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1. Semi-Supervised Diffusion Model for Brain Age Prediction

Author

Ijishakin, Ayodeji, Martin, Sophie, Townend, Florence, Agosta, Federica, Spinelli, Edoardo Gioele, Basaia, Silvia, Schito, Paride, Falzone, Yuri, Filippi, Massimo, Cole, James, and Malaspina, Andrea

Subjects
Electrical Engineering and Systems Science - Image and Video Processing, Computer Science - Computer Vision and Pattern Recognition
Abstract

Brain age prediction models have succeeded in predicting clinical outcomes in neurodegenerative diseases, but can struggle with tasks involving faster progressing diseases and low quality data. To enhance their performance, we employ a semi-supervised diffusion model, obtaining a 0.83(p<0.01) correlation between chronological and predicted age on low quality T1w MR images. This was competitive with state-of-the-art non-generative methods. Furthermore, the predictions produced by our model were significantly associated with survival length (r=0.24, p<0.05) in Amyotrophic Lateral Sclerosis. Thus, our approach demonstrates the value of diffusion-based architectures for the task of brain age prediction.

Published
2024

3. Interpretable Alzheimer's Disease Classification Via a Contrastive Diffusion Autoencoder

Author

Ijishakin, Ayodeji, Abdulaal, Ahmed, Hadjivasiliou, Adamos, Martin, Sophie, and Cole, James

Subjects
Computer Science - Computer Vision and Pattern Recognition, Computer Science - Machine Learning
Abstract

In visual object classification, humans often justify their choices by comparing objects to prototypical examples within that class. We may therefore increase the interpretability of deep learning models by imbuing them with a similar style of reasoning. In this work, we apply this principle by classifying Alzheimer's Disease based on the similarity of images to training examples within the latent space. We use a contrastive loss combined with a diffusion autoencoder backbone, to produce a semantically meaningful latent space, such that neighbouring latents have similar image-level features. We achieve a classification accuracy comparable to black box approaches on a dataset of 2D MRI images, whilst producing human interpretable model explanations. Therefore, this work stands as a contribution to the pertinent development of accurate and interpretable deep learning within medical imaging.

Published
2023

4. “Pink power”—the importance of coralline algal beds in the oceanic carbon cycle

Author

Schubert, Nadine, Tuya, Fernando, Peña, Viviana, Horta, Paulo A., Salazar, Vinícius W., Neves, Pedro, Ribeiro, Cláudia, Otero-Ferrer, Francisco, Espino, Fernando, Schoenrock, Kathryn, Ragazzola, Federica, Olivé, Irene, Giaccone, Thalassia, Nannini, Matteo, Mangano, M. Cristina, Sará, Gianluca, Mancuso, Francesco Paolo, Tantillo, Mario Francesco, Bosch-Belmar, Mar, Martin, Sophie, Le Gall, Line, Santos, Rui, and Silva, João

Published
2024
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7. IRE1 RNase controls CD95-mediated cell death

Author

Pelizzari-Raymundo, Diana, Maltret, Victoria, Nivet, Manon, Pineau, Raphael, Papaioannou, Alexandra, Zhou, Xingchen, Caradec, Flavie, Martin, Sophie, Le Gallo, Matthieu, Avril, Tony, Chevet, Eric, and Lafont, Elodie

Published
2024
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14. Development and evaluation of intraoperative ultrasound segmentation with negative image frames and multiple observer labels

Author

Chalcroft, Liam F, Qu, Jiongqi, Martin, Sophie A, Gayo, Iani JMB, Minore, Giulio V, Singh, Imraj RD, Saeed, Shaheer U, Yang, Qianye, Baum, Zachary MC, Altmann, Andre, and Hu, Yipeng

Subjects
Computer Science - Computer Vision and Pattern Recognition, Computer Science - Machine Learning
Abstract

