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Article ; Online: Comment on: Premenstrual and menstrual changes reported after COVID-19 vaccination: The EVA project.

Marques, Tiago A

2022 Volume 18, Page(s) 17455057221129395

MeSH term(s)	COVID-19/prevention & control ; COVID-19 Vaccines/adverse effects ; Extravehicular Activity ; Female ; Humans ; Menstrual Cycle ; Premenstrual Syndrome/epidemiology ; Vaccination
Chemical Substances	COVID-19 Vaccines
Language	English
Publishing date	2022-10-11
Publishing country	United States
Document type	Letter ; Research Support, Non-U.S. Gov't ; Comment
ZDB-ID	2274503-8
ISSN	1745-5065 ; 1745-5057
ISSN (online)	1745-5065
ISSN	1745-5057
DOI	10.1177/17455057221129395
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Article ; Online: A sperm whale cautionary tale about estimating acoustic cue rates for deep divers.

Marques, Tiago A / Marques, Carolina S / Gkikopoulou, Kalliopi C

The Journal of the Acoustical Society of America

2023 Volume 154, Issue 3, Page(s) 1577–1584

Abstract: Passive acoustic density estimation has been gaining traction in recent years. Cue counting uses detected acoustic cues to estimate animal abundance. A cue rate, the number of acoustic cues produced per animal per unit time, is required to convert cue ... ...

Abstract	Passive acoustic density estimation has been gaining traction in recent years. Cue counting uses detected acoustic cues to estimate animal abundance. A cue rate, the number of acoustic cues produced per animal per unit time, is required to convert cue density into animal density. Cue rate information can be obtained from animal borne acoustic tags. For deep divers, like beaked whales, data have been analyzed considering deep dive cycles as a natural sampling unit, based on either weighted averages or generalized estimating equations. Using a sperm whale DTAG (sound-and-orientation recording tag) example we compare different approaches of estimating cue rate from acoustic tags illustrating that both approaches used before might introduce biases and suggest that the natural unit of analysis should be the whole duration of the tag itself.
MeSH term(s)	Animals ; Sperm Whale ; Cues ; Acoustics ; Sound
Language	English
Publishing date	2023-09-12
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; 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	10.1121/10.0020910
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Article ; Online: Click detection rate variability of central North Pacific sperm whales from passive acoustic towed arrays.

Barkley, Yvonne M / Merkens, Karlina P B / Wood, Megan / Oleson, Erin M / Marques, Tiago A

The Journal of the Acoustical Society of America

2024 Volume 155, Issue 4, Page(s) 2627–2635

Abstract: Passive acoustic monitoring (PAM) is an optimal method for detecting and monitoring cetaceans as they frequently produce sound while underwater. Cue counting, counting acoustic cues of deep-diving cetaceans instead of animals, is an alternative method ... ...

Abstract	Passive acoustic monitoring (PAM) is an optimal method for detecting and monitoring cetaceans as they frequently produce sound while underwater. Cue counting, counting acoustic cues of deep-diving cetaceans instead of animals, is an alternative method for density estimation, but requires an average cue production rate to convert cue density to animal density. Limited information about click rates exists for sperm whales in the central North Pacific Ocean. In the absence of acoustic tag data, we used towed hydrophone array data to calculate the first sperm whale click rates from this region and examined their variability based on click type, location, distance of whales from the array, and group size estimated by visual observers. Our findings show click type to be the most important variable, with groups that include codas yielding the highest click rates. We also found a positive relationship between group size and click detection rates that may be useful for acoustic predictions of group size in future studies. Echolocation clicks detected using PAM methods are often the only indicator of deep-diving cetacean presence. Understanding the factors affecting their click rates provides important information for acoustic density estimation.
MeSH term(s)	Animals ; Sperm Whale ; Vocalization, Animal ; Acoustics ; Echolocation ; Whales ; Sound Spectrography
Language	English
Publishing date	2024-04-17
Publishing country	United States
Document type	Journal Article
ZDB-ID	219231-7
ISSN	1520-8524 ; 0001-4966
ISSN (online)	1520-8524
ISSN	0001-4966
DOI	10.1121/10.0025540
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Article ; Online: Estimating Florida manatee (Trichechus manatus latirostris) abundance using passive acoustic methods.

Rycyk, Athena M / Berchem, Cora / Marques, Tiago A

JASA express letters

2022 Volume 2, Issue 5, Page(s) 51202

Abstract: Manatees are difficult to detect, particularly cryptic populations that inhabit areas with limited water clarity. The effectiveness of using vocal detections to estimate manatee abundance was evaluated in a clear water spring where manatees congregate ... ...

