scholarly journals Species sensitivity analysis as a tool for interpreting diatom metabarcoding for WFD bioassessment

2021 ◽  
Vol 4 ◽  
Author(s):  
Rosa Trobajo ◽  
Javier Pérez Burillo ◽  
Valentin Vasselon ◽  
Frederic Rimet ◽  
Agnès Bouchez ◽  
...  
Keyword(s):  
Sensitivity Analysis ◽  
Ecological Status ◽  
Reference Database ◽  
Sensitivity Index ◽  
Reference Library ◽  
Mediterranean Rivers ◽  
River Stretch ◽  
Lower Status ◽  
Priority Species ◽  
Leave One Out

Recent metabarcoding work in European rivers, including our own studies of Mediterranean rivers in Catalonia (Pérez-Burillo et al. 2020), has shown promising agreement between morphology- (LM) and DNA-based (HTS) assessments of diatom periphyton for the Water Framework Directive. However, in 10 out of the 164 Catalan sites we analysed, the ecological status class was downgraded from “Good”/ “High” with LM to “Moderate”/ “Poor”/ “Bad”by HTS. We call these the “critical” sites and they are especially important because the WFD requires remedial action to be taken by water managers for any river stretch with Moderate or lower status. In order to discover the reasons for downgrading we investigated the contribution of each species to the Indice de Polluosensibilité Spécifique [Specific Pollution-sensitivity Index, IPS] using a “leave-one-out” sensitivity analysis, paying special attention to the critical sites. Discrepancies in IPS between LM and HTS were mainly due to the misidentification and overlooking in LM of a few species, which were better recovered by HTS. This bias was particularly important in the case of Fistulifera saprophila, whose clear underrepresentation in LM was important for explaining 8 out of the 10 critical sites and probably reflected destruction of its very weakly-silicified frustules during sample preparation for LM. Another important bias was brought about by differences between species in the rbcL copy number per cell, which for example affected the relative abundance obtained by HTS for Nitzschia inconspicua and Ulnaria ulna; these species were also identified by the sensitivity analysis as important for the WFD. However, blanket application of a correction factor based on cell volume did not lead to a clear improvement in the agreement between HTS and LM assessments. Only minor IPS discrepancies could be attributed to the incompleteness of the reference library, as most of the abundant and influential species (to the IPS) were well represented there. Finally, we propose that leave-one-out analysis is a valuable method for identifying priority species for isolation and barcoding that are currently not, or only poorly, represented in the DNA reference database.

scholarly journals Applicability of diatom metabarcoding in the ecological status assessment of Hungarian lotic and soda pan habitats

2021 ◽  
Vol 4 ◽  
Author(s):  
Mónika Duleba ◽  
Angéla Földi ◽  
Adrienn Micsinai ◽  
Anita Mohr ◽  
Rita Sipos ◽  
...  
Keyword(s):  
Ecological Status ◽  
Benthic Diatom ◽  
Reference Database ◽  
Sensitivity Index ◽  
Running Waters ◽  
Diatom Assemblages ◽  
Diatom Index ◽  
Rivers And Streams ◽  
Ecological Status Assessment ◽  
Status Assessment