When developing deep neural networks for segmenting intraoperative ultrasound images, several practical issues are encountered frequently, such as the presence of ultrasound frames that do not contain regions of interest and the high variance in ground-truth labels. In this study, we evaluate the utility of a pre-screening classification network prior to the segmentation network. Experimental results demonstrate that such a classifier, minimising frame classification errors, was able to directly impact the number of false positive and false negative frames. Importantly, the segmentation accuracy on the classifier-selected frames, that would be segmented, remains comparable to or better than those from standalone segmentation networks. Interestingly, the efficacy of the pre-screening classifier was affected by the sampling methods for training labels from multiple observers, a seemingly independent problem. We show experimentally that a previously proposed approach, combining random sampling and consensus labels, may need to be adapted to perform well in our application. Furthermore, this work aims to share practical experience in developing a machine learning application that assists highly variable interventional imaging for prostate cancer patients, to present robust and reproducible open-source implementations, and to report a set of comprehensive results and analysis comparing these practical, yet important, options in a real-world clinical application., Comment: Accepted to ASMUS@MICCAI 2021

Published
2021

15. Brain Matters: Exploring Bias in AI for Neuroimaging Research

Author

Martin, Sophie A., Biondo, Francesca, Cole, James H., Taylor, Beatrice, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Wesarg, Stefan, editor, Puyol Antón, Esther, editor, Baxter, John S. H., editor, Erdt, Marius, editor, Drechsler, Klaus, editor, Oyarzun Laura, Cristina, editor, Freiman, Moti, editor, Chen, Yufei, editor, Rekik, Islem, editor, Eagleson, Roy, editor, Feragen, Aasa, editor, King, Andrew P., editor, Cheplygina, Veronika, editor, Ganz-Benjaminsen, Melani, editor, Ferrante, Enzo, editor, Glocker, Ben, editor, Moyer, Daniel, editor, and Petersen, Eikel, editor

Published
2023
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18. The evolution of global health teaching in undergraduate medical curricula

Author

Rowson Mike, Smith Abi, Hughes Rob, Johnson Oliver, Maini Arti, Martin Sophie, Martineau Fred, Miranda J Jaime, Pollit Vicki, Wake Rae, Willott Chris, and Yudkin John S

Subjects
Global health, International health, Medical education, Undergraduate, Curriculum, Public aspects of medicine, RA1-1270
Abstract

Abstract Background Since the early 1990s there has been a burgeoning interest in global health teaching in undergraduate medical curricula. In this article we trace the evolution of this teaching and present recommendations for how the discipline might develop in future years. Discussion Undergraduate global health teaching has seen a marked growth over the past ten years, partly as a response to student demand and partly due to increasing globalization, cross-border movement of pathogens and international migration of health care workers. This teaching has many different strands and types in terms of topic focus, disciplinary background, the point in medical studies in which it is taught and whether it is compulsory or optional. We carried out a survey of medical schools across the world in an effort to analyse their teaching of global health. Results indicate that this teaching is rising in prominence, particularly through global health elective/exchange programmes and increasing teaching of subjects such as globalization and health and international comparison of health systems. Our findings indicate that global health teaching is moving away from its previous focus on tropical medicine towards issues of more global relevance. We suggest that there are three types of doctor who may wish to work in global health – the ‘globalised doctor’, ‘humanitarian doctor’ and ‘policy doctor’ – and that each of these three types will require different teaching in order to meet the required competencies. This teaching needs to be inserted into medical curricula in different ways, notably into core curricula, a special overseas doctor track, optional student selected components, elective programmes, optional intercalated degrees and postgraduate study. Summary We argue that teaching of global health in undergraduate medical curricula must respond to changing understandings of the term global health. In particular it must be taught from the perspective of more disciplines than just biomedicine, in order to reflect the social, political and economic causes of ill health. In this way global health can provide valuable training for all doctors, whether they choose to remain in their countries of origin or work abroad.

Published
2012
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19. Conceptualising global health: theoretical issues and their relevance for teaching

Author

Rowson Mike, Willott Chris, Hughes Rob, Maini Arti, Martin Sophie, Miranda J Jaime, Pollit Vicki, Smith Abi, Wake Rae, and Yudkin John S

Subjects
Global health, Medical education, Undergraduate, Curriculum, Globalization, Equity, Public aspects of medicine, RA1-1270
Abstract