Abstract	Manatees are difficult to detect, particularly cryptic populations that inhabit areas with limited water clarity. The effectiveness of using vocal detections to estimate manatee abundance was evaluated in a clear water spring where manatees congregate seasonally. Vocalizations were extracted by a detection classifier that clustered sounds with similar spectral properties. Vocalization counts from recordings in Blue Spring, FL, USA were strong predictors of manatee abundance. The link between independent visual counts and abundance estimates from passive acoustic monitoring was used to provide an estimate of 1.059 (95% confidence interval 0.963-1.127) vocalizations/manatee/5-min, which might be used elsewhere for cue counting of manatees.
MeSH term(s)	Acoustics ; Animals ; Sound ; Trichechus ; Trichechus manatus ; Water
Chemical Substances	Water (059QF0KO0R)
Language	English
Publishing date	2022-09-26
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ISSN	2691-1191
ISSN (online)	2691-1191
DOI	10.1121/10.0010495
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Article ; Online: Narwhal (Monodon monoceros) echolocation click rates to support cue counting passive acoustic density estimation.

Marques, Carolina S / Marques, Diana A / Blackwell, Susanna B / Heide-Jørgensen, Mads Peter / Malinka, Chloe E / Marques, Tiago A

The Journal of the Acoustical Society of America

2024 Volume 155, Issue 2, Page(s) 891–900

Abstract: Estimating animal abundance is fundamental for effective management and conservation. It is increasingly done by combining passive acoustics with knowledge about rates at which animals produce cues (cue rates). Narwhals (Monodon monoceros) are elusive ... ...

Abstract	Estimating animal abundance is fundamental for effective management and conservation. It is increasingly done by combining passive acoustics with knowledge about rates at which animals produce cues (cue rates). Narwhals (Monodon monoceros) are elusive marine mammals for which passive acoustic density estimation might be plausible, but for which cue rates are lacking. Clicking rates in narwhals were investigated using a dataset from sound and movement tag records collected in August 2013-2016 and 2019 in East Greenland. Clicking rates were quantified for ∼1200 one-second-long systematic random samples from 8 different whales. Generalized additive models were used to model (1) the probability of being in a clicking state versus depth and (2) the clicking rate while in a clicking state, versus time and depth. The probability of being in a clicking state increased with depth, reaching ∼1.0 at ∼500 m, while the number of clicks per second (while in a clicking state) increased with depth. The mean cue production rate, weighted by tag duration, was 1.28 clicks per second (se = 0.13, CV = 0.10). This first cue rate for narwhals may be used for cue counting density estimation, but care should be taken if applying it to other geographical areas or seasons, given sample size, geographical, and temporal limitations.
MeSH term(s)	Animals ; Echolocation ; Whales ; Cues ; Acoustics ; Sound ; Vocalization, Animal
Language	English
Publishing date	2024-02-01
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	219231-7
ISSN	1520-8524 ; 0001-4966
ISSN (online)	1520-8524
ISSN	0001-4966
DOI	10.1121/10.0024723
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Article ; Online: Implications of porpoise echolocation and dive behaviour on passive acoustic monitoring.

Macaulay, Jamie Donald John / Rojano-Doñate, Laia / Ladegaard, Michael / Tougaard, Jakob / Teilmann, Jonas / Marques, Tiago A / Siebert, Ursula / Madsen, Peter Teglberg

The Journal of the Acoustical Society of America

2023 Volume 154, Issue 4, Page(s) 1982–1995

Abstract: Harbour porpoises are visually inconspicuous but highly soniferous echolocating marine predators that are regularly studied using passive acoustic monitoring (PAM). PAM can provide quality data on animal abundance, human impact, habitat use, and ... ...

Abstract	Harbour porpoises are visually inconspicuous but highly soniferous echolocating marine predators that are regularly studied using passive acoustic monitoring (PAM). PAM can provide quality data on animal abundance, human impact, habitat use, and behaviour. The probability of detecting porpoise clicks within a given area (P̂) is a key metric when interpreting PAM data. Estimates of P̂ can be used to determine the number of clicks per porpoise encounter that may have been missed on a PAM device, which, in turn, allows for the calculation of abundance and ideally non-biased comparison of acoustic data between habitats and time periods. However, P̂ is influenced by several factors, including the behaviour of the vocalising animal. Here, the common implicit assumption that changes in animal behaviour have a negligible effect on P̂ between different monitoring stations or across time is tested. Using a simulation-based approach informed by acoustic biologging data from 22 tagged harbour porpoises, it is demonstrated that porpoise behavioural states can have significant (up to 3× difference) effects on P̂. Consequently, the behavioural state of the animals must be considered in analysis of animal abundance to avoid substantial over- or underestimation of the true abundance, habitat use, or effects of human disturbance.
MeSH term(s)	Animals ; Humans ; Echolocation ; Porpoises ; Phocoena ; Ecosystem ; Acoustics
Language	English
Publishing date	2023-10-17
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	219231-7
ISSN	1520-8524 ; 0001-4966
ISSN (online)	1520-8524
ISSN	0001-4966
DOI	10.1121/10.0021163
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Article ; Online: The influence of El Niño Southern Oscillation on the population dynamics of oceanic manta rays in the Mexican Pacific

