Optical microsystem for spectroscopy signals extraction applied to gastrointestinal dysplasia detection

Tese de Doutoramento em Engenharia BiomédicaThe early detection of gastrointestinal cancer, in the dysplastic stage, is essential to increase the patient survival rate. Spectroscopic techniques, particularly diffuse reflectance and fluorescence, can improve the gastrointestinal dysplasia detection, since these techniques can be used to extract biochemical and morphologic information related with the status of a gastrointestinal tissue. Several research groups have developed prototypes for the extraction of diffuse reflectance and fluorescence signals applied to gastrointestinal cancer detection. Despite their advantages associated with the gastrointestinal cancer identification, they have several disadvantages related with the use of complex, high-cost and sophisticate components such as xenon lamps, lasers, monochromators, optical fibers and high quantum efficiency detectors, which may hamper their wide use as well as their huge clinical value. Therefore, it is of utmost importance to develop a low-cost, miniaturized and minimal invasive microsystem for spectroscopic signals extraction. As a result, in this work it is proposed the implementation of a microsystem, which comprises in a single chip, an optical filter system for selection and extraction of the diffuse reflectance and fluorescence signals in relevant spectral bands, a silicon photodiodes matrix (4×4) and its readout electronics, and miniaturized light emitting diodes. The main applications of this microsystem are: its use as a portable device in a surgery room for inspection of total removing of the cancerous or dysplastic tissue; and its integration with the standard endoscopes and colonoscopes using it as an auxiliary, to the physician, in early gastrointestinal cancer detection. Along this thesis, important steps towards that microsystem implementation were achieved. In a first step experimental measurements were performed, with phantoms representative of the main absorbing, scattering and fluorescence properties of gastrointestinal tissues (containing hemoglobin, polystyrene microspheres to represent collagen fibers, and the fluorophores NADH and Carbostyril 124, the latter representing collagen), in order to study the diffuse reflectance and fluorescence typical spectra and their temperature dependence. Moreover, the viability of using only 16 spectral bands (between 350 and 750 nm) for signals extraction was discussed, proving the feasibility of an optical filter system implementation in the final microsystem. Therefore, it were designed, fabricated and characterized 16 MgO/TiO2 and SiO2/TiO2 based thin-film optical filters. Their characterization performed through optical transmittance, selectivity, profilometry and scanning electron microscopy, allowed understanding the deviations between the simulated characteristics and the ones experimentally obtained. Moreover, the optical filters results showed transmittances ranging from 50% to 90% approximately, and a full width half maximum (FWHM) averaging from 11 nm to 20 nm, which fits the required application. The fabricated optical filters had some deviations considering their simulated characteristics, which can be explained by the complexity of the optical filters design, for example, the materials refractive index dependence with wavelength and thin-film thickness. The diffuse reflectance and fluorescence signals that pass through the optical filters can be measured with an on-chip silicon photodetectors matrix (4×4), based on n+/p-epilayer junction photodiodes with an active area of 100 × 100 µm2, and a light-to-frequency converter, per each photodiode, that enables producing a digital signal with a frequency proportional to the photodiode current. As a result, the design and implementation of a CMOS microsystem comprising these components were performed. The photodiodes characterization