Abstract Background There has long been debate around the definition of the field of education, research and practice known as global health. In this article we step back from attempts at definition and instead ask what current definitions tell us about the evolution of the field, identifying gaps and points of debate and using these to inform discussions of how global health might be taught. Discussion What we now know as global health has its roots in the late 19th century, in the largely colonial, biomedical pursuit of ‘international health’. The twentieth century saw a change in emphasis of the field towards a much broader conceptualisation of global health, encompassing broader social determinants of health and a truly global focus. The disciplinary focus has broadened greatly to include economics, anthropology and political science, among others. There have been a number of attempts to define the new field of global health. We suggest there are three central areas of contention: what the object of knowledge of global health is, the types of knowledge to be used and around the purpose of knowledge in the field of global health. We draw a number of conclusions from this discussion. First, that definitions should pay attention to differences as well as commonalities in different parts of the world, and that the definitions of global health themselves depend to some extent on the position of the definer. Second, global health’s core strength lies in its interdisciplinary character, in particular the incorporation of approaches from outside biomedicine. This approach recognises that political, social and economic factors are central causes of ill health. Last, we argue that definition should avoid inclusion of values. In particular we argue that equity, a key element of many definitions of global health, is a value-laden concept and carries with it significant ideological baggage. As such, its widespread inclusion in the definitions of global health is inappropriate as it suggests that only people sharing these values may be seen as ‘doing’ global health. Nevertheless, discussion of values should be a key part of global health education. Summary Our discussions lead us to emphasise the importance of an approach to teaching global health that is flexible, interdisciplinary and acknowledges the different interpretations and values of those practising and teaching the field.

Published
2012
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21. A stochastic individual based model for the growth of a stand of Japanese knotweed including mowing as a management technique

Author

Lavallée, François, Smadi, Charline, Alvarez, Isabelle, Reineking, Björn, Martin, François-Marie, Dommanget, Fanny, and Martin, Sophie

Subjects
Quantitative Biology - Populations and Evolution
Abstract

Invasive alien species are a growing threat for environment and health. They also have a major economic impact, as they can damage many infrastructures. The Japanese knotweed (Fallopia japonica), present in North America, Northern and Central Europe as well as in Australia and New Zealand, is listed by the World Conservation Union as one of the world's worst invasive species. So far, most models have dealt with how the invasion spreads without management. This paper aims at providing a model able to study and predict the dynamics of a stand of Japanese knotweed taking into account mowing as a management technique. The model we propose is stochastic and individual-based, which allows us taking into account the behaviour of individuals depending on their size and location, as well as individual stochasticity. We set plant dynamics parameters thanks to a calibration with field data, and study the influence of the initial population size, the mean number of mowing events a year and the management project duration on mean area and mean number of crowns of stands. In particular, our results provide the sets of parameters for which it is possible to obtain the stand eradication, and the minimal duration of the management project necessary to achieve this latter.

Published
2019

25. 'It makes me feel a sense of belonging' : using person centred approaches to elicit and promote the voices of young women placed in a specialist SEMH provision

Author

Martin, Sophie

Subjects
371.9
Abstract

Evidence has indicated that pupils with social emotional and mental health (SEMH) needs are more likely to be excluded from mainstream school and placed in alternative provision (AP). Young women are a minority within this cohort and due to the differential prevalence rates, research exploring their experiences is restricted. Consequently, there is a paucity of knowledge on the impact SEMH and placement in AP has on young women's educational experiences, identities, lives and futures. Without such knowledge, opportunities to improve educational outcomes for this group of pupils is limited. This study adopted a longitudinal, participatory and person-centred approach, to elicit the voices and views of six young women placed within a specialist alternative provision (Riverford). Three sets of interviews were conducted with each young woman, to gain a rich and comprehensive understanding of their experiences in and out of school. Narrative analysis using Gilligan's listening guide (1982) enabled a dynamic exploration of each young woman's sense of self and identity. A thematic analysis was also used to extrapolate the commonalities in the young women's experiences. The findings drawn from the young women's narratives highlighted the complexity of their identities and self-concept. The longitudinal nature of the study allowed the temporality of their experiences to be explored. Relationships and self-concept were identified as integral to all the young women's stories. Riverford was presented as providing a distinctly different educational experience to mainstream school. Within this setting, the young women described a sense of belonging and the opportunity to see visions of 'hope for' future selves. Through a co-construction of knowledge, the current study offers new insight into young women placed in AP. The voices of the young women were integral to the research process and findings, and through their narrative's implications for professional educational practice and further research have been identified.

