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1. Exploring the Effects of Intersubunit Interface Mutations on Virus-Like Particle Structure and Stability.

Author

Pistono, Paige, Xu, Junyi, Huang, Paul, Fetzer, Jennifer, and Francis, Matthew

Abstract

Virus-like particles (VLPs) from bacteriophage MS2 provide a platform to study protein self-assembly and create engineered systems for drug delivery. Here, we aim to understand the impact of intersubunit interface mutations on the local and global structure and function of MS2-based VLPs. In previous work, our lab identified locally supercharged double mutants [T71K/G73R] that concentrate positive charge at capsid pores, enhancing uptake into mammalian cells. To study the effects of particle size on cellular internalization, we combined these double mutants with a single point mutation [S37P] that was previously reported to switch particle geometry from T = 3 to T = 1 icosahedral symmetry. These new variants retained their enhanced cellular uptake activity and could deliver small-molecule drugs with efficacy levels similar to our first-generation capsids. Surprisingly, these engineered triple mutants exhibit increased thermostability and unexpected geometry, producing T = 3 particles instead of the anticipated T = 1 assemblies. Transmission electron microscopy revealed various capsid assembly states, including wild-type (T = 3), T = 1, and rod-like particles, that could be accessed using different combinations of these point mutations. Molecular dynamics experiments recapitulated the structural rationale in silico for the single point mutation [S37P] forming a T = 1 virus-like particle and showed that this assembly state was not favored when combined with mutations that favor rod-like architectures. Through this work, we investigated how interdimer interface dynamics influence VLP size and morphology and how these properties affect particle function in applications such as drug delivery.

Published
2024

2. Editing the Mind of Giants: An In-Depth Exploration of Pitfalls of Knowledge Editing in Large Language Models

Author

Hsueh, Cheng-Hsun, Huang, Paul Kuo-Ming, Lin, Tzu-Han, Liao, Che-Wei, Fang, Hung-Chieh, Huang, Chao-Wei, and Chen, Yun-Nung

Subjects
Computer Science - Computation and Language
Abstract

Knowledge editing is a rising technique for efficiently updating factual knowledge in large language models (LLMs) with minimal alteration of parameters. However, recent studies have identified side effects, such as knowledge distortion and the deterioration of general abilities, that have emerged after editing. Despite these findings, evaluating the pitfalls of knowledge editing often relies on inconsistent metrics and benchmarks, lacking a uniform standard. In response, this survey presents a comprehensive study of these side effects, providing a unified perspective on the challenges of knowledge editing in LLMs by conducting experiments with consistent metrics and benchmarks. Additionally, we review related works and outline potential research directions to address these limitations. Our survey highlights the limitations of current knowledge editing methods, emphasizing the need for a deeper understanding of the inner knowledge structures of LLMs and improved knowledge editing methods. To foster future research, we have released the complementary materials publicly in https://github.com/MiuLab/EditLLM-Survey., Comment: EMNLP 2024 Findings

Published
2024

5. Prompting and Adapter Tuning for Self-supervised Encoder-Decoder Speech Model

Author

Chang, Kai-Wei, Chen, Ming-Hsin, Lin, Yun-Ping, Hsu, Jing Neng, Huang, Paul Kuo-Ming, Huang, Chien-yu, Li, Shang-Wen, and Lee, Hung-yi

Subjects
Electrical Engineering and Systems Science - Audio and Speech Processing, Computer Science - Computation and Language, Electrical Engineering and Systems Science - Signal Processing
Abstract

Prompting and adapter tuning have emerged as efficient alternatives to fine-tuning (FT) methods. However, existing studies on speech prompting focused on classification tasks and failed on more complex sequence generation tasks. Besides, adapter tuning is primarily applied with a focus on encoder-only self-supervised models. Our experiments show that prompting on Wav2Seq, a self-supervised encoder-decoder model, surpasses previous works in sequence generation tasks. It achieves a remarkable 53% relative improvement in word error rate for ASR and a 27% in F1 score for slot filling. Additionally, prompting competes with the FT method in the low-resource scenario. Moreover, we show the transferability of prompting and adapter tuning on Wav2Seq in cross-lingual ASR. When limited trainable parameters are involved, prompting and adapter tuning consistently outperform conventional FT across 7 languages. Notably, in the low-resource scenario, prompting consistently outperforms adapter tuning., Comment: Accepted to IEEE ASRU 2023

Published
2023

8. Score-based Conditional Generation with Fewer Labeled Data by Self-calibrating Classifier Guidance

Author

Huang, Paul Kuo-Ming, Chen, Si-An, and Lin, Hsuan-Tien

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

Score-based generative models (SGMs) are a popular family of deep generative models that achieve leading image generation quality. Early studies extend SGMs to tackle class-conditional generation by coupling an unconditional SGM with the guidance of a trained classifier. Nevertheless, such classifier-guided SGMs do not always achieve accurate conditional generation, especially when trained with fewer labeled data. We argue that the problem is rooted in the classifier's tendency to overfit without coordinating with the underlying unconditional distribution. To make the classifier respect the unconditional distribution, we propose improving classifier-guided SGMs by letting the classifier regularize itself. The key idea of our proposed method is to use principles from energy-based models to convert the classifier into another view of the unconditional SGM. Existing losses for unconditional SGMs can then be leveraged to achieve regularization by calibrating the classifier's internal unconditional scores. The regularization scheme can be applied to not only the labeled data but also unlabeled ones to further improve the classifier. Across various percentages of fewer labeled data, empirical results show that the proposed approach significantly enhances conditional generation quality. The enhancements confirm the potential of the proposed self-calibration technique for generative modeling with limited labeled data.

Published
2023

11. Fitness Landscape-Guided Engineering of Locally Supercharged Virus-like Particles with Enhanced Cell Uptake Properties

Author

Pistono, Paige E, Huang, Paul, Brauer, Daniel D, and Francis, Matthew B

Subjects
Biotechnology, Bioengineering, Nanotechnology, 5.1 Pharmaceuticals, Development of treatments and therapeutic interventions, Generic health relevance, Animals, Capsid, Capsid Proteins, Nanoparticles, Drug Delivery Systems, Mammals, Chemical Sciences, Biological Sciences, Organic Chemistry
Abstract

Protein-based nanoparticles are useful models for the study of self-assembly and attractive candidates for drug delivery. Virus-like particles (VLPs) are especially promising platforms for expanding the repertoire of therapeutics that can be delivered effectively as they can deliver many copies of a molecule per particle for each delivery event. However, their use is often limited due to poor uptake of VLPs into mammalian cells. In this study, we use the fitness landscape of the bacteriophage MS2 VLP as a guide to engineer capsid variants with positively charged surface residues to enhance their uptake into mammalian cells. By combining mutations with positive fitness scores that were likely to produce assembled capsids, we identified two key double mutants with internalization efficiencies as much as 67-fold higher than that of wtMS2. Internalization of these variants with positively charged surface residues depends on interactions with cell surface sulfated proteoglycans, and yet, they are biophysically similar to wtMS2 with low cytotoxicity and an overall negative charge. Additionally, the best-performing engineered MS2 capsids can deliver a potent anticancer small-molecule therapeutic with efficacy levels similar to antibody-drug conjugates. Through this work, we were able to establish fitness landscape-based engineering as a successful method for designing VLPs with improved cell penetration. These findings suggest that VLPs with positive surface charge could be useful in improving the delivery of small-molecule- and nucleic acid-based therapeutics.

Published
2022

12. Radiomic features of primary retroperitoneal sarcomas: a prognostic study

Author

Pasquali, Sandro, Iadecola, Sara, Vanzulli, Andrea, Infante, Gabriele, Bologna, Marco, Corino, Valentina, Greco, Gabriella, Vigorito, Raffaella, Morosi, Carlo, Beretta, Alessia, Percio, Stefano, Vallacchi, Viviana, Collini, Paola, Sanfilippo, Roberta, Fabbroni, Chiara, Stacchiotti, Silvia, Fiore, Marco, Huang, Paul, Benelli, Matteo, Mainardi, Luca, Miceli, Rosalba, Gronchi, Alessandro, and Callegaro, Dario

Published
2024
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15. Functional genomics of human clear cell sarcoma: genomic, transcriptomic and chemical biology landscape for clear cell sarcoma

Author

Rasmussen, Samuel V., Wozniak, Agnieszka, Lathara, Melvin, Goldenberg, Joshua M., Samudio, Benjamin M., Bickford, Lissett R., Nagamori, Kiyo, Wright, Hollis, Woods, Andrew D., Chauhan, Shefali, Lee, Che-Jui, Rudzinski, Erin R., Swift, Michael K., Kondo, Tadashi, Fisher, David E., Imyanitov, Evgeny, Machado, Isidro, Llombart-Bosch, Antonio, Andrulis, Irene L., Gokgoz, Nalan, Wunder, Jay, Mirotaki, Hiroshi, Nakamura, Takuro, Srinivasa, Ganapati, Thway, Khin, Jones, Robin L., Huang, Paul H., Berlow, Noah E., Schöffski, Patrick, and Keller, Charles

Published
2023
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16. The proteomic landscape of soft tissue sarcomas

Author

Burns, Jessica, Wilding, Christopher P., Krasny, Lukas, Zhu, Xixuan, Chadha, Madhumeeta, Tam, Yuen Bun, PS, Hari, Mahalingam, Aswanth H., Lee, Alexander T. J., Arthur, Amani, Guljar, Nafia, Perkins, Emma, Pankova, Valeriya, Jenks, Andrew, Djabatey, Vanessa, Szecsei, Cornelia, McCarthy, Frank, Ragulan, Chanthirika, Milighetti, Martina, Roumeliotis, Theodoros I., Crosier, Stephen, Finetti, Martina, Choudhary, Jyoti S., Judson, Ian, Fisher, Cyril, Schuster, Eugene F., Sadanandam, Anguraj, Chen, Tom W., Williamson, Daniel, Thway, Khin, Jones, Robin L., Cheang, Maggie C. U., and Huang, Paul H.