Diatoms, eukaryotic algae with silica cell wall have been proved to be reliable bioindicators and are applied in ecological status assessment of aquatic ecosystems using indices calculated from pollution sensitivity and indicator values of species. Traditional method of identification of diatom species is based on morphological features of frustule that requires in-depth taxonomical knowledge and expertise. Metabarcoding that combines barcodes and high-throughput sequencing offers a promising alternative. In this pilot study we tested the applicability of metabarcoding of benthic diatom assemblages for ecological status assessment of water bodies in Hungary comparing its performance to that of morphology-based identification of species. Samples from 78 rivers and streams arranged along a trophic gradient and 14 soda pans representing unique types of habitats were investigated. Sequences of the barcode region of rbcL gene suggested by Vasselon et al. (2017) were acquired revealing 1135 diatom amplicon sequence variants (ASVs) of which 54% could be assigned at species level using Diat.barcode (Rimet et al. 2019) as reference database. Morphological investigation detected more species and intraspecific taxa in the lotic and lentic samples (413 and 78, respectively) than metabarcoding (190 and 75). Correspondence between taxa detected based on morphology and DNA sequences was relatively low (on average 24% in lotic and 26% in lentic samples) but considerably increased (on average 66% and 56%, respectively) when taking into account only the taxa reaching higher than 5% relative abundance in microscopy counting. The differences mainly derived from that a considerable portion (59% and 32%, respectively) of the morphologically identified taxa were not recorded in the reference database. Community structure of samples from both running and standing waters based on microscopy and DNA sequence analysis showed significant correlation as revealed using Mantel test. For rivers and streams diatom index IPS (Specific Pollution Sensitivity Index, (Coste in Cemagref, 1982) for soda pans indices H (Ziemann et al., 2001) and IBD (Indice Biologique Diatomées, Lenoir and Coste, 1996) were calculated from the results of the two aspects. Strong correlation was found between morphology- and sequence-based indices and in about half of the samples, the ecological status class obtained with the two methods coincided. Our results suggest that metabarcoding inheres a great opportunity and could be successfully applied in benthic diatom-based ecological status assessment of Hungarian waters after the reference database is supplemented with taxa frequently occurring in these habitats. References Cemagref, 1982. Etude des méthodes biologiques quantitativesd’appréciation de la qualité des eaux, Rapport Division Qualité des Eaux Lyon. Agence financière de Bassin Rhône-Méditerranée-Corse, Pierre-Bénite, France. Lenoir, A., Coste, M., 1996. Development of a practical diatom index of overall water quality applicable to the French National Water Board Network. Presented at the International symposium, Volksbildungsheim Grilhof Vill, AUT, 17-19 September 1995, Universität Innsbruck, pp. 29–43. Rimet, F., Gusev, E., Kahlert, M., Kelly, M.G., Kulikovskiy, M., Maltsev, Y., Mann, D.G., Pfannkuchen, M., Trobajo, R., Vasselon, V., Zimmermann, J., Bouchez, A., 2019. Diat.barcode, an open-access curated barcode library for diatoms. Sci. Rep. 9, 15116. Vasselon, V., Rimet, F., Tapolczai, K., Bouchez, A., 2017. Assessing ecological status with diatoms DNA metabarcoding: Scaling-up on a WFD monitoring network (Mayotte island, France). Ecol. Indic. 82, 1–12. Ziemann, H., Kies, L., Schulz, C.-J., 2001. Desalinization of running waters: III. Changes in the structure of diatom assemblages caused by a decreasing salt load and changing ion spectra in the river Wipper (Thuringia, Germany). Limnologica 31, 257–280.

scholarly journals Sensitivity Analysis of Bistatic Scattering for Soil Moisture Retrieval

2021 ◽  
Vol 13 (2) ◽  
pp. 188
Author(s):  
Tingting Li ◽  
Irena Hajnsek ◽  
Kun-Shan Chen
Keyword(s):  
Sensitivity Analysis ◽  
Soil Moisture ◽  
Quality Index ◽  
High Sensitivity ◽  
Bare Soil ◽  
Sensitivity Index ◽  
Scattering Coefficients ◽  
Observation Systems ◽  
Bistatic Scattering ◽  
Scattering Response

Soil moisture is one of the vital environmental variables in the land–atmosphere cycle. A study of the sensitivity analysis of bistatic scattering coefficients from bare soil at the Ku-band is presented, with the aim of deepening our understanding of the bistatic scattering features and exploring its potential in soil moisture retrieval. First, a well-established advanced integral method was adopted for simulating the bistatic scattering response of bare soil. Secondly, a sensitivity index and a normalized weight quality index were proposed to evaluate the effect of soil moisture on the bistatic scattering coefficient in terms of polarization and angular diversity, and the combinations thereof. The results of single-polarized VV data show that the regions with the maximum sensitivity and high quality index, simultaneously, to soil moisture are in the forward off-specular direction. However, due to the effect of surface roughness and surface autocorrelation function (ACF), the single-polarized data have some limitations for soil moisture inversion. By contrast, the results of two different polarization combinations, as well as a dual-angular simulation of one transmitter and two receivers, show significant estimation benefits. It can be seen that they all provide better ACF suppression capabilities, larger high-sensitivity area, and higher quality indices compared to single-polarized estimation. In addition, dual polarization or dual angular combined measurement provides the possibility of retrieving soil moisture in backward regions. These results are expected to contribute to the design of future bistatic observation systems.

