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Article: Varying-Coefficient Stochastic Differential Equations with Applications in Ecology

Michelot, Théo / Glennie, Richard / Harris, Catriona / Thomas, Len

Journal of agricultural, biological, and environmental statistics. 2021 Sept., v. 26, no. 3

2021

Abstract: Stochastic differential equations (SDEs) are popular tools to analyse time series data in many areas, such as mathematical finance, physics, and biology. They provide a mechanistic description of the phenomenon of interest, and their parameters often ... ...

Abstract	Stochastic differential equations (SDEs) are popular tools to analyse time series data in many areas, such as mathematical finance, physics, and biology. They provide a mechanistic description of the phenomenon of interest, and their parameters often have a clear interpretation. These advantages come at the cost of requiring a relatively simple model specification. We propose a flexible model for SDEs with time-varying dynamics where the parameters of the process are nonparametric functions of covariates, similar to generalized additive models. Combining the SDE and nonparametric approaches allows for the SDE to capture more detailed, non-stationary, features of the data-generating process. We present a computationally efficient method of approximate inference, where the SDE parameters can vary according to fixed covariate effects, random effects, or basis-penalty smoothing splines. We demonstrate the versatility and utility of this approach with three applications in ecology, where there is often a modelling trade-off between interpretability and flexibility.Supplementary materials accompanying this paper appear online.
Keywords	ecology ; finance ; models ; physics ; statistics ; time series analysis
Language	English
Dates of publication	2021-09
Size	p. 446-463.
Publishing place	Springer US
Document type	Article
ZDB-ID	1324615-x
ISSN	1537-2693 ; 1085-7117
ISSN (online)	1537-2693
ISSN	1085-7117
DOI	10.1007/s13253-021-00450-6
Database	NAL-Catalogue (AGRICOLA)

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Article: Calibrating models of cancer invasion: parameter estimation using approximate Bayesian computation and gradient matching.

Xiao, Yunchen / Thomas, Len / Chaplain, Mark A J

Royal Society open science

2021 Volume 8, Issue 6, Page(s) 202237

Abstract: We present two different methods to estimate parameters within a partial differential equation model of cancer invasion. The model describes the spatio-temporal evolution of three variables-tumour cell density, extracellular matrix density and matrix ... ...

Abstract	We present two different methods to estimate parameters within a partial differential equation model of cancer invasion. The model describes the spatio-temporal evolution of three variables-tumour cell density, extracellular matrix density and matrix degrading enzyme concentration-in a one-dimensional tissue domain. The first method is a likelihood-free approach associated with approximate Bayesian computation; the second is a two-stage gradient matching method based on smoothing the data with a generalized additive model (GAM) and matching gradients from the GAM to those from the model. Both methods performed well on simulated data. To increase realism, additionally we tested the gradient matching scheme with simulated measurement error and found that the ability to estimate some model parameters deteriorated rapidly as measurement error increased.
Language	English
Publishing date	2021-06-16
Publishing country	England
Document type	Journal Article
ZDB-ID	2787755-3
ISSN	2054-5703
ISSN	2054-5703
DOI	10.1098/rsos.202237
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Article: Using dose–response functions to improve calculations of the impact of anthropogenic noise

Tyack, Peter L / Thomas, Len

Aquatic conservation. 2019 Sept., v. 29 Suppl S1

2019

Abstract: Estimating the number of animals impacted by a stressor typically involves combining a dose–response function with information about the distribution of animals and of the stressor. Regulators often prefer a single threshold to a full dose–response ... ...

Abstract	Estimating the number of animals impacted by a stressor typically involves combining a dose–response function with information about the distribution of animals and of the stressor. Regulators often prefer a single threshold to a full dose–response function, but much of the variability observed in the threshold at which different individuals respond to a stressor is an inherent characteristic of populations that needs to be taken into account to predict the effects of stressors. When selecting an exposure threshold, regulators need information on the proportion of the population that will be protected. Regulatory processes that calculate the number of animals impacted must draw from the dose–response function, the actual distribution of the animals, and a model mapping how the stressor intensity declines with distance from the source. Ignoring any of these factors can lead to significant errors in estimates of the area and numbers of animals affected. This paper focuses on behavioural responses of marine mammals to anthropogenic sound and demonstrates that a common approach of selecting the threshold at which half of the animals respond (RLp50) grossly underestimates the number of animals affected. We present an example, using a published dose–response function, where the number affected is underestimated by a factor of 280. Results would be similar for any stressor whose strength decreases following an inverse‐square function as it dilutes into the environment. This paper presents a method to use a dose–response function to derive a more accurate estimate of animals affected and to set a threshold (the Effective Response Level) that corrects the problem with the RLp50 estimate. Estimates of effects of stressors should include estimates of uncertainty, which can be used to adapt thresholds to different policy contexts and conservation problems.
Keywords	dose response ; issues and policy ; marine mammals ; models ; uncertainty
Language	English
Dates of publication	2019-09
Size	p. 242-253.
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	JOURNAL ARTICLE
ZDB-ID	1146285-1
ISSN	1052-7613
ISSN	1052-7613
DOI	10.1002/aqc.3149
Database	NAL-Catalogue (AGRICOLA)

