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5,641 results on '"Jenkins, Mark"'

1. Waveguide QED at the onset of spin-spin correlations

Author

Roca-Jerat, Sebastián, Rubín-Osanz, Marcos, Jenkins, Mark D., Camón, Agustín, Alonso, Pablo J., Zueco, David, and Luis, Fernando

Subjects
Quantum Physics, Condensed Matter - Materials Science
Abstract

We experimentally explore the competition between light-mediated and direct matter-matter interactions in waveguide quantum electrodynamics. For this, we couple a superconducting line to a model magnetic material, made of organic free radical DPPH molecules with a spin $S=1/2$ and a $g_{S}$ factor very close to that of a free electron. The microwave transmission has been measured in a wide range of temperatures ($0.013$ K $\leq T \leq 2$ K), magnetic fields ($0\leq B \leq 0.5$ T) and frequencies ($0 \leq \omega/2 \pi \leq 14$ GHz). We find that molecules belonging to the crystal sublattice B form one-dimensional spin chains. Temperature then controls intrinsic spin correlations along the chain in a continuous and monotonic way. In the paramagnetic region ($T > 0.7$ K), the microwave transmission shows evidences for the collective coupling of quasi-identical spins to the propagating photons, with coupling strengths that reach values close to the dissipation rates. As $T$ decreases, the growth of intrinsic spin correlations, combined with the anisotropy in the spin-spin exchange constants, break down the collective spin-photon coupling. In this regime, the temperature dependence of the spin resonance visibility reflects the change in the nature of the dominant spin excitations, from single spin flips to bosonic magnons, which is brought about by the magnetic correlation growth.

Published
2024

2. Genetic risk impacts the association of menopausal hormone therapy with colorectal cancer risk

Author

Tian, Yu, Lin, Yi, Qu, Conghui, Arndt, Volker, Baurley, James W., Berndt, Sonja I., Bien, Stephanie A., Bishop, D. Timothy, Brenner, Hermann, Buchanan, Daniel D., Budiarto, Arif, Campbell, Peter T., Carreras-Torres, Robert, Casey, Graham, Chan, Andrew T., Chen, Rui, Chen, Xuechen, Conti, David V., Díez-Obrero, Virginia, Dimou, Niki, Drew, David A., Figueiredo, Jane C., Gallinger, Steven, Giles, Graham G., Gruber, Stephen B., Gunter, Marc J., Harlid, Sophia, Harrison, Tabitha A., Hidaka, Akihisa, Hoffmeister, Michael, Huyghe, Jeroen R., Jenkins, Mark A., Jordahl, Kristina M., Joshi, Amit D., Keku, Temitope O., Kawaguchi, Eric, Kim, Andre E., Kundaje, Anshul, Larsson, Susanna C., Marchand, Loic Le, Lewinger, Juan Pablo, Li, Li, Moreno, Victor, Morrison, John, Murphy, Neil, Nan, Hongmei, Nassir, Rami, Newcomb, Polly A., Obón-Santacana, Mireia, Ogino, Shuji, Ose, Jennifer, Pardamean, Bens, Pellatt, Andrew J., Peoples, Anita R., Platz, Elizabeth A., Potter, John D., Prentice, Ross L., Rennert, Gad, Ruiz-Narvaez, Edward A., Sakoda, Lori C., Schoen, Robert E., Shcherbina, Anna, Stern, Mariana C., Su, Yu-Ru, Thibodeau, Stephen N., Thomas, Duncan C., Tsilidis, Konstantinos K., van Duijnhoven, Franzel J. B., Van Guelpen, Bethany, Visvanathan, Kala, White, Emily, Wolk, Alicja, Woods, Michael O., Wu, Anna H., Peters, Ulrike, Gauderman, W. James, Hsu, Li, and Chang-Claude, Jenny

Published
2024
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3. Intratumoral presence of the genotoxic gut bacteria pks+E. coli, Enterotoxigenic Bacteroides fragilis, and Fusobacterium nucleatum and their association with clinicopathological and molecular features of colorectal cancer

Author

Joo, Jihoon E., Chu, Yen Lin, Georgeson, Peter, Walker, Romy, Mahmood, Khalid, Clendenning, Mark, Meyers, Aaron L., Como, Julia, Joseland, Sharelle, Preston, Susan G., Diepenhorst, Natalie, Toner, Julie, Ingle, Danielle J., Sherry, Norelle L., Metz, Andrew, Lynch, Brigid M., Milne, Roger L., Southey, Melissa C., Hopper, John L., Win, Aung Ko, Macrae, Finlay A., Winship, Ingrid M., Rosty, Christophe, Jenkins, Mark A., and Buchanan, Daniel D.

Published
2024
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5. Lay Text Summarisation Using Natural Language Processing: A Narrative Literature Review

Author

Vinzelberg, Oliver, Jenkins, Mark David, Morison, Gordon, McMinn, David, and Tieges, Zoe

Subjects
Computer Science - Computation and Language
Abstract

Summarisation of research results in plain language is crucial for promoting public understanding of research findings. The use of Natural Language Processing to generate lay summaries has the potential to relieve researchers' workload and bridge the gap between science and society. The aim of this narrative literature review is to describe and compare the different text summarisation approaches used to generate lay summaries. We searched the databases Web of Science, Google Scholar, IEEE Xplore, Association for Computing Machinery Digital Library and arXiv for articles published until 6 May 2022. We included original studies on automatic text summarisation methods to generate lay summaries. We screened 82 articles and included eight relevant papers published between 2020 and 2021, all using the same dataset. The results show that transformer-based methods such as Bidirectional Encoder Representations from Transformers (BERT) and Pre-training with Extracted Gap-sentences for Abstractive Summarization (PEGASUS) dominate the landscape of lay text summarisation, with all but one study using these methods. A combination of extractive and abstractive summarisation methods in a hybrid approach was found to be most effective. Furthermore, pre-processing approaches to input text (e.g. applying extractive summarisation) or determining which sections of a text to include, appear critical. Evaluation metrics such as Recall-Oriented Understudy for Gisting Evaluation (ROUGE) were used, which do not consider readability. To conclude, automatic lay text summarisation is under-explored. Future research should consider long document lay text summarisation, including clinical trial reports, and the development of evaluation metrics that consider readability of the lay summary.

Published
2023

9. A mosaic pathogenic variant in MSH6 causes MSH6-deficient colorectal and endometrial cancer in a patient classified as suspected Lynch syndrome: a case report

Author

Walker, Romy, Clendenning, Mark, Joo, Jihoon E., Xue, Jessie, Mahmood, Khalid, Georgeson, Peter, Como, Julia, Joseland, Sharelle, Preston, Susan G., Chan, James M., Jenkins, Mark A., Rosty, Christophe, Macrae, Finlay A., Di Palma, Stephanie, Campbell, Ainsley, Winship, Ingrid M., and Buchanan, Daniel D.

