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2,162 results on '"Stevens, Molly"'

1. Biofabrication and biomanufacturing in Ireland and the UK

Author

Murphy, Jack F., Lavelle, Martha, Asciak, Lisa, Burdis, Ross, Levis, Hannah J., Ligorio, Cosimo, McGuire, Jamie, Polleres, Marlene, Smith, Poppy O., Tullie, Lucinda, Uribe-Gomez, Juan, Chen, Biqiong, Dawson, Jonathan I., Gautrot, Julien E., Hooper, Nigel M., Kelly, Daniel J., Li, Vivian S. W., Mata, Alvaro, Pandit, Abhay, Phillips, James B., Shu, Wenmiao, Stevens, Molly M., Williams, Rachel L., Armstrong, James P. K., and Huang, Yan Yan Shery

Published
2024
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2. Hyperspectral unmixing for Raman spectroscopy via physics-constrained autoencoders

Author

Georgiev, Dimitar, Fernández-Galiana, Álvaro, Pedersen, Simon Vilms, Papadopoulos, Georgios, Xie, Ruoxiao, Stevens, Molly M., and Barahona, Mauricio

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

Raman spectroscopy is widely used across scientific domains to characterize the chemical composition of samples in a non-destructive, label-free manner. Many applications entail the unmixing of signals from mixtures of molecular species to identify the individual components present and their proportions, yet conventional methods for chemometrics often struggle with complex mixture scenarios encountered in practice. Here, we develop hyperspectral unmixing algorithms based on autoencoder neural networks, and we systematically validate them using both synthetic and experimental benchmark datasets created in-house. Our results demonstrate that unmixing autoencoders provide improved accuracy, robustness and efficiency compared to standard unmixing methods. We also showcase the applicability of autoencoders to complex biological settings by showing improved biochemical characterization of volumetric Raman imaging data from a monocytic cell.

Published
2024
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3. Transfer Learning Bayesian Optimization to Design Competitor DNA Molecules for Use in Diagnostic Assays

Author

Sedgwick, Ruby, Goertz, John P., Stevens, Molly M., Misener, Ruth, and van der Wilk, Mark

Subjects
Quantitative Biology - Quantitative Methods, Computer Science - Machine Learning, Statistics - Machine Learning
Abstract

With the rise in engineered biomolecular devices, there is an increased need for tailor-made biological sequences. Often, many similar biological sequences need to be made for a specific application meaning numerous, sometimes prohibitively expensive, lab experiments are necessary for their optimization. This paper presents a transfer learning design of experiments workflow to make this development feasible. By combining a transfer learning surrogate model with Bayesian optimization, we show how the total number of experiments can be reduced by sharing information between optimization tasks. We demonstrate the reduction in the number of experiments using data from the development of DNA competitors for use in an amplification-based diagnostic assay. We use cross-validation to compare the predictive accuracy of different transfer learning models, and then compare the performance of the models for both single objective and penalized optimization tasks.

Published
2024

4. Non-invasive in vivo sensing of bacterial implant infection using catalytically-optimised gold nanocluster-loaded liposomes for urinary readout

Author

Chen, Kaili, Najer, Adrian, Charchar, Patrick, Saunders, Catherine, Thanapongpibul, Chalaisorn, Klöckner, Anna, Chami, Mohamed, Peeler, David J., Silva, Inês, Panariello, Luca, Karu, Kersti, Loynachan, Colleen N., Frenette, Leah C., Potter, Michael, Tregoning, John S., Parkin, Ivan P., Edwards, Andrew M., Clarke, Thomas B., Yarovsky, Irene, and Stevens, Molly M.

Published
2024
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8. RamanSPy: An open-source Python package for integrative Raman spectroscopy data analysis

Author

Georgiev, Dimitar, Pedersen, Simon Vilms, Xie, Ruoxiao, Fernández-Galiana, Álvaro, Stevens, Molly M., and Barahona, Mauricio

Subjects
Condensed Matter - Materials Science, Computer Science - Mathematical Software, Physics - Data Analysis, Statistics and Probability
Abstract

Raman spectroscopy is a non-destructive and label-free chemical analysis technique, which plays a key role in the analysis and discovery cycle of various branches of science. Nonetheless, progress in Raman spectroscopic analysis is still impeded by the lack of software, methodological and data standardisation, and the ensuing fragmentation and lack of reproducibility of analysis workflows thereof. To address these issues, we introduce RamanSPy, an open-source Python package for Raman spectroscopic research and analysis. RamanSPy provides a comprehensive library of ready-to-use tools for spectroscopic analysis, which streamlines day-to-day tasks, integrative analyses, as well as novel research and algorithmic development. RamanSPy is modular and open source, not tied to a particular technology or data format, and can be readily interfaced with the burgeoning ecosystem for data science, statistical analysis and machine learning in Python.

Published
2023
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10. Unsupervised hyperspectral data mining and bioimaging by information entropy and self-modeling curve resolution

Author

Pedersen, Simon Vilms, Walther, Anders R., Callanan, Anthony, Stevens, Molly M., Hedegaard, Martin A. B., and Arnspang, Eva C.

Subjects
Statistics - Computation, Quantitative Biology - Quantitative Methods
Abstract

Unsupervised estimation of the dimensionality of hyperspectral microspectroscopy datasets containing pure and mixed spectral features, and extraction of their representative endmember spectra, remains a challenge in biochemical data mining. We report a new versatile algorithm building on semi-nonnegativity constrained self-modeling curve resolution and information entropy, to estimate the quantity of separable biochemical species from hyperspectral microspectroscopy, and extraction of their representative spectra. The algorithm is benchmarked with established methods from satellite remote sensing, spectral unmixing, and clustering. To demonstrate the widespread applicability of the developed algorithm, we collected hyperspectral datasets using spontaneous Raman, Coherent Anti-stokes Raman Scattering and Fourier Transform IR, of seven reference compounds, an oil-in-water emulsion, and tissue-engineered extracellular matrices on poly-L-lactic acid and porcine jejunum-derived small intestine submucosa scaffolds seeded with bovine chondrocytes. We show the potential of the developed algorithm by consolidating hyperspectral molecular information with sample microstructure, pertinent to fields ranging from gastrophysics to regenerative medicine.

Published
2022

14. In vitro modeling of the human dopaminergic system using spatially arranged ventral midbrain–striatum–cortex assembloids

Author

Reumann, Daniel, Krauditsch, Christian, Novatchkova, Maria, Sozzi, Edoardo, Wong, Sakurako Nagumo, Zabolocki, Michael, Priouret, Marthe, Doleschall, Balint, Ritzau-Reid, Kaja I., Piber, Marielle, Morassut, Ilaria, Fieseler, Charles, Fiorenzano, Alessandro, Stevens, Molly M., Zimmer, Manuel, Bardy, Cedric, Parmar, Malin, and Knoblich, Jürgen A.

