Search

Your search keyword '"Chan, Andrew"' showing total 4,495 results
Start Over Author "Chan, Andrew" Search Limiters Full Text
4,495 results on '"Chan, Andrew"'

1. More than a piece of cake: Noun classifier processing in primary progressive aphasia

Author

Tee, Boon Lead, Li‐Ying, Lorinda Kwan‐Chen, Chen, Ta‐Fu, Yan, Connie TY, Tsoh, Joshua, Chan, Andrew Lung‐Tat, Wong, Adrian, Lo, Raymond Y, Lu, Chien Jung, Sun, Yu, Wang, Pei‐Ning, Lee, YiChen, Chiu, Ming‐Jang, Allen, Isabel Elaine, Battistella, Giovanni, Bak, Thomas H, Chuang, Yu‐Chen, García, Adolfo M, and Gorno‐Tempini, Maria Luisa

Subjects
Biological Psychology, Cognitive and Computational Psychology, Psychology, Frontotemporal Dementia (FTD), Neurodegenerative, Brain Disorders, Dementia, Clinical Research, Aphasia, Aging, Acquired Cognitive Impairment, 2.1 Biological and endogenous factors, Aetiology, Humans, Aphasia, Primary Progressive, Language, Gray Matter, Cerebral Cortex, Chinese language, lemma, lexical syntactic attributes, noun classifier, primary progressive aphasia, Clinical Sciences, Neurosciences, Geriatrics, Clinical sciences, Biological psychology
Abstract

IntroductionClinical understanding of primary progressive aphasia (PPA) has been primarily derived from Indo-European languages. Generalizing certain linguistic findings across languages is unfitting due to contrasting linguistic structures. While PPA patients showed noun classes impairments, Chinese languages lack noun classes. Instead, Chinese languages are classifier language, and how PPA patients manipulate classifiers is unknown.MethodsWe included 74 native Chinese speakers (22 controls, 52 PPA). For classifier production task, participants were asked to produce the classifiers of high-frequency items. In a classifier recognition task, participants were asked to choose the correct classifier.ResultsBoth semantic variant (sv) PPA and logopenic variant (lv) PPA scored significantly lower in classifier production task. In classifier recognition task, lvPPA patients outperformed svPPA patients. The classifier production scores were correlated to cortical volume over left temporal and visual association cortices.DiscussionThis study highlights noun classifiers as linguistic markers to discriminate PPA syndromes in Chinese speakers.HighlightsNoun classifier processing varies in the different primary progressive aphasia (PPA) variants. Specifically, semantic variant PPA (svPPA) and logopenic variant PPA (lvPPA) patients showed significantly lower ability in producing specific classifiers. Compared to lvPPA, svPPA patients were less able to choose the accurate classifiers when presented with choices. In svPPA, classifier production score was positively correlated with gray matter volume over bilateral temporal and left visual association cortices in svPPA. Conversely, classifier production performance was correlated with volumetric changes over left ventral temporal and bilateral frontal regions in lvPPA. Comparable performance of mass and count classifier were noted in Chinese PPA patients, suggesting a common cognitive process between mass and count classifiers in Chinese languages.

Published
2024

2. Anytime, Anywhere, Anyone: Investigating the Feasibility of Segment Anything Model for Crowd-Sourcing Medical Image Annotations

Author

Kulkarni, Pranav, Kanhere, Adway, Savani, Dharmam, Chan, Andrew, Chatterjee, Devina, Yi, Paul H., and Parekh, Vishwa S.

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

Curating annotations for medical image segmentation is a labor-intensive and time-consuming task that requires domain expertise, resulting in "narrowly" focused deep learning (DL) models with limited translational utility. Recently, foundation models like the Segment Anything Model (SAM) have revolutionized semantic segmentation with exceptional zero-shot generalizability across various domains, including medical imaging, and hold a lot of promise for streamlining the annotation process. However, SAM has yet to be evaluated in a crowd-sourced setting to curate annotations for training 3D DL segmentation models. In this work, we explore the potential of SAM for crowd-sourcing "sparse" annotations from non-experts to generate "dense" segmentation masks for training 3D nnU-Net models, a state-of-the-art DL segmentation model. Our results indicate that while SAM-generated annotations exhibit high mean Dice scores compared to ground-truth annotations, nnU-Net models trained on SAM-generated annotations perform significantly worse than nnU-Net models trained on ground-truth annotations ($p<0.001$, all).

