Development of MRI‐based axillary numerical models and estimation of axillary lymph node dielectric properties for microwave imaging

Purpose: Microwave imaging (MWI) has been studied as a complementary imaging modality to improve sensitivity and specificity of diagnosis of axillary lymph nodes (ALNs), which can be metastasized by breast cancer. The feasibility of such a system is based on the dielectric contrast between healthy and metastasized ALNs. However, reliable information such as anatomically realistic numerical models and matching dielectric properties of the axillary region and ALNs, which are crucial to develop MWI systems, are still limited in the literature. The purpose of this work is to develop a methodology to infer dielectric properties of structures from magnetic resonance imaging (MRI), in particular, ALNs. We further use this methodology, which is tailored for structures farther away from MR coils, to create MRI- based numerical models of the axillary region and share them with the scientific community, through an open- access repository. Methods: We use a dataset of breast MRI scans of 40 patients, 15 of them with metastasized ALNs. We apply image processing techniques to minimize the artifacts in MR images and segment the tissues of interest. The background, lung cavity, and skin are segmented using thresholding techniques and the remaining tissues are segmented using a K- means clustering algorithm. The ALNs are segmented combining the clustering results of two MRI sequences. The performance of this methodology was evaluated using qualitative criteria. We then apply a piecewise linear interpolation between voxel signal intensities and known dielectric properties, which allow us to create dielectric property maps within an MRI and consequently infer ALN properties. Finally, we compare healthy and metastasized ALN dielectric properties within and between patients, and we create an open- access repository of numerical axillary region numerical models which can be used for electromagnetic simulations. Results: The proposed methodology allowed creating anatomically realistic models of the axillary region, segmenting 80 ALNs and analyzing the corresponding dielectric properties. The estimated relative permittivity of those ALNs ranged from 16.6 to 49.3 at 5 GHz. We observe there is a high variability of dielectric properties of ALNs, which can be mainly related to the ALN size and, consequently, its composition. We verified an average dielectric contrast of 29% between healthy and metastasized ALNs. Our repository comprises 10 numerical models of the axillary region, from five patients, with variable number of metastasized ALNs and body mass index. Conclusions: The observed contrast between healthy and metastasized ALNs is a good indicator for the feasibility of a MWI system aiming to diagnose ALNs. This paper presents new contributions regarding anatomical modeling and dielectric properties' characterization, in particular for axillary region applications.info:eu-repo/semantics/publishedVersio

Development of 3D MRI-Based Anatomically Realistic Models of Breast Tissues and Tumours for Microwave Imaging Diagnosis

Breast cancer diagnosis using radar-based medical MicroWave Imaging (MWI) has been studied in recent years. Realistic numerical and physical models of the breast are needed for simulation and experimental testing of MWI prototypes. We aim to provide the scientific community with an online repository of multiple accurate realistic breast tissue models derived from Magnetic Resonance Imaging (MRI), including benign and malignant tumours. Such models are suitable for 3D printing, leveraging experimental MWI testing. We propose a pre-processing pipeline, which includes image registration, bias field correction, data normalisation, background subtraction, and median filtering. We segmented the fat tissue with the region growing algorithm in fat-weighted Dixon images. Skin, fibroglandular tissue, and the chest wall boundary were segmented from water-weighted Dixon images. Then, we applied a 3D region growing and Hoshen-Kopelman algorithms for tumour segmentation. The developed semi-automatic segmentation procedure is suitable to segment tissues with a varying level of heterogeneity regarding voxel intensity. Two accurate breast models with benign and malignant tumours, with dielectric properties at 3, 6, and 9 GHz frequencies have been made available to the research community. These are suitable for microwave diagnosis, i.e., imaging and classification, and can be easily adapted to other imaging modalities.info:eu-repo/semantics/publishedVersio

Development of an Anthropomorphic Phantom of the Axillary Region for Microwave Imaging Assessment