Published
2023
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18. Patient-Level Pooled Analysis of Endovascular Ultrasound Renal Denervation or a Sham Procedure 6 Months After Medication Escalation: The RADIANCE Clinical Trial Program

Author

Azizi, Michel, Sharp, Andrew S.P., Fisher, Naomi D.L., Weber, Michael A., Lobo, Melvin D., Daemen, Joost, Lurz, Philipp, Mahfoud, Felix, Schmieder, Roland E., Basile, Jan, Bloch, Michael J., Saxena, Manish, Wang, Yale, Sanghvi, Kintur, Jenkins, J. Stephen, Devireddy, Chandan, Rader, Florian, Gosse, Philippe, Claude, Lisa, Augustin, Dimitri A., McClure, Candace K., Kirtane, Ajay J., Wang, Yale, Skeik, Nedaa, Bae, Richard, McMeans, Amy, Goldman, JoAnne, Peterson, Rose, Stephen Jenkins, James, Tutor, Isabelle, Harrison, Michael, Penning, Angel, Devireddy, Chandan, Lea, Janice, Fiebach, Amanda, Merlin, Claudia, Rader, Florian, Dohad, Suhail, Tran, Anne, Bhatia, Kirin, Fisher, Naomi D.L., Sobieszczyk, Piotr, Halliday, Ian, Munson, Tay, Lindsey, Jason, Laster, Steven, Bunte, Mathew, Hart, Anthony, King, Dana, Hall, Jamie, Sanghvi, Kintur, Krathen, Courtney, Lewis, Luot, Willitts, Ashley, Todoran, Thomas, Basile, Jan, Awkar, Anthony, Palmer, Casey, Tecklenburg, Anna, Schindler, John, Pacella, John, Muldoon, Matthew, Albright, MaryJo, Nicholson, Tracy, Flack, John, Chami, Youseff, Hafiz, Abdul Moiz, Starkey, Emily, Adams, Kristal, Bernardo, Nelson, Veis, Judith, Hashim, Hayder, Singh, Suman, Whitman, Donna, Stouffer, Rick, Hinderliter, Alan, Allen, Meghan, Scholl, Tatum, Fong, Pete, Gainer, James, Crook, Sherron, Hatchcock, Ellen, Cohen, Debbie, Giri, Jay, Kobayashi, Taisei, Neubauer, Robin, Naidu, Suveeksha, Kirtane, Ajay J., Radhakrishnan, Jai, Batres, Candido, Edwards, Suzanne, Khuddus, Matheen, Zentko, Suzanne, Touchton, Abby, Roberson, Marti, Bloch, Michael J., Akinapelli, Abhilash, English, Lisa, Neumann, Bridget, Mendelsohn, Farrel, Brantley, Hutton, Cawthon, Thomas, DeRamus, Susan, Wade, Wesley, Fishman, Robert, Tuohy, Edward, LeBlanc, Jessica, McCurry, Tina, Krishnaswamy, Amar, Laffin, Luke, Bajzer, Christopher, Boros, Marilyn, Branche, Monica, Abraham, Josephine, Abraham, Anu, Stijleman, Inge, Hsi, David, Martin, Scott, Portnay, Edward, Fiebach, Maryann, Garavito, Carolina, Adams, Todd, Teklinski, Andrew, Leech, Adam, Drilling, Patrick, Tulik, Lynda, Benzuly, Keith, Paparello, James, Fintel, Dan, Ramirez, Haydee, Kats, Lauren, Huang, Paul, Biswas, Santanu, Risher, Serena, Pratt, Kristina, Ibebuogu, Uzoma, Johnson, Karen, Cushman, William, Jones, Lisa, Jackson, Leigh, Landers, David, Pasala, Tilak, Salazer, Thomas, Canino, Peter, Arakelian, Patricia, Yang, Yi-Ming, Khaliq, Asma, Weinberg, Mitchell, Abetu, Yihenew, Gulliver, Alana, Reilly, J.P., Garasic, Joseph, Chugh, Atul, Bertolet, Barry, Go, Brian, Gallapudi, Raghava, Cohn, Joel, Rogers, Kevin, Saxena, Manish, Mathur, Anthony, Jain, Ajay, Balawon, Armida, Zongo, Oliver, Topham, Christine, Sharp, Andrew, Anderson, Richard, Thompson, Elizabeth, Spiro, Nikki, Hodges, Elizabeth, Holder, Jaqueline, Ellam, Timothy, Bagnall, Alan, Jackson, Ralph, Bridgett, Victoria, Wilson, Peter, Das, Neelanjan, Doulton, Timothy, Loader, David, Hector, Gemma, Levy, Terry, Bent, Clare, Kodoth, Vivek, Horler, Stephanie, Nix, Sara, Robinson, Nicholas, Al-Janabi, Firas, Sayer, Jeremy, Ganesh Iyer, Sudha, Redman, Emily, Ramirez, Jonaifah, Padmanabhan, Sandosh, Sharif, Faisal, Alhmoudi, Aishah, Lunardi, Mattia, Coen, Eileen, Glynn, Nicola, Mahfoud, Felix, Lauder, Lucas, Kulenthiran, Saarraaken, Koch, Christina, Wachter, Angelika, Schmieder, Roland, Schmid, Axel, Kannenkeril, Dennis, Heinritz, Ulrike, Endres-Frohlich, Kerstin, Lurz, Philipp, Rommel, Karl, Fengler, Petzold, Martin, Büttner, Margit, Weil, Joachim, Agdirlioglu, Tolga, Köllner, Tanja, Stephan, Jeannine, Dagkonakis, Nikolaos, Hamann, Frank, Ettl, Ute, Petzsche, Ulrike, Reimer, Peter, Hausberg, Martin, Hinrichs, Ralf, Di Ponio-Voit, Isabella, Lutz, Matthias, Gosse, Philippe, Cremer, Antoine, Papadopoulos, Panteleimon, Gaudissard, Julie, Maire, Florent, Azizi, Michel, Sapoval, Marc, Livrozet, Marine, Regrag, Asma, Paquet, Valerie, Delsart, Pascal, Hennicaux, Justin, Sommeville, Coralie, Bertrand, Fabien, Daemen, Joost, Lafeber, Melvin, Zeijen, Victor, Ruiter, Amo, Huijskens, Elisabeth, van Ramshorst, Jan, Xaplanteris, Panagiotis, Briki, Rachid, de Hemptinne, Quentin, Pascal, Severine, Renard, Katty, Ferdinande, Bert, Iglesias, Juan F., Ehert, Georg, Gallego, Laetitia, Dobretz, Kevin, Bottone, Sylviane, Sanghvi, Kintur, Costello, Josh, Krathan, Courtney, Lewis, Luot, McElvarr, Andrew, Reilly, John, Jenkins, Stephen, Cash, Michael, Williams, Shannon, Jarvis, Maria, Fong, Pete, Laffer, Cheryl, Gainer, James, Robbins, Mark, Crook, Sherron, Maddel, Sarita, Hsi, David, Martin, Scott, Portnay, Edward, Ducey, Maryanne, Rose, Suzanne, DelMastro, Elizabeth, Bangalore, Sripal, Williams, Stephen, Cabos, Stanley, Rodriguez Alvarez, Carolina, Todoran, Thomas, Basile, Jan, Powers, Eric, Hodskins, Emily, Paladugu, Vijay, Tecklenburg, Anna, Devireddy, Chandan, Lea, Janice, Wells, Bryan, Fiebach, Amanda, Merlin, Claudia, Rader, Florian, Dohad, Suhail, Kim, Hyun-Min, Rashid, Mohammad, Abraham, Josephine, Owan, Theophilus, Abraham, Anu, Lavasani, Iran, Neilson, Hailey, Calhoun, David, McElderry, Thomas, Maddox, William, Oparil, Suzanne, Kinder, Sheila, Kirtane, Ajay J., Radhakrishnan, Jai, Batres, Candido, Edwards, Suzanne, Garasic, Joseph, Drachman, Doug, Zusman, Randy, Rosenfield, Kenneth, Do, Danny, Khuddus, Matheen, Zentko, Suzanne, O’Meara, James, Barb, Ilie, Foster, Abby, Boyette, Alice, Wang, Yale, Jay, Desmond, Skeik, Nedaa, Schwartz, Robert, Peterson, Rose, Goldman, Jo Anne, Goldman, Jessie, Ledley, Gary, Katof, Nancy, Potluri, Srinivasa, Biedermann, Scott, Ward, Jacquelyn, White, Megan, Fisher, Naomi D.L., Mauri, Laura, Sobieszczky, Piotr, Smith, Alex, Aseltine, Laura, Stouffer, Rick, Hinderliter, Alan, Pauley, Eric, Wade, Tyrone, Zidar, David, Shishehbor, Mehdi, Effron, Barry, Costa, Marco, Semenec, Terence, Bloch, Michael J., Roongsritong, Chanwit, Nelson, Priscilla, Neumann, Bridget, Cohen, Debbie, Giri, Jay, Neubauer, Robin, Vo, Thu, Chugh, Atul R., Huang, Pei-Hsiu, Jose, Powell, Flack, John, Fishman, Robert, Jones, Michael, Adams, Todd, Bajzer, Christopher, Saxena, Manish, Lobo, Melvin D., Mathur, Anthony, Jain, Ajay, Balawon, Armida, Zongo, Olivier, Levy, Terry, Bent, Clare, Beckett, David, Lakeman, Nicki, Kennard, Sarah, Sharp, Andrew, D’Souza, Richard J., Statton, Sarah, Wilkes, Lindsay, Anning, Christine, Sayer, Jeremy, Ganesh Iyer, Sudha, Robinson, Nicholas, Sevillano, Annaliza, Ocampo, Madelaine, Gerber, Robert, Faris, Mohamad, John Marshall, Andrew, Sinclair, Janet, Pepper, Hayley, Davies, Justin, Chapman, Neil, Burak, Paula, Carvelli, Paula, Jadhav, Sachin, Quinn, Jane, Christian Rump, Lars, Stegbauer, Johannes, Schimmöller, Lars, Potthoff, Sebastian, Schmid, Claudia, Roeder, Sylvia, Weil, Joachim, Hafer, Lukas, Agdirlioglu, Tolga, Köllner, Tanja, Mahfoud, Felix, Böhm, Michael, Ewen, Sebastian, Kulenthiran, Saarraaken, Wachter, Angelika, Koch, Christina, Lurz, Philipp, Fengler, Karl, Rommel, Karl-Philipp, Trautmann, Kai, Petzold, Martin, Schmieder, Roland E., Ott, Christian, Schmid, Axel, Uder, Michael, Heinritz, Ulrike, Fröhlich-Endres, Kerstin, Genth-Zotz, Sabine, Kämpfner, Denise, Grawe, Armin, Höhne, Johannes, Kaesberger, Bärbel, von zur Mühlen, Constantin, Wolf, Dennis, Welzel, Markus, Gosse, Philippe, Cremer, Antoine, Trillaud, Hervé, Papadopoulos, Panteleimon, Maire, Florent, Gaudissard, Julie, Azizi, Michel, Sapoval, Marc, Cornu, Erika, Fouassier, David, Livrozet, Marine, Lorthioir, Aurélien, Paquet, Valérie, Pathak, Atul, Honton, Benjamin, Cottin, Marianne, Petit, Frédéric, Lantelme, Pierre, Berge, Constance, Courand, Pierre-Yves, Langevin, Fatou, Delsart, Pascal, Longere, Benjamin, Ledieu, Guillaume, Pontana, François, Sommeville, Coralie, Bertrand, Fabien, Daemen, Joost, Feyz, Lida, Zeijen, Victor, Ruiter, Arno, Huyskens, Elisabeth, Blankestijn, Peter, Voskuil, Michiel, Rittersma, Zwaantina, Dolmans, Helma, Kroon, A.A., van Zwam, W.H., Vranken, Jeannique, de Haan, Claudia, Persu, Alexandre, Renkin, Jean, Maes, Frédéric, Beauloye, Christophe, Lengelé, Jean-Philippe, Huyberechts, Dominique, Bouvier, Anne, Witkowski, Adam, Januszewicz, Andrzej, Kądziela, Jacek, Prejbisj, Aleksander, Hering, Dagmara, Ciecwierz, Dariusz, Jaguszewski, Milosz J., Owczuk, Radoslaw, Ciecwierz, Dariusz, Jaguszewski, Milosz J., Wang, Yale, Jay, Desmond, Skeik, Nedaa, Schwartz, Robert, Rader, Florian, Dohad, Suhail, Victor, Ronald, Sanghvi, Kintur, Costello, Josh, Walsh, Courtney, Abraham, Josephine, Owan, Theophilus, Abraham, Anu, Fisher, Naomi D.L., Mauri, Laura, Sobieszczky, Piotr, Williams, Jonathan, Bloch, Michael J., Roongsritong, Chanwit, Todoran, Thomas, Basile, Jan, Powers, Eric, Hodskins, Emily, Fong, Pete, Laffer, Cheryl, Gainer, James, Robbins, Mark, Reilly, John, Cash, Michael, Goldman, Jessie, Aggarwal, Sandeep, Ledley, Gary, Hsi, David, Martin, Scott, Portnay, Edward, Calhoun, David, McElderry, Thomas, Maddox, William, Oparil, Suzanne, Huang, Pei-Hsiu, Jose, Powell, Khuddus, Matheen, Zentko, Suzanne, O’Meara, James, Barb, Ilie, Garasic, Joseph, Drachman, Doug, Zusman, Randy, Rosenfield, Kenneth, Devireddy, Chandan, Lea, Janice, Wells, Bryan, Stouffer, Rick, Hinderliter, Alan, Pauley, Eric, Potluri, Srinivasa, Biedermann, Scott, Bangalore, Sripal, Williams, Stephen, Zidar, David, Shishehbor, Mehdi, Effron, Barry, Costa, Marco, Kirtane, Ajay J., Radhakrishnan, Jai, Lobo, Melvin D., Mathur, Anthony, Jain, Ajay, Sayer, Jeremy, Ganesh Iyer, Sudha, Robinson, Nicholas, Ali Edroos, Sadat, Levy, Terry, Patel, Amit, Beckett, David, Bent, Clare, Davies, Justin, Chapman, Neil, Shun Shin, Matthew, Howard, James, Sharp, Andrew S.P., Joseph, Anil, D’Souza, Richard, Gerber, Robert, Faris, Mohamad, John Marshall, Andrew, Elorz, Cristina, Lurz, Philipp, Höllriegel, Robert, Fengler, Karl, Rommel, Karl-Philipp, Mahfoud, Felix, Böhm, Michael, Ewen, Sebastian, Lucic, Jelena, Schmieder, Roland E., Ott, Christian, Schmid, Axel, Uder, Michael, Rump, Christian, Stegbauer, Johannes, Kröpil, Patric, Azizi, Michel, Sapoval, Marc, Cornu, Erika, Fouassier, David, Gosse, Philippe, Cremer, Antoine, Trillaud, Hervé, Papadopoulos, Panteleimon, Pathak, Atul, Honton, Benjamin, Lantelme, Pierre, Berge, Constance, Courand, Pierre-Yves, Daemen, Joost, Feyz, Lida, Blankestijn, Peter, Voskuil, Michiel, Rittersma, Zwaantina, Kroon, A.A., van Zwam, W.H., Persu, Alexandre, and Renkin, Jean