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Article: A fine-scale marine mammal movement model for assessing long-term aggregate noise exposure

Joy, Ruth / Schick, Robert S. / Dowd, Michael / Margolina, Tetyana / Joseph, John E. / Thomas, Len

Ecological modelling. 2022 Feb., v. 464

2022

Abstract: Understanding the impacts of anthropogenic sound on marine mammals is important for effective mitigation and management. Sound impacts can cause behavioral changes that lead to displacement from preferred habitat and can have negative influence on vital ... ...

Abstract	Understanding the impacts of anthropogenic sound on marine mammals is important for effective mitigation and management. Sound impacts can cause behavioral changes that lead to displacement from preferred habitat and can have negative influence on vital rates. Here, we develop a movement model to better understand and simulate how whales respond to anthropogenic sound over ecologically meaningful space and time scales. The stochastic model is based on a sequential Monte Carlo sampler (a particle filter). The movement model takes account of vertical dive information and is influenced by the underwater soundscape and the historical whale distribution in the region. In the absence of noise disturbance, the simulator is shown to recover the historical whale distribution in the region. When noise disturbance is incorporated, the whale’s behavioral response is determined through a dose–response function dependent on the received level of sound. The aggregate impact is assessed by considering both the duration of foraging loss and the spatial shift to alternate (and potentially less favorable) habitat. Persistence of the behavioral response in time is treated through a ‘disruption’ parameter. We apply the approach to a population of fin whales whose distribution overlaps naval sonar testing activities beside the Southern California range complex. The simulation shows the consequences of one year of naval sonar disturbance are a function of: i) how loud the sound source is, ii) where the disturbed whales are relative to preferred (high density) habitat, and iii) how long a whale takes before returning to a pre-disturbance state. The movement simulator developed here is a generic movement modeling tool that can be adapted for different species, different regions, and any acoustic disturbances with known impacts on animal populations.
Keywords	acoustics ; dose response ; habitats ; models ; noise pollution ; sonar ; space and time ; stochastic processes ; whales ; California
Language	English
Dates of publication	2022-02
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	191971-4
ISSN	0304-3800
ISSN	0304-3800
DOI	10.1016/j.ecolmodel.2021.109798
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Alternative method for assessment of southwestern Atlantic humpback whale population status.

Bortolotto, Guilherme A / Thomas, Len / Hammond, Philip / Zerbini, Alexandre N

PloS one

2021 Volume 16, Issue 11, Page(s) e0259541

Abstract: The population of humpback whales (Megaptera novaeangliae) wintering off eastern South America was exploited by commercial whaling almost to the point of extinction in the mid-twentieth century. Since cessation of whaling in the 1970s it is recovering, ... ...

Abstract	The population of humpback whales (Megaptera novaeangliae) wintering off eastern South America was exploited by commercial whaling almost to the point of extinction in the mid-twentieth century. Since cessation of whaling in the 1970s it is recovering, but the timing and level of recovery is uncertain. We implemented a Bayesian population dynamics model describing the population's trajectory from 1901 and projecting it to 2040 to revise a previous population status assessment that used Sampling-Importance-Resampling in a Bayesian framework. Using our alternative method for model fitting (Markov chain Monte Carlo), which is more widely accessible to ecologists, we replicate a "base case scenario" to verify the effect on model results, and introduce additional data to update the status assessment. Our approach allowed us to widen the previous informative prior on carrying capacity to better reflect scientific uncertainty around historical population levels. The updated model provided more precise estimates for population sizes over the period considered (1901-2040) and suggests that carrying capacity (K: median 22,882, mean 22,948, 95% credible interval [CI] 22,711-23,545) and minimum population size (N1958: median 305, mean 319, 95% CI 271-444) might be lower than previously estimated (K: median 24,558, mean 25,110, 95% CI 22,791-31,118; N1958: median 503, mean 850, 95% CI 159-3,943). However, posterior 95% credible intervals of parameters in the updated model overlap those of the previous study. Our approach provides an accessible framework for investigating the status of depleted animal populations for which information is available on historical mortality (e.g., catches) and intermittent estimates of population size and/or trend.
MeSH term(s)	Animals ; Bayes Theorem ; Humpback Whale/physiology ; Population Density
Language	English
Publishing date	2021-11-17
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0259541
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Naturally Nano