showed a responsivity of 200 mA/W at 550 nm, approximately, and the light-to-frequency converter connected to the photodiode showed a linear response (R2>0.99) with a sensitivity of 25 Hz/nA at 550 nm, approximately. The behavior of the current-to-frequency converter, with an external current source directly injected in its input, was also studied allowing to confirm its linearity in the range of currents produced in this application, its power consumption of 1 mW, and its maximum input current, approximately 300 µA. This CMOS approach avoids the need of an expensive readout optical microsystem, since it is possible to integrate the photodiodes and the readout electronics in a small silicon area (275 × 100 µm2 per photodiode and its respective converter). The performance of the implemented microsystem and the fabricated optical filters was evaluated, using phantoms (also containing hemoglobin, polystyrene microspheres, NADH and Carbostyril 124). The obtained results have shown the viability of the microsystem (including the optical filter system) to extract diffuse reflectance and fluorescence signals. Some issues were noted on the sensitivity of the implemented optical setups for the on-chip measurements. However, some solutions were proposed for the remaining problems, specifically the future use of miniaturized light emitting diodes and the direct deposition of the optical filters on the top of the photodetection system. Finally, the direct integration of optical filters on top of the photodiodes was discussed and a new approach was tested.The author, Sara Filomena Ribeiro Pimenta, was supported by the Portuguese Foundation for Science and Technology (in portuguese FCT – Fundação para a Ciência e a Tecnologia) with the PhD grant SFRH/BD/87605/2012. This work is also funded by FEDER funds through the “Eixo I do Programa Operacional Fatores de Competitividade” (POFC) QREN, project reference COMPETE: FCOMP-01-0124-FEDER- 020241 and by FCT, project reference PTDC/EBB-EBI/120334/2010. Finally, the author thanks to the PEst-C/FIS/UI0607/2013, UID/FIS/04650/2013, UID/EEA/04436/2013 and POCI-01- 0145-FEDER-006941 for the use of equipment.A deteção precoce do cancro gastrointestinal, na fase de displasia, é essencial para o aumento da taxa de sobrevivência do paciente. As técnicas de espetroscopia, particularmente a refletância difusa e a fluorescência, permitem melhorar a deteção de displasia gastrointestinal, ao poderem ser utilizadas para a extração de informação bioquímica e morfológica associada ao estado do tecido gastrointestinal. Diversos grupos de investigação têm desenvolvido protótipos para a extração de sinais de refletância difusa e de fluorescência, para aplicação na deteção do cancro gastrointestinal. Apesar das vantagens associadas com a identificação do cancro gastrointestinal, esses sistemas apresentam várias desvantagens relacionadas com a utilização de componentes complexos, de elevado custo e sofisticados, como por exemplo, lâmpadas de xénon, lasers, monocromadores, fibras óticas e detetores de elevada eficiência, que podem dificultar a sua ampla utilização, bem como o seu elevado valor clínico. Portanto, é de extrema importância o desenvolvimento de um microssistema de baixo custo, miniaturizado e minimamente invasivo para a extração de sinais de espetroscopia. Assim, neste trabalho é proposta a implementação de um microssistema, num único chip, compreendendo: um sistema de filtros óticos para a seleção dos sinais de refletância difusa e de fluorescência em bandas espetrais relevantes; uma matriz de fotodíodos de silício (4×4) e a respetiva eletrónica de leitura; e díodos emissores de luz miniaturizados. As principais aplicações deste microssistema são: a sua utilização como sistema portátil numa sala de cirurgia para inspeção da remoção total do tecido maligno ou displásico; ou a sua integração com os sistemas de endoscopia e colonoscopia, servindo como auxiliar de diagnóstico, na