Published
2023
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10. Probing the diabetes and colorectal cancer relationship using gene – environment interaction analyses

Author

Dimou, Niki, Kim, Andre E., Flanagan, Orlagh, Murphy, Neil, Diez-Obrero, Virginia, Shcherbina, Anna, Aglago, Elom K., Bouras, Emmanouil, Campbell, Peter T., Casey, Graham, Gallinger, Steven, Gruber, Stephen B., Jenkins, Mark A., Lin, Yi, Moreno, Victor, Ruiz-Narvaez, Edward, Stern, Mariana C., Tian, Yu, Tsilidis, Kostas K., Arndt, Volker, Barry, Elizabeth L., Baurley, James W., Berndt, Sonja I., Bézieau, Stéphane, Bien, Stephanie A., Bishop, D. Timothy, Brenner, Hermann, Budiarto, Arif, Carreras-Torres, Robert, Cenggoro, Tjeng Wawan, Chan, Andrew T., Chang-Claude, Jenny, Chanock, Stephen J., Chen, Xuechen, Conti, David V., Dampier, Christopher H., Devall, Matthew, Drew, David A., Figueiredo, Jane C., Giles, Graham G., Gsur, Andrea, Harrison, Tabitha A., Hidaka, Akihisa, Hoffmeister, Michael, Huyghe, Jeroen R., Jordahl, Kristina, Kawaguchi, Eric, Keku, Temitope O., Larsson, Susanna C., Le Marchand, Loic, Lewinger, Juan Pablo, Li, Li, Mahesworo, Bharuno, Morrison, John, Newcomb, Polly A., Newton, Christina C., Obon-Santacana, Mireia, Ose, Jennifer, Pai, Rish K., Palmer, Julie R., Papadimitriou, Nikos, Pardamean, Bens, Peoples, Anita R., Pharoah, Paul D. P., Platz, Elizabeth A., Potter, John D., Rennert, Gad, Scacheri, Peter C., Schoen, Robert E., Su, Yu-Ru, Tangen, Catherine M., Thibodeau, Stephen N., Thomas, Duncan C., Ulrich, Cornelia M., Um, Caroline Y., van Duijnhoven, Franzel J. B., Visvanathan, Kala, Vodicka, Pavel, Vodickova, Ludmila, White, Emily, Wolk, Alicja, Woods, Michael O., Qu, Conghui, Kundaje, Anshul, Hsu, Li, Gauderman, W. James, Gunter, Marc J., and Peters, Ulrike

Published
2023
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11. Genetically proxied glucose-lowering drug target perturbation and risk of cancer: a Mendelian randomisation analysis

Author

Yarmolinsky, James, Bouras, Emmanouil, Constantinescu, Andrei, Burrows, Kimberley, Bull, Caroline J., Vincent, Emma E., Martin, Richard M., Dimopoulou, Olympia, Lewis, Sarah J., Moreno, Victor, Vujkovic, Marijana, Chang, Kyong-Mi, Voight, Benjamin F., Tsao, Philip S., Gunter, Marc J., Hampe, Jochen, Pellatt, Andrew J., Pharoah, Paul D. P., Schoen, Robert E., Gallinger, Steven, Jenkins, Mark A., Pai, Rish K., Gill, Dipender, and Tsilidis, Kostas K.

Published
2023
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12. What's Cracking? A Review and Analysis of Deep Learning Methods for Structural Crack Segmentation, Detection and Quantification

Author

König, Jacob, Jenkins, Mark, Mannion, Mike, Barrie, Peter, and Morison, Gordon

Subjects
Computer Science - Computer Vision and Pattern Recognition
Abstract

Surface cracks are a very common indicator of potential structural faults. Their early detection and monitoring is an important factor in structural health monitoring. Left untreated, they can grow in size over time and require expensive repairs or maintenance. With recent advances in computer vision and deep learning algorithms, the automatic detection and segmentation of cracks for this monitoring process have become a major topic of interest. This review aims to give researchers an overview of the published work within the field of crack analysis algorithms that make use of deep learning. It outlines the various tasks that are solved through applying computer vision algorithms to surface cracks in a structural health monitoring setting and also provides in-depth reviews of recent fully, semi and unsupervised approaches that perform crack classification, detection, segmentation and quantification. Additionally, this review also highlights popular datasets used for cracks and the metrics that are used to evaluate the performance of those algorithms. Finally, potential research gaps are outlined and further research directions are provided.

Published
2022

13. Genome-Wide Interaction Analysis of Genetic Variants With Menopausal Hormone Therapy for Colorectal Cancer Risk.

Author

Tian, Yu, Kim, Andre E, Bien, Stephanie A, Lin, Yi, Qu, Conghui, Harrison, Tabitha A, Carreras-Torres, Robert, Díez-Obrero, Virginia, Dimou, Niki, Drew, David A, Hidaka, Akihisa, Huyghe, Jeroen R, Jordahl, Kristina M, Morrison, John, Murphy, Neil, Obón-Santacana, Mireia, Ulrich, Cornelia M, Ose, Jennifer, Peoples, Anita R, Ruiz-Narvaez, Edward A, Shcherbina, Anna, Stern, Mariana C, Su, Yu-Ru, van Duijnhoven, Franzel JB, Arndt, Volker, Baurley, James W, Berndt, Sonja I, Bishop, D Timothy, Brenner, Hermann, Buchanan, Daniel D, Chan, Andrew T, Figueiredo, Jane C, Gallinger, Steven, Gruber, Stephen B, Harlid, Sophia, Hoffmeister, Michael, Jenkins, Mark A, Joshi, Amit D, Keku, Temitope O, Larsson, Susanna C, Le Marchand, Loic, Li, Li, Giles, Graham G, Milne, Roger L, Nan, Hongmei, Nassir, Rami, Ogino, Shuji, Budiarto, Arif, Platz, Elizabeth A, Potter, John D, Prentice, Ross L, Rennert, Gad, Sakoda, Lori C, Schoen, Robert E, Slattery, Martha L, Thibodeau, Stephen N, Van Guelpen, Bethany, Visvanathan, Kala, White, Emily, Wolk, Alicja, Woods, Michael O, Wu, Anna H, Campbell, Peter T, Casey, Graham, Conti, David V, Gunter, Marc J, Kundaje, Anshul, Lewinger, Juan Pablo, Moreno, Victor, Newcomb, Polly A, Pardamean, Bens, Thomas, Duncan C, Tsilidis, Konstantinos K, Peters, Ulrike, Gauderman, W James, Hsu, Li, and Chang-Claude, Jenny

Subjects
Humans, Colorectal Neoplasms, Estrogens, Progestins, Risk Factors, Case-Control Studies, Menopause, Polymorphism, Single Nucleotide, Female, Aging, Digestive Diseases, Estrogen, Colo-Rectal Cancer, Genetics, Prevention, Human Genome, Clinical Research, Cancer, 2.1 Biological and endogenous factors, Aetiology, Oncology and Carcinogenesis, Oncology & Carcinogenesis
Abstract

BackgroundThe use of menopausal hormone therapy (MHT) may interact with genetic variants to influence colorectal cancer (CRC) risk.MethodsWe conducted a genome-wide, gene-environment interaction between single nucleotide polymorphisms and the use of any MHT, estrogen only, and combined estrogen-progestogen therapy with CRC risk, among 28 486 postmenopausal women (11 519 CRC patients and 16 967 participants without CRC) from 38 studies, using logistic regression, 2-step method, and 2- or 3-degree-of-freedom joint test. A set-based score test was applied for rare genetic variants.ResultsThe use of any MHT, estrogen only and estrogen-progestogen were associated with a reduced CRC risk (odds ratio [OR] = 0.71, 95% confidence interval [CI] = 0.64 to 0.78; OR = 0.65, 95% CI = 0.53 to 0.79; and OR = 0.73, 95% CI = 0.59 to 0.90, respectively). The 2-step method identified a statistically significant interaction between a GRIN2B variant rs117868593 and MHT use, whereby MHT-associated CRC risk was statistically significantly reduced in women with the GG genotype (OR = 0.68, 95% CI = 0.64 to 0.72) but not within strata of GC or CC genotypes. A statistically significant interaction between a DCBLD1 intronic variant at 6q22.1 (rs10782186) and MHT use was identified by the 2-degree-of-freedom joint test. The MHT-associated CRC risk was reduced with increasing number of rs10782186-C alleles, showing odds ratios of 0.78 (95% CI = 0.70 to 0.87) for TT, 0.68 (95% CI = 0.63 to 0.73) for TC, and 0.66 (95% CI = 0.60 to 0.74) for CC genotypes. In addition, 5 genes in rare variant analysis showed suggestive interactions with MHT (2-sided P

Published
2022

16. SMARTERscreen protocol: a three-arm cluster randomised controlled trial of patient SMS messaging in general practice to increase participation in the Australian National Bowel Cancer Screening Program

Author

McIntosh, Jennifer G., Emery, Jon D., Wood, Anna, Chondros, Patty, Goodwin, Belinda C., Trevena, Judy, Wilson, Carlene, Chang, Shanton, Hocking, Jane, Campbell, Tina, Macrae, Finlay, Milley, Kristi, Lew, Jie-Bin, Nightingale, Claire, Dixon, Ian, Castelli, Makala, Lee, Nicholas, Innes, Lyle, Jolley, Tamara, Fletcher, Sabine, Buchanan, Lyn, Doncovio, Sally, Broun, Kate, Austin, Glenn, Jiang, Joyce, and Jenkins, Mark A.