Association Between Cigarette Smoking and Diabetic Foot Healing: A Systematic Review and Meta-Analysis

2018 ◽  
Vol 17 (4) ◽  
pp. 247-257 ◽  
Author(s):  
Xue-Lei Fu ◽  
Hui Ding ◽  
Wei-Wei Miao ◽  
Hong-Lin Chen
Keyword(s):  
Sensitivity Analysis ◽  
Wound Healing ◽  
Cigarette Smoking ◽  
Cohort Studies ◽  
Diabetic Foot ◽  
Healing Rate ◽  
Meta Analysis ◽  
Negative Effect ◽  
Retrospective Cohort Studies ◽  
Leave One Out

The role of smoking for wound healing in patients with diabetic foot has been unclear. This meta-analysis examined the relationship between cigarette smoking and diabetic foot wound healing. Observational studies for the association between smoking and diabetic foot wound healing of patients were systematically searched through PubMed and Wanfang Data, published up to June 2018. Healing rates of wounds were recognized as outcomes. Meta-analysis models were chosen by heterogeneity. A total of 3388 eligible studies were identified, of which 18 met all our inclusion criteria. In the smoking group, healing rate had an average of 62.1%, ranging from 20.0% to 89.6%; in the nonsmoking group, healing rate had an average of 71.5%, ranging from 40.2% to 93.8%. A significant association was found between smoking and the healing of diabetic foot wounds ( z = 3.08; P = .002), with an odds ratio (OR) of 0.70 (95% CI = 0.56-0.88), based on a random-effects model. Meta-regression analyses indicated that the heterogeneity did not come from publication year ( t = −0.50, P = .622) or overall healing rate ( t = 0.16, P = .872). The leave-one-out sensitivity analysis was robust; sensitivity analysis for pooled estimate of adjusted ORs had an OR of 0.20 (95% CI = 0.07-0.56; z = 3.08; P = .002). Subgroup analysis had an OR of 0.62 (95% CI = 0.41-0.95; z = 2.21; P = .027) in retrospective cohort studies and had an OR of 0.75 (95% CI = 0.57-0.99; z = 2.02; P = .043) in prospective cohort studies. Our meta-analysis indicated that smoking had an overall negative effect on the wound healing of diabetic foot individuals. This study provides evidence for the harm of smoking to diabetic foot and may help reduce the medical and economic burden on poor healing of diabetic foot.

scholarly journals A Three-Dimensional Coupled Hydrodynamic-Ecological Modeling to Assess the Planktonic Biomass in a Subalpine Lake

2021 ◽  
Vol 13 (22) ◽  
pp. 12377
Author(s):  
Wen-Cheng Liu ◽  
Hong-Ming Liu ◽  
Rita Sau-Wai Yam
Keyword(s):  
Water Quality ◽  
Sensitivity Analysis ◽  
Ecological Model ◽  
Three Dimensional ◽  
Ecological Status ◽  
Coupled Model ◽  
Zooplankton Biomass ◽  
Subalpine Lake ◽  
Depth Water ◽  
Temperature Water

In this study, a coupled three-dimensional hydrodynamic-ecological model was developed to comprehensively understand the interaction between the hydrodynamics and ecological status of a lake. The coupled model was utilized to explore the hydrodynamics, water quality, and ecological status in an ecologically rich subalpine lake (i.e., Tsuei-Feng Lake (TFL), located in north-central Taiwan). The measured data of water depth, water temperature, water quality, and planktonic biomass were gathered to validate the coupled model. The simulated results with a three-dimensional hydrodynamic and water quality-ecological model reasonably reproduced the variations in observed water depth, water temperature, water quality, and phytoplankton and zooplankton biomass. Sensitivity analysis was implemented to determine the most influential parameter affecting the planktonic biomass. The results of sensitivity analysis indicated that the predation rate on phytoplankton (PRP) significantly affects the phytoplankton biomass, while the basal metabolism rate of zooplankton (BMZ) importantly affects the zooplankton biomass. Furthermore, inflow discharge was the most important environmental factor dominating the phytoplankton and zooplankton biomass of TFL. This implies that the runoff in the catchment area caused by rainfall and the heavy rainfall induced by climate change may affect the planktonic biomass of the lake.