deteção precoce de cancro gastrointestinal. Com a realização desta tese foram dados passos importantes para a implementação desse microssistema. Numa primeira fase, foram realizados testes experimentais, com um grupo de fantomas representativos das propriedades de absorção, difusão e de fluorescência dos tecidos gastrointestinais (contendo hemoglobina, microesferas de polistireno representando as fibras de colagénio, e os fluoróforos NADH e Carbostyril 124, este último para representar o colagénio), de forma a obter os espetros típicos de refletância difusa e de fluorescência e a influência da temperatura do fantoma nos mesmos. Para além disso, a viabilidade de usar apenas 16 bandas espetrais (entre 350 e 750 nm) para a extração dos sinais espetroscópicos foi discutida, provando a exequibilidade da implementação de um sistema de filtros óticos no microssistema final. Assim, foram desenhados, fabricados e caracterizados 16 filtros óticos baseados em filmes finos de MgO/TiO2 e SiO2/TiO2. A sua caracterização do ponto de vista da transmitância ótica, seletividade, profilometria e microscopia eletrónica de varrimento, permitiu perceber os desvios verificados entre as características simuladas e as obtidas experimentalmente. Para além disso, os resultados da caracterização dos filtros óticos mostraram transmitâncias óticas que variam entre 50% e 90%, aproximadamente, e uma largura a meia-altura (FWHM) média entre 11 nm e 20 nm, o que é adequado para a aplicação pretendida. Os filtros óticos fabricados possuem alguns desvios das suas características simuladas, o que pode ser explicado pela complexidade no projeto de filtros óticos, por exemplo, a dependência dos índices de refração com o comprimento de onda e espessura do filme fino. Os sinais de refletância difusa e fluorescência que atravessam os filtros óticos podem ser medidos através de uma matriz de fotodetetores de silício (4×4), baseada em fotodíodos do tipo n+/p-epilayer com uma área ativa de 100 × 100 µm2, e um conversor luz-frequência, um por cada fotodíodo, que permite produzir um sinal digital com uma frequência proporcional à corrente gerada pelo fotodíodo. Assim, o projeto e a implementação de um microssistema CMOS incluindo esses componentes foram executados. A caracterização dos fotodíodos da matriz resultou num valor de responsividade de 200 mA/W a 550 nm, aproximadamente, e a do conversor luz-frequência, quando ligado a um fotodíodo, resultou numa resposta linear (R2>0.99) com uma sensibilidade de 25 Hz/nA a 550 nm, aproximadamente. O comportamento do conversor corrente-frequência, com uma fonte de corrente externa diretamente injetada na sua entrada, foi também estudado, permitindo confirmar a sua linearidade na gama de correntes envolvidas nesta aplicação, a sua potência de consumo de 1 mW, e a sua corrente de entrada máxima, aproximadamente 300 µA. Esta abordagem em tecnologia CMOS evita a utilização de um microssistema ótico de leitura de elevado custo, uma vez que torna possível a integração dos fotodíodos e respetiva eletrónica de leitura numa área de silício pequena (275 × 100 µm2 por fotodíodo e respetivo conversor). Foi avaliado o desempenho do microssistema implementado e dos filtros óticos fabricados usando fantomas (mais uma vez contendo hemoglobina, microesferas de polistireno, NADH e Carbostyril 124). Os resultados obtidos provaram a viabilidade do microssistema (incluindo o sistema de filtros óticos) para a extração de sinais de refletância difusa e de fluorescência. Foram notados alguns problemas na sensibilidade dos setups óticos implementados para as medições on-chip. No entanto, foram também propostas algumas soluções para os respetivos problemas, especificamente o uso futuro de díodos emissores de luz miniaturizados e a deposição direta dos filtros óticos no sistema de fotodeteção. Finalmente, a integração dos filtros óticos depositados diretamente em cima dos fotodíodos foi discutida e uma nova abordagem foi testada