Published
2024
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20. A CT-based radiomics classification model for the prediction of histological type and tumour grade in retroperitoneal sarcoma (RADSARC-R): a retrospective multicohort analysis

Author

Arthur, Amani, Orton, Matthew R, Emsley, Robby, Vit, Sharon, Kelly-Morland, Christian, Strauss, Dirk, Lunn, Jason, Doran, Simon, Lmalem, Hafida, Nzokirantevye, Axelle, Litiere, Saskia, Bonvalot, Sylvie, Haas, Rick, Gronchi, Alessandro, Van Gestel, Dirk, Ducassou, Anne, Raut, Chandrajit P, Meeus, Pierre, Spalek, Mateusz, Hatton, Matthew, Le Pechoux, Cecile, Thway, Khin, Fisher, Cyril, Jones, Robin, Huang, Paul H, and Messiou, Christina

Published
2023
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21. Genetic Determinants of Electrocardiographic P-Wave Duration and Relation to Atrial Fibrillation

Author

Weng, Lu-Chen, Hall, Amelia Weber, Choi, Seung Hoan, Jurgens, Sean J, Haessler, Jeffrey, Bihlmeyer, Nathan A, Grarup, Niels, Lin, Honghuang, Teumer, Alexander, Li-Gao, Ruifang, Yao, Jie, Guo, Xiuqing, Brody, Jennifer A, Müller-Nurasyid, Martina, Schramm, Katharina, Verweij, Niek, van den Berg, Marten E, van Setten, Jessica, Isaacs, Aaron, Ramírez, Julia, Warren, Helen R, Padmanabhan, Sandosh, Kors, Jan A, de Boer, Rudolf A, van der Meer, Peter, Sinner, Moritz F, Waldenberger, Melanie, Psaty, Bruce M, Taylor, Kent D, Völker, Uwe, Kanters, Jørgen K, Li, Man, Alonso, Alvaro, Perez, Marco V, Vaartjes, Ilonca, Bots, Michiel L, Huang, Paul L, Heckbert, Susan R, Lin, Henry J, Kornej, Jelena, Munroe, Patricia B, van Duijn, Cornelia M, Asselbergs, Folkert W, Stricker, Bruno H, van der Harst, Pim, Kääb, Stefan, Peters, Annette, Sotoodehnia, Nona, Rotter, Jerome I, Mook-Kanamori, Dennis O, Dörr, Marcus, Felix, Stephan B, Linneberg, Allan, Hansen, Torben, Arking, Dan E, Kooperberg, Charles, Benjamin, Emelia J, Lunetta, Kathryn L, Ellinor, Patrick T, and Lubitz, Steven A

Subjects
Biomedical and Clinical Sciences, Cardiovascular Medicine and Haematology, Clinical Research, Genetics, Heart Disease, Cardiovascular, Human Genome, 2.1 Biological and endogenous factors, Aetiology, Atrial Fibrillation, Cardiac Myosins, Connectin, Electrocardiography, Genetic Variation, Genome-Wide Association Study, Homeodomain Proteins, Humans, Myosin Heavy Chains, NAV1.8 Voltage-Gated Sodium Channel, Quantitative Trait Loci, Transcription Factors, atrial fibrillation, electrophysiology, exome, genetic, genome-wide association studies, population, Medical Biotechnology, Cardiorespiratory Medicine and Haematology, Cardiovascular System & Hematology, Cardiovascular medicine and haematology
Abstract

BackgroundThe P-wave duration (PWD) is an electrocardiographic measurement that represents cardiac conduction in the atria. Shortened or prolonged PWD is associated with atrial fibrillation (AF). We used exome-chip data to examine the associations between common and rare variants with PWD.MethodsFifteen studies comprising 64 440 individuals (56 943 European, 5681 African, 1186 Hispanic, 630 Asian) and ≈230 000 variants were used to examine associations with maximum PWD across the 12-lead ECG. Meta-analyses summarized association results for common variants; gene-based burden and sequence kernel association tests examined low-frequency variant-PWD associations. Additionally, we examined the associations between PWD loci and AF using previous AF genome-wide association studies.ResultsWe identified 21 common and low-frequency genetic loci (14 novel) associated with maximum PWD, including several AF loci (TTN, CAND2, SCN10A, PITX2, CAV1, SYNPO2L, SOX5, TBX5, MYH6, RPL3L). The top variants at known sarcomere genes (TTN, MYH6) were associated with longer PWD and increased AF risk. However, top variants at other loci (eg, PITX2 and SCN10A) were associated with longer PWD but lower AF risk.ConclusionsOur results highlight multiple novel genetic loci associated with PWD, and underscore the shared mechanisms of atrial conduction and AF. Prolonged PWD may be an endophenotype for several different genetic mechanisms of AF.

Published
2020

22. Multi-ancestry GWAS of the electrocardiographic PR interval identifies 202 loci underlying cardiac conduction.

Author

Ntalla, Ioanna, Weng, Lu-Chen, Cartwright, James H, Hall, Amelia Weber, Sveinbjornsson, Gardar, Tucker, Nathan R, Choi, Seung Hoan, Chaffin, Mark D, Roselli, Carolina, Barnes, Michael R, Mifsud, Borbala, Warren, Helen R, Hayward, Caroline, Marten, Jonathan, Cranley, James J, Concas, Maria Pina, Gasparini, Paolo, Boutin, Thibaud, Kolcic, Ivana, Polasek, Ozren, Rudan, Igor, Araujo, Nathalia M, Lima-Costa, Maria Fernanda, Ribeiro, Antonio Luiz P, Souza, Renan P, Tarazona-Santos, Eduardo, Giedraitis, Vilmantas, Ingelsson, Erik, Mahajan, Anubha, Morris, Andrew P, Del Greco M, Fabiola, Foco, Luisa, Gögele, Martin, Hicks, Andrew A, Cook, James P, Lind, Lars, Lindgren, Cecilia M, Sundström, Johan, Nelson, Christopher P, Riaz, Muhammad B, Samani, Nilesh J, Sinagra, Gianfranco, Ulivi, Sheila, Kähönen, Mika, Mishra, Pashupati P, Mononen, Nina, Nikus, Kjell, Caulfield, Mark J, Dominiczak, Anna, Padmanabhan, Sandosh, Montasser, May E, O'Connell, Jeff R, Ryan, Kathleen, Shuldiner, Alan R, Aeschbacher, Stefanie, Conen, David, Risch, Lorenz, Thériault, Sébastien, Hutri-Kähönen, Nina, Lehtimäki, Terho, Lyytikäinen, Leo-Pekka, Raitakari, Olli T, Barnes, Catriona LK, Campbell, Harry, Joshi, Peter K, Wilson, James F, Isaacs, Aaron, Kors, Jan A, van Duijn, Cornelia M, Huang, Paul L, Gudnason, Vilmundur, Harris, Tamara B, Launer, Lenore J, Smith, Albert V, Bottinger, Erwin P, Loos, Ruth JF, Nadkarni, Girish N, Preuss, Michael H, Correa, Adolfo, Mei, Hao, Wilson, James, Meitinger, Thomas, Müller-Nurasyid, Martina, Peters, Annette, Waldenberger, Melanie, Mangino, Massimo, Spector, Timothy D, Rienstra, Michiel, van de Vegte, Yordi J, van der Harst, Pim, Verweij, Niek, Kääb, Stefan, Schramm, Katharina, Sinner, Moritz F, Strauch, Konstantin, Cutler, Michael J, Fatkin, Diane, London, Barry, Olesen, Morten, and Roden, Dan M

Subjects
Humans, Cardiovascular Diseases, Genetic Predisposition to Disease, Electrocardiography, Gene Expression, Multifactorial Inheritance, Quantitative Trait Loci, Female, Male, Arrhythmias, Cardiac, Genetic Variation, Genome-Wide Association Study, Genetic Loci, Endophenotypes, Arrhythmias, Cardiac
Abstract

The electrocardiographic PR interval reflects atrioventricular conduction, and is associated with conduction abnormalities, pacemaker implantation, atrial fibrillation (AF), and cardiovascular mortality. Here we report a multi-ancestry (N = 293,051) genome-wide association meta-analysis for the PR interval, discovering 202 loci of which 141 have not previously been reported. Variants at identified loci increase the percentage of heritability explained, from 33.5% to 62.6%. We observe enrichment for cardiac muscle developmental/contractile and cytoskeletal genes, highlighting key regulation processes for atrioventricular conduction. Additionally, 8 loci not previously reported harbor genes underlying inherited arrhythmic syndromes and/or cardiomyopathies suggesting a role for these genes in cardiovascular pathology in the general population. We show that polygenic predisposition to PR interval duration is an endophenotype for cardiovascular disease, including distal conduction disease, AF, and atrioventricular pre-excitation. These findings advance our understanding of the polygenic basis of cardiac conduction, and the genetic relationship between PR interval duration and cardiovascular disease.