scholarly journals Intima heterogeneity in stress assessment of atherosclerotic plaques

2017 ◽  
Vol 8 (1) ◽  
pp. 20170008 ◽  
Author(s):  
Ali C. Akyildiz ◽  
Lambert Speelman ◽  
Bas van Velzen ◽  
Raoul R. F. Stevens ◽  
Antonius F. W. van der Steen ◽  
...  
Keyword(s):  
Sensitivity Analysis ◽  
Plaque Rupture ◽  
Homogeneous Model ◽  
Sensitivity Analyses ◽  
Homogeneous Material ◽  
Sensitivity Index ◽  
Stress Assessment ◽  
Heterogeneous Models ◽  
Homogeneous Models ◽  
Accuracy Stress

Atherosclerotic plaque rupture is recognized as the primary cause of cardiac and cerebral ischaemic events. High structural plaque stresses have been shown to strongly correlate with plaque rupture. Plaque stresses can be computed with finite-element (FE) models. Current FE models employ homogeneous material properties for the heterogeneous atherosclerotic intima. This study aimed to evaluate the influence of intima heterogeneity on plaque stress computations. Two-dimensional FE models with homogeneous and heterogeneous intima were constructed from histological images of atherosclerotic human coronaries ( n = 12). For homogeneous models, a single stiffness value was employed for the entire intima. For heterogeneous models, the intima was subdivided into four clusters based on the histological information and different stiffness values were assigned to the clusters. To cover the reported local intima stiffness range, 100 cluster stiffness combinations were simulated. Peak cap stresses (PCSs) from the homogeneous and heterogeneous models were analysed and compared. By using a global variance-based sensitivity analysis, the influence of the cluster stiffnesses on the PCS variation in the heterogeneous intima models was determined. Per plaque, the median PCS values of the heterogeneous models ranged from 27 to 160 kPa, and the PCS range varied between 43 and 218 kPa. On average, the homogeneous model PCS values differed from the median PCS values of heterogeneous models by 14%. A positive correlation ( R 2 = 0.72) was found between the homogeneous model PCS and the PCS range of the heterogeneous models. Sensitivity analysis showed that the highest main sensitivity index per plaque ranged from 0.26 to 0.83, and the average was 0.47. Intima heterogeneity resulted in substantial changes in PCS, warranting stress analyses with heterogeneous intima properties for plaque-specific, high accuracy stress assessment. Yet, computations with homogeneous intima assumption are still valuable to perform sensitivity analyses or parametric studies for testing the effect of plaque geometry on PCS. Moreover, homogeneous intima models can help identify low PCS, stable type plaques with thick caps. Yet, for thin cap plaques, accurate stiffness measurements of the clusters in the cap and stress analysis with heterogeneous cap properties are required to characterize the plaque stability.

scholarly journals Parametric Sensitivity Analysis for Importance Measure on Failure Probability and Its Efficient Kriging Solution

2015 ◽  
Vol 2015 ◽  
pp. 1-13 ◽  
Author(s):  
Yishang Zhang ◽  
Yongshou Liu ◽  
Xufeng Yang
Keyword(s):  
Sensitivity Analysis ◽  
Failure Probability ◽  
Computational Effort ◽  
Importance Measure ◽  
Sensitivity Index ◽  
Reliability Engineering ◽  
Parametric Sensitivity ◽  
Distribution Parameters ◽  
The Moment ◽  
Sensitivity Indicator

The moment-independent importance measure (IM) on the failure probability is important in system reliability engineering, and it is always influenced by the distribution parameters of inputs. For the purpose of identifying the influential distribution parameters, the parametric sensitivity of IM on the failure probability based on local and global sensitivity analysis technology is proposed. Then the definitions of the parametric sensitivities of IM on the failure probability are given, and their computational formulae are derived. The parametric sensitivity finds out how the IM can be changed by varying the distribution parameters, which provides an important reference to improve or modify the reliability properties. When the sensitivity indicator is larger, the basic distribution parameter becomes more important to the IM. Meanwhile, for the issue that the computational effort of the IM and its parametric sensitivity is usually too expensive, an active learning Kriging (ALK) solution is established in this study. Two numerical examples and two engineering examples are examined to demonstrate the significance of the proposed parametric sensitivity index, as well as the efficiency and precision of the calculation method.