Desenvolvimento de um sistema à escala reduzida para determinação do tipo de sangue humano

Dissertação de mestrado integrado em Engenharia Biomédica (área de especialização em Eletrónica Médica)A determinação do tipo sanguíneo é um dos testes clínicos mais importantes que precede uma transfusão de sangue. Em situações de emergência, as transfusões sanguíneas são críticas, especialmente quando não há tempo para determinar o tipo de sangue do paciente, devido ao seu estado clínico, sendo a transfusão realizada com base no dador universal (tipo sanguíneo O negativo). Esta situação pode acarretar um conjunto de complicações clínicas para o paciente. Os sistemas e métodos existentes, atualmente, para a determinação do tipo sanguíneo apresentam algumas limitações, nomeadamente: subjetividade no caso dos métodos manuais; e elevado custo e tempo de resposta, no caso dos sistemas automáticos. Assim, no âmbito desta dissertação foi desenhado e construído um dispositivo automático para a determinação do tipo sanguíneo ABO-Rh, com as seguintes características: pequenas dimensões, 150 mm × 120 mm × 70 mm; portátil, permitindo a realização de análises próxima do paciente; baixo custo, em relação aos sistemas automáticos existentes no mercado; e tempo de resposta curto, permitindo a realização de uma análise em menos de 5 minutos. Estas características tornam o dispositivo vantajoso para operar especialmente em situações de emergência e fora dos laboratórios de análises clínicas, minimizando algumas das limitações dos sistemas/métodos atuais. O dispositivo implementado recorre à espetrofotometria, por absorção ótica, para detetar a reação de aglutinação em amostras sanguíneas, previamente preparadas e introduzidas no sistema. O protocolo experimental utilizado baseia-se na preparação de quatro amostras de teste, recorrendo ao protocolo convencional em lâmina, em que são utilizadas amostras de sangue total misturadas com soluções comerciais de anticorpos tipo A, B, AB e D. Uma vez introduzidas, simultaneamente, as amostras de teste no dispositivo, este determina três valores de densidade ótica (DO) por amostra, em comprimentos de onda específicos. Com base nestes valores, o sistema classifica cada uma das amostras em aglutinada ou não aglutinada e determina o tipo sanguíneo em análise, por aplicação de um algoritmo de decisão implementado no dispositivo. Os elementos base do dispositivo são: um sistema de LEDs e a sua eletrónica de controlo; fotodíodos e a sua eletrónica de leitura e um microcontrolador com display táctil (interface do utilizador com o dispositivo). O sistema foi testado e validado em ambiente laboratorial utilizando amostras padronizadas cedidas pelo Instituto Português de Sangue, correspondentes a diferentes tipos de sangue ABO-Rh.Blood type determination is one of the most important clinical tests that precede a blood transfusion. In emergency situations, blood transfusions are critical, once usually, due to the patient condition there is no time to blood typing and it is administered the universal donor blood type (O negative). This situation can bring some clinical risks to the patient. The systems and methods available nowadays to blood typing have some limitations, such as, the subjectivity of the manual tests and the high cost and time response of the automatic systems. Therefore, in this thesis, it is presented an automatic electronic device to ABO-Rh human blood typing with the following features: miniaturized, 150 mm × 120 mm × 70 mm; portable, allowing blood type determination near the patient; low-cost, comparing to the automatic systems available today; and fast response time, allowing performing analysis in less than 5 minutes. With these features the system is especially advantageous to operate in emergency situations and outside a conventional clinical laboratory, decreasing some limitations of the existents systems/methods. The developed device is based on a spectrophotometric approach and in the detection of agglutination reaction in the test samples, previously prepared and introduced into the device. The experimental procedure is based on the conventional plate protocol, i.e., preparation of four test samples by mixing blood samples with commercial antibodies solutions type A, B, AB and D. The samples are, simultaneously, introduced into the system and three discrete values of optical density (for each sample) are obtained at specific wavelengths. Based on these values, the device classifies each sample in agglutinated or non-agglutinated and determines the blood type by the application of a decision algorithm, based on the samples classification. The basic elements of the implemented device are: a group of LEDs and its electronic control system, photodiodes and their electronic reading system and a microcontroller with a touchscreen (user interface with the device). The system has been tested and validated in the laboratory using standardized samples, corresponding to different blood types ABO-Rh, provided by the Portuguese Blood Institute

Flexible neural probes: a review of the current advantages, drawbacks, and future demands

Brain diseases affect millions of people and have a huge social and economic impact. The use of neural probes for studies in animals has been the main approach to increasing knowledge about neural network functioning. Ultimately, neuroscientists are trying to develop new and more effective therapeutic approaches to treating neurological disorders. The implementation of neural probes with multifunctionalities (electrical, optical, and fluidic interactions) has been increasing in the last few years, leading to the creation of devices with high temporal and spatial resolution. Increasing the applicability of, and elements integrated into, neural probes has also led to the necessity to create flexible interfaces, reducing neural tissue damage during probe implantation and increasing the quality of neural acquisition data. In this paper, we review the fabrication, characterization, and validation of several types of flexible neural probes, exploring the main advantages and drawbacks of these devices. Finally, future developments and applications are covered. Overall, this review aims to present the currently available flexible devices and future appropriate avenues for development as possible guidance for future engineered devices.This work was supported by the CMEMS-UMinho Strategic Project (Nos. UIDB/04436/2020 and UIDP/04436/2020) and the MPhotonBiopsy (No. PTDC/FIS-OTI/1259/2020; https:// doi.org/10.54499/PTDC/FIS-OTI/1259/2020). João R. FREITAS thanks Fundação para a Ciência e a Tecnologia (FCT) for the Ph.D. grant (No. 2020.07708.BD). Sara PIMENTA thanks FCT for the grant (No. 2022.00101.CEECIND/CP1718/CT0008; https:// doi.org/10.54499/2022.00101.CEECIND/CP1718/CT0008)