Published
2023
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15. Cellular shape reinforces niche to stem cell signaling in the small intestine

Author

Pentinmikko, Nalle, Lozano, Rodrigo, Scharaw, Sandra, Andersson, Simon, Englund, Johanna I, Castillo-Azofeifa, David, Gallagher, Aaron, Broberg, Martin, Song, Ki-Young, Carvajal, Agustín Sola, Speidel, Alessondra T, Sundstrom, Michael, Allbritton, Nancy, Stevens, Molly M, Klein, Ophir D, Teixeira, Ana, and Katajisto, Pekka

Subjects
Biochemistry and Cell Biology, Biomedical and Clinical Sciences, Biological Sciences, Stem Cell Research - Nonembryonic - Non-Human, Stem Cell Research, Digestive Diseases, Regenerative Medicine, 1.1 Normal biological development and functioning
Abstract

Niche-derived factors regulate tissue stem cells, but apart from the mechanosensory pathways, the effect of niche geometry is not well understood. We used organoids and bioengineered tissue culture platforms to demonstrate that the conical shape of Lgr5+ small intestinal stem cells (ISCs) facilitate their self-renewal and function. Inhibition of non-muscle myosin II (NM II)-driven apical constriction altered ISC shape and reduced niche curvature and stem cell capacity. Niche curvature is decreased in aged mice, suggesting that suboptimal interactions between old ISCs and their niche develop with age. We show that activation of NM IIC or physical restriction to young topology improves in vitro regeneration by old epithelium. We propose that the increase in lateral surface area of ISCs induced by apical constriction promotes interactions between neighboring cells, and the curved topology of the intestinal niche has evolved to maximize signaling between ISCs and neighboring cells.

Published
2022

19. Versailles project on advanced materials and standards (VAMAS) interlaboratory study on measuring the number concentration of colloidal gold nanoparticles

Author

Minelli, Caterina, Wywijas, Magdalena, Bartczak, Dorota, Cuello-Nuñez, Susana, Infante, Heidi Goenaga, Deumer, Jerome, Gollwitzer, Christian, Krumrey, Michael, Murphy, Karen E, Johnson, Monique E, Montoro Bustos, Antonio R, Strenge, Ingo H, Faure, Bertrand, Høghøj, Peter, Tong, Vivian, Burr, Loïc, Norling, Karin, Höök, Fredrik, Roesslein, Matthias, Kocic, Jovana, Hendriks, Lyndsey, Kestens, Vikram, Ramaye, Yannic, Contreras Lopez, Maria C, Auclair, Guy, Mehn, Dora, Gilliland, Douglas, Potthoff, Annegret, Oelschlägel, Kathrin, Tentschert, Jutta, Jungnickel, Harald, Krause, Benjamin C, Hachenberger, Yves U, Reichardt, Philipp, Luch, Andreas, Whittaker, Thomas E, Stevens, Molly M, Gupta, Shalini, Singh, Akash, Lin, Fang-Hsin, Liu, Yi-Hung, Costa, Anna Luisa, Baldisserri, Carlo, Jawad, Rid, Andaloussi, Samir EL, Holme, Margaret N, Lee, Tae Geol, Kwak, Minjeong, Kim, Jaeseok, Ziebel, Johanna, Guignard, Cedric, Cambier, Sebastien, Contal, Servane, Gutleb, Arno C, Kuba Tatarkiewicz, Jan, Jankiewicz, Bartłomiej J, Bartosewicz, Bartosz, Wu, Xiaochun, Fagan, Jeffrey A, Elje, Elisabeth, Rundén-Pran, Elise, Dusinska, Maria, Kaur, Inder Preet, Price, David, Nesbitt, Ian, O Reilly, Sarah, Peters, Ruud JB, Bucher, Guillaume, Coleman, Dennis, Harrison, Angela J, Ghanem, Antoine, Gering, Anne, McCarron, Eileen, Fitzgerald, Niamh, Cornelis, Geert, Tuoriniemi, Jani, Sakai, Midori, Tsuchida, Hidehisa, Maguire, Ciarán, Prina-Mello, Adriele, Lawlor, Alan J, Adams, Jessica, Schultz, Carolin L, Constantin, Doru, Thanh, Nguyen Thi Kim, Tung, Le Duc, Panariello, Luca, Damilos, Spyridon, Gavriilidis, Asterios, Lynch, Iseult, Fryer, Benjamin, Carrazco Quevedo, Ana, Guggenheim, Emily, Briffa, Sophie, Valsami-Jones, Eugenia, Huang, Yuxiong, Keller, Arturo A, Kinnunen, Virva-Tuuli, Perämäki, Siiri, and Krpetic, Zeljka

Subjects
Nanotechnology, Bioengineering, Physical Sciences, Chemical Sciences, Technology, Nanoscience & Nanotechnology
Abstract

We describe the outcome of a large international interlaboratory study of the measurement of particle number concentration of colloidal nanoparticles, project 10 of the technical working area 34, "Nanoparticle Populations" of the Versailles Project on Advanced Materials and Standards (VAMAS). A total of 50 laboratories delivered results for the number concentration of 30 nm gold colloidal nanoparticles measured using particle tracking analysis (PTA), single particle inductively coupled plasma mass spectrometry (spICP-MS), ultraviolet-visible (UV-Vis) light spectroscopy, centrifugal liquid sedimentation (CLS) and small angle X-ray scattering (SAXS). The study provides quantitative data to evaluate the repeatability of these methods and their reproducibility in the measurement of number concentration of model nanoparticle systems following a common measurement protocol. We find that the population-averaging methods of SAXS, CLS and UV-Vis have high measurement repeatability and reproducibility, with between-labs variability of 2.6%, 11% and 1.4% respectively. However, results may be significantly biased for reasons including inaccurate material properties whose values are used to compute the number concentration. Particle-counting method results are less reproducibile than population-averaging methods, with measured between-labs variability of 68% and 46% for PTA and spICP-MS respectively. This study provides the stakeholder community with important comparative data to underpin measurement reproducibility and method validation for number concentration of nanoparticles.

Published
2022

20. Design of Experiments for Verifying Biomolecular Networks

Author

Sedgwick, Ruby, Goertz, John, Stevens, Molly, Misener, Ruth, and van der Wilk, Mark

Subjects
Quantitative Biology - Quantitative Methods, Computer Science - Machine Learning, Statistics - Machine Learning
Abstract

There is a growing trend in molecular and synthetic biology of using mechanistic (non machine learning) models to design biomolecular networks. Once designed, these networks need to be validated by experimental results to ensure the theoretical network correctly models the true system. However, these experiments can be expensive and time consuming. We propose a design of experiments approach for validating these networks efficiently. Gaussian processes are used to construct a probabilistic model of the discrepancy between experimental results and the designed response, then a Bayesian optimization strategy used to select the next sample points. We compare different design criteria and develop a stopping criterion based on a metric that quantifies this discrepancy over the whole surface, and its uncertainty. We test our strategy on simulated data from computer models of biochemical processes., Comment: Comment: Updated to correct typo "that that" => "that"

Published
2020

21. High-throughput molecular imaging via deep learning enabled Raman spectroscopy

Author

Horgan, Conor C., Jensen, Magnus, Nagelkerke, Anika, St-Pierre, Jean-Phillipe, Vercauteren, Tom, Stevens, Molly M., and Bergholt, Mads S.