Rick A. D. Arancon / Zeid A. Al Othman / Thomas Len / Kaimin Shih / Leonid Voskressensky / Rafael Luque

Catalysts, Vol 12, Iss 1337, p

Magnetically Separable Nanocomposites from Natural Resources for Advanced Catalytic Applications

2022 Volume 1337

Abstract: The present manuscript describes the use of silk cocoons as a structuring agent for the formation of an iron-based active phase for the controlled oxidation of benzyl alcohol. Different samples were prepared using different calcination temperatures. X- ... ...

Abstract	The present manuscript describes the use of silk cocoons as a structuring agent for the formation of an iron-based active phase for the controlled oxidation of benzyl alcohol. Different samples were prepared using different calcination temperatures. X-ray diffraction and transmission electron microscopy showed a higher proportion of alpha-Fe 2 O 3 phase and a higher global crystallinity at superior calcination temperature. In terms of catalytic activity, the sample treated at 500 °C presented the highest conversion reaching 47%, with selectivity in benzaldehyde of 75.9%.
Keywords	nanomaterials ; silk cocoons ; oxidation ; Fe ; Chemical technology ; TP1-1185 ; Chemistry ; QD1-999
Language	English
Publishing date	2022-11-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Microwave-Assisted Homogeneous Acid Catalysis and Chemoenzymatic Synthesis of Dialkyl Succinate in a Flow Reactor

Laura Daviot / Thomas Len / Carol Sze Ki Lin / Christophe Len

Catalysts, Vol 9, Iss 3, p

2019 Volume 272

Abstract: Two new continuous flow systems for the production of dialkyl succinates were developed via the esterification of succinic acid, and via the trans-esterification of dimethyl succinate. The first microwave-assisted continuous esterification of succinic ... ...

Abstract	Two new continuous flow systems for the production of dialkyl succinates were developed via the esterification of succinic acid, and via the trans-esterification of dimethyl succinate. The first microwave-assisted continuous esterification of succinic acid with H2SO4 as a chemical homogeneous catalyst was successfully achieved via a single pass (ca 320 s) at 65–115 °C using a MiniFlow 200ss Sairem Technology. The first continuous trans-esterification of dimethyl succinate with lipase Cal B as an enzymatic catalyst was developed using a Syrris Asia Technology, with an optimal reaction condition of 14 min at 40 °C. Dialkyl succinates were produced with the two technologies, but higher productivity was observed for the microwave-assisted continuous esterification using chemical catalysts. The continuous flow trans-esterification demonstrated a number of advantages, but it resulted in lower yield of the target esters.
Keywords	continuous flow ; dialkyl succinates ; homogeneous catalysis ; lipase Cal B ; succinate ; Chemical technology ; TP1-1185 ; Chemistry ; QD1-999
Subject code	660 ; 540
Language	English
Publishing date	2019-03-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Voltammetric Sensor Based on Waste‐Derived Carbon Nanodots for Enhanced Detection of Nitrobenzene

Dr. Viviana Bressi / Prof. Isabella Chiarotto / Dr. Angelo Ferlazzo / Dr. Consuelo Celesti / Dr. Cinzia Michenzi / Dr. Thomas Len / Prof. Daniela Iannazzo / Prof. Giovanni Neri / Prof. Claudia Espro

ChemElectroChem, Vol 10, Iss 13, Pp n/a-n/a (2023)

2023

Abstract: Abstract Carbon dots (CDs) samples were synthesized from orange peel waste (OPW) via a simple and eco‐friendly hydrothermal carbonization (HTC) and electrochemical (EC) bottom‐up synthesis integrated approach. The comprehensive chemical‐physical ... ...