Detection of low-magnetic fields by rubidium (87Rb) vapor cell

Journal of Physics: Conference Series, Volume 1837, 30th Micromechanics and Microsystems Europe Workshop (MME) 2019 18-20 August 2019, Wolfson College, Oxford, United KingdomThis paper describes the work carried out to assess the use of a quartz reference rubidium (87Rb) vapor cell for non-invasively magnetoencephalography, avoiding cryogenically cooled sensors as the Superconducting Quantum Interference Devices (SQUIDs). An experimental setup based on a cylindrical glass vapor cell of 87Rb (l = 75 mm, d =19 mm) was developed. The 87Rb cell was heated to around 75°C and it was optically pumped with polarized light (range 750-850 nm), tuned to the D1 transition of rubidium, for spin-polarization of the atoms, and the intensity of the light transmitted through the cell was detected using a photodiode. Without magnetic field, the photodiode current is maximized but when a small transverse magnetic field is present a measurable drop in light transmission occurs. A Magnetic Shielded Box (MSB) made by a nickel-iron ferromagnetic alloy, was used for nulling background magnetic fields and the transmittance light versus transverse magnetic field intensity (100-1000 nT) was measured.This work is supported by: Project MME reference 105399, FCT Strategic Project UID/EEA/04436/2019, Infrastructures Micro&NanoFabs@PT, reference NORTE-01-0145-FEDER-022090, POR Norte, Portugal 2020, SARSPEC Lda, V.N. Gaia-Portugal

Silicon nitride thin-films deposited by radiofrequency reactive sputtering: refractive index optimization with substrate cooling in a nitrogen-rich atmosphere

Silicon nitride (SiN) is widely used as a core material in optical waveguides due to its optical properties. The deposition of SiN thin-films by radiofrequency (RF) reactive sputtering is commonly used in low-temperature processes, where the thin-films optical properties can be optimized by controlling the deposition parameters (sputtering power, gases ratio, etc.). This work presents the deposition of several SiN thin-films by RF reactive sputtering with different sputtering powers (ranging from 180 W to 300 W), with a nitrogen-argon ratio of 16:4, and performing substrate cooling in a nitrogen-rich atmosphere immediately after deposition, consisting in keeping the substrate under 16 sccm of nitrogen until it reaches 25 ◦C. The refractive indices of the SiN thin-films were assessed through ellipsometry, obtaining a maximum refractive index of 1.906 at 400 nm. SiN thin-films were also analyzed by energy-dispersive spectroscopy (EDS) and atomic force microscopy (AFM).This work is supported by: MPhotonBiopsy, PTDC/FISOTI/1259/2020, http://doi.org/10.54499/PTDC/FIS-OTI/1259/2020; and CMEMS-UMinho Strategic Project UIDB/04436/2020 and UIDP/ 04436/2020. João R. Freitas thanks FCT (Fundação para a Ciência e a Tecnologia) for the Ph.D. grant, 2020.07708.BD. Sara Pimenta thanks FCT for the grant 2022.00101.CEECIND/CP1718/CT0008, https://doi.org/10.54499/2022.00101.CEECIND/CP1718/CT0008

Photodynamic therapy review: principles, photosensitizers, applications, and future directions

