scholarly journals Transect sampling promotes higher detection rates compared to discrete sampling for environmental DNA applications

2021 ◽  
Vol 4 ◽  
Author(s):  
Thiago Sanches

The use of environmental DNA (eDNA) to monitor species in aquatic environments has rapidly increased over the past decade. eDNA has consistently outperformed other methods of detection, yet eDNA relies on an indirect measure to estimate the real distribution of a species. Therefore, understanding the environmental factors that disperse eDNA is of major importance. Here we modeled the use of transect sampling for eDNA studies and also model the impact of river advection on detection radius and the expected probability of detection. Our model suggests that transect sampling: 1) increases the detection probability for both rare and common species, thus reducing the frequency of false negatives, 2) diminishes the standard deviation of the detection probability, which in most cases means higher reproducibility of eDNA studies, 3) better estimates systemwide trends of fish population distinguishing zones of multiple fishes from zones where few fishes are present, and 4) diminishes the effects of eddies and river velocity on the detection probability and detection radius. We propose the use of transect sampling as an alternative method of eDNA sampling with benefits that surpass the disadvantages of not being able to pinpoint the exact fish location. Our model also suggests that even short transects (less than 100 m) can yield considerable benefits compared to point sampling.

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5871 ◽  
Author(s):  
Robert S. Cornman ◽  
James E. McKenna ◽  
Jennifer Fike ◽  
Sara J. Oyler-McCance ◽  
Robin Johnson

Use of environmental DNA (eDNA) to assess distributions of aquatic and semi-aquatic macroorganisms is promising, but sampling schemes may need to be tailored to specific objectives. Given the potentially high variance in aquatic eDNA among replicate grab samples, compositing smaller water volumes collected over a period of time may be more effective for some applications. In this study, we compared eDNA profiles from composite water samples aggregated over three hours with grab water samples. Both sampling patterns were performed with identical autosamplers paired at two different sites in a headwater stream environment, augmented with exogenous fish eDNA from an upstream rearing facility. Samples were filtered through 0.8 μm cellulose nitrate filters and DNA was extracted with a cetyl trimethylammonium bromide procedure. Eukaryotic and bacterial community profiles were derived by amplicon sequencing of 12S ribosomal, 16S ribosomal, and cytochrome oxidase I loci. Operational taxa were assigned to genus with a lowest common ancestor approach for eukaryotes and to family with the RDP Classifier software for prokaryotes. Eukaryotic community profiles were more consistent with composite sampling than grab sampling. Downstream, rarefaction curves suggested faster taxon accumulation for composite samples, and estimated richness was higher for composite samples as a set than for grab samples. Upstream, composite sampling produced lower estimated richness than grab samples, but with overlapping standard errors. Furthermore, a bimodal pattern of richness as a function of sequence counts suggested the impact of clumped particles on upstream samples. Bacterial profiles were insensitive to sample method, consistent with the more even dispersion expected for bacteria compared with eukaryotic eDNA. Overall, samples composited over 3 h performed equal to or better than triplicate grab sampling for quantitative community metrics, despite the higher total sequencing effort provided to grab replicates. On the other hand, taxon-specific detection rates did not differ appreciably and the two methods gave similar estimates of the ratio of the common fish genera Salmo and Coregonus at each site. Unexpectedly, Salmo eDNA dropped out substantially faster than Coregonus eDNA between the two sites regardless of sampling method, suggesting that differential settling affects the estimation of relative abundance. We identified bacterial patterns that were associated with eukaryotic diversity, suggesting potential roles as biomarkers of sample representativeness.


2021 ◽  
Vol 11 (5) ◽  
pp. 2198
Author(s):  
Junwoo Jung ◽  
Jaesung Lim ◽  
Sungyeol Park ◽  
Haengik Kang ◽  
Seungbok Kwon

A frequency hopping orthogonal frequency division multiple access (FH-OFDMA) can provide low probability of detection (LPD) and anti-jamming capabilities to users against adversary detectors. To obtain an extreme LPD capability that cannot be provided by the basic symbol-by-symbol (SBS)-based FH pattern, we proposed two FH patterns, namely chaotic standard map (CSM) and cat map for FH-OFDMA systems. In our previous work, through analysis of complexity to regenerate the transmitted symbol sequence, at the point of adversary detectors, we found that the CSM had a lower probability of intercept than the cat map and SBS. It is possible when a detector already knows symbol and frame structures, and the detector has been synchronized to the FH-OFDMA system. Unlike the previous work, here, we analyze whether the CSM provides greater LPD capability than the cat map and SBS by detection probability using spectrum sensing technique. We analyze the detection probability of the CSM and provide detection probabilities of the cat map and SBS compared to the CSM. Based on our analysis of the detection probability and numerical results, it is evident that the CSM provides greater LPD capability than both the cat map and SBS-based FH-OFDMA systems.