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

Raman spectroscopy enables non-destructive, label-free imaging with unprecedented molecular contrast but is limited by slow data acquisition, largely preventing high-throughput imaging applications. Here, we present a comprehensive framework for higher-throughput molecular imaging via deep learning enabled Raman spectroscopy, termed DeepeR, trained on a large dataset of hyperspectral Raman images, with over 1.5 million spectra (400 hours of acquisition) in total. We firstly perform denoising and reconstruction of low signal-to-noise ratio Raman molecular signatures via deep learning, with a 9x improvement in mean squared error over state-of-the-art Raman filtering methods. Next, we develop a neural network for robust 2-4x super-resolution of hyperspectral Raman images that preserves molecular cellular information. Combining these approaches, we achieve Raman imaging speed-ups of up to 160x, enabling high resolution, high signal-to-noise ratio cellular imaging in under one minute. Finally, transfer learning is applied to extend DeepeR from cell to tissue-scale imaging. DeepeR provides a foundation that will enable a host of higher-throughput Raman spectroscopy and molecular imaging applications across biomedicine.

Published
2020
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22. Fluorescence-Guided Raman Spectroscopy for Tumour Margin Delineation

Author

Horgan, Conor C., Bergholt, Mads S., Thin, May Zaw, Nagelkerke, Anika, Kennedy, Robert, Kalber, Tammy L., Stuckey, Daniel J., and Stevens, Molly M.

Subjects
Physics - Medical Physics
Abstract

The initial detection and identification of suspicious lesions and the precise delineation of tumour mar-gins are essential for successful tumour resection, with progression-free survival linked to rates of complete resection. However, post-surgical positive margin rates remain high for many cancers and despite numerous advances in intraoperative imaging and diagnostic technologies, there exists no single modality that can adequately perform both tumoural detection and delineation. Here, we demonstrate a multimodal computer vision-based diagnostic system capable of both the gross detection and identification of suspicious lesions and the precise delineation of disease margins. We first show that through visual tracking of a spectroscopic probe, we enable real-time tumour margin delineation both for ex vivo human tumour biopsies and for an in vivo tumour xenograft mouse model. We then demonstrate that the combination of Raman spectroscopic diagnoses with protoporphyrin IX (PPIX) fluorescence imaging enables fluorescence-guided Raman spectroscopic margin delineation. Our fluorescence-guided Raman spectroscopic system achieves superior margin delineation accuracy to fluorescence imaging alone, demonstrating the potential for our system to achieve improved clinical outcomes for tumour resection surgeries.

Published
2020

23. Integrated Photodynamic Raman Theranostics for Cancer Diagnosis, Treatment, and Post-Treatment Molecular Monitoring

Author

Horgan, Conor C., Bergholt, Mads S., Nagelkerke, Anika, Thin, May Zaw, Pence, Isaac J., Kauscher, Ulrike, Kalber, Tammy L., Stuckey, Daniel J., and Stevens, Molly M.

Subjects
Physics - Medical Physics, Physics - Optics
Abstract

Theranostics, the combination of diagnosis and therapy, has long held promise as a means to achieving personalised precision cancer treatments. However, despite its potential, theranostics has yet to realise significant clinical translation, largely due the complexity and overriding toxicity concerns of existing theranostic nanoparticle strategies. Here, we present an alternative nanoparticle-free theranostic approach based on simultaneous Raman spectroscopy and photodynamic therapy (PDT) in an integrated clinical platform for cancer theranostics. We detail the compatibility of Raman spectroscopy and PDT for cancer theranostics, whereby Raman spectroscopic diagnosis can be performed on PDT photosensitiser-positive cells and tissues without inadvertent photosensitiser activation/photobleaching or impaired diagnostic capacity. We further demonstrate that our theranostic platform enables in vivo tumour diagnosis, treatment, and post-treatment molecular monitoring in real-time. This system thus achieves effective theranostic performance, providing a promising new avenue towards the clinical realisation of theranostics.

Published
2020

27. A multi-platform approach to identify a blood-based host protein signature for distinguishing between bacterial and viral infections in febrile children (PERFORM): a multi-cohort machine learning study