Published
2020

25. Validation of a novel risk score to predict early and late recurrence in solitary fibrous tumour

Author

Georgiesh, Tatiana, Aggerholm-Pedersen, Ninna, Schöffski, Patrick, Zhang, Yifan, Napolitano, Andrea, Bovée, Judith V. M. G., Hjelle, Åse, Tang, Gordon, Spalek, Mateusz, Nannini, Margherita, Swanson, David, Baad-Hansen, Thomas, Sciot, Raf, Hesla, Asle C., Huang, Paul, Dorleijn, Desiree, Haugland, Hans Kristian, Lacambra, Maribel, Skoczylas, Jacek, Pantaleo, Maria A., Haas, Rick L., Meza-Zepeda, Leonardo A., Haller, Florian, Czarnecka, Anna M., Loong, Herbert, Jebsen, Nina L., van de Sande, Michiel, Jones, Robin L., Haglund, Felix, Timmermans, Iris, Safwat, Akmal, Bjerkehagen, Bodil, and Boye, Kjetil

Published
2022
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26. A saturated map of common genetic variants associated with human height

Author

Yengo, Loïc, Vedantam, Sailaja, Marouli, Eirini, Sidorenko, Julia, Bartell, Eric, Sakaue, Saori, Graff, Marielisa, Eliasen, Anders U., Jiang, Yunxuan, Raghavan, Sridharan, Miao, Jenkai, Arias, Joshua D., Graham, Sarah E., Mukamel, Ronen E., Spracklen, Cassandra N., Yin, Xianyong, Chen, Shyh-Huei, Ferreira, Teresa, Highland, Heather H., Ji, Yingjie, Karaderi, Tugce, Lin, Kuang, Lüll, Kreete, Malden, Deborah E., Medina-Gomez, Carolina, Machado, Moara, Moore, Amy, Rüeger, Sina, Sim, Xueling, Vrieze, Scott, Ahluwalia, Tarunveer S., Akiyama, Masato, Allison, Matthew A., Alvarez, Marcus, Andersen, Mette K., Ani, Alireza, Appadurai, Vivek, Arbeeva, Liubov, Bhaskar, Seema, Bielak, Lawrence F., Bollepalli, Sailalitha, Bonnycastle, Lori L., Bork-Jensen, Jette, Bradfield, Jonathan P., Bradford, Yuki, Braund, Peter S., Brody, Jennifer A., Burgdorf, Kristoffer S., Cade, Brian E., Cai, Hui, Cai, Qiuyin, Campbell, Archie, Cañadas-Garre, Marisa, Catamo, Eulalia, Chai, Jin-Fang, Chai, Xiaoran, Chang, Li-Ching, Chang, Yi-Cheng, Chen, Chien-Hsiun, Chesi, Alessandra, Choi, Seung Hoan, Chung, Ren-Hua, Cocca, Massimiliano, Concas, Maria Pina, Couture, Christian, Cuellar-Partida, Gabriel, Danning, Rebecca, Daw, E. Warwick, Degenhard, Frauke, Delgado, Graciela E., Delitala, Alessandro, Demirkan, Ayse, Deng, Xuan, Devineni, Poornima, Dietl, Alexander, Dimitriou, Maria, Dimitrov, Latchezar, Dorajoo, Rajkumar, Ekici, Arif B., Engmann, Jorgen E., Fairhurst-Hunter, Zammy, Farmaki, Aliki-Eleni, Faul, Jessica D., Fernandez-Lopez, Juan-Carlos, Forer, Lukas, Francescatto, Margherita, Freitag-Wolf, Sandra, Fuchsberger, Christian, Galesloot, Tessel E., Gao, Yan, Gao, Zishan, Geller, Frank, Giannakopoulou, Olga, Giulianini, Franco, Gjesing, Anette P., Goel, Anuj, Gordon, Scott D., Gorski, Mathias, Grove, Jakob, Guo, Xiuqing, Gustafsson, Stefan, Haessler, Jeffrey, Hansen, Thomas F., Havulinna, Aki S., Haworth, Simon J., He, Jing, Heard-Costa, Nancy, Hebbar, Prashantha, Hindy, George, Ho, Yuk-Lam A., Hofer, Edith, Holliday, Elizabeth, Horn, Katrin, Hornsby, Whitney E., Hottenga, Jouke-Jan, Huang, Hongyan, Huang, Jie, Huerta-Chagoya, Alicia, Huffman, Jennifer E., Hung, Yi-Jen, Huo, Shaofeng, Hwang, Mi Yeong, Iha, Hiroyuki, Ikeda, Daisuke D., Isono, Masato, Jackson, Anne U., Jäger, Susanne, Jansen, Iris E., Johansson, Ingegerd, Jonas, Jost B., Jonsson, Anna, Jørgensen, Torben, Kalafati, Ioanna-Panagiota, Kanai, Masahiro, Kanoni, Stavroula, Kårhus, Line L., Kasturiratne, Anuradhani, Katsuya, Tomohiro, Kawaguchi, Takahisa, Kember, Rachel L., Kentistou, Katherine A., Kim, Han-Na, Kim, Young Jin, Kleber, Marcus E., Knol, Maria J., Kurbasic, Azra, Lauzon, Marie, Le, Phuong, Lea, Rodney, Lee, Jong-Young, Leonard, Hampton L., Li, Shengchao A., Li, Xiaohui, Li, Xiaoyin, Liang, Jingjing, Lin, Honghuang, Lin, Shih-Yi, Liu, Jun, Liu, Xueping, Lo, Ken Sin, Long, Jirong, Lores-Motta, Laura, Luan, Jian’an, Lyssenko, Valeriya, Lyytikäinen, Leo-Pekka, Mahajan, Anubha, Mamakou, Vasiliki, Mangino, Massimo, Manichaikul, Ani, Marten, Jonathan, Mattheisen, Manuel, Mavarani, Laven, McDaid, Aaron F., Meidtner, Karina, Melendez, Tori L., Mercader, Josep M., Milaneschi, Yuri, Miller, Jason E., Millwood, Iona Y., Mishra, Pashupati P., Mitchell, Ruth E., Møllehave, Line T., Morgan, Anna, Mucha, Soeren, Munz, Matthias, Nakatochi, Masahiro, Nelson, Christopher P., Nethander, Maria, Nho, Chu Won, Nielsen, Aneta A., Nolte, Ilja M., Nongmaithem, Suraj S., Noordam, Raymond, Ntalla, Ioanna, Nutile, Teresa, Pandit, Anita, Christofidou, Paraskevi, Pärna, Katri, Pauper, Marc, Petersen, Eva R. B., Petersen, Liselotte V., Pitkänen, Niina, Polašek, Ozren, Poveda, Alaitz, Preuss, Michael H., Pyarajan, Saiju, Raffield, Laura M., Rakugi, Hiromi, Ramirez, Julia, Rasheed, Asif, Raven, Dennis, Rayner, Nigel W., Riveros, Carlos, Rohde, Rebecca, Ruggiero, Daniela, Ruotsalainen, Sanni E., Ryan, Kathleen A., Sabater-Lleal, Maria, Saxena, Richa, Scholz, Markus, Sendamarai, Anoop, Shen, Botong, Shi, Jingchunzi, Shin, Jae Hun, Sidore, Carlo, Sitlani, Colleen M., Slieker, Roderick C., Smit, Roelof A. J., Smith, Albert V., Smith, Jennifer A., Smyth, Laura J., Southam, Lorraine, Steinthorsdottir, Valgerdur, Sun, Liang, Takeuchi, Fumihiko, Tallapragada, Divya Sri Priyanka, Taylor, Kent D., Tayo, Bamidele O., Tcheandjieu, Catherine, Terzikhan, Natalie, Tesolin, Paola, Teumer, Alexander, Theusch, Elizabeth, Thompson, Deborah J., Thorleifsson, Gudmar, Timmers, Paul R. H. J., Trompet, Stella, Turman, Constance, Vaccargiu, Simona, van der Laan, Sander W., van der Most, Peter J., van Klinken, Jan B., van Setten, Jessica, Verma, Shefali S., Verweij, Niek, Veturi, Yogasudha, Wang, Carol A., Wang, Chaolong, Wang, Lihua, Wang, Zhe, Warren, Helen R., Bin Wei, Wen, Wickremasinghe, Ananda R., Wielscher, Matthias, Wiggins, Kerri L., Winsvold, Bendik S., Wong, Andrew, Wu, Yang, Wuttke, Matthias, Xia, Rui, Xie, Tian, Yamamoto, Ken, Yang, Jingyun, Yao, Jie, Young, Hannah, Yousri, Noha A., Yu, Lei, Zeng, Lingyao, Zhang, Weihua, Zhang, Xinyuan, Zhao, Jing-Hua, Zhao, Wei, Zhou, Wei, Zimmermann, Martina E., Zoledziewska, Magdalena, Adair, Linda S., Adams, Hieab H. H., Aguilar-Salinas, Carlos A., Al-Mulla, Fahd, Arnett, Donna K., Asselbergs, Folkert W., Åsvold, Bjørn Olav, Attia, John, Banas, Bernhard, Bandinelli, Stefania, Bennett, David A., Bergler, Tobias, Bharadwaj, Dwaipayan, Biino, Ginevra, Bisgaard, Hans, Boerwinkle, Eric, Böger, Carsten A., Bønnelykke, Klaus, Boomsma, Dorret I., Børglum, Anders D., Borja, Judith B., Bouchard, Claude, Bowden, Donald W., Brandslund, Ivan, Brumpton, Ben, Buring, Julie E., Caulfield, Mark J., Chambers, John C., Chandak, Giriraj R., Chanock, Stephen J., Chaturvedi, Nish, Chen, Yii-Der Ida, Chen, Zhengming, Cheng, Ching-Yu, Christophersen, Ingrid E., Ciullo, Marina, Cole, John W., Collins, Francis S., Cooper, Richard S., Cruz, Miguel, Cucca, Francesco, Cupples, L. Adrienne, Cutler, Michael J., Damrauer, Scott M., Dantoft, Thomas M., de Borst, Gert J., de Groot, Lisette C. P. G. M., De Jager, Philip L., de Kleijn, Dominique P. V., Janaka de Silva, H., Dedoussis, George V., den Hollander, Anneke I., Du, Shufa, Easton, Douglas F., Elders, Petra J. M., Eliassen, A. Heather, Ellinor, Patrick T., Elmståhl, Sölve, Erdmann, Jeanette, Evans, Michele K., Fatkin, Diane, Feenstra, Bjarke, Feitosa, Mary F., Ferrucci, Luigi, Ford, Ian, Fornage, Myriam, Franke, Andre, Franks, Paul W., Freedman, Barry I., Gasparini, Paolo, Gieger, Christian, Girotto, Giorgia, Goddard, Michael E., Golightly, Yvonne M., Gonzalez-Villalpando, Clicerio, Gordon-Larsen, Penny, Grallert, Harald, Grant, Struan F. A., Grarup, Niels, Griffiths, Lyn, Gudnason, Vilmundur, Haiman, Christopher, Hakonarson, Hakon, Hansen, Torben, Hartman, Catharina A., Hattersley, Andrew T., Hayward, Caroline, Heckbert, Susan R., Heng, Chew-Kiat, Hengstenberg, Christian, Hewitt, Alex W., Hishigaki, Haretsugu, Hoyng, Carel B., Huang, Paul L., Huang, Wei, Hunt, Steven C., Hveem, Kristian, Hyppönen, Elina, Iacono, William G., Ichihara, Sahoko, Ikram, M. Arfan, Isasi, Carmen R., Jackson, Rebecca D., Jarvelin, Marjo-Riitta, Jin, Zi-Bing, Jöckel, Karl-Heinz, Joshi, Peter K., Jousilahti, Pekka, Jukema, J. Wouter, Kähönen, Mika, Kamatani, Yoichiro, Kang, Kui Dong, Kaprio, Jaakko, Kardia, Sharon L. R., Karpe, Fredrik, Kato, Norihiro, Kee, Frank, Kessler, Thorsten, Khera, Amit V., Khor, Chiea Chuen, Kiemeney, Lambertus A. L. M., Kim, Bong-Jo, Kim, Eung Kweon, Kim, Hyung-Lae, Kirchhof, Paulus, Kivimaki, Mika, Koh, Woon-Puay, Koistinen, Heikki A., Kolovou, Genovefa D., Kooner, Jaspal S., Kooperberg, Charles, Köttgen, Anna, Kovacs, Peter, Kraaijeveld, Adriaan, Kraft, Peter, Krauss, Ronald M., Kumari, Meena, Kutalik, Zoltan, Laakso, Markku, Lange, Leslie A., Langenberg, Claudia, Launer, Lenore J., Le Marchand, Loic, Lee, Hyejin, Lee, Nanette R., Lehtimäki, Terho, Li, Huaixing, Li, Liming, Lieb, Wolfgang, Lin, Xu, Lind, Lars, Linneberg, Allan, Liu, Ching-Ti, Liu, Jianjun, Loeffler, Markus, London, Barry, Lubitz, Steven A., Lye, Stephen J., Mackey, David A., Mägi, Reedik, Magnusson, Patrik K. E., Marcus, Gregory M., Vidal, Pedro Marques, Martin, Nicholas G., März, Winfried, Matsuda, Fumihiko, McGarrah, Robert W., McGue, Matt, McKnight, Amy Jayne, Medland, Sarah E., Mellström, Dan, Metspalu, Andres, Mitchell, Braxton D., Mitchell, Paul, Mook-Kanamori, Dennis O., Morris, Andrew D., Mucci, Lorelei A., Munroe, Patricia B., Nalls, Mike A., Nazarian, Saman, Nelson, Amanda E., Neville, Matt J., Newton-Cheh, Christopher, Nielsen, Christopher S., Nöthen, Markus M., Ohlsson, Claes, Oldehinkel, Albertine J., Orozco, Lorena, Pahkala, Katja, Pajukanta, Päivi, Palmer, Colin N. A., Parra, Esteban J., Pattaro, Cristian, Pedersen, Oluf, Pennell, Craig E., Penninx, Brenda W. J. H., Perusse, Louis, Peters, Annette, Peyser, Patricia A., Porteous, David J., Posthuma, Danielle, Power, Chris, Pramstaller, Peter P., Province, Michael A., Qi, Qibin, Qu, Jia, Rader, Daniel J., Raitakari, Olli T., Ralhan, Sarju, Rallidis, Loukianos S., Rao, Dabeeru C., Redline, Susan, Reilly, Dermot F., Reiner, Alexander P., Rhee, Sang Youl, Ridker, Paul M., Rienstra, Michiel, Ripatti, Samuli, Ritchie, Marylyn D., Roden, Dan M., Rosendaal, Frits R., Rotter, Jerome I., Rudan, Igor, Rutters, Femke, Sabanayagam, Charumathi, Saleheen, Danish, Salomaa, Veikko, Samani, Nilesh J., Sanghera, Dharambir K., Sattar, Naveed, Schmidt, Börge, Schmidt, Helena, Schmidt, Reinhold, Schulze, Matthias B., Schunkert, Heribert, Scott, Laura J., Scott, Rodney J., Sever, Peter, Shiroma, Eric J., Shoemaker, M. Benjamin, Shu, Xiao-Ou, Simonsick, Eleanor M., Sims, Mario, Singh, Jai Rup, Singleton, Andrew B., Sinner, Moritz F., Smith, J. Gustav, Snieder, Harold, Spector, Tim D., Stampfer, Meir J., Stark, Klaus J., Strachan, David P., ‘t Hart, Leen M., Tabara, Yasuharu, Tang, Hua, Tardif, Jean-Claude, Thanaraj, Thangavel A., Timpson, Nicholas J., Tönjes, Anke, Tremblay, Angelo, Tuomi, Tiinamaija, Tuomilehto, Jaakko, Tusié-Luna, Maria-Teresa, Uitterlinden, Andre G., van Dam, Rob M., van der Harst, Pim, Van der Velde, Nathalie, van Duijn, Cornelia M., van Schoor, Natasja M., Vitart, Veronique, Völker, Uwe, Vollenweider, Peter, Völzke, Henry, Wacher-Rodarte, Niels H., Walker, Mark, Wang, Ya Xing, Wareham, Nicholas J., Watanabe, Richard M., Watkins, Hugh, Weir, David R., Werge, Thomas M., Widen, Elisabeth, Wilkens, Lynne R., Willemsen, Gonneke, Willett, Walter C., Wilson, James F., Wong, Tien-Yin, Woo, Jeong-Taek, Wright, Alan F., Wu, Jer-Yuarn, Xu, Huichun, Yajnik, Chittaranjan S., Yokota, Mitsuhiro, Yuan, Jian-Min, Zeggini, Eleftheria, Zemel, Babette S., Zheng, Wei, Zhu, Xiaofeng, Zmuda, Joseph M., Zonderman, Alan B., Zwart, John-Anker, Chasman, Daniel I., Cho, Yoon Shin, Heid, Iris M., McCarthy, Mark I., Ng, Maggie C. Y., O’Donnell, Christopher J., Rivadeneira, Fernando, Thorsteinsdottir, Unnur, Sun, Yan V., Tai, E. Shyong, Boehnke, Michael, Deloukas, Panos, Justice, Anne E., Lindgren, Cecilia M., Loos, Ruth J. F., Mohlke, Karen L., North, Kari E., Stefansson, Kari, Walters, Robin G., Winkler, Thomas W., Young, Kristin L., Loh, Po-Ru, Yang, Jian, Esko, Tõnu, Assimes, Themistocles L., Auton, Adam, Abecasis, Goncalo R., Willer, Cristen J., Locke, Adam E., Berndt, Sonja I., Lettre, Guillaume, Frayling, Timothy M., Okada, Yukinori, Wood, Andrew R., Visscher, Peter M., and Hirschhorn, Joel N.

