽  
Hiroya Harino ◽  
Masayuki K. Sakata ◽  
Makoto Hatakeyama ◽  
...  
Keyword(s):  
Marine Sediment ◽  
Oil Spills ◽  
Sediment Cores ◽  
Environmental Dna ◽  
Target Species ◽  
Tank Experiment ◽  
Polycyclic Aromatic ◽  
Flow Through ◽  
High Concentrations ◽  
One Year

AbstractEnvironmental DNA (eDNA) can be a powerful tool for detecting the distribution and abundance of target species. This study aimed to test the longevity of eDNA in marine sediment through a tank experiment and to use this information to reconstruct past faunal occurrence. In the tank experiment, juvenile jack mackerel (Trachurus japonicus) were kept in flow-through tanks with marine sediment for two weeks. Water and sediment samples from the tanks were collected after the removal of fish. In the field trial, sediment cores were collected in Moune Bay, northeast Japan, where unusual blooms of jellyfish (Aurelia sp.) occurred after a tsunami. The samples were analyzed by layers to detect the eDNA of jellyfish. The tank experiment revealed that after fish were removed, eDNA was not present in the water the next day, or subsequently, whereas eDNA was detectable in the sediment for 12 months. In the sediment core samples, jellyfish eDNA was detected at high concentrations above the layer with the highest content of polycyclic aromatic hydrocarbons, reflecting tsunami-induced oil spills. Thus, marine sediment eDNA preserves a record of target species for at least one year and can be used to reconstruct past faunal occurrence.

scholarly journals Safety and Efficacy of All-In-One Percutaneous Pedicle Screw System

2021 ◽  
pp. 219256822110114
Author(s):  
Atsushi Kojima ◽  
Takato Aihara ◽  
Makoto Urushibara ◽  
Kenji Hatakeyama ◽  
Tomonori Sodeyama
Keyword(s):  
Pedicle Screw ◽  
Conventional Method ◽  
Surgical Time ◽  
Computed Tomography Images ◽  
Spine Stabilization ◽  
Percutaneous Pedicle Screw ◽  
Minimally Invasive Spine ◽  
Conventional Methods ◽  
Speed And Accuracy ◽  
Minimally Invasive Spine Stabilization

Study Design: Retrospective study of the prospectively collected outcomes data. Objective: The indications for PPS placement during minimally invasive spine stabilization (MISt) procedures have increased in recent years. To the best of our knowledge, no studies have documented the outcomes of PPS insertion using the all-in-one PPS system. This study compared the conventional methods and the use of all-in-one percutaneous pedicle screw (PPS) system with respect to the speed and accuracy of PPS placement. We also determined the advantages associated with the use of the all-in-one PPS system. Methods: We evaluated 54 patients who underwent PPS insertion using the conventional method and the all-in-one PPS system during MISt procedures. We also assessed the number of implanted PPSs, the time taken to implant PPSs, and the accuracy of PPS placement based on postoperative computed tomography images. Results: A total of 254 PPSs were inserted (126 using the conventional method and 128 using the all-in-one PPS system). The PPS insertion time with the all-in-one PPS system (mean, 25.3 ± 9.1 s) was significantly shorter than that using the conventional method (mean, 63.1 ± 13.0 s; P < 0.01). With respect to the accuracy of PPS insertion, ≥ 2 mm pedicle breach was noted in one case each in both groups. Conclusions: PPS placement using the all-in-one PPS system is as safe as conventional methods and has the potential to save the surgical time of MISt procedures.

Knowledge Graph Completion to Solve University Campus Issues

2020 ◽  
Vol 1 (3) ◽  
pp. 333-350
Author(s):  
Yuto Tsukagoshi ◽  
Takahiro Kawamura ◽  
Yuichi Sei ◽  
Yasuyuki Tahara ◽  
Akihiko Ohsuga
Keyword(s):  
Data Integration ◽  
Conventional Method ◽  
Current Literature ◽  
Statistical Data ◽  
Mean Absolute Error ◽  
Absolute Error ◽  
Knowledge Graph ◽  
University Campus ◽  
Combining Data ◽  
Conventional Methods

A number of urban challenges are encountered by modern societies. Governments, businesses and public bodies need to make statistical data widely available in order to tackle these challenges. Nonetheless, current literature and data are problematic; they have inaccuracies which lead to less effective methods of resolving these issues. This research aims to solve this challenge by thinking of a university campus as a microcosm of society, implementing a data integration schema, and combining data into a knowledge graph. Existing completion methods will then be applied and updated. Especially in regards to bicycle environment, our knowledge graph was tailored and evaluated in line with conventional methods, and secondly with our proposed derivative methods. Roughly 650 pieces of parking data, with various dates and times, was contrasted with each time's mean absolute error. Our approach accurately projected 54.5 more bicycles than the conventional method.