Author

Jackson, Heather Ruth, Zandstra, Judith, Menikou, Stephanie, Hamilton, Shea, McArdle, Andrew J, De, Tisham, Agyeman, Philipp K A, Von Both, Ulrich, Carrol, Enitan D, Emonts, Marieke, Eleftheriou, Irini, Van der Flier, Michiel, Fink, Colin, De Groot, Ronald, Moll, Henriette A, Pokorn, Marko, Pollard, Andrew, Schlapbach, Luregn J, Tsolia, Maria, Usuf, Effua, Wright, Victoria, Yeung, Shunmay, Zavadska, Dace, Zenz, Werner, Coin, Lachlan JM, Cunnington, Aubrey J, Martinon-Torres, Federico, Herberg, Jethro, De Jonge, Marien I, Levin, Michael, Kuijpers, Taco, Kaforou, Myrsini, Abdulla, Amina, Aebi, Christoph, Agbeko, Rachel, Ali, Ladan, Alkema, Wynand, Allen, Karen, Anderson, Suzanne, Ansari, Imran, Arif, Tasnim, Avramoska, Tanja, Baas, Bryan, Bahovec, Natalija, Balode, Anda, Bãrdzdina, Arta, Barendregt, A M, Barral-Arca, Ruth, Bath, David, Bauchinger, Sebastian, Baumard, Lucas, Baumgart, Hinrich, Baxter, Frances, Bell, Kathryn, Bell, Ashley, Bello, Xabier, Bellos, Evangelos, Benesch, Martin, Bennet, Joshua, Berger, Christoph, Bernhard-Stirnemann, Sara, Bibi, Sagida, Bidlingmaier, Christoph, Binder, Alexander, Binder, Vera, Blackmore, Jennifer, Bojang, Kalifa, Borensztajn, Dorine M, Brengel-Pesce, Karen, Broderick, Claire, Buschbeck, Judith, Calvo-Bado, Leonides, Carnota, Sandra, Carter, Michael J, Castro, María Barreiro, Cebey-López, Miriam, Ceesay, Samba, Ceolotto, Astrid, Chan, Adora, Cocklin, Elizabeth, Collings, Kalvin, Crulley, Stephen, Curras-Tuala, María José, D'alessandro, Umberto, D'Souza, Giselle, Danhauser, Katharina, Darboe, Saffiatou, Darnell, Sarah, De Haan, L, De Vries, Gabriella, Deksne, Dãrta, Devine, Kirsty, Dewez, Juan Emmanuel, Dik, W, Dudley, Julia, Eber, Ernst, Fabian, Daniel, Farto, Cristina Balo, Fernández, Sonia Serén, Fidler, Katy, Fitchett, Elizabeth, Galassini, Rachel, Gallisti, Siegfried, García, Mirian Ben, Gardovska, Dace, Geissler, J, Gerrits, G P J M, Giannoni, Eric, Gloerich, Jolein, Gómez-Carballa, Alberto, González, Fernando Álves, Gores, Gunther, Grãvele, Dagne, Griese, Matthias, Grope, Ilze, Gurung, Meeru, Haas, Nikolaus, Habgood-Coote, Dominic, Hagedoorn, Nienke N, Haidl, Harald, Harrison, Rebekah, Hauer, Almuthe, Heidema, J, Heininger, Ulrich, Henriet, Stefanie, Hibberd, Martin, Hoggart, Cllive, Hösele, Susanne, Hourmat, Sara, Hude, Christa, Huijnen, Martijn, Iglesias, Pilar Leboráns, Iglesias, Marisol Vilas, Jennings, Rebecca, Johnson, Joanne, Jongerius, Ilse, Jorgensen, Rikke, Kahlert, Christian, Kandasamy, Rama, Kappler, Matthias, Keldorfer, Markus, Kelly, Dominic F, Khanijau, Aakash, Kim, Nayoung, Kim, Eunjung, King, Sharon, Kolberg, Laura, Kolnik, Mojca, Kloosterhuis, Lieke, Kohlfürst, Daniela S, Kohlmaier, Benno, Krenn, Larissa, Leigh, Simon, Leitner, Manuel, Leurent, Baptiste, Lim, Emma, Lin, Naomi, Liu, Ching-Chuan, Löffler, Sabine, Lurz, Eberhard, Mackerness, Christine, Maconochie, Ian, Mallet, Francois, Marmarinos, Antonis, Martin, Alex, Martin, Mike, Martinón Sánchez, José María, Martinón-Torres, Nazareth, McAlinden, Paul, McDonald, Sam, McDonell, Anne, Meiere, Anija, Meierford, Anne, Miedema, C J, Miners, Alec, Mistry, Ravi, Mommert, Marine, Morris, Sophie, Muench, Georg, Murdoch, David R, Mustafa, Sobia, Natalucci, Giancarlo, Neeleman, C, Newall, Karen, Nichols, Samuel, Niederer-Loher, Anita, Niedrist, Tobias, Nijman, Ruud, Nokalna, Ieve, Nordberg, Gudrun, O'Connor, Daniel, Obihara, C C, Oliver, Zoe, Oosthoek, Wilma, Ora, Miguel Sadiki, Osterman, Veronika, Pachot, Alexandre, Pajkrt, D, Pardo-Seco, Jacobo, Pavãre, Jana, Paz, Ivonne Pena, Paulus, Stéphane, Pérez, Belén Mosquera, Persand, Salina, Pfleger, Andreas, Pfurtscheller, Klaus, Philipsen, Ria, Pickering, Alisa, Pierce, Benjamin, Pilch, Heidemarie, Pischedda, Sara, Pölz, Lena, Posfay-Barbe, Klara M, Powell, Oliver, Prunk, Petra, Pučuka, Zanda, Rajic, Glorija, Rashid, Aqeela, Redondo-Collazo, Lorenzo, Reiter, Karl, Relly, Christa, Rhodes, Mathew, Rial, Jose Gómez, Richmond, Vivien, Riedel, Thomas, Rivero Calle, Irene, Roca, Anna, Rödl, Siegfried, Rodríguez, Lidia Piñeiro, Rodríguez-Tenreiro, Carmen, Romaine, Sam, Rowlands, Emily, Rudzate, Aleksandra, Sagmeister, Manfred, Saidykhan, Momodou, Sallas, Antonio, Sarr, Isatou, Schoen, Carola, Schonenberg, D, Schweintzger, Nina, Secka, Fatou, Selecka, Katrīna, Shah, Priyen, Shen, Ching-Fen, Shrestha, Shrijana, Skrabl-Baumgartner, Andrea, Soon, Joshua, Sperl, Matthias, Sprenkeler, Evelien, Spyridis, Nikos, Srovin, Tina Plankar, Stampfer, Laura, Stevens, Molly, Stocker, Martin, Strenger, Volker, Suárez, Carlos Durán, Svile, Dace, Syggelou, Kelly, Tal, Chantal, Tambouratzi, Maria, Tavliavini, Emma, Thakker, Clare, Thomson, Evelyn, Throson, Stephen, Till, Holger, Tramper-Stranders, G A, Trasorras, Cristina Serén, Trobisch, Andreas, Urbãne, Urzula Nora, Usman, Mariama, Valentine, Lucille, Van Aerde, Koen, Van den Berg, J M, Van den Broek, Bryan, Van der Giessen, Ilona, Van der Kuip, M, Van der Velden, Fabian, Van Furth, A M, Van Gool, Alain J, Van Leur, M, van Mierlo, G, Vázquez, Sara Ray, Vermont, Clementien, Vicente, Luisa García, Vincek, Katarina, Vito, Ortensia, Voice, Marie, Wallia, Diane, Walsh, Ben, Wang, Shih-Min, Wedderburn, Catherine, Willems, Esther, Wilson, Clare, Wood, Amanda, Woodsford, Phil, Wyss, Verena, Xagorari, Marietta, Zachariasse, Joany, Zaman, Syed M A, Zurl, Christoph, Zwerenz, Manuela, Jackson, Heather R, Hamilton, Melissa Shea, Fischer, Roman, Thorne, Adam M, Huang, Honglei, Tanck, Michael W, Jansen, Machiel H, Pollard, Andrew J, Tsolia, Maria N, Wright, Victoria J, Coin, Lachlan J M, Casals-Pascual, Climent, Herberg, Jethro A, de Jonge, Marien I, and Kuijpers, Taco W

Published
2023
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28. Relationship between molecular pathogen detection and clinical disease in febrile children across Europe: a multicentre, prospective observational study