Published
2022
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27. Involvement of Endothelial Nitric Oxide Synthase in Cerebral Microcirculation and Oxygenation in Traumatic Brain Injury

Author

Bragin, Denis E., Bragina, Olga A., Trofimov, Alex O., Huang, Paul L., Atochin, Dmitriy N., Crusio, Wim E., Series Editor, Dong, Haidong, Series Editor, Radeke, Heinfried H., Series Editor, Rezaei, Nima, Series Editor, Steinlein, Ortrud, Series Editor, Xiao, Junjie, Series Editor, Scholkmann, Felix, editor, LaManna, Joseph, editor, and Wolf, Ursula, editor

Published
2022
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28. Multi Modal Fusion for Radiogenomics Classification of Brain Tumor

Author

Mun, Timothy Sum Hon, Doran, Simon, Huang, Paul, Messiou, Christina, Blackledge, Matthew, 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, Crimi, Alessandro, editor, and Bakas, Spyridon, editor

Published
2022
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30. Controversies in the management of patients with soft tissue sarcoma: Recommendations of the Conference on State of Science in Sarcoma 2022

Author

Andreou, Dimosthenis, Barth, Thomas, Bauer, Sebastian, Blay, Jean-Yves, Blum, Veronika, Bode, Beata, Bonvalot, Sylvie, Bovee, Judith, Braam, Petra, Brodowicz, Thomas, Broto, Jean Martin, Dei Tos, Angelo, Denschlag, Dominik, Desar, Ingrid, Digklia, Antonia, Dileo, Palma, Dirksen, Uta, Douchy, Thomas, Duffaud, Florence, Eriksson, Mikael, Fröhling, Stefan, Gelderblom, Hans, Gronchi, Alessandro, Haas, Rick, Hardes, Jenrik, Hartmann, Wolfgang, Hofer, Silvia, Hohenberger, Peter, Hompes, Daphne, Huang, Paul, Italiano, Antoine, Jakob, Jens, Jones, Robin, Judson, Ian, Köhler, Günter, Kollàr, Attila, Krasniqi, Fatime, Krol, Stijn, Kunz, Wolfgang, Le Grange, Franel, Le Pechoux, Cécile, LeCesne, Alexandre, Leithner, Andreas, Liegl-Atzwanger, Bernadette, Lindner, Lars, Mechtersheimer, Gunhild, Messiou, Christina, Miah, Aisha, Pink, Daniel, Reichardt, Peter, Romagosa, Cleo, Rothermundt, Christian, Rutkowski, Piotr, Safwat, Akmel, Sangalli, Claudia, Szkandera, Joanna, Thway, Khin, Tunn, Per-Ulf, Van der Graaf, Winette, Van Houdt, Winan, Wardelmann, Eva, Zachariah, Ralph, Botter, Sander, Cerny, Thomas, Desar, Ingrid M.E., Jones, Robin L., Kunz, Wolfgang G., Liegl-Atzwanger, Berndadette, Lindner, Lars H., Miah, Aisha B., van der Graaf, Winette T.A., and van Houdt, Winan J.