Published
2023
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18. Combining Asian and European genome-wide association studies of colorectal cancer improves risk prediction across racial and ethnic populations

Author

Thomas, Minta, Su, Yu-Ru, Rosenthal, Elisabeth A., Sakoda, Lori C., Schmit, Stephanie L., Timofeeva, Maria N., Chen, Zhishan, Fernandez-Rozadilla, Ceres, Law, Philip J., Murphy, Neil, Carreras-Torres, Robert, Diez-Obrero, Virginia, van Duijnhoven, Franzel J. B., Jiang, Shangqing, Shin, Aesun, Wolk, Alicja, Phipps, Amanda I., Burnett-Hartman, Andrea, Gsur, Andrea, Chan, Andrew T., Zauber, Ann G., Wu, Anna H., Lindblom, Annika, Um, Caroline Y., Tangen, Catherine M., Gignoux, Chris, Newton, Christina, Haiman, Christopher A., Qu, Conghui, Bishop, D. Timothy, Buchanan, Daniel D., Crosslin, David R., Conti, David V., Kim, Dong-Hyun, Hauser, Elizabeth, White, Emily, Siegel, Erin, Schumacher, Fredrick R., Rennert, Gad, Giles, Graham G., Hampel, Heather, Brenner, Hermann, Oze, Isao, Oh, Jae Hwan, Lee, Jeffrey K., Schneider, Jennifer L., Chang-Claude, Jenny, Kim, Jeongseon, Huyghe, Jeroen R., Zheng, Jiayin, Hampe, Jochen, Greenson, Joel, Hopper, John L., Palmer, Julie R., Visvanathan, Kala, Matsuo, Keitaro, Matsuda, Koichi, Jung, Keum Ji, Li, Li, Le Marchand, Loic, Vodickova, Ludmila, Bujanda, Luis, Gunter, Marc J., Matejcic, Marco, Jenkins, Mark A., Slattery, Martha L., D’Amato, Mauro, Wang, Meilin, Hoffmeister, Michael, Woods, Michael O., Kim, Michelle, Song, Mingyang, Iwasaki, Motoki, Du, Mulong, Udaltsova, Natalia, Sawada, Norie, Vodicka, Pavel, Campbell, Peter T., Newcomb, Polly A., Cai, Qiuyin, Pearlman, Rachel, Pai, Rish K., Schoen, Robert E., Steinfelder, Robert S., Haile, Robert W., Vandenputtelaar, Rosita, Prentice, Ross L., Küry, Sébastien, Castellví-Bel, Sergi, Tsugane, Shoichiro, Berndt, Sonja I., Lee, Soo Chin, Brezina, Stefanie, Weinstein, Stephanie J., Chanock, Stephen J., Jee, Sun Ha, Kweon, Sun-Seog, Vadaparampil, Susan, Harrison, Tabitha A., Yamaji, Taiki, Keku, Temitope O., Vymetalkova, Veronika, Arndt, Volker, Jia, Wei-Hua, Shu, Xiao-Ou, Lin, Yi, Ahn, Yoon-Ok, Stadler, Zsofia K., Van Guelpen, Bethany, Ulrich, Cornelia M., Platz, Elizabeth A., Potter, John D., Li, Christopher I., Meester, Reinier, Moreno, Victor, Figueiredo, Jane C., Casey, Graham, Lansdorp Vogelaar, Iris, Dunlop, Malcolm G., Gruber, Stephen B., Hayes, Richard B., Pharoah, Paul D. P., Houlston, Richard S., Jarvik, Gail P., Tomlinson, Ian P., Zheng, Wei, Corley, Douglas A., Peters, Ulrike, and Hsu, Li

Published
2023
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19. Author Correction: Application of Mendelian randomization to explore the causal role of the human gut microbiome in colorectal cancer

Author

Hatcher, Charlie, Richenberg, George, Waterson, Samuel, Nguyen, Long H., Joshi, Amit D., Carreras-Torres, Robert, Moreno, Victor, Chan, Andrew T., Gunter, Marc, Lin, Yi, Qu, Conghui, Song, Mingyang, Casey, Graham, Figueiredo, Jane C., Gruber, Stephen B., Hampe, Jochen, Hampel, Heather, Jenkins, Mark A., Keku, Temitope O., Peters, Ulrike, Tangen, Catherine M., Wu, Anna H., Hughes, David A., Rühlemann, Malte C., Raes, Jeroen, Timpson, Nicholas J., and Wade, Kaitlin H.

Published
2023
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20. A tumor focused approach to resolving the etiology of DNA mismatch repair deficient tumors classified as suspected Lynch syndrome

Author

Walker, Romy, Mahmood, Khalid, Joo, Jihoon E., Clendenning, Mark, Georgeson, Peter, Como, Julia, Joseland, Sharelle, Preston, Susan G., Antill, Yoland, Austin, Rachel, Boussioutas, Alex, Bowman, Michelle, Burke, Jo, Campbell, Ainsley, Daneshvar, Simin, Edwards, Emma, Gleeson, Margaret, Goodwin, Annabel, Harris, Marion T., Henderson, Alex, Higgins, Megan, Hopper, John L., Hutchinson, Ryan A., Ip, Emilia, Isbister, Joanne, Kasem, Kais, Marfan, Helen, Milnes, Di, Ng, Annabelle, Nichols, Cassandra, O’Connell, Shona, Pachter, Nicholas, Pope, Bernard J., Poplawski, Nicola, Ragunathan, Abiramy, Smyth, Courtney, Spigelman, Allan, Storey, Kirsty, Susman, Rachel, Taylor, Jessica A., Warwick, Linda, Wilding, Mathilda, Williams, Rachel, Win, Aung K., Walsh, Michael D., Macrae, Finlay A., Jenkins, Mark A., Rosty, Christophe, Winship, Ingrid M., and Buchanan, Daniel D.

Published
2023
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21. Application of Mendelian randomization to explore the causal role of the human gut microbiome in colorectal cancer

Author

Hatcher, Charlie, Richenberg, George, Waterson, Samuel, Nguyen, Long H., Joshi, Amit D., Carreras-Torres, Robert, Moreno, Victor, Chan, Andrew T., Gunter, Marc, Lin, Yi, Qu, Conghui, Song, Mingyang, Casey, Graham, Figueiredo, Jane C., Gruber, Stephen B., Hampe, Jochen, Hampel, Heather, Jenkins, Mark A., Keku, Temitope O., Peters, Ulrike, Tangen, Catherine M., Wu, Anna H., Hughes, David A., Rühlemann, Malte C., Raes, Jeroen, Timpson, Nicholas J., and Wade, Kaitlin H.