Author

Shah, Priyen, Voice, Marie, Calvo-Bado, Leonides, Calle, Irene Rivero, Morris, Sophie, Nijman, Ruud, Broderick, Claire, De, Tisham, Eleftheriou, Irini, Galassini, Rachel, Khanijau, Aakash, Kolberg, Laura, Kolnik, Mojca, Rudzate, Aleksandra, Sagmeister, Manfred, Schweintzger, Nina, Secka, Fatou, Thakker, Clare, Van der Velden, Fabian, Vermont, Clementien, Vincek, Katarina, Agyeman, Philipp K.A., Cunnington, Aubrey J., De Groot, Ronald, Emonts, Marieke, Fidler, Katy, Kuijpers, Taco, Mommert-Tripon, Marine, Brengel-Pesce, Karen, Mallet, Francois, Moll, Henriette, Paulus, Stéphane, Pokorn, Marko, Pollard, Andrew, Schlapbach, Luregn J., Shen, Ching-Fen, Tsolia, Maria, Usuf, Effua, Van der Flier, Michiel, Von Both, Ulrich, Yeung, Shunmay, Zavadska, Dace, Zenz, Werner, Wright, Victoria, Carrol, Enitan D., Kaforou, Myrsini, Martinon-Torres, Federico, Fink, Colin, Levin, Michael, Herberg, Jethro, Baumard, Lucas, Bellos, Evangelos, Coin, Lachlan, D'Souza, Giselle, Habgood-Coote, Dominic, Hamilton, Shea, Hoggart, Cllive, Hourmat, Sara, Jackson, Heather, Lin, Naomi, Menikou, Stephanie, Nichols, Samuel, Paz, Ivonne Pena, Powell, Oliver, Vito, Ortensia, Wilson, Clare, Abdulla, Amina, Ali, Ladan, Darnell, Sarah, Jorgensen, Rikke, Maconochie, Ian, Mustafa, Sobia, Persand, Salina, Walsh, Ben, Stevens, Molly, Kim, Nayoung, Kim, Eunjung, Pierce, Benjamin, Dudley, Julia, Richmond, Vivien, Tavliavini, Emma, Liu, Ching-Chuan, Wang, Shih-Min, González, Fernando Álves, Farto, Cristina Balo, Barral-Arca, Ruth, Castro, María Barreiro, Bello, Xabier, Ben García, Mirian, Carnota, Sandra, Cebey-López, Miriam, Curras-Tuala, María José, Suárez, Carlos Durán, Vicente, Luisa García, Gómez-Carballa, Alberto, Rial, Jose Gómez, Iglesias, Pilar Leboráns, Martinón-Torres, Nazareth, Martinón Sánchez, José María, Pérez, Belén Mosquera, Pardo-Seco, Jacobo, Rodríguez, Lidia Piñeiro, Pischedda, Sara, Vázquez, Sara Ray, Rodríguez-Tenreiro, Carmen, Redondo-Collazo, Lorenzo, Ora, Miguel Sadiki, Sallas, Antonio, Fernández, Sonia Serén, Trasorras, Cristina Serén, Iglesias, Marisol Vilas, Balode, Anda, Bãrdzdina, Arta, Deksne, Dãrta, Gardovska, Dace, Grãvele, Dagne, Grope, Ilze, Meiere, Anija, Nokalna, Ieve, Pavãre, Jana, Pučuka, Zanda, Selecka, Katrīna, Svile, Dace, Urbãne, Urzula Nora, Bojang, Kalifa, Zaman, Syed M.A., Anderson, Suzanne, Roca, Anna, Sarr, Isatou, Saidykhan, Momodou, Darboe, Saffiatou, Ceesay, Samba, D'alessandro, Umberto, Borensztajn, Dorine M., Hagedoorn, Nienke N., Tal, Chantal, Zachariasse, Joany, Dik, W., Aebi, Christoph, Berger, Christoph, Wyss, Verena, Usman, Mariama, Giannoni, Eric, Stocker, Martin, Posfay-Barbe, Klara M., Heininger, Ulrich, Bernhard-Stirnemann, Sara, Niederer-Loher, Anita, Kahlert, Christian, Natalucci, Giancarlo, Relly, Christa, Riedel, Thomas, Cocklin, Elizabeth, Jennings, Rebecca, Johnson, Joanne, Leigh, Simon, Newall, Karen, Romaine, Sam, Tambouratzi, Maria, Marmarinos, Antonis, Xagorari, Marietta, Syggelou, Kelly, Spyridis, Nikos, Blackmore, Jennifer, Harrison, Rebekah, Kohlmaier, Benno, Kohlfürst, Daniela S., Zurl, Christoph, Binder, Alexander, Hösele, Susanne, Leitner, Manuel, Pölz, Lena, Rajic, Glorija, Bauchinger, Sebastian, Baumgart, Hinrich, Benesch, Martin, Ceolotto, Astrid, Eber, Ernst, Gallisti, Siegfried, Gores, Gunther, Haidl, Harald, Hauer, Almuthe, Hude, Christa, Keldorfer, Markus, Krenn, Larissa, Pilch, Heidemarie, Pfleger, Andreas, Pfurtscheller, Klaus, Nordberg, Gudrun, Niedrist, Tobias, Rödl, Siegfried, Skrabl-Baumgartner, Andrea, Sperl, Matthias, Stampfer, Laura, Strenger, Volker, Till, Holger, Trobisch, Andreas, Löffler, Sabine, Dewez, Juan Emmanuel, Hibberd, Martin, Bath, David, Miners, Alec, Fitchett, Elizabeth, Wedderburn, Catherine, Meierford, Anne, Leurent, Baptiste, De Jonge, Marien I., van Aerde, Koen, Alkema, Wynand, van den Broek, Bryan, Gloerich, Jolein, Van Gool, Alain J., Henriet, Stefanie, Huijnen, Martijn, Philipsen, Ria, Willems, Esther, Gerrits, G.P.J.M., Van Leur, M., Heidema, J., De Haan, L., Miedema, C.J., Neeleman, C., Obihara, C.C., Tramper-Stranders, G.A., Kandasamy, Rama, Carter, Michael J., O'Connor, Daniel, Bibi, Sagida, Kelly, Dominic F., Gurung, Meeru, Throson, Stephen, Ansari, Imran, Murdoch, David R., Shrestha, Shrijana, Oliver, Zoe, Lim, Emma, Valentine, Lucille, Allen, Karen, Bell, Kathryn, Chan, Adora, Crulley, Stephen, Devine, Kirsty, Fabian, Daniel, King, Sharon, McAlinden, Paul, McDonald, Sam, McDonell, Anne, Pickering, Alisa, Thomson, Evelyn, Wood, Amanda, Wallia, Diane, Woodsford, Phil, Baxter, Frances, Bell, Ashley, Rhodes, Mathew, Agbeko, Rachel, Mackerness, Christine, Baas, Bryan, Kloosterhuis, Lieke, Oosthoek, Wilma, Arif, Tasnim, Bennet, Joshua, Collings, Kalvin, Van der Giessen, Ilona, Martin, Alex, Rashid, Aqeela, Rowlands, Emily, Soon, Joshua, De Vries, Gabriella, van der Velden, Fabian, Martin, Mike, Mistry, Ravi, Zwerenz, Manuela, Buschbeck, Judith, Bidlingmaier, Christoph, Binder, Vera, Danhauser, Katharina, Haas, Nikolaus, Griese, Matthias, Kappler, Matthias, Lurz, Eberhard, Muench, Georg, Reiter, Karl, Schoen, Carola, Pachot, Alexandre, Mommert, Marine, Srovin, Tina Plankar, Bahovec, Natalija, Prunk, Petra, Osterman, Veronika, Avramoska, Tanja, Jongerius, Ilse, van den Berg, J.M., Schonenberg, D., Barendregt, A.M., Pajkrt, D., van der Kuip, M., van Furth, A.M., Sprenkeler, Evelien, Zandstra, Judith, van Mierlo, G., Geissler, J., Rivero-Calle, Irene, Sagmeister, Manfred G., Schweintzger, Nina A., Kuijpers, Taco W., van der Flier, Michiel, and von Both, Ulrich