We produced an anatomically and dielectrically realistic phantom of the axillary region to enable the experimental assessment of Axillary Lymph Node (ALN) imaging using microwave imaging technology. We segmented a thoracic Computed Tomography (CT) scan and created a computer-aided designed file containing the anatomical configuration of the axillary region. The phantom comprises five 3D-printed parts representing the main tissues of interest of the axillary region for the purpose of microwave imaging: fat, muscle, bone, ALNs, and lung. The phantom allows the experimental assessment of multiple anatomical configurations, by including ALNs of different size, shape, and number in several locations. Except for the bone mimicking organ, which is made of solid conductive polymer, we 3D-printed cavities to represent the fat, muscle, ALN, and lung and filled them with appropriate tissue-mimicking liquids. Existing studies about complex permittivity of ALNs have reported limitations. To address these, we measured the complex permittivity of both human and animal lymph nodes using the standard open-ended coaxial-probe technique, over the 0.5 GHz-8.5 GHz frequency band, thus extending current knowledge on dielectric properties of ALNs. Lastly, we numerically evaluated the effect of the polymer which constitutes the cavities of the phantom and compared it to the realistic axillary region. The results showed a maximum difference of 7 dB at 4 GHz in the electric field magnitude coupled to the tissues and a maximum of 10 dB difference in the ALN response. Our results showed that the phantom is a good representation of the axillary region and a viable tool for pre-clinical assessment of microwave imaging technology.info:eu-repo/semantics/publishedVersio

Expression of Developmentally Important Axon Guidance Cues in the Adult Optic Chiasm.

Funder: Wellcome TrustPURPOSE: Regeneration of optic nerve axons after injury can be facilitated by several approaches, but misguidance at the optic chiasm is often observed. We characterized guidance cues in the embryonic visual system and adult optic chiasm before and after optic nerve crush (ONC) injury to better understand barriers to optic nerve regeneration in adults. METHODS: Radial glial (RC2/BLBP/Slit1), developmental (Pax2) and extracellular markers (CSPG: H2B/CS-56) were assessed in C57BL/6J mice by immunohistochemistry. RC2, BLBP, Slit1, and CSPG are known inhibitory guidance cues while Pax2 is a permissive guidance cue. RESULTS: At embryonic day 15.5 (E.15.5), RC2 and BLBP were identified superior to, and extending through, the optic chiasm. The optic chiasm was BLBP-ve in adult uninjured mice but BLBP+ve in adult mice 10 days after ONC injury. The reverse was true for RC2. Both BLBP and RC2 were absent in adult mice 6 weeks post-ONC. Slit1 was present in the optic chiasm midline and optic tracts in embryonic samples but was absent in uninjured adult tissue. Slit1 was observed superior to and at the midline of the optic chiasm 10 days post-ONC but absent 6 weeks after injury. Pax2 was expressed at the junction between the optic nerve and optic chiasm in embryonic brain tissue. In embryonic sections, CS-56 was observed at the junction between the optic chiasm and optic tract, and immediately superior to the optic chiasm. Both 2H6 and CS-56 staining was absent in uninjured and ONC-injured adult brains. CONCLUSION: Differences in guidance cue expression during development, in adulthood and after injury may contribute to misguidance of regenerating RGC axons in the adult optic chiasm

User satisfaction on the use of hypermedia in a health-education mobile device application

O uso da tecnologia na área da saúde tem crescido cada vez mais. Os dispositivos móveis possibilitam que as pessoas aprendam em qualquer lugar e a qualquer tempo. OBJETIVO: investigar a satisfação do usuário quanto ao uso de hipermídias para a aprendizagem de educação em saúde por meio de dispositivo móvel. MÉTODO: contou com 4 partes. Na primeira, foi aplicado um questionário pré-teste, em seguida houve a interação com as hipermídias, posteriormente aplicou-se o questionário pós-teste. Por fim, os participantes avaliaram a satisfação quanto ao uso das hipermídias. RESULTADOS: os resultados obtidos demonstraram que os participantes consideraram as hipermídias atraentes, desejadas, que elas promovem o sentimento de integração e aproximação, bem como tem um enorme valor em sua aplicação. CONCLUSÕES: a pesquisa demonstrou que o uso das hipermídias em dispositivos móveis para o aprendizado em cuidados em saúde é uma solução criativa, atrativa e eficaz e aprimora o processo ensino-aprendizagem.The use of technology in healthcare has been growing more each day. Mobile devices make it possible for anyone to learn anywhere, anytime. OBJECTIVE: to investigate user satisfaction regarding the use of hypermedia for learning health education through mobile devices. METHODS: It consisted of 4 parts. At first, a pre-test questionnaire was applied, then there was the interaction with the hypermedia, later the post-test questionnaire was conducted. Finally, participants rated their satisfaction in regard to the use of hypermedia. RESULTS: findings showed that the participants considered the hypermedia appealing, desirable, promoted a feeling of integration and closeness, and had an enormous value in their application. CONCLUSIONS: this study demonstrated that the use of hypermedia on mobile devices for learning in healthcare is a creative, appealing, and effective solution. Also, it improves the teaching-learning process