Published
2023
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25. Weakly-Supervised Surface Crack Segmentation by Generating Pseudo-Labels using Localization with a Classifier and Thresholding

Author

König, Jacob, Jenkins, Mark, Mannion, Mike, Barrie, Peter, and Morison, Gordon

Subjects
Computer Science - Computer Vision and Pattern Recognition
Abstract

Surface cracks are a common sight on public infrastructure nowadays. Recent work has been addressing this problem by supporting structural maintenance measures using machine learning methods. Those methods are used to segment surface cracks from their background, making them easier to localize. However, a common issue is that to create a well-functioning algorithm, the training data needs to have detailed annotations of pixels that belong to cracks. Our work proposes a weakly supervised approach that leverages a CNN classifier in a novel way to create surface crack pseudo labels. First, we use the classifier to create a rough crack localization map by using its class activation maps and a patch based classification approach and fuse this with a thresholding based approach to segment the mostly darker crack pixels. The classifier assists in suppressing noise from the background regions, which commonly are incorrectly highlighted as cracks by standard thresholding methods. Then, the pseudo labels can be used in an end-to-end approach when training a standard CNN for surface crack segmentation. Our method is shown to yield sufficiently accurate pseudo labels. Those labels, incorporated into segmentation CNN training using multiple recent crack segmentation architectures, achieve comparable performance to fully supervised methods on four popular crack segmentation datasets., Comment: This work has been submitted to the IEEE for possible publication. Copyright may be transferred without notice, after which this version may no longer be accessible

Published
2021

26. Body size and risk of colorectal cancer molecular defined subtypes and pathways: Mendelian randomization analyses

Author

Papadimitriou, Nikos, Qu, Conghui, Harrison, Tabitha A., Bever, Alaina M., Martin, Richard M., Tsilidis, Konstantinos K., Newcomb, Polly A., Thibodeau, Stephen N., Newton, Christina C., Um, Caroline Y., Obón-Santacana, Mireia, Moreno, Victor, Brenner, Hermann, Mandic, Marko, Chang-Claude, Jenny, Hoffmeister, Michael, Pellatt, Andrew J., Schoen, Robert E., Harlid, Sophia, Ogino, Shuji, Ugai, Tomotaka, Buchanan, Daniel D., Lynch, Brigid M., Gruber, Stephen B., Cao, Yin, Hsu, Li, Huyghe, Jeroen R., Lin, Yi, Steinfelder, Robert S., Sun, Wei, Van Guelpen, Bethany, Zaidi, Syed H., Toland, Amanda E., Berndt, Sonja I., Huang, Wen-Yi, Aglago, Elom K., Drew, David A., French, Amy J., Georgeson, Peter, Giannakis, Marios, Hullar, Meredith, Nowak, Johnathan A., Thomas, Claire E., Le Marchand, Loic, Cheng, Iona, Gallinger, Steven, Jenkins, Mark A., Gunter, Marc J., Campbell, Peter T., Peters, Ulrike, Song, Mingyang, Phipps, Amanda I., and Murphy, Neil

Published
2024
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27. Weight, Blood Pressure, and Dietary Benefits After 12 Months of a Web-based Nutrition Education Program (DASH for Health): Longitudinal Observational Study

Author

Moore, Thomas J, Alsabeeh, Nour, Apovian, Caroline M, Murphy, Megan C, Coffman, Gerald A, Cullum-Dugan, Diana, Jenkins, Mark, and Cabral, Howard

Subjects
Computer applications to medicine. Medical informatics, R858-859.7, Public aspects of medicine, RA1-1270
Abstract

Background The dietary habits of Americans are creating serious health concerns, including obesity, hypertension, diabetes, cardiovascular disease, and even some types of cancer. While considerable attention has been focused on calorie reduction and weight loss, approaches are needed that will not only help the population reduce calorie intake but also consume the type of healthy, well-balanced diet that would prevent this array of medical complications. Objective To design an Internet-based nutrition education program and to explore its effect on weight, blood pressure, and eating habits after 12 months of participation. Methods We designed the DASH for Health program to provide weekly articles about healthy nutrition via the Internet. Dietary advice was based on the DASH diet (Dietary Approaches to Stop Hypertension). The program was offered as a free benefit to the employees of EMC Corporation, and 2834 employees and spouses enrolled. Enrollees voluntarily entered information about themselves on the website (food intake), and we used these self-entered data to determine if the program had any effect. Analyses were based upon the change in weight, blood pressure, and food intake between the baseline period (before the DASH program began) and the 12th month. To be included in an outcome, a subject had to have provided both a baseline and 12th-month entry. Results After 12 months, 735 of 2834 original enrollees (26%) were still actively using the program. For subjects who were overweight/obese (body mass index > 25; n = 151), weight change at 12 months was -4.2 lbs (95% CI: -2.2, -6.2; P < .001). For subjects with hypertension or prehypertension at baseline (n = 62), systolic blood pressure fell 6.8 mmHg at 12 months (CI: -2.6, -11.0; P < .001; n = 62). Diastolic pressure fell 2.1 mmHg (P = .16). Based upon self-entered food surveys, enrollees (n = 181) at 12 months were eating significantly more fruits, more vegetables, and fewer grain products. They also reduced consumption of carbonated beverages. Enrollees who had visited the website more often tended to have greater blood pressure and weight loss effect, suggesting that use of the DASH for Health program was at least partially responsible for the benefits we observed. Conclusions We have found that continued use of a nutrition education program delivered totally via the Internet, with no person-to-person contact with health professionals, is associated with significant weight loss, blood pressure lowering, and dietary improvements after 12 months. Effective programs like DASH for Health, delivered via the Internet, can provide benefit to large numbers of subjects at low cost and may help address the nutritional public health crisis.

Published
2008
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28. Genome-wide association study identifies tumor anatomical site-specific risk variants for colorectal cancer survival

Author

Labadie, Julia D, Savas, Sevtap, Harrison, Tabitha A, Banbury, Barb, Huang, Yuhan, Buchanan, Daniel D, Campbell, Peter T, Gallinger, Steven J, Giles, Graham G, Gunter, Marc J, Hoffmeister, Michael, Hsu, Li, Jenkins, Mark A, Lin, Yi, Ogino, Shuji, Phipps, Amanda I, Slattery, Martha L, Steinfelder, Robert S, Sun, Wei, Van Guelpen, Bethany, Hua, Xinwei, Figuieredo, Jane C, Pai, Rish K, Nassir, Rami, Qi, Lihong, Chan, Andrew T, Peters, Ulrike, and Newcomb, Polly A

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Genetics, Epidemiology, Health Sciences, Oncology and Carcinogenesis, Human Genome, Cancer, Colo-Rectal Cancer, Prevention, Digestive Diseases, Aetiology, 2.1 Biological and endogenous factors, Adult, Aged, Aged, 80 and over, Biomarkers, Tumor, Colorectal Neoplasms, Databases, Genetic, Female, Genetic Loci, Genome-Wide Association Study, Humans, Male, Middle Aged, Neoplasm Staging, Polymorphism, Single Nucleotide, Risk Assessment, Risk Factors, Young Adult
Abstract

Identification of new genetic markers may improve the prediction of colorectal cancer prognosis. Our objective was to examine genome-wide associations of germline genetic variants with disease-specific survival in an analysis of 16,964 cases of colorectal cancer. We analyzed genotype and colorectal cancer-specific survival data from a consortium of 15 studies. Approximately 7.5 million SNPs were examined under the log-additive model using Cox proportional hazards models, adjusting for clinical factors and principal components. Additionally, we ran secondary analyses stratifying by tumor site and disease stage. We used a genome-wide p-value threshold of 5 × 10-8 to assess statistical significance. No variants were statistically significantly associated with disease-specific survival in the full case analysis or in the stage-stratified analyses. Three SNPs were statistically significantly associated with disease-specific survival for cases with tumors located in the distal colon (rs698022, HR = 1.48, CI 1.30-1.69, p = 8.47 × 10-9) and the proximal colon (rs189655236, HR = 2.14, 95% CI 1.65-2.77, p = 9.19 × 10-9 and rs144717887, HR = 2.01, 95% CI 1.57-2.58, p = 3.14 × 10-8), whereas no associations were detected for rectal tumors. Findings from this large genome-wide association study highlight the potential for anatomical-site-stratified genome-wide studies to identify germline genetic risk variants associated with colorectal cancer-specific survival. Larger sample sizes and further replication efforts are needed to more fully interpret these findings.