Published
2023
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31. Machine learning for rhabdomyosarcoma histopathology

Author

Frankel, Arthur O., Lathara, Melvin, Shaw, Celine Y., Wogmon, Owen, Jackson, Jacob M., Clark, Mattie M., Eshraghi, Navah, Keenen, Stephanie E., Woods, Andrew D., Purohit, Reshma, Ishi, Yukitomo, Moran, Nirupama, Eguchi, Mariko, Ahmed, Farhat Ul Ain, Khan, Sara, Ioannou, Maria, Perivoliotis, Konstantinos, Li, Pin, Zhou, Huixia, Alkhaledi, Ahmad, Davis, Elizabeth J., Galipeau, Danielle, Randall, R. L., Wozniak, Agnieszka, Schoffski, Patrick, Lee, Che-Jui, Huang, Paul H., Jones, Robin L., Rubin, Brian P., Darrow, Morgan, Srinivasa, Ganapati, Rudzinski, Erin R., Chen, Sonja, Berlow, Noah E., and Keller, Charles

Published
2022
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33. Self-Powered Wireless Sensor

Author

Huang, Paul Ryuji Chuen-Ying, Nguang, Sing Kiong, and Partridge, Ashton

Subjects
Computer Science - Systems and Control
Abstract

This paper develops a novel power harvesting system to harvest ambient RF energy to power a wireless sensor. Harvesting ambient RF energy is a very difficult task as the power levels are extremely weak. Simulation results show zero threshold MOSFETs are essential in the RF to DC conversion process. 0.5VDC at the output of the RF to DC conversion stage is the minimum voltage which must be achieved for the micro-power sensor circuitry to operate. The weakest power level the proposed system can successfully harvest is -37dBm. The measured available power from the FM band has been measured to fluctuate between -33 to -43dBm using a ribbon FM dipole antenna. Ambient RF energy would best be used in conjunction with other forms of harvested ambient energy to increase diversity and dependability. The potential economic and environmental benefits make such endeavors truly worthwhile.

Published
2017

35. Exome-chip meta-analysis identifies novel loci associated with cardiac conduction, including ADAMTS6

Author

Prins, Bram P, Mead, Timothy J, Brody, Jennifer A, Sveinbjornsson, Gardar, Ntalla, Ioanna, Bihlmeyer, Nathan A, van den Berg, Marten, Bork-Jensen, Jette, Cappellani, Stefania, Van Duijvenboden, Stefan, Klena, Nikolai T, Gabriel, George C, Liu, Xiaoqin, Gulec, Cagri, Grarup, Niels, Haessler, Jeffrey, Hall, Leanne M, Iorio, Annamaria, Isaacs, Aaron, Li-Gao, Ruifang, Lin, Honghuang, Liu, Ching-Ti, Lyytikäinen, Leo-Pekka, Marten, Jonathan, Mei, Hao, Müller-Nurasyid, Martina, Orini, Michele, Padmanabhan, Sandosh, Radmanesh, Farid, Ramirez, Julia, Robino, Antonietta, Schwartz, Molly, van Setten, Jessica, Smith, Albert V, Verweij, Niek, Warren, Helen R, Weiss, Stefan, Alonso, Alvaro, Arnar, David O, Bots, Michiel L, de Boer, Rudolf A, Dominiczak, Anna F, Eijgelsheim, Mark, Ellinor, Patrick T, Guo, Xiuqing, Felix, Stephan B, Harris, Tamara B, Hayward, Caroline, Heckbert, Susan R, Huang, Paul L, Jukema, JW, Kähönen, Mika, Kors, Jan A, Lambiase, Pier D, Launer, Lenore J, Li, Man, Linneberg, Allan, Nelson, Christopher P, Pedersen, Oluf, Perez, Marco, Peters, Annette, Polasek, Ozren, Psaty, Bruce M, Raitakari, Olli T, Rice, Kenneth M, Rotter, Jerome I, Sinner, Moritz F, Soliman, Elsayed Z, Spector, Tim D, Strauch, Konstantin, Thorsteinsdottir, Unnur, Tinker, Andrew, Trompet, Stella, Uitterlinden, André, Vaartjes, Ilonca, van der Meer, Peter, Völker, Uwe, Völzke, Henry, Waldenberger, Melanie, Wilson, James G, Xie, Zhijun, Asselbergs, Folkert W, Dörr, Marcus, van Duijn, Cornelia M, Gasparini, Paolo, Gudbjartsson, Daniel F, Gudnason, Vilmundur, Hansen, Torben, Kääb, Stefan, Kanters, Jørgen K, Kooperberg, Charles, Lehtimäki, Terho, Lin, Henry J, Lubitz, Steven A, Mook-Kanamori, Dennis O, Conti, Francesco J, Newton-Cheh, Christopher H, Rosand, Jonathan, Rudan, Igor, and Samani, Nilesh J

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Genetics, Human Genome, Heart Disease, Cardiovascular, 2.1 Biological and endogenous factors, Aetiology, ADAMTS Proteins, Animals, Black People, Connexin 43, Electrocardiography, Exome, Female, Gene Expression, Gene Expression Profiling, Genetic Loci, Genome-Wide Association Study, Heart Conduction System, Humans, Male, Mice, Middle Aged, Myocardium, Open Reading Frames, Polymorphism, Single Nucleotide, White People, Exome Sequencing, Exome chip, Conduction, ADAMTS6, Meta-analysis, Environmental Sciences, Information and Computing Sciences, Bioinformatics
Abstract

BackgroundGenome-wide association studies conducted on QRS duration, an electrocardiographic measurement associated with heart failure and sudden cardiac death, have led to novel biological insights into cardiac function. However, the variants identified fall predominantly in non-coding regions and their underlying mechanisms remain unclear.ResultsHere, we identify putative functional coding variation associated with changes in the QRS interval duration by combining Illumina HumanExome BeadChip genotype data from 77,898 participants of European ancestry and 7695 of African descent in our discovery cohort, followed by replication in 111,874 individuals of European ancestry from the UK Biobank and deCODE cohorts. We identify ten novel loci, seven within coding regions, including ADAMTS6, significantly associated with QRS duration in gene-based analyses. ADAMTS6 encodes a secreted metalloprotease of currently unknown function. In vitro validation analysis shows that the QRS-associated variants lead to impaired ADAMTS6 secretion and loss-of function analysis in mice demonstrates a previously unappreciated role for ADAMTS6 in connexin 43 gap junction expression, which is essential for myocardial conduction.ConclusionsOur approach identifies novel coding and non-coding variants underlying ventricular depolarization and provides a possible mechanism for the ADAMTS6-associated conduction changes.

Published
2018

36. Multi-ethnic genome-wide association study for atrial fibrillation

Author

Roselli, Carolina, Chaffin, Mark D, Weng, Lu-Chen, Aeschbacher, Stefanie, Ahlberg, Gustav, Albert, Christine M, Almgren, Peter, Alonso, Alvaro, Anderson, Christopher D, Aragam, Krishna G, Arking, Dan E, Barnard, John, Bartz, Traci M, Benjamin, Emelia J, Bihlmeyer, Nathan A, Bis, Joshua C, Bloom, Heather L, Boerwinkle, Eric, Bottinger, Erwin B, Brody, Jennifer A, Calkins, Hugh, Campbell, Archie, Cappola, Thomas P, Carlquist, John, Chasman, Daniel I, Chen, Lin Y, Chen, Yii-Der Ida, Choi, Eue-Keun, Choi, Seung Hoan, Christophersen, Ingrid E, Chung, Mina K, Cole, John W, Conen, David, Cook, James, Crijns, Harry J, Cutler, Michael J, Damrauer, Scott M, Daniels, Brian R, Darbar, Dawood, Delgado, Graciela, Denny, Joshua C, Dichgans, Martin, Dörr, Marcus, Dudink, Elton A, Dudley, Samuel C, Esa, Nada, Esko, Tonu, Eskola, Markku, Fatkin, Diane, Felix, Stephan B, Ford, Ian, Franco, Oscar H, Geelhoed, Bastiaan, Grewal, Raji P, Gudnason, Vilmundur, Guo, Xiuqing, Gupta, Namrata, Gustafsson, Stefan, Gutmann, Rebecca, Hamsten, Anders, Harris, Tamara B, Hayward, Caroline, Heckbert, Susan R, Hernesniemi, Jussi, Hocking, Lynne J, Hofman, Albert, Horimoto, Andrea RVR, Huang, Jie, Huang, Paul L, Huffman, Jennifer, Ingelsson, Erik, Ipek, Esra Gucuk, Ito, Kaoru, Jimenez-Conde, Jordi, Johnson, Renee, Jukema, J Wouter, Kääb, Stefan, Kähönen, Mika, Kamatani, Yoichiro, Kane, John P, Kastrati, Adnan, Kathiresan, Sekar, Katschnig-Winter, Petra, Kavousi, Maryam, Kessler, Thorsten, Kietselaer, Bas L, Kirchhof, Paulus, Kleber, Marcus E, Knight, Stacey, Krieger, Jose E, Kubo, Michiaki, Launer, Lenore J, Laurikka, Jari, Lehtimäki, Terho, Leineweber, Kirsten, Lemaitre, Rozenn N, Li, Man, Lim, Hong Euy, Lin, Henry J, and Lin, Honghuang

Subjects
Biological Sciences, Genetics, Heart Disease, Cardiovascular, Human Genome, Biotechnology, 2.1 Biological and endogenous factors, Aetiology, Atrial Fibrillation, Case-Control Studies, Ethnicity, Genetic Predisposition to Disease, Genome-Wide Association Study, Humans, Quantitative Trait Loci, Transcriptome, Medical and Health Sciences, Developmental Biology, Agricultural biotechnology, Bioinformatics and computational biology
Abstract

Atrial fibrillation (AF) affects more than 33 million individuals worldwide1 and has a complex heritability2. We conducted the largest meta-analysis of genome-wide association studies (GWAS) for AF to date, consisting of more than half a million individuals, including 65,446 with AF. In total, we identified 97 loci significantly associated with AF, including 67 that were novel in a combined-ancestry analysis, and 3 that were novel in a European-specific analysis. We sought to identify AF-associated genes at the GWAS loci by performing RNA-sequencing and expression quantitative trait locus analyses in 101 left atrial samples, the most relevant tissue for AF. We also performed transcriptome-wide analyses that identified 57 AF-associated genes, 42 of which overlap with GWAS loci. The identified loci implicate genes enriched within cardiac developmental, electrophysiological, contractile and structural pathways. These results extend our understanding of the biological pathways underlying AF and may facilitate the development of therapeutics for AF.