Published
2019

26. Lack of the human choline transporter‐like protein SLC44A2 causes hearing impairment and a rare red blood phenotype

Author

Koehl, Bérengère, Vrignaud, Cédric, Mikdar, Mahmoud, Nair, Thankam S, Yang, Lucy, Landry, Seyve, Laiguillon, Guy, Giroux‐Lathuile, Claudine, Anselme‐Martin, Sophie, El Kenz, Hanane, Hermine, Olivier, Mohandas, Narla, Cartron, Jean Pierre, Colin, Yves, Detante, Olivier, Marlu, Raphaël, Le Van Kim, Caroline, Carey, Thomas E, Azouzi, Slim, and Peyrard, Thierry

Published
2023
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32. Development and Evaluation of Intraoperative Ultrasound Segmentation with Negative Image Frames and Multiple Observer Labels

Author

Chalcroft, Liam F., Qu, Jiongqi, Martin, Sophie A., Gayo, Iani JMB, Minore, Giulio V., Singh, Imraj RD, Saeed, Shaheer U., Yang, Qianye, Baum, Zachary M. C., Altmann, Andre, Hu, Yipeng, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Woeginger, Gerhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Noble, J. Alison, editor, Aylward, Stephen, editor, Grimwood, Alexander, editor, Min, Zhe, editor, Lee, Su-Lin, editor, and Hu, Yipeng, editor

Published
2021
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35. Attenuated Codon Optimality Contributes to Neural-Specific mRNA Decay in Drosophila

Author

Burow, Dana A, Martin, Sophie, Quail, Jade F, Alhusaini, Najwa, Coller, Jeff, and Cleary, Michael D

Subjects
Biological Sciences, Genetics, Neurosciences, Animals, Animals, Genetically Modified, Codon, Computational Biology, Drosophila melanogaster, Embryo, Nonmammalian, Gene Expression Regulation, Developmental, Half-Life, Humans, Neurogenesis, Protein Biosynthesis, RNA Stability, RNA, Messenger, RNA, Transfer, Zygote, Drosophila, codon optimality, development, mRNA stability, nervous system, tRNA, Biochemistry and Cell Biology, Medical Physiology, Biological sciences
Abstract

Tissue-specific mRNA stability is important for cell fate and physiology, but the mechanisms involved are not fully understood. We found that zygotic mRNA stability in Drosophila correlates with codon content: optimal codons are enriched in stable transcripts associated with metabolic functions like translation, while non-optimal codons are enriched in unstable transcripts, including those associated with neural development. Bioinformatic analyses and reporter assays revealed that similar codons stabilize or destabilize mRNAs in the nervous system and other tissues, but the link between codon content and stability is attenuated in the nervous system. We confirmed that optimal codons are decoded by abundant tRNAs while non-optimal codons are decoded by less abundant tRNAs in embryos and in the nervous system. We conclude that codon optimality is a general determinant of zygotic mRNA stability, and attenuation of codon optimality allows trans-acting factors to exert greater influence over mRNA decay in the nervous system.

Published
2018

37. Metastatic cancer patients hospitalized at initial diagnosis: when does rescue systemic therapy make sense?

Author

Vercueil, Colin, primary, Varnier, Romain, additional, Seban, Romain, additional, Ciaptacz, Lisa, additional, Pavillet, Julien, additional, Fraisse, Cléa, additional, Darbas, Tiffany, additional, Abdallahoui, Safa, additional, Cox, David, additional, Martin, Sophie, additional, Trensz, Philippe, additional, Kurtz, Jean-Emmanuel, additional, Gantzer, Justine, additional, Amé, Shanti, additional, Bouleuc, Carole, additional, Chvetzoff, Gisèle, additional, and Eberst, Lauriane, additional

Published
2024
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43. Amniotic fluid peptides predict postnatal kidney survival in developmental kidney disease