Published
2022

30. Prognostic role of detailed colorectal location and tumor molecular features: analyses of 13,101 colorectal cancer patients including 2994 early-onset cases

Author

Ugai, Tomotaka, Akimoto, Naohiko, Haruki, Koichiro, Harrison, Tabitha A., Cao, Yin, Qu, Conghui, Chan, Andrew T., Campbell, Peter T., Berndt, Sonja I., Buchanan, Daniel D., Cross, Amanda J., Diergaarde, Brenda, Gallinger, Steven J., Gunter, Marc J., Harlid, Sophia, Hidaka, Akihisa, Hoffmeister, Michael, Brenner, Hermann, Chang-Claude, Jenny, Hsu, Li, Jenkins, Mark A., Lin, Yi, Milne, Roger L., Moreno, Victor, Newcomb, Polly A., Nishihara, Reiko, Obon-Santacana, Mireia, Pai, Rish K., Sakoda, Lori C., Schoen, Robert E., Slattery, Martha L., Sun, Wei, Amitay, Efrat L., Alwers, Elizabeth, Thibodeau, Stephen N., Toland, Amanda E., Van Guelpen, Bethany, Zaidi, Syed H., Potter, John D., Meyerhardt, Jeffrey A., Giannakis, Marios, Song, Mingyang, Nowak, Jonathan A., Peters, Ulrike, Phipps, Amanda I., and Ogino, Shuji

Published
2023
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31. Otherworldly fiber art at the Renwick evokes space, sea and flesh

Author

Jenkins, Mark

Subjects
Renwick Gallery, Textile fabrics, General interest, News, opinion and commentary
Abstract

Byline: Mark Jenkins The 33 artworks in the Renwick Gallery's 'Subversive, Skilled, Sublime: Fiber Art by Women' are not quite so rebellious as the show's title suggests. But they do [...]

Published
2024

32. âNew Worlds' is a sweeping art show mash-up of sci-fi and ancient myth

Author

Jenkins, Mark

Subjects
Sculpture -- Exhibitions -- United States, Handicraft -- Exhibitions, Women artists -- Exhibitions, Installations (Art) -- Exhibitions, Video art -- Exhibitions, General interest, News, opinion and commentary
Abstract

Byline: Mark Jenkins Biological and ecological concerns are as common as cultural ones in âNew Worlds: Women to Watch 2024,â the seventh and largest of the triennial surveys of emerging [...]

Published
2024

33. A fascinating look at Japan's gorgeous ghost stories

Author

Jenkins, Mark

Subjects
Painting, General interest, News, opinion and commentary
Abstract

Byline: Mark Jenkins Some of the best-known examples of Ukiyo-e, the popular and influential Japanese genre exemplified by Hokusai's âThe Great Wave Off Kanagawa,â depict notable locations in a stylized [...]

Published
2024

35. Long-term cost-effectiveness of a melanoma prevention program using genomic risk information compared with standard prevention advice in Australia

Author

Newson, Ainsley J., Morton, Rachael L., Kimlin, Michael, Keogh, Louise, Law, Matthew, Kirk, Judy, Dobbinson, Suzanne J., Kanetsky, Peter, Mann, Graham, Dawkins, Hugh, Savard, Jacqueline, Dunlop, Kate, Trevena, Lyndal, Jenkins, Mark, Allen, Martin, Butow, Phyllis, Wordsworth, Sarah, Lo, Serigne, Low, Cynthia, Smit, Amelia K., Espinoza, David, Cust, Anne E., Law, Chi Kin, Fernandez-Penas, Pablo, Nieweg, Omgo E., and Menzies, Alexander M.

Published
2023
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36. Optimized Deep Encoder-Decoder Methods for Crack Segmentation

Author

König, Jacob, Jenkins, Mark, Mannion, Mike, Barrie, Peter, and Morison, Gordon

Subjects
Computer Science - Computer Vision and Pattern Recognition
Abstract

Surface crack segmentation poses a challenging computer vision task as background, shape, colour and size of cracks vary. In this work we propose optimized deep encoder-decoder methods consisting of a combination of techniques which yield an increase in crack segmentation performance. Specifically we propose a decoder-part for an encoder-decoder based deep learning architecture for semantic segmentation and study its components to achieve increased performance. We also examine the use of different encoder strategies and introduce a data augmentation policy to increase the amount of available training data. The performance evaluation of our method is carried out on four publicly available crack segmentation datasets. Additionally, we introduce two techniques into the field of surface crack segmentation, previously not used there: Generating results using test-time-augmentation and performing a statistical result analysis over multiple training runs. The former approach generally yields increased performance results, whereas the latter allows for more reproducible and better representability of a methods results. Using those aforementioned strategies with our proposed encoder-decoder architecture we are able to achieve new state of the art results in all datasets., Comment: Accepted Manuscript at Digital Signal Processing (Elsevier)

Published
2020
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37. Genetically predicted circulating concentrations of micronutrients and risk of colorectal cancer among individuals of European descent: a Mendelian randomization study

Author

Tsilidis, Konstantinos K, Papadimitriou, Nikos, Dimou, Niki, Gill, Dipender, Lewis, Sarah J, Martin, Richard M, Murphy, Neil, Markozannes, Georgios, Zuber, Verena, Cross, Amanda J, Burrows, Kimberley, Lopez, David S, Key, Timothy J, Travis, Ruth C, Perez-Cornago, Aurora, Hunter, David J, van Duijnhoven, Fränzel JB, Albanes, Demetrius, Arndt, Volker, Berndt, Sonja I, Bézieau, Stéphane, Bishop, D Timothy, Boehm, Juergen, Brenner, Hermann, Burnett-Hartman, Andrea, Campbell, Peter T, Casey, Graham, Castellví-Bel, Sergi, Chan, Andrew T, Chang-Claude, Jenny, de la Chapelle, Albert, Figueiredo, Jane C, Gallinger, Steven J, Giles, Graham G, Goodman, Phyllis J, Gsur, Andrea, Hampe, Jochen, Hampel, Heather, Hoffmeister, Michael, Jenkins, Mark A, Keku, Temitope O, Kweon, Sun-Seog, Larsson, Susanna C, Le Marchand, Loic, Li, Christopher I, Li, Li, Lindblom, Annika, Martín, Vicente, Milne, Roger L, Moreno, Victor, Nan, Hongmei, Nassir, Rami, Newcomb, Polly A, Offit, Kenneth, Pharoah, Paul DP, Platz, Elizabeth A, Potter, John D, Qi, Lihong, Rennert, Gad, Sakoda, Lori C, Schafmayer, Clemens, Slattery, Martha L, Snetselaar, Linda, Schenk, Jeanette, Thibodeau, Stephen N, Ulrich, Cornelia M, Van Guelpen, Bethany, Harlid, Sophia, Visvanathan, Kala, Vodickova, Ludmila, Wang, Hansong, White, Emily, Wolk, Alicja, Woods, Michael O, Wu, Anna H, Zheng, Wei, Bueno-de-Mesquita, Bas, Boutron-Ruault, Marie-Christine, Hughes, David J, Jakszyn, Paula, Kühn, Tilman, Palli, Domenico, Riboli, Elio, Giovannucci, Edward L, Banbury, Barbara L, Gruber, Stephen B, Peters, Ulrike, Gunter, Marc J, and on behalf of GECCO, CORECT

Subjects
Complementary and Integrative Health, Digestive Diseases, Clinical Research, Clinical Trials and Supportive Activities, Cancer, Colo-Rectal Cancer, Prevention, Nutrition, Prevention of disease and conditions, and promotion of well-being, 3.3 Nutrition and chemoprevention, Case-Control Studies, Colorectal Neoplasms, Dietary Supplements, Genetic Predisposition to Disease, Humans, Mendelian Randomization Analysis, Micronutrients, Risk Factors, Selenium, Vitamin B 12, White People, Mendelian randomization, genes, nutrition, supplements, colorectal cancer, Engineering, Medical and Health Sciences, Nutrition & Dietetics
Abstract