Photodynamic therapy (PDT) is a minimally invasive therapeutic modality that has gained great attention in the past years as a new therapy for cancer treatment. PDT uses photosensitizers that, after being excited by light at a specific wavelength, react with the molecular oxygen to create reactive oxygen species in the target tissue, resulting in cell death. Compared to conventional therapeutic modalities, PDT presents greater selectivity against tumor cells, due to the use of photosensitizers that are preferably localized in tumor lesions, and the precise light irradiation of these lesions. This paper presents a review of the principles, mechanisms, photosensitizers, and current applications of PDT. Moreover, the future path on the research of new photosensitizers with enhanced tumor selectivity, featuring the improvement of PDT effectiveness, has also been addressed. Finally, new applications of PDT have been covered.This work was supported by FCT with project OpticalBrain reference PTDC/CTMREF/28406/2017, operation code POCI-01-0145-FEDER-028406, through the COMPETE 2020; CMEMSUMinho Strategic Project UIDB/04436/2020; Infrastructures Micro&NanoFabs@PT, operation code NORTE 01-0145-FEDER-022090, POR Norte, Portugal 2020; and MPhotonBiopsy, PTDC/FIS-OTI/1259/2020. The authors thank Biolitec research GmbH (Jena, Germany) for providing the photosensitizer Foscan®.The APC was funded by Chongqing Technology and Business University (CTBU)

SU-8 based waveguide for optrodes

Neural probes can be equipped with light for optogenetics applications. Different approaches are used for delivering light to the tissue: an optical fiber coupled to the probe, a µLED or a waveguide integrated on the probe. Small probe dimensions, adequate optical power for photostimulation and good tissue penetration for in-vivo experiments are critical requirements. Thus, integrating a waveguide is a promising solution. This work shows the design and simulation of a SU-8 based waveguide for integration in a neural probe. The waveguide contains 3 apertures, spaced by 0.5 mm, which will allow the photostimulation of different brain regions simultaneously.ANI supports this work through the Brain-Lighting project by FEDER funds through Portugal 2020, COMPETE 2020 with the reference POCI-01-0247-FEDER-003416. S. B. Goncalves is supported by the Portuguese Foundation for Science and Technology, grant PD/BD/105931/2014, MIT-Portugal program.info:eu-repo/semantics/publishedVersio

Differentiation between normal and tumor mammary glands with depth-resolved attenuation coefficient from optical coherence tomography

Optical coherence tomography (OCT) is a well-established imaging technology for high-resolution, cross-sectional imaging of biological tissues. Imaging processing and light attenuation coefficient estimation allows to further improve the OCT diagnostic capability. In this paper we use a commercial OCT system, Telesto II-1325LR from Thorlabs, and demonstrate its ability to differentiate normal and tumor mammary mouse glands with the OCT attenuation coefficient. Using several OCT images of normal and tumor mammary mouse glands (n = 26), a statistical analysis was performed. The attenuation coefficient was calculated in depth, considering a slope of 0.5 mm. The normal glands present a median attenuation coefficient of 0.403 mm-1, comparatively to 0.561 mm-1obtained for tumor mammary glands. This translates in an attenuation coefficient approximately 39% higher for tumor mammary glands when compared to normal mammary glands. The OCT attenuation coefficient estimation eliminates the subjective analysis provided by direct visualization of the OCT images.This work is supported by:-OCT-RAMAN, PTDC/FISOTI/28296/2017 with the operation code NORTE-01- 0145-FEDER-028296;—MPhotonBiopsy, PTDC/FISOTI/1259/2020;—CMEMS-UMinho Strategic Project UIDB/04436/2020;- Infrastructures Micro&NanoFabs@PT, operation code NORTE 01-0145-FEDER022090, POR Norte, Portugal

MAMMALS IN PORTUGAL : A data set of terrestrial, volant, and marine mammal occurrences in P ortugal