Author(s):  
Jeff Nawrocki ◽  
Katherine Olin ◽  
Martin C Holdrege ◽  
Joel Hartsell ◽  
Lindsay Meyers ◽  
...  

Abstract Background The initial focus of the US public health response to COVID-19 was the implementation of numerous social distancing policies. While COVID-19 was the impetus for imposing these policies, it is not the only respiratory disease affected by their implementation. This study aimed to assess the impact of social distancing policies on non-SARS-CoV-2 respiratory pathogens typically circulating across multiple US states. Methods Linear mixed-effect models were implemented to explore the effects of five social distancing policies on non-SARS-CoV-2 respiratory pathogens across nine states from January 1 through May 1, 2020. The observed 2020 pathogen detection rates were compared week-by-week to historical rates to determine when the detection rates were different. Results Model results indicate that several social distancing policies were associated with a reduction in total detection rate, by nearly 15%. Policies were associated with decreases in pathogen circulation of human rhinovirus/enterovirus and human metapneumovirus, as well as influenza A, which typically decrease after winter. Parainfluenza viruses failed to circulate at historical levels during the spring. Total detection rate in April 2020 was 35% less than historical average. Many of the pathogens driving this difference fell below historical detection rate ranges within two weeks of initial policy implementation. Conclusion This analysis investigated the effect of multiple social distancing policies implemented to reduce transmission of SARS-CoV-2 on non-SARS-CoV-2 respiratory pathogens. These findings suggest that social distancing policies may be used as an impactful public health tool to reduce communicable respiratory illness.


2014 ◽  
Vol 138 (1) ◽  
pp. 76-87 ◽  
Author(s):  
Charanjeet Singh ◽  
J. Carlos Manivel ◽  
Alexander M. Truskinovsky ◽  
Kay Savik ◽  
Samy Amirouche ◽  
...  

Context.—The use of p16 in cervical biopsies improves the accuracy of cervical intraepithelial neoplasia (CIN) diagnosis and grading and decreases its interpathologist variability. Objective.—To determine the impact of the frequency of use of p16 immunostains in cervical biopsies on pathologists' diagnoses of CIN grade 1 and grade 2 or above (CIN1 and CIN2+) and on cytohistologic correlations. Design.—We identified all cervical biopsy specimens with cytologic correlations subjected or not to p16 staining from January 1, 2005, to September 30, 2010; calculated each pathologist's percentage of p16 use; and correlated it with their major cytohistologic discrepancy rates, CIN2+ diagnoses, and CIN1/CIN2+ ratios. Results.—During the study period, each of the 23 pathologists interpreted 59 to 1811 (mean, 518) of 11 850 cervical biopsy specimens, used p16 for 0% to 21.31% (mean, 10.14%) of these, had CIN2+ detection rates of 9.5% to 24.1% (mean, 18.9%), and CIN1/CIN2+ ratios of 0.7 to 4.5 (mean, 1.5). Compared to the 12 “low users” of p16, who used p16 fewer times than the institution's mean for p16 use, the 11 “high users” of p16 diagnosed more biopsies (8391 versus 3459), had a lower rate of major cytohistologic discrepancies (12.62% versus 14.92%, P < .001), a higher rate of CIN2+ diagnoses (19.9% versus 16.4%, P < .001), a lower range of CIN2+ rates (15.0%–23.1% versus 9.5%–24.1%), and lower CIN1/CIN2+ ratios (1.2 versus 2.3). Conclusions.—We found a high intrainstitutional variability of p16 use in cervical biopsies, CIN2+ rates, and CIN1/CIN2+ ratios. Use of p16 for greater than 10% of cervical biopsies was associated with improved cytohistologic correlation rates and with lower variability in the frequencies of histologic diagnoses.