Published
2023
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29. Impact of infection on proteome-wide glycosylation revealed by distinct signatures for bacterial and viral pathogens

Author

Abdulla, Amina, Aebi, Christoph, van Aerde, Koen, Agbeko, Rachel, Agyeman, Philipp, D’alessandro, Umberto, Ali, Ladan, Alkema, Wynand, Allen, Karen, González, Fernando Álvez, Anderson, Suzanne, Ansari, Imran, Araf, Tasnim, Avramoska, Tanja, Baas, Bryan, Bahovec, Natalija, Farto, Cristina Balo, Balode, Anda, Barendregt, A.M., Barral-Arca, Ruth, Castro, María Barreiro, Bārzdiņa, Arta, Bath, David, Bauchinger, Sebastian, Baumard, Lucas, Baumgart, Hinrich, Baxter, Frances, Bell, Ashley, Bell, Kathryn, Bello, Xabier, Bellos, Evangelos, Benesch, Martin, Ben García, Mirian, Bennet, Joshua, Berger, Christoph, van den Berg, J.M., Bernhard-Stirnemann, Sara, Bibi, Sagida, Bidlingmaier, Christoph, Binder, Alexander, Binder, Vera, Bojang, Kalifa, Borensztajn, Dorine M., von Both, Ulrich, Brengel-Pesce, Karen, van den Broek, Bryan, Buschbeck, Judith, Calvo-Bado, Leo, Carnota, Sandra, Carrol, Enitan D., Carter, Michael J., Cebey-López, Miriam, Ceesay, Samba, Ceolotto, Astrid, Chan, Adora, Cocklin, Elizabeth, Collings, Kalvin, Crulley, Stephen, Cunnington, Aubrey, Curras-Tuala, María José, Danhauser, Katharina, Darboe, Saffiatou, Darnell, Sarah, De, Tisham, Deksne, Dārta, Devine, Kirsty, Dewez, Juan Emmanuel, Dudley, Julia, Suárez, Carlos Durán, Eber, Ernst, Eleftheriou, Irini, Emonts, Marieke, Fabian, Daniel, Feuchtinger, Tobias, Fidler, Katy, Fink, Colin, van der Flier, Michiel, van Furth, A.M., Galassini, Rachel, Gallistl, Siegfried, Vicente, Luisa García, Gardovska, Dace, Geissler, J., Gerrits, G.P.J.M., Giannoni, Eric, van der Giessen, Ilona, Gloerich, Jolein, Gómez-Carballa, Alberto, Rial, Jose Gómez, van Gool, Alain J., Gores, Gunther, Grāvele, Dagne, Griese, Matthias, Grope, Ilze, de Groot, Ronald, Gurung, Meeru, de Haan, L., Haas, Nikolaus, Habgood-Coote, Dominic, Hagedoorn, Nienke N., Haidl, Harald, Hamilton, Shea, Hauer, Almuthe, Heidema, J., Heininger, Ulrich, Henriet, Stefanie, Herberg, Jethro, Hoggart, Clive, Hösele, Susanne, Hourmat, Sara, Hude, Christa, Huijnen, Martijn, Jackson, Heather, Jennings, Rebecca, Johnston, Joanne, de Jonge, Marien I., Jongerius, Ilse, Jorgensen, Rikke, Kaforou, Myrsini, Kahlert, Christian, Kandasamy, Rama, Kappler, Matthias, Keil, Julia, Keldorfer, Markus, Kell, Dominic F., Kim, Eunjung, King, Sharon, Kloosterhuis, Lieke, Kohlfürst, Daniela S., Kohlmaier, Benno, Kolberg, Laura, Kolnik, Mojca, Krenn, Larissa, Kuijpers, Taco, van der Kuip, M., Iglesias, Pilar Leboráns, Leigh, Simon, Leitner, Manuel, van Leur, M., Lim, Emma, Lin, Naomi, Liu, Ching-Chuan, Löffler, Sabine, Lurz, Eberhard, Maconochie, Ian, Mackerness, Christine, Mallet, François, Martinón-Torres, Federico, Marmarinos, Antonis, Martin, Alex, Martin, Mike, Martinón Sánchez, José María, Martinón-Torres, Nazareth, McAlinden, Paul, McDonnell, Anne, McDonald, Sam, Miedema, C.J., Meiere, Anija, Menikou, Stephanie, van Mierlo, G., Miners, Alec, Mistry, Ravi, Moll, Henriëtte A., Mommert, Marine, Pérez, Belén Mosquera, Murdoch, David R., Mustafa, Sobia, Natalucci, Giancarlo, Neeleman, C., Newall, Karen, Nichols, Samuel, Niedrist, Tobias, Niederer-Loher, Anita, Nijman, Ruud, Nokalna, Ieva, Urbāne, Urzula Nora, Nordberg, Gudrun, Obihara, C.C., O'Connor, Daniel, Oosthoek, Wilma, Osterman, Veronika, Pachot, Alexandre, Pajkrt, D., Pardo-Seco, Jacobo, Paulus, Stéphane, Pavāre, Jana, Paz, Ivonne Pena, Persand, Salina, Pfleger, Andreas, Pfurtscheller, Klaus, Philipsen, Ria, Pickering, Ailsa, Pierce, Benjamin, Pilch, Heidemarie, Rodríguez, Lidia Piñeiro, Pischedda, Sara, Srovin, Tina Plankar, Pokorn, Marko, Pollard, Andrew J., Pölz, Lena, Posfay-Barbe, Klara M., Prunk, Petra, Pučuka, Zanda, Rajic, Glorija, Rashid, Aqeela, Redondo-Collazo, Lorenzo, Relly, Christa, Calle, Irene Rivero, Vázquez, Sara Rey, Rhodes, Mathew, Richmond, Vivien, Riedel, Thomas, RocaIsatou Sarr, Anna, Rödl, Siegfried, Rodríguez-Tenreiro, Carmen, Romaine, Sam, Rowlands, Emily, Ora, Miguel Sadiki, Sagmeister, Manfred G., Saidykhan, Momodou, Salas, Antonio, Schlapbach, Luregn J., Schonenberg, D., Secka, Fatou, Selecka, Katrīna, Fernández, Sonia Serén, Trasorras, Cristina Serén, Shah, Priyen, Shen, Ching-Fen, Shrestha, Shrijana, Sidorova, Aleksandra, Skrabl-Baumgartner, Andrea, D’Souza, Giselle, Sperl, Matthias, Sprenkeler, Evelien, Schweintzger, Nina A., Stampfer, Laura, Stevens, Molly, Stocker, Martin, Strenger, Volker, Svile, Dace, Syggelou, Kelly, Tambouratzi, Maria, Tan, Chantal, Tavliavini, Emma, Thomson, Evelyn, Thorson, Stephen, Till, Holger, Tramper-Stranders, G.A., Trobisch, Andreas, Tsolia, Maria, Usuf, Effua, Valentine, Lucille, Vermont, Clementien L., Iglesias, Marisol Vilas, Vincek, Katarina, Voice, Marie, de Vries, Gabriella, Wallia, Diane, Wang, Shih-Min, Willems, Esther, Wilson, Clare, Wood, Amanda, Woodsford, Phil, Wright, Victoria, Xagorari, Marietta, Yeung, Shunmay, Zachariasse, Joany, Zavadska, Dace, Zaman, Syed M.A., Zandstra, Judith, Zenz, Werner, Zurl, Christoph, Zwerenz, Manuela, Suppers, Anouk, van den Heuvel, Lambert P., van de Kar, Nicole, Philipsen, Ria H.L.A., van Dael, Maurice, Wright, Victoria J., Herberg, Jethro A., Torres, Federico Martinon, Levin, Michael, Lefeber, Dirk J., and Wessels, Hans J.C.T.