BackgroundThe literature on associations of circulating concentrations of minerals and vitamins with risk of colorectal cancer is limited and inconsistent. Evidence from randomized controlled trials (RCTs) to support the efficacy of dietary modification or nutrient supplementation for colorectal cancer prevention is also limited.ObjectivesTo complement observational and RCT findings, we investigated associations of genetically predicted concentrations of 11 micronutrients (β-carotene, calcium, copper, folate, iron, magnesium, phosphorus, selenium, vitamin B-6, vitamin B-12, and zinc) with colorectal cancer risk using Mendelian randomization (MR).MethodsTwo-sample MR was conducted using 58,221 individuals with colorectal cancer and 67,694 controls from the Genetics and Epidemiology of Colorectal Cancer Consortium, Colorectal Cancer Transdisciplinary Study, and Colon Cancer Family Registry. Inverse variance-weighted MR analyses were performed with sensitivity analyses to assess the impact of potential violations of MR assumptions.ResultsNominally significant associations were noted for genetically predicted iron concentration and higher risk of colon cancer [ORs per SD (ORSD): 1.08; 95% CI: 1.00, 1.17; P value = 0.05] and similarly for proximal colon cancer, and for vitamin B-12 concentration and higher risk of colorectal cancer (ORSD: 1.12; 95% CI: 1.03, 1.21; P value = 0.01) and similarly for colon cancer. A nominally significant association was also noted for genetically predicted selenium concentration and lower risk of colon cancer (ORSD: 0.98; 95% CI: 0.96, 1.00; P value = 0.05) and similarly for distal colon cancer. These associations were robust to sensitivity analyses. Nominally significant inverse associations were observed for zinc and risk of colorectal and distal colon cancers, but sensitivity analyses could not be performed. None of these findings survived correction for multiple testing. Genetically predicted concentrations of β-carotene, calcium, copper, folate, magnesium, phosphorus, and vitamin B-6 were not associated with disease risk.ConclusionsThese results suggest possible causal associations of circulating iron and vitamin B-12 (positively) and selenium (inversely) with risk of colon cancer.

Published
2021

38. Deciphering colorectal cancer genetics through multi-omic analysis of 100,204 cases and 154,587 controls of European and east Asian ancestries

Author

Fernandez-Rozadilla, Ceres, Timofeeva, Maria, Chen, Zhishan, Law, Philip, Thomas, Minta, Schmit, Stephanie, Díez-Obrero, Virginia, Hsu, Li, Fernandez-Tajes, Juan, Palles, Claire, Sherwood, Kitty, Briggs, Sarah, Svinti, Victoria, Donnelly, Kevin, Farrington, Susan, Blackmur, James, Vaughan-Shaw, Peter, Shu, Xiao-ou, Long, Jirong, Cai, Qiuyin, Guo, Xingyi, Lu, Yingchang, Broderick, Peter, Studd, James, Huyghe, Jeroen, Harrison, Tabitha, Conti, David, Dampier, Christopher, Devall, Mathew, Schumacher, Fredrick, Melas, Marilena, Rennert, Gad, Obón-Santacana, Mireia, Martín-Sánchez, Vicente, Moratalla-Navarro, Ferran, Oh, Jae Hwan, Kim, Jeongseon, Jee, Sun Ha, Jung, Keum Ji, Kweon, Sun-Seog, Shin, Min-Ho, Shin, Aesun, Ahn, Yoon-Ok, Kim, Dong-Hyun, Oze, Isao, Wen, Wanqing, Matsuo, Keitaro, Matsuda, Koichi, Tanikawa, Chizu, Ren, Zefang, Gao, Yu-Tang, Jia, Wei-Hua, Hopper, John, Jenkins, Mark, Win, Aung Ko, Pai, Rish, Figueiredo, Jane, Haile, Robert, Gallinger, Steven, Woods, Michael, Newcomb, Polly, Duggan, David, Cheadle, Jeremy, Kaplan, Richard, Maughan, Timothy, Kerr, Rachel, Kerr, David, Kirac, Iva, Böhm, Jan, Mecklin, Lukka-Pekka, Jousilahti, Pekka, Knekt, Paul, Aaltonen, Lauri, Rissanen, Harri, Pukkala, Eero, Eriksson, Johan, Cajuso, Tatiana, Hänninen, Ulrika, Kondelin, Johanna, Palin, Kimmo, Tanskanen, Tomas, Renkonen-Sinisalo, Laura, Zanke, Brent, Männistö, Satu, Albanes, Demetrius, Weinstein, Stephanie, Ruiz-Narvaez, Edward, Palmer, Julie, Buchanan, Daniel, Platz, Elizabeth, Visvanathan, Kala, Ulrich, Cornelia, Siegel, Erin, Brezina, Stefanie, Gsur, Andrea, Campbell, Peter, Chang-Claude, Jenny, Hoffmeister, Michael, Brenner, Hermann, Slattery, Martha, Potter, John, Tsilidis, Konstantinos, Schulze, Matthias, Gunter, Marc, Murphy, Neil, Castells, Antoni, Castellví-Bel, Sergi, Moreira, Leticia, Arndt, Volker, Shcherbina, Anna, Stern, Mariana, Pardamean, Bens, Bishop, Timothy, Giles, Graham, Southey, Melissa, Idos, Gregory, McDonnell, Kevin, Abu-Ful, Zomoroda, Greenson, Joel, Shulman, Katerina, Lejbkowicz, Flavio, Offit, Kenneth, Su, Yu-Ru, Steinfelder, Robert, Keku, Temitope, van Guelpen, Bethany, Hudson, Thomas, Hampel, Heather, Pearlman, Rachel, Berndt, Sonja, Hayes, Richard, Martinez, Marie Elena, Thomas, Sushma, Corley, Douglas, Pharoah, Paul, Larsson, Susanna, Yen, Yun, Lenz, Heinz-Josef, White, Emily, Li, Li, Doheny, Kimberly, Pugh, Elizabeth, Shelford, Tameka, Chan, Andrew, Cruz-Correa, Marcia, Lindblom, Annika, Hunter, David, Joshi, Amit, Schafmayer, Clemens, Scacheri, Peter, Kundaje, Anshul, Nickerson, Deborah, Schoen, Robert, Hampe, Jochen, Stadler, Zsofia, Vodicka, Pavel, Vodickova, Ludmila, Vymetalkova, Veronika, Papadopoulos, Nickolas, Edlund, Chistopher, Gauderman, William, Thomas, Duncan, Shibata, David, Toland, Amanda, Markowitz, Sanford, Kim, Andre, Chanock, Stephen, van Duijnhoven, Franzel, Feskens, Edith, Sakoda, Lori, Gago-Dominguez, Manuela, Wolk, Alicja, Naccarati, Alessio, Pardini, Barbara, FitzGerald, Liesel, Lee, Soo Chin, Ogino, Shuji, Bien, Stephanie, Kooperberg, Charles, Li, Christopher, Lin, Yi, Prentice, Ross, Qu, Conghui, Bézieau, Stéphane, Tangen, Catherine, Mardis, Elaine, Yamaji, Taiki, Sawada, Norie, Iwasaki, Motoki, Haiman, Christopher, Le Marchand, Loic, Wu, Anna, Qu, Chenxu, McNeil, Caroline, Coetzee, Gerhard, Hayward, Caroline, Deary, Ian, Harris, Sarah, Theodoratou, Evropi, Reid, Stuart, Walker, Marion, Ooi, Li Yin, Moreno, Victor, Casey, Graham, Gruber, Stephen, Tomlinson, Ian, Zheng, Wei, Dunlop, Malcolm, Houlston, Richard, and Peters, Ulrike

Published
2023
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39. Probing the current-phase relation of graphene Josephson junctions using microwave measurements

Author

Schmidt, Felix E., Jenkins, Mark D., Watanabe, Kenji, Taniguchi, Takashi, and Steele, Gary A.

Subjects
Condensed Matter - Mesoscale and Nanoscale Physics, Condensed Matter - Superconductivity
Abstract

We perform extensive analysis of graphene Josephson junctions embedded in microwave circuits. By comparing a diffusive junction at 15 mK with a ballistic one at 15 mK and 1 K, we are able to reconstruct the current-phase relation.

Published
2020

40. Current detection using a Josephson parametric upconverter

Author

Schmidt, Felix E., Bothner, Daniel, Rodrigues, Ines C., Gely, Mario F., Jenkins, Mark D., and Steele, Gary A.