Segregation distortion of wild-type alleles at the Machado-Joseph disease locus: a study in normal families from the Azores islands (Portugal)

Machado-Joseph disease (MJD) is caused by an expansion of a triplet repeat with a CAG motif at the ATXN3 gene. The putative segregation ratio distortion (SRD) of alleles can play an important role in the non-Mendelian behaviour of triplet repeat loci. To study the stability and infer the segregation patterns of wild-type MJD alleles, the size of the (CAG)(n) tract was analysed in 102 normal sibships, representing 428 meioses. No mutational events were detected during the transmission of alleles. Segregation analysis showed that the smaller alleles were preferentially transmitted (56.9%). Considering maternal meioses alone, such preference was still detected (55.7%) but without statistical significance. A positive correlation was observed for the difference in length between the two alleles constituting the transmitters' genotype (D) and the frequency of transmission of the smaller alleles. The results suggest that small D values are not enough to modify the probability of allele transmission. When transmissions involving genotypes with D <or= 2 were excluded, SRD in favour of the smaller allele became significant for both maternal and paternal transmissions. Therefore, the genotypic composition of the transmitters in a sample to be analysed should influence the ability to detect SRD, acting as a confounding factor.This work was supported by ‘‘Projecto Regional Integrado— DMJ (PRI-DMJ)’’ (funded by Regional Government of the Azores), ‘‘Construyendo una Bio-Región Europea—Biopolis’’ (05/MAC/2.3/ C14, funded by PIC Interreg III B, Azores—Madeira—Canarias) and MANSEEBMO (MI.2.1/004/2005, funded by ‘‘Direcção Regional da Ciência e Tecnologia’’). CB (SFRH/BD/21875/2005) is a recipient of a Ph.D. grant, and RM (SFRH/BPD/32473/2006) and CS (SFRH/BPD/ 20944/2004) are postdoctoral fellows from ‘‘Fundação para a Ciência e a Tecnologia’’ (FCT)

SARS-CoV-2 introductions and early dynamics of the epidemic in Portugal

Genomic surveillance of SARS-CoV-2 in Portugal was rapidly implemented by the National Institute of Health in the early stages of the COVID-19 epidemic, in collaboration with more than 50 laboratories distributed nationwide. Methods By applying recent phylodynamic models that allow integration of individual-based travel history, we reconstructed and characterized the spatio-temporal dynamics of SARSCoV-2 introductions and early dissemination in Portugal. Results We detected at least 277 independent SARS-CoV-2 introductions, mostly from European countries (namely the United Kingdom, Spain, France, Italy, and Switzerland), which were consistent with the countries with the highest connectivity with Portugal. Although most introductions were estimated to have occurred during early March 2020, it is likely that SARS-CoV-2 was silently circulating in Portugal throughout February, before the first cases were confirmed. Conclusions Here we conclude that the earlier implementation of measures could have minimized the number of introductions and subsequent virus expansion in Portugal. This study lays the foundation for genomic epidemiology of SARS-CoV-2 in Portugal, and highlights the need for systematic and geographically-representative genomic surveillance.We gratefully acknowledge to Sara Hill and Nuno Faria (University of Oxford) and Joshua Quick and Nick Loman (University of Birmingham) for kindly providing us with the initial sets of Artic Network primers for NGS; Rafael Mamede (MRamirez team, IMM, Lisbon) for developing and sharing a bioinformatics script for sequence curation (https://github.com/rfm-targa/BioinfUtils); Philippe Lemey (KU Leuven) for providing guidance on the implementation of the phylodynamic models; Joshua L. Cherry (National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health) for providing guidance with the subsampling strategies; and all authors, originating and submitting laboratories who have contributed genome data on GISAID (https://www.gisaid.org/) on which part of this research is based. The opinions expressed in this article are those of the authors and do not reflect the view of the National Institutes of Health, the Department of Health and Human Services, or the United States government. This study is co-funded by Fundação para a Ciência e Tecnologia and Agência de Investigação Clínica e Inovação Biomédica (234_596874175) on behalf of the Research 4 COVID-19 call. Some infrastructural resources used in this study come from the GenomePT project (POCI-01-0145-FEDER-022184), supported by COMPETE 2020 - Operational Programme for Competitiveness and Internationalisation (POCI), Lisboa Portugal Regional Operational Programme (Lisboa2020), Algarve Portugal Regional Operational Programme (CRESC Algarve2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF), and by Fundação para a Ciência e a Tecnologia (FCT).info:eu-repo/semantics/publishedVersio

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