Published
2018

37. ExomeChip-Wide Analysis of 95 626 Individuals Identifies 10 Novel Loci Associated With QT and JT Intervals

Author

Bihlmeyer, Nathan A, Brody, Jennifer A, Smith, Albert Vernon, Warren, Helen R, Lin, Honghuang, Isaacs, Aaron, Liu, Ching-Ti, Marten, Jonathan, Radmanesh, Farid, Hall, Leanne M, Grarup, Niels, Mei, Hao, Müller-Nurasyid, Martina, Huffman, Jennifer E, Verweij, Niek, Guo, Xiuqing, Yao, Jie, Li-Gao, Ruifang, van den Berg, Marten, Weiss, Stefan, Prins, Bram P, van Setten, Jessica, Haessler, Jeffrey, Lyytikäinen, Leo-Pekka, Li, Man, Alonso, Alvaro, Soliman, Elsayed Z, Bis, Joshua C, Austin, Tom, Chen, Yii-Der Ida, Psaty, Bruce M, Harrris, Tamara B, Launer, Lenore J, Padmanabhan, Sandosh, Dominiczak, Anna, Huang, Paul L, Xie, Zhijun, Ellinor, Patrick T, Kors, Jan A, Campbell, Archie, Murray, Alison D, Nelson, Christopher P, Tobin, Martin D, Bork-Jensen, Jette, Hansen, Torben, Pedersen, Oluf, Linneberg, Allan, Sinner, Moritz F, Peters, Annette, Waldenberger, Melanie, Meitinger, Thomas, Perz, Siegfried, Kolcic, Ivana, Rudan, Igor, de Boer, Rudolf A, van der Meer, Peter, Lin, Henry J, Taylor, Kent D, de Mutsert, Renée, Trompet, Stella, Jukema, J Wouter, Maan, Arie C, Stricker, Bruno HC, Rivadeneira, Fernando, Uitterlinden, André, Völker, Uwe, Homuth, Georg, Völzke, Henry, Felix, Stephan B, Mangino, Massimo, Spector, Timothy D, Bots, Michiel L, Perez, Marco, Raitakari, Olli T, Kähönen, Mika, Mononen, Nina, Gudnason, Vilmundur, Munroe, Patricia B, Lubitz, Steven A, van Duijn, Cornelia M, Newton-Cheh, Christopher H, Hayward, Caroline, Rosand, Jonathan, Samani, Nilesh J, Kanters, Jørgen K, Wilson, James G, Kääb, Stefan, Polasek, Ozren, van der Harst, Pim, Heckbert, Susan R, Rotter, Jerome I, Mook-Kanamori, Dennis O, Eijgelsheim, Mark, Dörr, Marcus, Jamshidi, Yalda, Asselbergs, Folkert W, Kooperberg, Charles, Lehtimäki, Terho, Arking, Dan E, and Sotoodehnia, Nona

Subjects
Biomedical and Clinical Sciences, Cardiovascular Medicine and Haematology, Heart Disease, Prevention, Genetics, Cardiovascular, 2.1 Biological and endogenous factors, Aetiology, Antiporters, DNA-Binding Proteins, Electrocardiography, Exome, Genome-Wide Association Study, Humans, Long QT Syndrome, Oligonucleotide Array Sequence Analysis, Polymorphism, Single Nucleotide, Quantitative Trait Loci, Receptors, Calcium-Sensing, Transcription Factors, arrhythmias, cardiac, death, sudden, cardiac, genetics, genome, humans, Medical Biotechnology, Cardiorespiratory Medicine and Haematology, Cardiovascular System & Hematology, Cardiovascular medicine and haematology
Abstract

BackgroundQT interval, measured through a standard ECG, captures the time it takes for the cardiac ventricles to depolarize and repolarize. JT interval is the component of the QT interval that reflects ventricular repolarization alone. Prolonged QT interval has been linked to higher risk of sudden cardiac arrest.Methods and resultsWe performed an ExomeChip-wide analysis for both QT and JT intervals, including 209 449 variants, both common and rare, in 17 341 genes from the Illumina Infinium HumanExome BeadChip. We identified 10 loci that modulate QT and JT interval duration that have not been previously reported in the literature using single-variant statistical models in a meta-analysis of 95 626 individuals from 23 cohorts (comprised 83 884 European ancestry individuals, 9610 blacks, 1382 Hispanics, and 750 Asians). This brings the total number of ventricular repolarization associated loci to 45. In addition, our approach of using coding variants has highlighted the role of 17 specific genes for involvement in ventricular repolarization, 7 of which are in novel loci.ConclusionsOur analyses show a role for myocyte internal structure and interconnections in modulating QT interval duration, adding to previous known roles of potassium, sodium, and calcium ion regulation, as well as autonomic control. We anticipate that these discoveries will open new paths to the goal of making novel remedies for the prevention of lethal ventricular arrhythmias and sudden cardiac arrest.

Published
2018

38. Genetic Evidence That Carbohydrate-Stimulated Insulin Secretion Leads to Obesity.

Author

Astley, Christina M, Todd, Jennifer N, Salem, Rany M, Vedantam, Sailaja, Ebbeling, Cara B, Huang, Paul L, Ludwig, David S, Hirschhorn, Joel N, and Florez, Jose C

Subjects
Humans, Insulin Resistance, Obesity, Dietary Carbohydrates, Glucose, Body Mass Index, Fasting, Cohort Studies, Reproducibility of Results, Polymorphism, Single Nucleotide, Models, Biological, Genome-Wide Association Study, Mendelian Randomization Analysis, Insulin Secretion, Polymorphism, Single Nucleotide, Models, Biological, Medical Biotechnology, Medical Biochemistry and Metabolomics, Clinical Sciences, General Clinical Medicine
Abstract

BACKGROUND:A fundamental precept of the carbohydrate-insulin model of obesity is that insulin secretion drives weight gain. However, fasting hyperinsulinemia can also be driven by obesity-induced insulin resistance. We used genetic variation to isolate and estimate the potentially causal effect of insulin secretion on body weight. METHODS:Genetic instruments of variation of insulin secretion [assessed as insulin concentration 30 min after oral glucose (insulin-30)] were used to estimate the causal relationship between increased insulin secretion and body mass index (BMI), using bidirectional Mendelian randomization analysis of genome-wide association studies. Data sources included summary results from the largest published metaanalyses of predominantly European ancestry for insulin secretion (n = 26037) and BMI (n = 322154), as well as individual-level data from the UK Biobank (n = 138541). Data from the Cardiology and Metabolic Patient Cohort study at Massachusetts General Hospital (n = 1675) were used to validate genetic associations with insulin secretion and to test the observational association of insulin secretion and BMI. RESULTS:Higher genetically determined insulin-30 was strongly associated with higher BMI (β = 0.098, P = 2.2 × 10-21), consistent with a causal role in obesity. Similar positive associations were noted in sensitivity analyses using other genetic variants as instrumental variables. By contrast, higher genetically determined BMI was not associated with insulin-30. CONCLUSIONS:Mendelian randomization analyses provide evidence for a causal relationship of glucose-stimulated insulin secretion on body weight, consistent with the carbohydrate-insulin model of obesity.

Published
2018

39. Genetic analyses of the electrocardiographic QT interval and its components identify additional loci and pathways

Author

Young, William J., Lahrouchi, Najim, Isaacs, Aaron, Duong, ThuyVy, Foco, Luisa, Ahmed, Farah, Brody, Jennifer A., Salman, Reem, Noordam, Raymond, Benjamins, Jan-Walter, Haessler, Jeffrey, Lyytikäinen, Leo-Pekka, Repetto, Linda, Concas, Maria Pina, van den Berg, Marten E., Weiss, Stefan, Baldassari, Antoine R., Bartz, Traci M., Cook, James P., Evans, Daniel S., Freudling, Rebecca, Hines, Oliver, Isaksen, Jonas L., Lin, Honghuang, Mei, Hao, Moscati, Arden, Müller-Nurasyid, Martina, Nursyifa, Casia, Qian, Yong, Richmond, Anne, Roselli, Carolina, Ryan, Kathleen A., Tarazona-Santos, Eduardo, Thériault, Sébastien, van Duijvenboden, Stefan, Warren, Helen R., Yao, Jie, Raza, Dania, Aeschbacher, Stefanie, Ahlberg, Gustav, Alonso, Alvaro, Andreasen, Laura, Bis, Joshua C., Boerwinkle, Eric, Campbell, Archie, Catamo, Eulalia, Cocca, Massimiliano, Cutler, Michael J., Darbar, Dawood, De Grandi, Alessandro, De Luca, Antonio, Ding, Jun, Ellervik, Christina, Ellinor, Patrick T., Felix, Stephan B., Froguel, Philippe, Fuchsberger, Christian, Gögele, Martin, Graff, Claus, Graff, Mariaelisa, Guo, Xiuqing, Hansen, Torben, Heckbert, Susan R., Huang, Paul L., Huikuri, Heikki V., Hutri-Kähönen, Nina, Ikram, M. Arfan, Jackson, Rebecca D., Junttila, Juhani, Kavousi, Maryam, Kors, Jan A., Leal, Thiago P., Lemaitre, Rozenn N., Lin, Henry J., Lind, Lars, Linneberg, Allan, Liu, Simin, MacFarlane, Peter W., Mangino, Massimo, Meitinger, Thomas, Mezzavilla, Massimo, Mishra, Pashupati P., Mitchell, Rebecca N., Mononen, Nina, Montasser, May E., Morrison, Alanna C., Nauck, Matthias, Nauffal, Victor, Navarro, Pau, Nikus, Kjell, Pare, Guillaume, Patton, Kristen K., Pelliccione, Giulia, Pittman, Alan, Porteous, David J., Pramstaller, Peter P., Preuss, Michael H., Raitakari, Olli T., Reiner, Alexander P., Ribeiro, Antonio Luiz P., Rice, Kenneth M., Risch, Lorenz, Schlessinger, David, Schotten, Ulrich, Schurmann, Claudia, Shen, Xia, Shoemaker, M. Benjamin, Sinagra, Gianfranco, Sinner, Moritz F., Soliman, Elsayed Z., Stoll, Monika, Strauch, Konstantin, Tarasov, Kirill, Taylor, Kent D., Tinker, Andrew, Trompet, Stella, Uitterlinden, André, Völker, Uwe, Völzke, Henry, Waldenberger, Melanie, Weng, Lu-Chen, Whitsel, Eric A., Wilson, James G., Avery, Christy L., Conen, David, Correa, Adolfo, Cucca, Francesco, Dörr, Marcus, Gharib, Sina A., Girotto, Giorgia, Grarup, Niels, Hayward, Caroline, Jamshidi, Yalda, Järvelin, Marjo-Riitta, Jukema, J. Wouter, Kääb, Stefan, Kähönen, Mika, Kanters, Jørgen K., Kooperberg, Charles, Lehtimäki, Terho, Lima-Costa, Maria Fernanda, Liu, Yongmei, Loos, Ruth J. F., Lubitz, Steven A., Mook-Kanamori, Dennis O., Morris, Andrew P., O’Connell, Jeffrey R., Olesen, Morten Salling, Orini, Michele, Padmanabhan, Sandosh, Pattaro, Cristian, Peters, Annette, Psaty, Bruce M., Rotter, Jerome I., Stricker, Bruno, van der Harst, Pim, van Duijn, Cornelia M., Verweij, Niek, Wilson, James F., Arking, Dan E., Ramirez, Julia, Lambiase, Pier D., Sotoodehnia, Nona, Mifsud, Borbala, Newton-Cheh, Christopher, and Munroe, Patricia B.