Published
2024

3. Hidden in Plain Sight: Undetectable Adversarial Bias Attacks on Vulnerable Patient Populations

Author

Kulkarni, Pranav, Chan, Andrew, Navarathna, Nithya, Chan, Skylar, Yi, Paul H., and Parekh, Vishwa S.

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

The proliferation of artificial intelligence (AI) in radiology has shed light on the risk of deep learning (DL) models exacerbating clinical biases towards vulnerable patient populations. While prior literature has focused on quantifying biases exhibited by trained DL models, demographically targeted adversarial bias attacks on DL models and its implication in the clinical environment remains an underexplored field of research in medical imaging. In this work, we demonstrate that demographically targeted label poisoning attacks can introduce undetectable underdiagnosis bias in DL models. Our results across multiple performance metrics and demographic groups like sex, age, and their intersectional subgroups show that adversarial bias attacks demonstrate high-selectivity for bias in the targeted group by degrading group model performance without impacting overall model performance. Furthermore, our results indicate that adversarial bias attacks result in biased DL models that propagate prediction bias even when evaluated with external datasets., Comment: 29 pages, 4 figures

Published
2024

5. Strain-specific gut microbial signatures in type 2 diabetes identified in a cross-cohort analysis of 8,117 metagenomes

Author

Mei, Zhendong, Wang, Fenglei, Bhosle, Amrisha, Dong, Danyue, Mehta, Raaj, Ghazi, Andrew, Zhang, Yancong, Liu, Yuxi, Rinott, Ehud, Ma, Siyuan, Rimm, Eric B., Daviglus, Martha, Willett, Walter C., Knight, Rob, Hu, Frank B., Qi, Qibin, Chan, Andrew T., Burk, Robert D., Stampfer, Meir J., Shai, Iris, Kaplan, Robert C., Huttenhower, Curtis, and Wang, Dong D.

Published
2024
Full Text
View/download PDF

6. 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
Full Text
View/download PDF

8. Genome-wide interaction analysis of folate for colorectal cancer risk.

Author

Bouras, Emmanouil, Kim, Andre, Lin, Yi, Morrison, John, Du, Mengmeng, Albanes, Demetrius, Barry, Elizabeth, Baurley, James, Berndt, Sonja, Bien, Stephanie, Bishop, Timothy, Brenner, Hermann, Budiarto, Arif, Burnett-Hartman, Andrea, Campbell, Peter, Carreras-Torres, Robert, Casey, Graham, Cenggoro, Tjeng, Chan, Andrew, Chang-Claude, Jenny, Conti, David, Cotterchio, Michelle, Devall, Matthew, Diez-Obrero, Virginia, Dimou, Niki, Drew, David, Figueiredo, Jane, Giles, Graham, Gruber, Stephen, Gunter, Marc, Harrison, Tabitha, Hidaka, Akihisa, Hoffmeister, Michael, Huyghe, Jeroen, Joshi, Amit, Kawaguchi, Eric, Keku, Temitope, Kundaje, Anshul, Le Marchand, Loic, Lewinger, Juan, Li, Li, Lynch, Brigid, Mahesworo, Bharuno, Männistö, Satu, Moreno, Victor, Murphy, Neil, Newcomb, Polly, Obón-Santacana, Mireia, Ose, Jennifer, Palmer, Julie, Papadimitriou, Nikos, Pardamean, Bens, Pellatt, Andrew, Peoples, Anita, Platz, Elizabeth, Potter, John, Qi, Lihong, Qu, Conghui, Rennert, Gad, Ruiz-Narvaez, Edward, Sakoda, Lori, Schmit, Stephanie, Shcherbina, Anna, Stern, Mariana, Su, Yu-Ru, Tangen, Catherine, Thomas, Duncan, Tian, Yu, Um, Caroline, van Duijnhoven, Franzel, Van Guelpen, Bethany, Visvanathan, Kala, Wang, Jun, White, Emily, Wolk, Alicja, Woods, Michael, Ulrich, Cornelia, Hsu, Li, Gauderman, W, Peters, Ulrike, and Tsilidis, Konstantinos

Subjects
CRC, European, GWIS, SYN2, TIMP4, colorectal cancer, folate, folic acid, genome-wide, interaction, synapsin, tissue inhibitor of metalloproteinase 4, Humans, Folic Acid, Risk Factors, Colorectal Neoplasms, Case-Control Studies, Dietary Supplements
Abstract