scholarly journals A sensitivity analysis of the PAWN sensitivity index

2020 ◽  
Vol 127 ◽  
pp. 104679 ◽  
Author(s):  
Arnald Puy ◽  
Samuele Lo Piano ◽  
Andrea Saltelli
Keyword(s):  
Sensitivity Analysis ◽  
Sensitivity Index

scholarly journals Assessing the ecological status in species-poor systems: A fish-based index for Mediterranean Rivers (Guadiana River, SW Spain)

2010 ◽  
Vol 10 (6) ◽  
pp. 1152-1161 ◽  
Author(s):  
Virgilio Hermoso ◽  
Miguel Clavero ◽  
Francisco Blanco-Garrido ◽  
José Prenda
Keyword(s):  
Ecological Status ◽  
Mediterranean Rivers ◽  
Sw Spain

Accuracy design of high precision machine tools using error sensitivity analysis methodology

2016 ◽  
Vol 231 (18) ◽  
pp. 3401-3413 ◽  
Author(s):  
Wenjie Tian ◽  
Shaopeng Liu ◽  
Xingxing Liu
Keyword(s):  
Sensitivity Analysis ◽  
Machine Tool ◽  
Machine Tools ◽  
Geometric Error ◽  
Sensitivity Index ◽  
Assembly Accuracy ◽  
Machining Test ◽  
Precision Machine Tools ◽  
Design And Manufacture ◽  
Source Errors

Geometric accuracy is a crucially important performance factor for machine tools. Theoretically, the effects of source errors on pose accuracy (positional and angular accuracy) of 3-, 4- or 5-axis machine tools cannot fully be compensated by software, and only those pose errors associated with the permission motions are compensatable by means of error compensation. Therefore, the uncompensatable pose errors should be strictly guaranteed in the processes of design and manufacture. In this paper, after the geometric error model is established, the source errors affecting the uncompensatable pose accuracy are identified out of all the source errors. In order to enhance the understanding of which source errors have more influences on the pose accuracy, a probabilistic sensitivity analysis method is proposed, and the global sensitivity index is defined to evaluate the influence in the overall workspace. According to the sensitivity analysis results, the uncompensatable pose accuracy index is allocated to each source error. And then, assembly accuracy acceptance criteria are proposed as a guideline for machine assemblers. As an application example, the presented approaches are applied to the accuracy design and manufacture of a 4-axis machine tool, and double ball bar measurement and machining test are carried out to check the accuracy of the designed machine tool.

scholarly journals Sensitivity-guided evaluation of the HBV hydrological model parameterization

2012 ◽  
Vol 15 (3) ◽  
pp. 967-990 ◽  
Author(s):  
M. B. Zelelew ◽  
K. Alfredsen
Keyword(s):  
Sensitivity Analysis ◽  
Hydrological Model ◽  
River Basin Management ◽  
Low Flow ◽  
Model Parameters ◽  
Sensitivity Index ◽  
Analysis Method ◽  
Flow Conditions ◽  
Model Parameterization ◽  
Sensitivity Analysis Method

Applying hydrological models for river basin management depends on the availability of the relevant data information to constrain the model residuals. The estimation of reliable parameter values for parameterized models is not guaranteed. Identification of influential model parameters controlling the model response variations either by main or interaction effects is therefore critical for minimizing model parametric dimensions and limiting prediction uncertainty. In this study, the Sobol variance-based sensitivity analysis method was applied to quantify the importance of the HBV conceptual hydrological model parameterization. The analysis was also supplemented by the generalized sensitivity analysis method to assess relative model parameter sensitivities in cases of negative Sobol sensitivity index computations. The study was applied to simulate runoff responses at twelve catchments varying in size. The result showed that varying up to a minimum of four to six influential model parameters for high flow conditions, and up to a minimum of six influential model parameters for low flow conditions can sufficiently capture the catchments' responses characteristics. To the contrary, varying more than nine out of 15 model parameters will not make substantial model performance changes on any of the case studies.

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