scholarly journals Content Visualization: An Evaluation of PowerPoint Effectiveness as a Learning Tool for Students

2018 ◽  
Vol 7 (2.29) ◽  
pp. 840
Author(s):  
Devi Pratami ◽  
Asti Amalia Nur Fajrillah ◽  
Tien Fabrianti Kusumasari
Keyword(s):  
Conventional Method ◽  
Test Score ◽  
Visual Presentation ◽  
Statistical Test ◽  
Learning Tool ◽  
The World ◽  
Slide Show ◽  
Conventional Methods ◽  
Education Field

PowerPoint is a slide show presentation program from Microsoft, which also one of the most widely used programs to develop visual presentation all over the world. PowerPoint has become enormously popular because of the functionalities offered and since it is designed to be easy to use. Previous researchers stated PowerPoint as one of the best tool to facilitate users to deliver idea/objective/goal, especially in education field. But some of the researchers argue that in today’s environment, PowerPoint no longer be the best tool to deliver information. This research aims to evaluate and design the content of the slide which influences the level of students understanding on information being presented. This research will be comparing three methods at once, which are a conventional method where the material course will be presented without any PowerPoint and are limited to boards and books. The second method will be a material-course presentation using a PowerPoint where it was using an aesthetically pleasing and methodically correct PowerPoint. And the last method would be the combination between the two. By using a statistical test ANOVA that among three methods there is no significance impact to the students understanding. Nevertheless, based on the test score that are done after treatment the results show that the quality of PowerPoint slide has an influence to the level of students understanding compared to conventional methods (blackboard and textbook). But only attractive slide itself is insufficient to improve students understanding, this study will incorporate conventional method and attractive slide through content visualization in order to gives a better impact on students understanding.  

scholarly journals Estimation accuracy of species abundance based on environmental DNA with relation to its production source, state, and assay methodology suggested by meta-analyses

2021 ◽  
Author(s):  
Toshiaki Jo ◽  
Hiroki Yamanaka
Keyword(s):  
Meta Analysis ◽  
Empirical Studies ◽  
Species Abundance ◽  
Environmental Dna ◽  
Efficient Estimation ◽  
Estimation Accuracy ◽  
Accurate Estimation ◽  
Abundance Estimation ◽  
Natural Environments ◽  
Promising Tool

Environmental DNA (eDNA) analysis is a promising tool for non-disruptive and cost-efficient estimation of species abundance. However, its practical applicability in natural environments is limited because it is unclear whether eDNA concentrations actually represent species abundance in the field. Although the importance of accounting for eDNA dynamics, such as transport and degradation, has been discussed, the influences of eDNA characteristics, including production source and state, and methodology, including collection and quantification strategy and abundance metrics, on the accuracy of eDNA-based abundance estimation were entirely overlooked. We conducted a meta-analysis using 56 previous eDNA literature and investigated the relationships between the accuracy (R2) of eDNA-based abundance estimation and eDNA characteristics and methodology. Our meta-regression analysis found that R2 values were significantly lower for crustaceans than fish, suggesting that less frequent eDNA production owing to their external morphology and physiology may impede accurate estimation of their abundance via eDNA. Moreover, R2 values were positively associated with filter pore size, indicating that selective collection of larger-sized eDNA, which is typically fresher, could improve the estimation accuracy of species abundance. Furthermore, R2 values were significantly lower for natural than laboratory conditions, while there was no difference in the estimation accuracy among natural environments. Our findings shed a new light on the importance of what characteristics of eDNA should be targeted for more accurate estimation of species abundance. Further empirical studies are required to validate our findings and fully elucidate the relationship between eDNA characteristics and eDNA-based abundance estimation.

scholarly journals Estimation of the relative abundance of species in artificial mixtures of insects using low-coverage shotgun metagenomics

2020 ◽  
Vol 4 ◽  
Author(s):  
Lidia Garrido-Sanz ◽  
Miquel Àngel Senar ◽  
Josep Piñol
Keyword(s):  
Relative Abundance ◽  
Species Abundance ◽  
Single Species ◽  
Insect Species ◽  
Individual Species ◽  
Advanced Degree ◽  
Mixed Species ◽  
Species List ◽  
Shotgun Metagenomics ◽  
Low Coverage