Subjects
Condensed Matter - Mesoscale and Nanoscale Physics, Condensed Matter - Superconductivity, Physics - Instrumentation and Detectors, Quantum Physics
Abstract

We present the design, measurement and analysis of a current sensor based on a process of Josephson parametric upconversion in a superconducting microwave cavity. Terminating a coplanar waveguide with a nanobridge constriction Josephson junction, we observe modulation sidebands from the cavity that enable highly sensitive, frequency-multiplexed output of small currents for applications such as transition-edge sensor array readout. We derive an analytical model to reproduce the measurements over a wide range of bias currents, detunings and input powers. Tuning the frequency of the cavity by more than \SI{100}{\mega\hertz} with DC current, our device achieves a minimum current sensitivity of \SI{8.9}{\pico\ampere\per\sqrt{\hertz}}. Extrapolating the results of our analytical model, we predict an improved device based on our platform, capable of achieving sensitivities down to \SI{50}{\femto\ampere\per\sqrt{\hertz}}}, or even lower if one could take advantage of parametric amplification in the Josephson cavity. Taking advantage of the Josephson architecture, our approach can provide higher sensitivity than kinetic inductance designs, and potentially enables detection of currents ultimately limited by quantum noise.

Published
2020
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43. Fine-mapping analysis including over 254,000 East Asian and European descendants identifies 136 putative colorectal cancer susceptibility genes

Author

Chen, Zhishan, Guo, Xingyi, Tao, Ran, Huyghe, Jeroen R., Law, Philip J., Fernandez-Rozadilla, Ceres, Ping, Jie, Jia, Guochong, Long, Jirong, Li, Chao, Shen, Quanhu, Xie, Yuhan, Timofeeva, Maria N., Thomas, Minta, Schmit, Stephanie L., Díez-Obrero, Virginia, Devall, Matthew, Moratalla-Navarro, Ferran, Fernandez-Tajes, Juan, Palles, Claire, Sherwood, Kitty, Briggs, Sarah E. W., Svinti, Victoria, Donnelly, Kevin, Farrington, Susan M., Blackmur, James, Vaughan-Shaw, Peter G., Shu, Xiao-Ou, Lu, Yingchang, Broderick, Peter, Studd, James, Harrison, Tabitha A., Conti, David V., Schumacher, Fredrick R., Melas, Marilena, Rennert, Gad, Obón-Santacana, Mireia, Martín-Sánchez, Vicente, Oh, Jae Hwan, Kim, Jeongseon, Jee, Sun Ha, Jung, Keum Ji, Kweon, Sun-Seog, Shin, Min-Ho, Shin, Aesun, Ahn, Yoon-Ok, Kim, Dong-Hyun, Oze, Isao, Wen, Wanqing, Matsuo, Keitaro, Matsuda, Koichi, Tanikawa, Chizu, Ren, Zefang, Gao, Yu-Tang, Jia, Wei-Hua, Hopper, John L., Jenkins, Mark A., Win, Aung Ko, Pai, Rish K., Figueiredo, Jane C., Haile, Robert W., Gallinger, Steven, Woods, Michael O., Newcomb, Polly A., Duggan, David, Cheadle, Jeremy P., Kaplan, Richard, Kerr, Rachel, Kerr, David, Kirac, Iva, Böhm, Jan, Mecklin, Jukka-Pekka, Jousilahti, Pekka, Knekt, Paul, Aaltonen, Lauri A., Rissanen, Harri, Pukkala, Eero, Eriksson, Johan G., Cajuso, Tatiana, Hänninen, Ulrika, Kondelin, Johanna, Palin, Kimmo, Tanskanen, Tomas, Renkonen-Sinisalo, Laura, Männistö, Satu, Albanes, Demetrius, Weinstein, Stephanie J., Ruiz-Narvaez, Edward, Palmer, Julie R., Buchanan, Daniel D., Platz, Elizabeth A., Visvanathan, Kala, Ulrich, Cornelia M., Siegel, Erin, Brezina, Stefanie, Gsur, Andrea, Campbell, Peter T., Chang-Claude, Jenny, Hoffmeister, Michael, Brenner, Hermann, Slattery, Martha L., Potter, John D., Tsilidis, Kostas K., Schulze, Matthias B., Gunter, Marc J., Murphy, Neil, Castells, Antoni, Castellví-Bel, Sergi, Moreira, Leticia, Arndt, Volker, Shcherbina, Anna, Bishop, D. Timothy, Giles, Graham G., Southey, Melissa C., Idos, Gregory E., McDonnell, Kevin J., Abu-Ful, Zomoroda, Greenson, Joel K., Shulman, Katerina, Lejbkowicz, Flavio, Offit, Kenneth, Su, Yu-Ru, Steinfelder, Robert, Keku, Temitope O., van Guelpen, Bethany, Hudson, Thomas J., Hampel, Heather, Pearlman, Rachel, Berndt, Sonja I., Hayes, Richard B., Martinez, Marie Elena, Thomas, Sushma S., Pharoah, Paul D. P., Larsson, Susanna C., Yen, Yun, Lenz, Heinz-Josef, White, Emily, Li, Li, Doheny, Kimberly F., Pugh, Elizabeth, Shelford, Tameka, Chan, Andrew T., Cruz-Correa, Marcia, Lindblom, Annika, Hunter, David J., Joshi, Amit D., Schafmayer, Clemens, Scacheri, Peter C., Kundaje, Anshul, Schoen, Robert E., Hampe, Jochen, Stadler, Zsofia K., Vodicka, Pavel, Vodickova, Ludmila, Vymetalkova, Veronika, Edlund, Christopher K., Gauderman, W. James, Shibata, David, Toland, Amanda, Markowitz, Sanford, Kim, Andre, Chanock, Stephen J., van Duijnhoven, Franzel, Feskens, Edith J. M., Sakoda, Lori C., Gago-Dominguez, Manuela, Wolk, Alicja, Pardini, Barbara, FitzGerald, Liesel M., Lee, Soo Chin, Ogino, Shuji, Bien, Stephanie A., Kooperberg, Charles, Li, Christopher I., Lin, Yi, Prentice, Ross, Qu, Conghui, Bézieau, Stéphane, Yamaji, Taiki, Sawada, Norie, Iwasaki, Motoki, Le Marchand, Loic, Wu, Anna H., Qu, Chenxu, McNeil, Caroline E., Coetzee, Gerhard, Hayward, Caroline, Deary, Ian J., Harris, Sarah E., Theodoratou, Evropi, Reid, Stuart, Walker, Marion, Ooi, Li Yin, Lau, Ken S., Zhao, Hongyu, Hsu, Li, Cai, Qiuyin, Dunlop, Malcolm G., Gruber, Stephen B., Houlston, Richard S., Moreno, Victor, Casey, Graham, Peters, Ulrike, Tomlinson, Ian, and Zheng, Wei

Published
2024
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44. Elucidating the Risk of Colorectal Cancer for Variants in Hereditary Colorectal Cancer Genes

Author

Wang, Xiaoliang, Huyghe, Jeroen R., Joo, Jihoon E., Georgeson, Peter, Arndt, Volker, Berndt, Sonja I., Bézieau, Stéphane, Bien, Stephanie A., Bishop, D. Timothy, Brenner, Hermann, Brezina, Stefanie, Burnett-Hartman, Andrea, Campbell, Peter T., Casey, Graham, Castellví-Bel, Sergi, Chan, Andrew T., Chang-Claude, Jenny, Chen, Xuechen, Conti, David V., Cremolini, Chiara, Diergaarde, Brenda, Figueiredo, Jane C., FitzGerald, Liesel M., Gago-Dominguez, Manuela, Gallinger, Steven, Giles, Graham G., Gsu, Andrea, Gunter, Marc J., Hampe, Jochen, Hampel, Heather, Harrison, Tabitha A., Hoffmeister, Michael, Keku, Temitope O., Kundaje, Anshul, Le Marchand, Loic, Lenz, Heinz-Josef, Li, Christopher I., Li, Li, Lin, Yi, Lindblom, Annika, Moreno, Victor, Murphy, Neil, Newcomb, Polly A., Newton, Christina C., Obón-Santacana, Mireia, Ogino, Shuji, Pai, Rish K., Palmer, Julie R., Pearlman, Rachel, Pharoah, Paul D.P., Phipps, Amanda I., Platz, Elizabeth A., Potter, John D., Rennert, Gad, Sakoda, Lori C., Schafmayer, Clemens, Schmit, Stephanie L., Schoen, Robert E., Slattery, Martha L., Stadler, Zsofia K., Steinfelder, Robert S., Thibodeau, Stephen N., Ulrich, Cornelia M., Um, Caroline Y., van Duijnhoven, Franzel J.B., Van Guelpen, Bethany, Visvanathan, Kala, Vodicka, Pavel, Vodickova, Ludmila, Vymetalkova, Veronika, Weinstein, Stephanie J., White, Emily, Winship, Ingrid M., Wolk, Alicja, Gruber, Stephen B., Jenkins, Mark A., Mahmood, Khalid, Thomas, Minta, Qu, Conghui, Hsu, Li, Buchanan, Daniel D., and Peters, Ulrike