Abstract	Abstract Carbon dots (CDs) samples were synthesized from orange peel waste (OPW) via a simple and eco‐friendly hydrothermal carbonization (HTC) and electrochemical (EC) bottom‐up synthesis integrated approach. The comprehensive chemical‐physical characterization of CDs samples, carried out by various techniques such as TEM, EDX, XRD, FT‐IR, underlined their morphological and microstructural features. The CDs exhibited attractive electrochemical properties, and thus an electrochemical sensor by modifying a screen printed carbon electrode (CDs/SPCE) for the detection of nitrobenzene (NB) in water was developed. Electroanalytical performances of CDs/SPCE sensor using differential pulse voltammetry (DPV) demonstrated its high sensitivity (9.36 μA μM−1 cm−2) towards NB in a wide linear dynamic range (0.1–2000 μM) and a low limit of detection (LOD=13 nM). The electrochemical sensor also shown high selectivity, long‐term stability, and repeatability. This paper might open the way to a new synergistic HTC‐EC approach for the synthesis of CDs from waste biomass material and their advanced application in highly efficient electrochemical sensors.
Keywords	carbon nanodots ; electrochemical sensor ; electrochemical bottom-up synthesis ; waste valorization ; nitrobenzene ; Industrial electrochemistry ; TP250-261 ; Chemistry ; QD1-999
Subject code	620
Language	English
Publishing date	2023-07-01T00:00:00Z
Publisher	Wiley-VCH
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Acoustic detection range and population density of Cuvier's beaked whales estimated from near-surface hydrophones.

Barlow, Jay / Fregosi, Selene / Thomas, Len / Harris, Danielle / Griffiths, Emily T

The Journal of the Acoustical Society of America

2021 Volume 149, Issue 1, Page(s) 111

Abstract: The population density of Cuvier's beaked whales is estimated acoustically with drifting near-surface hydrophone recorders in the Catalina Basin. Three empirical approaches (trial-based, distance-sampling, and spatially explicit capture-recapture) are ... ...

Abstract	The population density of Cuvier's beaked whales is estimated acoustically with drifting near-surface hydrophone recorders in the Catalina Basin. Three empirical approaches (trial-based, distance-sampling, and spatially explicit capture-recapture) are used to estimate the probability of detecting the echolocation pulses as a function of range. These detection functions are used with two point-transect methods (snapshot and dive-cue) to estimate density. Measurement errors result in a small range of density estimates (3.9-5.4 whales per 1000 km
Language	English
Publishing date	2021-01-29
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	219231-7
ISSN	1520-8524 ; 0001-4966
ISSN (online)	1520-8524
ISSN	0001-4966
DOI	10.1121/10.0002881
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Article: Using density surface models to estimate spatio‐temporal changes in population densities and trend

Camp, Richard J / Miller, David L / Thomas, Len / Buckland, Stephen T / Kendall, Steve J

Ecography. 2020 July, v. 43, no. 7

2020

Abstract: Precise measures of population abundance and trend are needed for species conservation; these are most difficult to obtain for rare and rapidly changing populations. We compare uncertainty in densities estimated from spatio–temporal models with that from ...

Abstract	Precise measures of population abundance and trend are needed for species conservation; these are most difficult to obtain for rare and rapidly changing populations. We compare uncertainty in densities estimated from spatio–temporal models with that from standard design‐based methods. Spatio–temporal models allow us to target priority areas where, and at times when, a population may most benefit. Generalised additive models were fitted to a 31‐year time series of point‐transect surveys of an endangered Hawaiian forest bird, the Hawai‘i ‘ākepa Loxops coccineus. This allowed us to estimate bird densities over space and time. We used two methods to quantify uncertainty in density estimates from the spatio–temporal model: the delta method (which assumes independence between detection and distribution parameters) and a variance propagation method. With the delta method we observed a 52% decrease in the width of the design‐based 95% confidence interval (CI), while we observed a 37% decrease in CI width when propagating the variance. We mapped bird densities as they changed across space and time, allowing managers to evaluate management actions. Integrating detection function modelling with spatio–temporal modelling exploits survey data more efficiently by producing finer‐grained abundance estimates than are possible with design‐based methods as well as producing more precise abundance estimates. Model‐based approaches require switching from making assumptions about the survey design to assumptions about bird distribution. Such a switch warrants consideration. In this case the model‐based approach benefits conservation planning through improved management efficiency and reduced costs by taking into account both spatial shifts and temporal changes in population abundance and distribution.
Keywords	Loxops coccineus ; confidence interval ; endangered species ; forest birds ; managers ; models ; planning ; population density ; species abundance ; surveys ; temporal variation ; time series analysis ; uncertainty
Language	English
Dates of publication	2020-07
Size	p. 1079-1089.
Publishing place	Blackwell Publishing Ltd
Document type	Article
Note	JOURNAL ARTICLE
ZDB-ID	1112659-0
ISSN	0906-7590
ISSN	0906-7590
DOI	10.1111/ecog.04859
Database	NAL-Catalogue (AGRICOLA)

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