Author

Allegaert, Karel, Aubard, Yves, Basmaison, Odile, Benevent, Jean-Baptiste, Biquard, Florence, Champion, Gérard, Delbosc, Jean-Marie, Eckart, Philippe, Froute, Marie-Françoise, Gaucherand, Pascal, Groussolles, Marion, Guigonis, Vincent, Hougas, Blandine, Le Bouar, Gwenaelle, Martin, Alain, Martin, Sophie, Maupin-Hyvonnet, Mariannick, Merveille, Marina, Mousty, Eve, Nobili, François, Ryckewaert, Amelie, Sartor, Agnes, Taque, Sophie, Winer, Norbert, Klein, Julie, Buffin-Meyer, Bénédicte, Boizard, Franck, Moussaoui, Nabila, Lescat, Ophélie, Breuil, Benjamin, Fedou, Camille, Feuillet, Guylène, Casemayou, Audrey, Neau, Eric, Hindryckx, An, Decatte, Luc, Levtchenko, Elena, Raaijmakers, Anke, Vayssière, Christophe, Goua, Valérie, Lucas, Charlotte, Perrotin, Franck, Cloarec, Sylvie, Benachi, Alexandra, Manca-Pellissier, Marie-Christine, Delmas, Hélène Laurichesse, Bessenay, Lucie, Le Vaillant, Claudine, Allain-Launay, Emma, Gondry, Jean, Boudailliez, Bernard, Simon, Elisabeth, Prieur, Fabienne, Lavocat, Marie-Pierre, Saliou, Anne-Hélène, De Parscau, Loic, Bidat, Laurent, Noel, Catherine, Floch, Corinne, Bourdat-Michel, Guylène, Favre, Romain, Weingertner, Anne-Sophie, Oury, Jean-François, Baudouin, Véronique, Bory, Jean-Paul, Pietrement, Christine, Fiorenza, Maryse, Massardier, Jérôme, Kessler, Sylvie, Lounis, Nadia, Auriol, Françoise Conte, Marcorelles, Pascale, Collardeau-Frachon, Sophie, Zürbig, Petra, Mischak, Harald, Magalhães, Pedro, Batut, Julie, Blader, Patrick, Saulnier Blache, Jean-Sebastien, Bascands, Jean-Loup, Schaefer, Franz, Decramer, Stéphane, and Schanstra, Joost P.

Published
2021
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44. Positive species interactions structure rhodolith bed communities at a global scale

Author

Bulleri, Fabio, Schubert, Nadine, Hall-Spencer, Jason M., Basso, Daniela, Burdett, Heidi, Francini-Filho, Ronaldo B., Grall, Jacques, Horta, Paulo A., Kamenos, Nicholas A., Martin, Sophie, Nannini, Matteo, Neves, Pedro, Olivé, Irene, Peña, Viviana, Ragazzola, Federica, Ribeiro, Cláudia, Rinde, Eli, Sissini, Marina, Tuya, Fernando, Silva, João, Bulleri, Fabio, Schubert, Nadine, Hall-Spencer, Jason M., Basso, Daniela, Burdett, Heidi, Francini-Filho, Ronaldo B., Grall, Jacques, Horta, Paulo A., Kamenos, Nicholas A., Martin, Sophie, Nannini, Matteo, Neves, Pedro, Olivé, Irene, Peña, Viviana, Ragazzola, Federica, Ribeiro, Cláudia, Rinde, Eli, Sissini, Marina, Tuya, Fernando, and Silva, João

Abstract

Rhodolith beds are diverse and globally distributed habitats. Nonetheless, the role of rhodoliths in structuring the associated species community through a hierarchy of positive interactions is yet to be recognised. In this review, we provide evidence that rhodoliths can function as foundation species of multi-level facilitation cascades and, hence, are fundamental for the persistence of hierarchically structured communities within coastal oceans. Rhodoliths generate facilitation cascades by buffering physical stress, reducing consumer pressure and enhancing resource availability. Due to large variations in their shape, size and density, a single rhodolith bed can support multiple taxonomically distant and architecturally distinct habitat-forming species, such as primary producers, sponges or bivalves, thus encompassing a broad range of functional traits and providing a wealth of secondary microhabitat and food resources. In addition, rhodoliths are often mobile, and thus can redistribute associated species, potentially expanding the distribution of species with short-distance dispersal abilities. Key knowledge gaps we have identified include: the experimental assessment of the role of rhodoliths as basal facilitators; the length and temporal stability of facilitation cascades; variations in species interactions within cascades across environmental gradients; and the role of rhodolith beds as climate refugia. Addressing these research priorities will allow the development of evidence-based policy decisions and elevate rhodolith beds within marine conservation strategies.