2017 ◽  
Vol 14 ◽  
pp. 187-194 ◽  
Author(s):  
Stefano Federico ◽  
Marco Petracca ◽  
Giulia Panegrossi ◽  
Claudio Transerici ◽  
Stefano Dietrich

Abstract. This study investigates the impact of the assimilation of total lightning data on the precipitation forecast of a numerical weather prediction (NWP) model. The impact of the lightning data assimilation, which uses water vapour substitution, is investigated at different forecast time ranges, namely 3, 6, 12, and 24 h, to determine how long and to what extent the assimilation affects the precipitation forecast of long lasting rainfall events (> 24 h). The methodology developed in a previous study is slightly modified here, and is applied to twenty case studies occurred over Italy by a mesoscale model run at convection-permitting horizontal resolution (4 km). The performance is quantified by dichotomous statistical scores computed using a dense raingauge network over Italy. Results show the important impact of the lightning assimilation on the precipitation forecast, especially for the 3 and 6 h forecast. The probability of detection (POD), for example, increases by 10 % for the 3 h forecast using the assimilation of lightning data compared to the simulation without lightning assimilation for all precipitation thresholds considered. The Equitable Threat Score (ETS) is also improved by the lightning assimilation, especially for thresholds below 40 mm day−1. Results show that the forecast time range is very important because the performance decreases steadily and substantially with the forecast time. The POD, for example, is improved by 1–2 % for the 24 h forecast using lightning data assimilation compared to 10 % of the 3 h forecast. The impact of the false alarms on the model performance is also evidenced by this study.


2020 ◽  
Vol 642 ◽  
pp. A157 ◽  
Author(s):  
N. Meunier ◽  
A.-M. Lagrange

Context. The detectability of exoplanets and the determination of their projected mass in radial velocity are affected by stellar magnetic activity and photospheric dynamics. Among those processes, the effect of granulation, and even more so of supergranulation, has been shown to be significant in the solar case. The impact for other spectral types has not yet been characterised. Aims. Our study is aimed at quantifying the impact of these flows for other stars and estimating how such contributions affect their performance. Methods. We analysed a broad array of extended synthetic time series that model these processes to characterise the impact of these flows on exoplanet detection for main sequence stars with spectral types from F6 to K4. We focussed on Earth-mass planets orbiting within the habitable zone around those stars. We estimated the expected detection rates and detection limits, tested the tools that are typically applied to such observations, and performed blind tests. Results. We find that both granulation and supergranulation on these stars significantly affect planet mass characterisation in radial velocity when performing a follow-up of a transit detection: the uncertainties on these masses are sometimes below 20% for a 1 MEarth (for granulation alone or for low-mass stars), but they are much larger in other configurations (supergranulation, high-mass stars). For granulation and low levels of supergranulation, the detection rates are good for K and late G stars (if the number of points is large enough), but poor for more massive stars. The highest level of supergranulation leads to a very poor performance, even for K stars; this is both due to low detection rates and to high levels of false positives, even for a very dense temporal sampling over 10 yr. False positive levels estimated from standard false alarm probabilities sometimes significantly overestimate or underestimate the true level, depending on the number of points: it is, therefore, crucial to take this effect into account when analysing observations. Conclusions. We conclude that granulation and supergranulation significantly affect the performance of exoplanet detectability. Future works will focus on improving the following three aspects: decreasing the number of false positives, increasing detection rates, and improving the false alarm probability estimations from observations.


2020 ◽  
Author(s):  
Johannes Fischer ◽  
I Debski ◽  
GA Taylor ◽  
Heiko Wittmer

© The Ornithological Society of New Zealand Inc. We assessed the impact of interspecific interactions on the breeding success of the South Georgian diving petrel (Pelecanoides georgicus; SGDP), a Nationally Critical seabird species, by monitoring 20 burrows at Codfish Island (Whenua Hou), with remote cameras. Additionally, we tested the utility of remote cameras to study the breeding biology and activity patterns of the SGDP by pairing 5 remote cameras with RFID readers. We recorded 7 different species at SGDP burrow entrances. The common diving petrel (P. urinatrix) likely caused two monitored burrows to fail. These results suggest that remote cameras are useful tools to study such interactions. However, the cameras had extremely low SGDP detection rates (mean = 10.86%; se = 7.62%) when compared to RFID readers. These low detection rates may be explained by the small body size and the speed at which SGDPs enter/leave burrows. Therefore, remote cameras, or at least the model and setup we used, appear unsuitable to study breeding biology and activity patterns in this seabird species.