Published
2023
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46. Two genome-wide interaction loci modify the association of nonsteroidal anti-inflammatory drugs with colorectal cancer

Author

Drew, David A., primary, Kim, Andre E., additional, Lin, Yi, additional, Qu, Conghui, additional, Morrison, John, additional, Lewinger, Juan Pablo, additional, Kawaguchi, Eric, additional, Wang, Jun, additional, Fu, Yubo, additional, Zemlianskaia, Natalia, additional, Díez-Obrero, Virginia, additional, Bien, Stephanie A., additional, Dimou, Niki, additional, Albanes, Demetrius, additional, Baurley, James W., additional, Wu, Anna H., additional, Buchanan, Daniel D., additional, Potter, John D., additional, Prentice, Ross L., additional, Harlid, Sophia, additional, Arndt, Volker, additional, Barry, Elizabeth L., additional, Berndt, Sonja I., additional, Bouras, Emmanouil, additional, Brenner, Hermann, additional, Budiarto, Arif, additional, Burnett-Hartman, Andrea, additional, Campbell, Peter T., additional, Carreras-Torres, Robert, additional, Casey, Graham, additional, Chang-Claude, Jenny, additional, Conti, David V., additional, Devall, Matthew A.M., additional, Figueiredo, Jane C., additional, Gruber, Stephen B., additional, Gsur, Andrea, additional, Gunter, Marc J., additional, Harrison, Tabitha A., additional, Hidaka, Akihisa, additional, Hoffmeister, Michael, additional, Huyghe, Jeroen R., additional, Jenkins, Mark A., additional, Jordahl, Kristina M., additional, Kundaje, Anshul, additional, Le Marchand, Loic, additional, Li, Li, additional, Lynch, Brigid M., additional, Murphy, Neil, additional, Nassir, Rami, additional, Newcomb, Polly A., additional, Newton, Christina C., additional, Obón-Santacana, Mireia, additional, Ogino, Shuji, additional, Ose, Jennifer, additional, Pai, Rish K., additional, Palmer, Julie R., additional, Papadimitriou, Nikos, additional, Pardamean, Bens, additional, Pellatt, Andrew J., additional, Peoples, Anita R., additional, Platz, Elizabeth A., additional, Rennert, Gad, additional, Ruiz-Narvaez, Edward, additional, Sakoda, Lori C., additional, Scacheri, Peter C., additional, Schmit, Stephanie L., additional, Schoen, Robert E., additional, Stern, Mariana C., additional, Su, Yu-Ru, additional, Thomas, Duncan C., additional, Tian, Yu, additional, Tsilidis, Konstantinos K., additional, Ulrich, Cornelia M., additional, Um, Caroline Y., additional, van Duijnhoven, Fränzel J.B., additional, Van Guelpen, Bethany, additional, White, Emily, additional, Hsu, Li, additional, Moreno, Victor, additional, Peters, Ulrike, additional, Chan, Andrew T., additional, and Gauderman, W. James, additional

Published
2024
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47. Supplementary Table S1 from Use of Deep Learning to Evaluate Tumor Microenvironmental Features for Prediction of Colon Cancer Recurrence

Author

Sinicrope, Frank A., primary, Nelson, Garth D., primary, Saberzadeh-Ardestani, Bahar, primary, Segovia, Diana I., primary, Graham, Rondell P., primary, Wu, Christina, primary, Hagen, Catherine E., primary, Shivji, Sameer, primary, Savage, Paul, primary, Buchanan, Dan D., primary, Jenkins, Mark A., primary, Phipps, Amanda I., primary, Swallow, Carol, primary, LeMarchand, Loic, primary, Gallinger, Steven, primary, Grant, Robert C., primary, Pai, Reetesh K., primary, Sinicrope, Stephen N., primary, Yan, Dongyao, primary, Shanmugam, Kandavel, primary, Conner, James, primary, Cyr, David P., primary, Kirsch, Richard, primary, Banerjee, Imon, primary, Alberts, Steve R., primary, Shi, Qian, primary, and Pai, Rish K., primary

Published
2024
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48. TABLE 2 from Use of Deep Learning to Evaluate Tumor Microenvironmental Features for Prediction of Colon Cancer Recurrence

Author

Sinicrope, Frank A., primary, Nelson, Garth D., primary, Saberzadeh-Ardestani, Bahar, primary, Segovia, Diana I., primary, Graham, Rondell P., primary, Wu, Christina, primary, Hagen, Catherine E., primary, Shivji, Sameer, primary, Savage, Paul, primary, Buchanan, Dan D., primary, Jenkins, Mark A., primary, Phipps, Amanda I., primary, Swallow, Carol, primary, LeMarchand, Loic, primary, Gallinger, Steven, primary, Grant, Robert C., primary, Pai, Reetesh K., primary, Sinicrope, Stephen N., primary, Yan, Dongyao, primary, Shanmugam, Kandavel, primary, Conner, James, primary, Cyr, David P., primary, Kirsch, Richard, primary, Banerjee, Imon, primary, Alberts, Steve R., primary, Shi, Qian, primary, and Pai, Rish K., primary

Published
2024
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49. FIGURE 2 from Use of Deep Learning to Evaluate Tumor Microenvironmental Features for Prediction of Colon Cancer Recurrence

Author

Sinicrope, Frank A., primary, Nelson, Garth D., primary, Saberzadeh-Ardestani, Bahar, primary, Segovia, Diana I., primary, Graham, Rondell P., primary, Wu, Christina, primary, Hagen, Catherine E., primary, Shivji, Sameer, primary, Savage, Paul, primary, Buchanan, Dan D., primary, Jenkins, Mark A., primary, Phipps, Amanda I., primary, Swallow, Carol, primary, LeMarchand, Loic, primary, Gallinger, Steven, primary, Grant, Robert C., primary, Pai, Reetesh K., primary, Sinicrope, Stephen N., primary, Yan, Dongyao, primary, Shanmugam, Kandavel, primary, Conner, James, primary, Cyr, David P., primary, Kirsch, Richard, primary, Banerjee, Imon, primary, Alberts, Steve R., primary, Shi, Qian, primary, and Pai, Rish K., primary

Published
2024
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50. FIGURE 1 from Use of Deep Learning to Evaluate Tumor Microenvironmental Features for Prediction of Colon Cancer Recurrence

Author

Sinicrope, Frank A., primary, Nelson, Garth D., primary, Saberzadeh-Ardestani, Bahar, primary, Segovia, Diana I., primary, Graham, Rondell P., primary, Wu, Christina, primary, Hagen, Catherine E., primary, Shivji, Sameer, primary, Savage, Paul, primary, Buchanan, Dan D., primary, Jenkins, Mark A., primary, Phipps, Amanda I., primary, Swallow, Carol, primary, LeMarchand, Loic, primary, Gallinger, Steven, primary, Grant, Robert C., primary, Pai, Reetesh K., primary, Sinicrope, Stephen N., primary, Yan, Dongyao, primary, Shanmugam, Kandavel, primary, Conner, James, primary, Cyr, David P., primary, Kirsch, Richard, primary, Banerjee, Imon, primary, Alberts, Steve R., primary, Shi, Qian, primary, and Pai, Rish K., primary

Published
2024
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