Published
2024
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45. French coastal network for carbonate system monitoring: The CocoriCO2 dataset

Author

Petton, Sébastien, Pernet, Fabrice, Le Roy, Valerian, Huber, Matthias, Martin, Sophie, Mace, Eric, Bozec, Yann, Loisel, Stephane, Rimmelin-maury, Peggy, Grossteffan, Emilie, Repecaud, Michel, Quemener, Loïc, Retho, Michael, Manach, Soazig, Papin, Mathias, Pineau, Philippe, Lacoue-labarthe, Thomas, Deborde, Jonathan, Costes, Louis, Polsenaere, Pierre, Rigouin, Loic, Benhamou, Jeremy, Gouriou, Laure, Lequeux, Josephine, Labourdette, Nathalie, Savoye, Nicolas, Messiaen, Gregory, Foucault, Elodie, Ouisse, Vincent, Richard, Marion, Lagarde, Franck, Voron, Florian, Kempf, Valentin, Mas, Sebastien, Giannecchini, Lea, Vidussi, Francesca, Mostajir, Behzad, Leredde, Yann, Alliouane, Samir, Gattuso, Jean-pierre, Gazeau, Frederic, Petton, Sébastien, Pernet, Fabrice, Le Roy, Valerian, Huber, Matthias, Martin, Sophie, Mace, Eric, Bozec, Yann, Loisel, Stephane, Rimmelin-maury, Peggy, Grossteffan, Emilie, Repecaud, Michel, Quemener, Loïc, Retho, Michael, Manach, Soazig, Papin, Mathias, Pineau, Philippe, Lacoue-labarthe, Thomas, Deborde, Jonathan, Costes, Louis, Polsenaere, Pierre, Rigouin, Loic, Benhamou, Jeremy, Gouriou, Laure, Lequeux, Josephine, Labourdette, Nathalie, Savoye, Nicolas, Messiaen, Gregory, Foucault, Elodie, Ouisse, Vincent, Richard, Marion, Lagarde, Franck, Voron, Florian, Kempf, Valentin, Mas, Sebastien, Giannecchini, Lea, Vidussi, Francesca, Mostajir, Behzad, Leredde, Yann, Alliouane, Samir, Gattuso, Jean-pierre, and Gazeau, Frederic

Abstract

Since the beginning of the industrial revolution, atmospheric carbon dioxide (CO2) concentrations have risen steadily and have induced a decrease of the averaged surface ocean pH by 0.1 units, corresponding to an increase in ocean acidity of about 30 %. In addition to ocean warming, ocean acidification poses a tremendous challenge to some marine organisms, especially calcifiers. The need for long-term oceanic observations of pH and temperature is a key element to assess the vulnerability of marine communities and ecosystems to these pressures. Nearshore productive environments, where a large majority of shellfish farming activities are conducted, are known to present pH levels as well as amplitudes of daily and seasonal variations that are much larger than those observed in the open ocean. Yet, to date, there are very few coastal observation sites where these parameters are measured simultaneously and at high frequency. To bridge this gap, an observation network was initiated in 2021 in the framework of the CocoriCO(2) project. Six sites were selected along the French Atlantic and Mediterranean coastlines based on their importance in terms of shellfish production and the presence of high- and low-frequency monitoring activities. At each site, autonomous pH sensors were deployed, both inside and outside shellfish production areas, next to high-frequency CTD (conductivity-temperature-depth) probes operated through two operating monitoring networks. pH sensors were set to an acquisition rate of 15 min, and discrete seawater samples were collected biweekly in order to control the quality of pH data (laboratory spectrophotometric measurements) as well as to measure total alkalinity and dissolved inorganic carbon concentrations for full characterization of the carbonate system. While this network has been up and running for more than 2 years, the acquired dataset has already revealed important differences in terms of pH variations between monitored sites related to the in

Published
2024
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