Cabral, Madalena Mesquitela Pereira / Stewart, Joshua D. / Marques, Tiago A. / Ketchum, James T. / Ayala-Bocos, Arturo / Hoyos-Padilla, Edgar Mauricio / Reyes-Bonilla, Héctor

Hydrobiologia. 2023 Jan., v. 850, no. 2 p.257-267

2023

Abstract: Oceanic manta rays Mobula birostris are declining globally due to fisheries. Past work has shown that movements and distributions of oceanic manta ray populations are sensitive to climatic fluctuations such as the El Niño Southern Oscillation. The ... ...

Abstract	Oceanic manta rays Mobula birostris are declining globally due to fisheries. Past work has shown that movements and distributions of oceanic manta ray populations are sensitive to climatic fluctuations such as the El Niño Southern Oscillation. The Revillagigedo National Park (RNP), Mexico, is a well-known aggregation site for oceanic manta rays. However, published baseline data on population structure and dynamics, and the influence of oceanographic variables on the abundance of oceanic manta rays in the region are lacking. We used 2015–2019 photo-identification data to describe baseline demographic characteristics of this population and to evaluate the influence of environmental factors on population dynamics. A significant sex bias was found with a female:male ratio of 1.4:1. Mark-recapture (MR) was used to estimate monthly abundance and provided the first superpopulation size estimate of 1172 (± 90), representing all individuals using the RNP during the survey period. The MR analysis suggests a significant relationship between the multivariate ENSO index and monthly survival probabilities, and chlorophyll-a as a driver of recruitment in surveyed dive sites. These findings provide a baseline to support effective conservation and management plans for this endangered species in the Mexican Pacific.
Keywords	El Nino ; Manta ; Mobula ; chlorophyll ; endangered species ; mark-recapture studies ; national parks ; population dynamics ; population structure ; surveys ; Mexico
Language	English
Dates of publication	2023-01
Size	p. 257-267.
Publishing place	Springer International Publishing
Document type	Article ; Online
ZDB-ID	214428-1
ISSN	1573-5117 ; 0018-8158
ISSN (online)	1573-5117
ISSN	0018-8158
DOI	10.1007/s10750-022-05047-9
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: COVID-19: Nothing is Normal in this Pandemic.

Gonçalves, Luzia / Turkman, Maria Antónia Amaral / Geraldes, Carlos / Marques, Tiago A / Sousa, Lisete

Journal of epidemiology and global health

2021 Volume 11, Issue 2, Page(s) 146–149

Abstract: This manuscript brings attention to inaccurate epidemiological concepts that emerged during the COVID-19 pandemic. In social media and scientific journals, some wrong references were given to a "normal epidemic curve" and also to a "log-normal curve/ ... ...

Abstract	This manuscript brings attention to inaccurate epidemiological concepts that emerged during the COVID-19 pandemic. In social media and scientific journals, some wrong references were given to a "normal epidemic curve" and also to a "log-normal curve/distribution". For many years, textbooks and courses of reputable institutions and scientific journals have disseminated misleading concepts. For example, calling histogram to plots of epidemic curves or using epidemic data to introduce the concept of a Gaussian distribution, ignoring its temporal indexing. Although an epidemic curve may look like a Gaussian curve and be eventually modelled by a Gauss function, it is not a normal distribution or a log-normal, as some authors claim. A pandemic produces highly-complex data and to tackle it effectively statistical and mathematical modelling need to go beyond the "one-size-fits-all solution". Classical textbooks need to be updated since pandemics happen and epidemiology needs to provide reliable information to policy recommendations and actions.
MeSH term(s)	COVID-19/epidemiology ; Epidemiologic Research Design ; Humans ; Models, Statistical ; Normal Distribution ; Pandemics/statistics & numerical data ; Reproducibility of Results ; SARS-CoV-2
Language	English
Publishing date	2021-01-20
Publishing country	France
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2645324-1
ISSN	2210-6014 ; 2210-6014
ISSN (online)	2210-6014
ISSN	2210-6014
DOI	10.2991/jegh.k.210108.001
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Article: Trends in cetacean research in the Eastern North Atlantic

Cartagena‐Matos, Bárbara / Lugué, Klervi / Fonseca, Paulo / Marques, Tiago A / Prieto, Rui / Alves, Filipe

Mammal review. 2021 July, v. 51, no. 3

2021

Abstract: Cetaceans are considered ecosystem engineers and useful bioindicators of the health of marine environments. The Eastern North Atlantic is an area of great geographical and oceanographic complexity that favours ecosystem richness and, consequently, ... ...