2021 ◽  
Vol 4 ◽  
Author(s):  
Karolina Bacela-Spychalska ◽  
Annette Taugbøl ◽  
Wiesław Babik ◽  
Maciej Pabijan ◽  
David Strand ◽  
...  

Pond ecosystems are hotspots of freshwater biodiversity, often containing many rare and protected species that are not commonly found elsewhere (Harper et al. 2018;Harper et al. 2019). However, even if they constitute c.a. 30% of freshwaters by area, still not enough effort has been put into pond monitoring and management and pond ecosystems are hence relatively poorly understood. Results of ECOPOND project will lead to add valuable knowledge upon pond diversity in geographic gradient taking for consideration human impact by comparing rural and urban areas. The sample design in ECOPOND includes six geographic regions, spanning from the south of Poland to the middle of Norway, where we will sample five replicates of urban and rural ponds in close geographic proximity, making it possible to test the impact of urbanization on biodiversity and biotic homogenization across latitude. We will sample all ponds at spring and late summer, making it possible to assess also seasonality in biodiversity. ECOPOND will utilize environmental DNA and RNA to perform biodiversity screening. The extracted eDNA and eRNA fragments will be amplified with the use of several selected markers for vertebrates, invertebrates, fungi and bacteria. Comparisons between eDNA and eRNA metabarcoding are hypothesized to allow inference between present and past diversity, as eRNA is thought to be only available from live organisms in the community. Moreover, ECOPOND aims at testing the effects of selected invasives species that can have on whole ecosystems. By sampling a range of biotic and abiotic parameters describing studied ponds, we will incorporate the available data for the ponds and employ occupancy modelling methods to assess the habitat preferences of selected invasive alien species. Then we will develop a method that can contribute towards an earlywarning system of evaluating threats to ecosystem status. One of the focus species will be the parasitic fungus Batrachochytrium dendrobatidis (Bd), an infectious fungal pathogen that has caused a number of amphibian declines and extinctions. The European amphibians seem less affected by the parasite at present. However, the fungi could be a direct driver of reduced genetic variation due to selection, or directly reduce the infected amphibian’s overall fitness by reducing the microbiotic diversity on their skin, which in many cases acts as a second immune system. ECOPOND will therefore provide data on genomic variation (using RADseq) for two amphibian species: the smooth newt (Lissotriton vulgaris) and the common toad (Bufo bufo). We will investigate populations of these species inhabiting ponds that are infected and not infected by Bd as well as collect data on their skin microbes (identified using metabarcoding). We will also contrast the genomic diversity between the replicated urban/rural setup and look for repeatable genomic changes. This setup will also be compared for the genomic variation for a potential native prey, the blue-tailed dragonfly, as will ponds with and without fish and/or amphibians (possibly also comparing between native and IAS top-predators) in order to look for predatory selective sweeps in the genome and transcriptome (experimental setup). All ponds will also be analyzed for over 20 water quality parameters and include data on a range of site characteristics that will be used as explanatory variables in all models. ECOPOND will compare large datasets across large geographic regions and will provide detailed knowledge of biodiversity patterns in vertebrates, invertebrates, fungal and microbial species, as well as genomic composition and skin biodiversity for animals inhabiting the same ponds set in an urban context. As a total, ECOPOND will obtain data on the location and status of biodiversity interests, gather data that can help in preventing the establishment of invasive alien species, and eradicating or controlling species that have already become established. And finally, ECOPOND will work closely with stakeholders and develop statistical techniques that can be used for monitoring, detection and protection of biodiversity.


Photonics ◽  
2021 ◽  
Vol 8 (12) ◽  
pp. 545
Author(s):  
Yang Yu ◽  
Zhangjun Wang ◽  
Kuntai Ma ◽  
Chao Chen ◽  
Xiufen Wang ◽  
...  

With the wide application of lidar in the future, the problem of crosstalk between lidars will become more serious. True random coding photon counting lidar with high anti-crosstalk ability will play an important role in solving this problem. In this paper, based on the working principle of Gm-APD, the detection probability theoretical model of true random coding photon counting lidar is built, and the impact of jitter on detection probability is considered for the first time. The influence of mean echo photon number, mean pulse count density, sequence length and pulse width on detection probability is analyzed. Monte Carlo simulation and experimental results are highly consistent with the theoretical model, which proves the correctness of the detection probability theoretical model. This theoretical model provides an effective means to evaluate the system performance.


Sign in / Sign up

Export Citation Format

Share Document