BACKGROUND: Epidemiological and experimental evidence suggests that higher folate intake is associated with decreased colorectal cancer (CRC) risk; however, the mechanisms underlying this relationship are not fully understood. Genetic variation that may have a direct or indirect impact on folate metabolism can provide insights into folates role in CRC. OBJECTIVES: Our aim was to perform a genome-wide interaction analysis to identify genetic variants that may modify the association of folate on CRC risk. METHODS: We applied traditional case-control logistic regression, joint 3-degree of freedom, and a 2-step weighted hypothesis approach to test the interactions of common variants (allele frequency >1%) across the genome and dietary folate, folic acid supplement use, and total folate in relation to risk of CRC in 30,550 cases and 42,336 controls from 51 studies from 3 genetic consortia (CCFR, CORECT, GECCO). RESULTS: Inverse associations of dietary, total folate, and folic acid supplement with CRC were found (odds ratio [OR]: 0.93; 95% confidence interval [CI]: 0.90, 0.96; and 0.91; 95% CI: 0.89, 0.94 per quartile higher intake, and 0.82 (95% CI: 0.78, 0.88) for users compared with nonusers, respectively). Interactions (P-interaction < 5×10-8) of folic acid supplement and variants in the 3p25.2 locus (in the region of Synapsin II [SYN2]/tissue inhibitor of metalloproteinase 4 [TIMP4]) were found using traditional interaction analysis, with variant rs150924902 (located upstream to SYN2) showing the strongest interaction. In stratified analyses by rs150924902 genotypes, folate supplementation was associated with decreased CRC risk among those carrying the TT genotype (OR: 0.82; 95% CI: 0.79, 0.86) but increased CRC risk among those carrying the TA genotype (OR: 1.63; 95% CI: 1.29, 2.05), suggesting a qualitative interaction (P-interaction = 1.4×10-8). No interactions were observed for dietary and total folate. CONCLUSIONS: Variation in 3p25.2 locus may modify the association of folate supplement with CRC risk. Experimental studies and studies incorporating other relevant omics data are warranted to validate this finding.

Published
2023

9. The Development of Ofatumumab, a Fully Human Anti-CD20 Monoclonal Antibody for Practical Use in Relapsing Multiple Sclerosis Treatment.

Author

Kappos, Ludwig, Bar-Or, Amit, Wiendl, Heinz, Paling, David, Williams, Mitzi, Gold, Ralf, Chan, Andrew, Milo, Ron, Das Gupta, Ayan, Karlsson, Goeril, Sullivan, Roseanne, Graham, Gordon, Merschhemke, Martin, Häring, Dieter, Vermersch, Patrick, and Hauser, Stephen

Subjects
ALITHIOS, ASCLEPIOS I/II, Anti-CD20 monoclonal antibody, Benefit-risk, Ofatumumab, Relapsing multiple sclerosis, Self-administration, Subcutaneous
Abstract

The importance of B cells in multiple sclerosis (MS) has been demonstrated through the advent of B-cell-depleting anti-CD20 antibody therapies. Ofatumumab is the first fully human anti-CD20 monoclonal antibody (mAb) developed and tested for subcutaneous (SC) self-administration at monthly doses of 20 mg, and has been approved in the US, UK, EU, and other regions and countries worldwide for the treatment of relapsing MS. The development goal of ofatumumab was to obtain a highly efficacious anti-CD20 therapy, with a safety and tolerability profile that allows for self-administration by MS patients at home and a positive benefit-risk balance for use in the broad relapsing MS population. This development goal was enabled by the unique binding site, higher affinity to B cells, and higher potency of ofatumumab compared to previous anti-CD20 mAbs; these properties of ofatumumab facilitate rapid B-cell depletion and maintenance with a low dose at a low injection volume (20 mg/0.4 ml). The high potency in turn enables the selective targeting of B cells that reside in the lymphatic system via subcutaneous (SC) administration. Through a comprehensive dose-finding program in two phase 2 studies (one intravenous and one SC) and model simulations, it was found that safety and tolerability can be further improved, and the risk of systemic injection-related reactions (IRRs) minimized, by avoiding doses ≥ 30 mg, and by reaching initial and rapid B-cell depletion via stepwise weekly administration of ofatumumab at Weeks 0, 1, and 2 (instead of a single high dose). Once near-complete B-cell depletion is reached, it can be maintained by monthly doses of 20 mg/0.4 ml. Indeed, in phase 3 trials (ASCLEPIOS I/II), rapid and sustained near-complete B-cell depletion (largely independent of body weight, race and other factors) was observed with this dosing regimen, which resulted in superior efficacy of ofatumumab versus teriflunomide on relapse rates, disability worsening, neuronal injury (serum neurofilament light chain), and imaging outcomes. Likely due to its fully human nature, ofatumumab has a low immunogenic risk profile-only 2 of 914 patients receiving ofatumumab in ASCLEPIOS I/II developed anti-drug antibodies-and this may also underlie the infrequent IRRs (20% with ofatumumab vs. 15% with the placebo injection in the teriflunomide arm) that were mostly (99.8%) mild to moderate in severity. The overall rates of infections and serious infections in patients treated with ofatumumab were similar to those in patients treated with teriflunomide (51.6% vs. 52.7% and 2.5% vs. 1.8%, respectively). The benefit-risk profile of ofatumumab was favorable compared to teriflunomide in the broad RMS population, and also in the predefined subgroups of both recently diagnosed and/or treatment-naïve patients, as well as previously disease-modifying therapy-treated patients. Interim data from the ongoing extension study (ALITHIOS) have shown that long-term treatment with ofatumumab up to 4 years is well-tolerated in RMS patients, with no new safety risks identified. In parallel to the phase 3 trials in which SC administration was carried out with a pre-filled syringe, an autoinjector pen for more convenient self-administration of the ofatumumab 20 mg dose was developed and is available for use in clinical practice.