Mammals are threatened worldwide, with 26% of all species being includedin the IUCN threatened categories. This overall pattern is primarily associatedwith habitat loss or degradation, and human persecution for terrestrial mam-mals, and pollution, open net fishing, climate change, and prey depletion formarine mammals. Mammals play a key role in maintaining ecosystems func-tionality and resilience, and therefore information on their distribution is cru-cial to delineate and support conservation actions. MAMMALS INPORTUGAL is a publicly available data set compiling unpublishedgeoreferenced occurrence records of 92 terrestrial, volant, and marine mam-mals in mainland Portugal and archipelagos of the Azores and Madeira thatincludes 105,026 data entries between 1873 and 2021 (72% of the data occur-ring in 2000 and 2021). The methods used to collect the data were: live obser-vations/captures (43%), sign surveys (35%), camera trapping (16%),bioacoustics surveys (4%) and radiotracking, and inquiries that represent lessthan 1% of the records. The data set includes 13 types of records: (1) burrowsjsoil moundsjtunnel, (2) capture, (3) colony, (4) dead animaljhairjskullsjjaws, (5) genetic confirmation, (6) inquiries, (7) observation of live animal (8),observation in shelters, (9) photo trappingjvideo, (10) predators dietjpelletsjpine cones/nuts, (11) scatjtrackjditch, (12) telemetry and (13) vocalizationjecholocation. The spatial uncertainty of most records ranges between 0 and100 m (76%). Rodentia (n=31,573) has the highest number of records followedby Chiroptera (n=18,857), Carnivora (n=18,594), Lagomorpha (n=17,496),Cetartiodactyla (n=11,568) and Eulipotyphla (n=7008). The data setincludes records of species classified by the IUCN as threatened(e.g.,Oryctolagus cuniculus[n=12,159],Monachus monachus[n=1,512],andLynx pardinus[n=197]). We believe that this data set may stimulate thepublication of other European countries data sets that would certainly contrib-ute to ecology and conservation-related research, and therefore assisting onthe development of more accurate and tailored conservation managementstrategies for each species. There are no copyright restrictions; please cite thisdata paper when the data are used in publications.info:eu-repo/semantics/publishedVersio

Mammals in Portugal: a data set of terrestrial, volant, and marine mammal occurrences in Portugal

Mammals are threatened worldwide, with ~26% of all species being included in the IUCN threatened categories. This overall pattern is primarily associated with habitat loss or degradation, and human persecution for terrestrial mammals, and pollution, open net fishing, climate change, and prey depletion for marine mammals. Mammals play a key role in maintaining ecosystems functionality and resilience, and therefore information on their distribution is crucial to delineate and support conservation actions. MAMMALS IN PORTUGAL is a publicly available data set compiling unpublished georeferenced occurrence records of 92 terrestrial, volant, and marine mammals in mainland Portugal and archipelagos of the Azores and Madeira that includes 105,026 data entries between 1873 and 2021 (72% of the data occurring in 2000 and 2021). The methods used to collect the data were: live observations/captures (43%), sign surveys (35%), camera trapping (16%), bioacoustics surveys (4%) and radiotracking, and inquiries that represent less than 1% of the records. The data set includes 13 types of records: (1) burrows | soil mounds | tunnel, (2) capture, (3) colony, (4) dead animal | hair | skulls | jaws, (5) genetic confirmation, (6) inquiries, (7) observation of live animal (8), observation in shelters, (9) photo trapping | video, (10) predators diet | pellets | pine cones/nuts, (11) scat | track | ditch, (12) telemetry and (13) vocalization | echolocation. The spatial uncertainty of most records ranges between 0 and 100 m (76%). Rodentia (n =31,573) has the highest number of records followed by Chiroptera (n = 18,857), Carnivora (n = 18,594), Lagomorpha (n = 17,496), Cetartiodactyla (n = 11,568) and Eulipotyphla (n = 7008). The data set includes records of species classified by the IUCN as threatened (e.g., Oryctolagus cuniculus [n = 12,159], Monachus monachus [n = 1,512], and Lynx pardinus [n = 197]). We believe that this data set may stimulate the publication of other European countries data sets that would certainly contribute to ecology and conservation-related research, and therefore assisting on the development of more accurate and tailored conservation management strategies for each species. There are no copyright restrictions; please cite this data paper when the data are used in publications