Published
2022
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40. Clinical implications and molecular features of extracellular matrix networks in soft tissue sarcomas

Author

Pankova, Valeriya, primary, Krasny, Lukas, additional, Kerrison, William, additional, Tam, Yuen Bun, additional, Chadha, Madhumeeta, additional, Burns, Jessica, additional, Wilding, Christopher P., additional, Chen, Liang, additional, Chowdhury, Avirup, additional, Perkins, Emma, additional, Lee, Alexander T.J., additional, Howell, Louise, additional, Guljar, Nafia, additional, Sisley, Karen, additional, Fisher, Cyril, additional, Chudasama, Priya, additional, Thway, Khin, additional, Jones, Robin L., additional, and Huang, Paul H., additional

Published
2024
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41. MRI/CT guided multiregional ‘smart’ biopsy in sarcomas: a prospective development study

Author

Johnston, Edward William, primary, Winfield, Jessica M, additional, Arthur, Amani, additional, Blackledge, Matthew, additional, Basso, Jodie, additional, Chowdhury, Avirup, additional, Hannay, Jonathan, additional, Hayes, Andrew, additional, Kelly-Morland, Christian, additional, Napolitano, Andrea, additional, Richardson, Cheryl, additional, Smith, Myles, additional, Strauss, Dirk, additional, Koh, Dow-Mu, additional, Jones, Robin Lewis, additional, Thway, Khin, additional, Huang, Paul, additional, Messiou, Christina, additional, and Fotiadis, Nicos, additional

Published
2024
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44. Evaluating Effectiveness of DART Buoy Networks

Author

Percival, Donald B., Denbo, Donald W., Gica, Edison, Huang, Paul Y., Mofjeld, Harold O., Spillane, Michael C., and Titov, Vasily V.

Subjects
Physics - Atmospheric and Oceanic Physics, Statistics - Applications
Abstract

A performance measure for a DART tsunami buoy network has been developed. The measure is based on a statistical analysis of simulated forecasts of wave heights outside an impact site and how much the forecasts are degraded in accuracy when one or more buoys are inoperative. The analysis uses simulated tsunami height time series collected at each buoy from selected source segments in the Short-term Inundation Forecast for Tsunamis (SIFT) database and involves a set for 1000 forecasts for each buoy/segment pair at sites just offshore of selected impact communities. Random error-producing scatter in the time series is induced by uncertainties in the source location, addition of real oceanic noise, and imperfect tidal removal. Comparison with an error-free standard leads to root-mean-square errors (RMSEs) for DART buoys located near a subduction zone. The RMSEs indicate which buoy provides the best forecast (lowest RMSE) for sections of the zone, under a warning-time constraint for the forecasts of 3 hrs. The analysis also shows how the forecasts are degraded (larger minimum RMSE among the remaining buoys) when one or more buoys become inoperative. The RMSEs also provide a way to assess array augmentation or redesign such as moving buoys to more optimal locations. Examples are shown for buoys off the Aleutian Islands and off the West Coast of South America for impact sites at Hilo HI and along the U.S. West Coast (Crescent City CA and Port San Luis CA). A simple measure (coded green, yellow or red) of the current status of the network's ability to deliver accurate forecasts is proposed to flag the urgency of buoy repair., Comment: 31 pages, 18 figures

Published
2016

47. Discovery of novel heart rate-associated loci using the Exome Chip

Author

van den Berg, Marten E, Warren, Helen R, Cabrera, Claudia P, Verweij, Niek, Mifsud, Borbala, Haessler, Jeffrey, Bihlmeyer, Nathan A, Fu, Yi-Ping, Weiss, Stefan, Lin, Henry J, Grarup, Niels, Li-Gao, Ruifang, Pistis, Giorgio, Shah, Nabi, Brody, Jennifer A, Müller-Nurasyid, Martina, Lin, Honghuang, Mei, Hao, Smith, Albert V, Lyytikäinen, Leo-Pekka, Hall, Leanne M, van Setten, Jessica, Trompet, Stella, Prins, Bram P, Isaacs, Aaron, Radmanesh, Farid, Marten, Jonathan, Entwistle, Aiman, Kors, Jan A, Silva, Claudia T, Alonso, Alvaro, Bis, Joshua C, de Boer, Rudolf, de Haan, Hugoline G, de Mutsert, Renée, Dedoussis, George, Dominiczak, Anna F, Doney, Alex SF, Ellinor, Patrick T, Eppinga, Ruben N, Felix, Stephan B, Guo, Xiuqing, Hagemeijer, Yanick, Hansen, Torben, Harris, Tamara B, Heckbert, Susan R, Huang, Paul L, Hwang, Shih-Jen, Kähönen, Mika, Kanters, Jørgen K, Kolcic, Ivana, Launer, Lenore J, Li, Man, Yao, Jie, Linneberg, Allan, Liu, Simin, Macfarlane, Peter W, Mangino, Massimo, Morris, Andrew D, Mulas, Antonella, Murray, Alison D, Nelson, Christopher P, Orrú, Marco, Padmanabhan, Sandosh, Peters, Annette, Porteous, David J, Poulter, Neil, Psaty, Bruce M, Qi, Lihong, Raitakari, Olli T, Rivadeneira, Fernando, Roselli, Carolina, Rudan, Igor, Sattar, Naveed, Sever, Peter, Sinner, Moritz F, Soliman, Elsayed Z, Spector, Timothy D, Stanton, Alice V, Stirrups, Kathleen E, Taylor, Kent D, Tobin, Martin D, Uitterlinden, André, Vaartjes, Ilonca, Hoes, Arno W, van der Meer, Peter, Völker, Uwe, Waldenberger, Melanie, Xie, Zhijun, Zoledziewska, Magdalena, Tinker, Andrew, Polasek, Ozren, Rosand, Jonathan, Jamshidi, Yalda, van Duijn, Cornelia M, Zeggini, Eleftheria, Jukema, J Wouter, Asselbergs, Folkert W, Samani, Nilesh J, and Lehtimäki, Terho

Subjects
Biological Sciences, Genetics, Human Genome, Biotechnology, Heart Disease, Prevention, Cardiovascular, Stem Cell Research, Clinical Research, Aetiology, 2.1 Biological and endogenous factors, Adult, Alleles, Exome, Female, Gene Frequency, Genetic Loci, Genetic Predisposition to Disease, Genome-Wide Association Study, Genotype, Heart Rate, Humans, Male, Middle Aged, Oligonucleotide Array Sequence Analysis, Polymorphism, Single Nucleotide, Risk Factors, White People, Medical and Health Sciences, Genetics & Heredity
Abstract

Resting heart rate is a heritable trait, and an increase in heart rate is associated with increased mortality risk. Genome-wide association study analyses have found loci associated with resting heart rate, at the time of our study these loci explained 0.9% of the variation. This study aims to discover new genetic loci associated with heart rate from Exome Chip meta-analyses.Heart rate was measured from either elecrtrocardiograms or pulse recordings. We meta-analysed heart rate association results from 104 452 European-ancestry individuals from 30 cohorts, genotyped using the Exome Chip. Twenty-four variants were selected for follow-up in an independent dataset (UK Biobank, N = 134 251). Conditional and gene-based testing was undertaken, and variants were investigated with bioinformatics methods.We discovered five novel heart rate loci, and one new independent low-frequency non-synonymous variant in an established heart rate locus (KIAA1755). Lead variants in four of the novel loci are non-synonymous variants in the genes C10orf71, DALDR3, TESK2 and SEC31B. The variant at SEC31B is significantly associated with SEC31B expression in heart and tibial nerve tissue. Further candidate genes were detected from long-range regulatory chromatin interactions in heart tissue (SCD, SLF2 and MAPK8). We observed significant enrichment in DNase I hypersensitive sites in fetal heart and lung. Moreover, enrichment was seen for the first time in human neuronal progenitor cells (derived from embryonic stem cells) and fetal muscle samples by including our novel variants.Our findings advance the knowledge of the genetic architecture of heart rate, and indicate new candidate genes for follow-up functional studies.

Published
2017

49. Proteomic profiling improves prognostic risk stratification of the Sarculator nomogram in soft tissue sarcomas of the extremities and trunk wall.

Author

Chadha, Madhumeeta, Iadecola, Sara, Jenks, Andrew, Pankova, Valeriya, Tam, Yuen Bun, Burns, Jessica, Arthur, Amani, Wilding, Christopher P., Chen, Liang, Chudasama, Priya, Callegaro, Dario, Strauss, Dirk C., Thway, Khin, Gronchi, Alessandro, Jones, Robin L., Miceli, Rosalba, Pasquali, Sandro, and Huang, Paul H.

Subjects
CELL cycle proteins, SARCOMA, DNA replication, OVERALL survival, DRUG target
Abstract

Background: High‐risk soft tissue sarcomas of the extremities and trunk wall (eSTS), as defined by the Sarculator nomogram, are more likely to benefit from (neo)adjuvant anthracycline‐based therapy compared to low/intermediate‐risk patients. The biology underpinning these differential treatment outcomes remain unknown. Methods: We analysed proteomic profiles and clinical outcomes of 123 eSTS patients. A Cox model for overall survival including the Sarculator was fitted to individual data to define four risk groups. A DNA replication protein signature‐Sarcoma Proteomic Module 6 (SPM6) was evaluated for association with clinicopathological factors and risk groups. SPM6 was added as a covariate together with Sarculator in a multivariable Cox model to assess improvement in prognostic risk stratification. Results: DNA replication and cell cycle proteins were upregulated in high‐risk versus very low‐risk patients. Evaluation of the functional effects of CRISPR‐Cas9 gene knockdown of proteins enriched in high‐risk patients using the cancer cell line encyclopaedia database identified candidate drug targets. SPM6 was significantly associated with tumour malignancy grade (p = 1.6e‐06), histology (p = 1.4e‐05) and risk groups (p = 2.6e‐06). Cox model analysis showed that SPM6 substantially contributed to a better calibration of the Sarculator nomogram (Index of Prediction Accuracy = 0.109 for Sarculator alone versus 0.165 for Sarculator + SPM6). Conclusions: Risk stratification of patient with STS is defined by distinct biological pathways across a range of cancer hallmarks. Incorporation of SPM6 protein signature improves prognostic risk stratification of the Sarculator nomogram. This study highlights the utility of integrating protein signatures for the development of next‐generation nomograms. [ABSTRACT FROM AUTHOR]

Published
2024
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