Published
2023
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30. DNA origami protection and molecular interfacing through engineered sequence-defined peptoids

Author

Wang, Shih-Ting, Gray, Melissa A, Xuan, Sunting, Lin, Yiyang, Byrnes, James, Nguyen, Andy I, Todorova, Nevena, Stevens, Molly M, Bertozzi, Carolyn R, Zuckermann, Ronald N, and Gang, Oleg

Subjects
Biological Sciences, Engineering, Chemical Sciences, Biomedical Engineering, Cancer, Nanotechnology, Bioengineering, Genetics, Biotechnology, Generic health relevance, DNA, Drug Delivery Systems, Molecular Dynamics Simulation, Molecular Structure, Nanostructures, Peptoids, Static Electricity, DNA nanotechnology, peptoid, molecular coating
Abstract

DNA nanotechnology has established approaches for designing programmable and precisely controlled nanoscale architectures through specific Watson-Crick base-pairing, molecular plasticity, and intermolecular connectivity. In particular, superior control over DNA origami structures could be beneficial for biomedical applications, including biosensing, in vivo imaging, and drug and gene delivery. However, protecting DNA origami structures in complex biological fluids while preserving their structural characteristics remains a major challenge for enabling these applications. Here, we developed a class of structurally well-defined peptoids to protect DNA origamis in ionic and bioactive conditions and systematically explored the effects of peptoid architecture and sequence dependency on DNA origami stability. The applicability of this approach for drug delivery, bioimaging, and cell targeting was also demonstrated. A series of peptoids (PE1-9) with two types of architectures, termed as "brush" and "block," were built from positively charged monomers and neutral oligo-ethyleneoxy monomers, where certain designs were found to greatly enhance the stability of DNA origami. Through experimental and molecular dynamics studies, we demonstrated the role of sequence-dependent electrostatic interactions of peptoids with the DNA backbone. We showed that octahedral DNA origamis coated with peptoid (PE2) can be used as carriers for anticancer drug and protein, where the peptoid modulated the rate of drug release and prolonged protein stability against proteolytic hydrolysis. Finally, we synthesized two alkyne-modified peptoids (PE8 and PE9), conjugated with fluorophore and antibody, to make stable DNA origamis with imaging and cell-targeting capabilities. Our results demonstrate an approach toward functional and physiologically stable DNA origami for biomedical applications.

Published
2020

31. Lateral flow test engineering and lessons learned from COVID-19

Author

Budd, Jobie, Miller, Benjamin S., Weckman, Nicole E., Cherkaoui, Dounia, Huang, Da, Decruz, Alyssa Thomas, Fongwen, Noah, Han, Gyeo-Re, Broto, Marta, Estcourt, Claudia S., Gibbs, Jo, Pillay, Deenan, Sonnenberg, Pam, Meurant, Robyn, Thomas, Michael R., Keegan, Neil, Stevens, Molly M., Nastouli, Eleni, Topol, Eric J., Johnson, Anne M., Shahmanesh, Maryam, Ozcan, Aydogan, Collins, James J., Fernandez Suarez, Marta, Rodriguez, Bill, Peeling, Rosanna W., and McKendry, Rachel A.

Published
2023
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37. Micro and nanoscale technologies in oral drug delivery

Author

Ahadian, Samad, Finbloom, Joel A, Mofidfar, Mohammad, Diltemiz, Sibel Emir, Nasrollahi, Fatemeh, Davoodi, Elham, Hosseini, Vahid, Mylonaki, Ioanna, Sangabathuni, Sivakoti, Montazerian, Hossein, Fetah, Kirsten, Nasiri, Rohollah, Dokmeci, Mehmet Remzi, Stevens, Molly M, Desai, Tejal A, and Khademhosseini, Ali

Subjects
Medical Biotechnology, Biomedical and Clinical Sciences, Bioengineering, Biotechnology, Dental/Oral and Craniofacial Disease, Nanotechnology, 5.1 Pharmaceuticals, Underpinning research, Development of treatments and therapeutic interventions, 1.3 Chemical and physical sciences, 5.9 Resources and infrastructure (treatment development), Administration, Oral, Animals, Drug Carriers, Drug Delivery Systems, Humans, Hydrophobic and Hydrophilic Interactions, Microspheres, Microtechnology, Nanoparticles, Pharmaceutical Preparations, Drug delivery devices, Micro and nanocarriers, Micro and nanoscale technologies, Oral drug delivery, Tissue models, Pharmacology and Pharmaceutical Sciences, Pharmacology & Pharmacy, Pharmacology and pharmaceutical sciences
Abstract

Oral administration is a pillar of the pharmaceutical industry and yet it remains challenging to administer hydrophilic therapeutics by the oral route. Smart and controlled oral drug delivery could bypass the physiological barriers that limit the oral delivery of these therapeutics. Micro- and nanoscale technologies, with an unprecedented ability to create, control, and measure micro- or nanoenvironments, have found tremendous applications in biology and medicine. In particular, significant advances have been made in using these technologies for oral drug delivery. In this review, we briefly describe biological barriers to oral drug delivery and micro and nanoscale fabrication technologies. Micro and nanoscale drug carriers fabricated using these technologies, including bioadhesives, microparticles, micropatches, and nanoparticles, are described. Other applications of micro and nanoscale technologies are discussed, including fabrication of devices and tissue engineering models to precisely control or assess oral drug delivery in vivo and in vitro, respectively. Strategies to advance translation of micro and nanotechnologies into clinical trials for oral drug delivery are mentioned. Finally, challenges and future prospects on further integration of micro and nanoscale technologies with oral drug delivery systems are highlighted.