Abstract	Cetaceans are considered ecosystem engineers and useful bioindicators of the health of marine environments. The Eastern North Atlantic is an area of great geographical and oceanographic complexity that favours ecosystem richness and, consequently, cetacean occurrence. Although this occurrence has led to relevant scientific research on this taxon, information on the composition of this research has not been assessed. We aimed to describe and quantify the evolution of research on cetaceans in the Eastern North Atlantic, highlighting the main focal areas and trends. We considered 380 peer‐reviewed publications between 1900 and 2018. For each paper, we collected publication year, research topics and regions, and species studied. We assessed differences among regions with distinct socio‐economic landscapes, and between coastal and oceanic habitats. To evaluate the changes in scientific production over time, we fitted a General Additive Model to the time series of numbers of papers. Although research in this region has been increasing, the results show relatively little research output in North African and coastal regions within the study area. Moreover, except for four studies, research was restricted to a few miles around the coast of the main islands, leaving offshore regions less well surveyed. There was little research on genetics, acoustics, and behaviour. Most papers were focused on the Azores and Canary Islands, and mostly involved Tursiops truncatus, Delphinus delphis, and Physeter macrocephalus. Species considered Endangered or Near Threatened were the subjects of only 10% of the studies. We suggest a greater research focus on beaked whales (Ziphiidae) in Macaronesia, as well as collaborative efforts between research teams in the region, by sharing data sets, and aiming to produce long‐term research. Moreover, a Delphi method approach, based on questionnaires answered by experts, could be attempted to identify priority research for cetaceans in these areas.
Keywords	Delphi method ; Delphinus delphis ; Physeter macrocephalus ; Tursiops truncatus ; Ziphiidae ; acoustics ; coasts ; ecosystems ; evolution ; genetics ; mammals ; models ; socioeconomics ; time series analysis ; Azores
Language	English
Dates of publication	2021-07
Size	p. 436-453.
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	NAL-AP-2-clean ; REVIEW
ZDB-ID	2020637-9
ISSN	1365-2907 ; 0305-1838
ISSN (online)	1365-2907
ISSN	0305-1838
DOI	10.1111/mam.12238
Database	NAL-Catalogue (AGRICOLA)

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Article: Aeromonas spp. Prevalence, Virulence, and Antimicrobial Resistance in an Ex Situ Program for Threatened Freshwater Fish—A Pilot Study with Protective Measures

Grilo, Miguel L. / Amaro, Guadalupe / Chambel, Lélia / Marques, Carolina S. / Marques, Tiago A. / Gil, Fátima / Sousa-Santos, Carla / Robalo, Joana I. / Oliveira, Manuela

Animals. 2022 Feb. 11, v. 12, no. 4

2022

Abstract: Ex situ breeding programs are important conservation tools for endangered freshwater fish. However, developing husbandry techniques that decrease the likelihood of disease, antimicrobial resistance, and virulence determinants acquisition during this ... ...

Abstract	Ex situ breeding programs are important conservation tools for endangered freshwater fish. However, developing husbandry techniques that decrease the likelihood of disease, antimicrobial resistance, and virulence determinants acquisition during this process is challenging. In this pilot study, we conducted a captivity experiment with Portuguese nase (Iberochondrostoma lusitanicum), a critically endangered leuciscid species, to investigate the influence of simple protective measures (i.e., material disinfection protocols and animal handling with gloves) on the dynamics of a potential pathogenic genus, Aeromonas, as well as its virulence profiles and antimicrobial resistance signatures. Our findings show that antimicrobial resistance in Aeromonas spp. collected from I. lusitanicum significantly increased during the extent of the assay (5 weeks), with all isolates collected at the end of the study classified as multidrug-resistant. Additionally, humans handling fishes without protective measures were colonized by Aeromonas spp. The use of protective measures suggested a decreasing trend in Aeromonas spp. prevalence in I. lusitanicum, while bacterial isolates displayed significantly lower virulence index values when virulence phenotypical expression was tested at 22 °C. Despite this study representing an initial trial, which needs support from further research, protective measures tested are considered a simple tool to be applied in ex situ breeding programs for aquatic animals worldwide. Furthermore, current results raise concern regarding antimicrobial resistance amplification and zoonotic transmission of Aeromonas spp. in aquatic ex situ programs.
Keywords	Aeromonas ; Iberochondrostoma ; antibiotic resistance ; disinfection ; freshwater ; freshwater fish ; multiple drug resistance ; virulence
Language	English
Dates of publication	2022-0211
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
ZDB-ID	2606558-7
ISSN	2076-2615
ISSN	2076-2615
DOI	10.3390/ani12040436
Database	NAL-Catalogue (AGRICOLA)

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