Amplicon metabarcoding is an established technique to analyse the taxonomic composition of communities of organisms using high-throughput DNA sequencing, but there are doubts about its ability to quantify the relative proportions of the species, as opposed to the species list. Here, we bypass the enrichment step and avoid the PCR-bias, by directly sequencing the extracted DNA using shotgun metagenomics. This approach is common practice in prokaryotes, but not in eukaryotes, because of the low number of sequenced genomes of eukaryotic species. We tested the metagenomics approach using insect species whose genome is already sequenced and assembled to an advanced degree. We shotgun-sequenced, at low-coverage, 18 species of insects in 22 single-species and 6 mixed-species libraries and mapped the reads against 110 reference genomes of insects. We used the single-species libraries to calibrate the process of assignation of reads to species and the libraries created from species mixtures to evaluate the ability of the method to quantify the relative species abundance. Our results showed that the shotgun metagenomic method is easily able to set apart closely-related insect species, like four species of Drosophila included in the artificial libraries. However, to avoid the counting of rare misclassified reads in samples, it was necessary to use a rather stringent detection limit of 0.001, so species with a lower relative abundance are ignored. We also identified that approximately half the raw reads were informative for taxonomic purposes. Finally, using the mixed-species libraries, we showed that it was feasible to quantify with confidence the relative abundance of individual species in the mixtures.

Extracellular DNA in environmental samples: Occurrence, extraction, quantification, and impact on microbial biodiversity assessment

2021 ◽  
Author(s):  
Sakcham Bairoliya ◽  
Jonas Koh Zhi Xiang ◽  
Bin Cao
Keyword(s):  
Dna Sequencing ◽  
Microbial Communities ◽  
Dna Extraction ◽  
Environmental Samples ◽  
Environmental Dna ◽  
Extracellular Dna ◽  
Biodiversity Assessment ◽  
Microbial Biodiversity ◽  
Technical Details ◽  
The Impact

Environmental DNA, i.e., DNA directly extracted from environmental samples, has been applied to understand microbial communities in the environments and to monitor contemporary biodiversity in the conservation context. Environmental DNA often contains both intracellular DNA (iDNA) and extracellular DNA (eDNA). eDNA can persist in the environment and complicate environmental DNA sequencing-based analyses of microbial communities and biodiversity. Although several studies acknowledged the impact of eDNA on DNA-based profiling of environmental communities, eDNA is still being neglected or ignored in most studies dealing with environmental samples. In this article, we summarize key findings on eDNA in environmental samples and discuss the methods used to extract and quantify eDNA as well as the importance of eDNA on the interpretation of experimental results. We then suggest several factors to consider when designing experiments and analyzing data to negate or determine the contribution of eDNA to environmental DNA-based community analyses. This field of research will be driven forward by: (i) carefully designing environmental DNA extraction pipelines by taking into consideration technical details in methods for eDNA extraction/removal and membrane-based filtration and concentration; (ii) quantifying eDNA in extracted environmental DNA using multiple methods including qPCR and fluorescent DNA binding dyes; (iii) carefully interpretating effect of eDNA on DNA-based community analyses at different taxonomic levels; and (iv) when possible, removing eDNA from environmental samples for DNA-based community analyses.

Temperature Measurement—Gold Standard

PEDIATRICS ◽  
1992 ◽  
Vol 90 (4) ◽  
pp. 649-649
Author(s):  
MARTIN E. WEISSE
Keyword(s):  
Temperature Measurement ◽  
Core Temperature ◽  
Conventional Method ◽  
Study Design ◽  
Rectal Temperature ◽  
Gold Standard ◽  
Relative Accuracy ◽  
Temperature Determination ◽  
Conventional Methods

To the Editor.— I would like to comment on the article by Freed and Fraley in the March 1992 issue of Pediatrics.1 I have no argument with their study design and in fact applaud them for using Altman and Bland's method of analysis. Their conclusions, as written, are correct, that the tympanic thermometer "is unreliable compared with conventional methods of temperature determination." The three issues that I would like to raise are: (1) the relative accuracy of rectal and tympanic temperatures in predicting core temperature, (2) rectal temperature as the "gold standard," and (3) axillary thermometry as an acceptable conventional method of clinical temperature.

Drones for conservation

2021 ◽  
pp. 35-52
Author(s):  
Serge A. Wich ◽  
Mike Hudson ◽  
Herizo Andrianandrasana ◽  
Steven N. Longmore
Keyword(s):  
Data Collection ◽  
Land Cover ◽  
Land Cover Change ◽  
Conservation Management ◽  
Habitat Mapping ◽  
Data Collection Tool ◽  
Target Species ◽  
Animal Distribution

Conservation management benefits from having accurate and timely data on land-cover change, animal distribution and density, as well as the ability to detect poachers before they reach their target species. In addition to other methods, drones have become a data collection tool for all three of these aspects and are becoming rapidly more widespread in conservation management and research. This chapter discusses these three issues and provides a case study in which a drone was used for habitat mapping. The chapter will also go over some of the sensors and drone systems currently used in conservation. To conclude, it will discuss the current challenges with the usage of drones in conservation settings.

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