Published
2020

38. Shape-controlled synthesis and in situ characterisation of anisotropic Au nanomaterials using liquid cell transmission electron microscopy

Author

Wang, Shih-Ting, Lin, Yiyang, Nielsen, Michael H, Song, Cheng Yu, Thomas, Michael R, Spicer, Christopher D, Kröger, Roland, Ercius, Peter, Aloni, Shaul, and Stevens, Molly M

Subjects
Chemical Sciences, Physical Chemistry, Engineering, Physical Sciences, Nanotechnology, Bioengineering, 1.1 Normal biological development and functioning, Technology, Nanoscience & Nanotechnology, Chemical sciences, Physical sciences
Abstract

Understanding the mechanisms behind crystal nucleation and growth is a fundamental requirement for the design and production of bespoke nanomaterials with controlled sizes and morphologies. Herein, we select gold (Au) nanoparticles as the model system for our study due to their representative applications in biology, electronics and optoelectronics. We investigate the radiation-induced in situ growth of gold (Au) particles using liquid cell transmission electron microscopy (LCTEM) and study the growth kinetics of non-spherical Au structures. Under controlled electron fluence, liquid flow rate and Au3+ ion supply, we show the favoured diffusion-limited growth of multi-twinned nascent Au seed particles into branched structures when using thin liquid cells (100 nm and 250 nm) in LCTEM, whereas faceted structures (e.g., spheres, rods, and prisms) formed when using a 1 μm thick liquid cell. In addition, we observed that anisotropic Au growth could be modulated by Au-binding amyloid fibrils, which we ascribe to their capability to regulate Au3+ ion diffusion and mass transfer in solution. We anticipate that this study will provide new perspectives on the shape-controlled synthesis of anisotropic metallic nanomaterials using LCTEM.

Published
2019

42. Bioactive Coatings on 3D Printed Polycaprolactone Scaffolds for Bone Regeneration: A Novel Murine Femur Defect Model for Examination of the Biomaterial Capacity for Repair.

Author

Marshall, Karen M., Wojciechowski, Jonathan P., Jayawarna, Vineetha, Hasan, Abshar, Echalier, Cécile, Callens, Sebastien J. P., Yang, Tao, Kanczler, Janos M., Dawson, Jonathan I., Mata, Alvaro, Salmeron‐Sanchez, Manuel, Stevens, Molly M., and Oreffo, Richard O. C.

Subjects
BONE growth, BONE grafting, ETHYL acrylate, BONE regeneration, TISSUE engineering, POLYCAPROLACTONE
Abstract

Bone tissue engineering seeks to develop treatment approaches for nonhealing and large bone defects. An ideal biodegradable scaffold will induce and support bone formation. The current study examines bone augmentation in critical‐sized bone defects, using functionalized scaffolds, with the hypothesized potential to induce skeletal cell differentiation. 3D printed, porous poly(caprolactone) trimethacrylate (PCL‐TMA900) scaffolds are applied within a murine femur defect, stabilized by a polyimide intramedullary (IM) pin. The PCL‐TMA900 scaffolds are coated with i) elastin‐like polypeptide (ELP), ii) poly(ethyl acrylate) (PEA)/fibronectin (FN)/bone morphogenetic protein‐2 (PEA/FN/BMP‐2), iii) both ELP and PEA/FN/BMP‐2, or iv) Laponite nanoclay binding BMP‐2. Sequential microcomputed tomography (µCT) and histological analysis are performed. PCL‐TMA900 is robust and biocompatible and when coated with the nanoclay material Laponite and BMP‐2 induce consistent, significant bone formation compared to the uncoated PCL‐TMA900 scaffold. Critically, the BMP‐2 is retained, due to the Laponite, producing bone around the scaffold in the desired shape and volume, compared to bone formation observed with the positive control (collagen sponge/BMP‐2). The ELP and/or PEA/FN/BMP‐2 scaffolds do not demonstrate significant or consistent bone formation. In summary, Laponite/BMP‐2 coated PCL‐TMA900 scaffolds offer a biodegradable, osteogenic construct for bone augmentation with potential for development into a large scale polymer scaffold for clinical translation. [ABSTRACT FROM AUTHOR]

Published
2025
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43. Transfer learning Bayesian optimization for competitor DNA molecule design for use in diagnostic assays.

Author

Sedgwick, Ruby, Goertz, John P., Stevens, Molly M., Misener, Ruth, and van der Wilk, Mark

Abstract

With the rise in engineered biomolecular devices, there is an increased need for tailor‐made biological sequences. Often, many similar biological sequences need to be made for a specific application meaning numerous, sometimes prohibitively expensive, lab experiments are necessary for their optimization. This paper presents a transfer learning design of experiments workflow to make this development feasible. By combining a transfer learning surrogate model with Bayesian optimization, we show how the total number of experiments can be reduced by sharing information between optimization tasks. We demonstrate the reduction in the number of experiments using data from the development of DNA competitors for use in an amplification‐based diagnostic assay. We use cross‐validation to compare the predictive accuracy of different transfer learning models, and then compare the performance of the models for both single objective and penalized optimization tasks. [ABSTRACT FROM AUTHOR]

Published
2025
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47. The 15th Anniversary of the U.S. National Nanotechnology Initiative

Author

Chan, Warren CW, Chhowalla, Manish, Farokhzad, Omid, Glotzer, Sharon, Gogotsi, Yury, Hammond, Paula T, Hersam, Mark C, Javey, Ali, Kagan, Cherie R, Kataoka, Kazunori, Khademhosseini, Ali, Kotov, Nicholas A, Lee, Shuit-Tong, Lee, Young Hee, Li, Yan, Millstone, Jill E, Mulvaney, Paul, Nel, Andre E, Nordlander, Peter J, Parak, Wolfgang J, Penner, Reginald M, Rogach, Andrey L, Schaak, Raymond E, Sood, Ajay K, Stevens, Molly M, Wee, Andrew TS, Weil, Tanja, Willson, C Grant, and Weiss, Paul S

Subjects
Nanoscience & Nanotechnology
Published
2018

48. Novel endosomolytic compounds enable highly potent delivery of antisense oligonucleotides

Author

Bost, Jeremy P., Ojansivu, Miina, Munson, Michael J., Wesén, Emelie, Gallud, Audrey, Gupta, Dhanu, Gustafsson, Oskar, Saher, Osama, Rädler, Julia, Higgins, Stuart G., Lehto, Taavi, Holme, Margaret N., Dahlén, Anders, Engkvist, Ola, Strömstedt, Per-Erik, Andersson, Shalini, Edvard Smith, C. I., Stevens, Molly M., Esbjörner, Elin K., Collén, Anna, and El Andaloussi, Samir

Published
2022
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