Published
2023

10. Computationally designed Spike antigens induce neutralising responses against the breadth of SARS-COV-2 variants

Author

Vishwanath, Sneha, Carnell, George William, Billmeier, Martina, Ohlendorf, Luis, Neckermann, Patrick, Asbach, Benedikt, George, Charlotte, Sans, Maria Suau, Chan, Andrew, Olivier, Joey, Nadesalingam, Angalee, Einhauser, Sebastian, Temperton, Nigel, Cantoni, Diego, Grove, Joe, Jordan, Ingo, Sandig, Volker, Tonks, Paul, Geiger, Johannes, Dohmen, Christian, Mummert, Verena, Samuel, Anne Rosalind, Plank, Christian, Kinsley, Rebecca, Wagner, Ralf, and Heeney, Jonathan Luke

Published
2024
Full Text
View/download PDF

11. Calcium intake and genetic variants in the calcium sensing receptor in relation to colorectal cancer mortality: an international consortium study of 18,952 patients

Author

Wesselink, Evertine, Gauderman, William, Berndt, Sonja I., Brenner, Hermann, Buchanan, Daniel D., Campbell, Peter T., Chan, Andrew T., Chang-Claude, Jenny, Cotterchoi, Michelle, Gunter, Marc J., Hoffmeister, Michael, Joshi, Amit D., Newton, Christina C., Pai, Rish K., Pellatt, Andrew J., Phipps, Amanda I., Song, Mingyang, Um, Caroline Y., van Guelpen, Bethany, White, Emily, Peters, Ulrike, and van Duijnhoven, Fränzel J. B.

Published
2024
Full Text
View/download PDF

15. 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
Full Text
View/download PDF

16. Germline genetic regulation of the colorectal tumor immune microenvironment

Author

Schmit, Stephanie L., Tsai, Ya-Yu, Bonner, Joseph D., Sanz-Pamplona, Rebeca, Joshi, Amit D., Ugai, Tomotaka, Lindsey, Sidney S., Melas, Marilena, McDonnell, Kevin J., Idos, Gregory E., Walker, Christopher P., Qu, Chenxu, Kast, W. Martin, Da Silva, Diane M., Glickman, Jonathan N., Chan, Andrew T., Giannakis, Marios, Nowak, Jonathan A., Rennert, Hedy S., Robins, Harlan S., Ogino, Shuji, Greenson, Joel K., Moreno, Victor, Rennert, Gad, and Gruber, Stephen B.

Published
2024
Full Text
View/download PDF

17. Circulating markers of microbial translocation and host response to bacteria with risk of colorectal cancer: a prospective, nested case-control study in men

Author

Shi, Mengyao, Zong, Xiaoyu, Hur, Jinhee, Birmann, Brenda M, Martinez-Maza, Otoniel, Epeldegui, Marta, Chan, Andrew T, Giovannucci, Edward L, and Cao, Yin

Subjects
Epidemiology, Biomedical and Clinical Sciences, Health Sciences, Infectious Diseases, Digestive Diseases, Colo-Rectal Cancer, Clinical Research, Prevention, Cancer, Aetiology, 2.2 Factors relating to the physical environment, Detection, screening and diagnosis, 2.1 Biological and endogenous factors, 4.1 Discovery and preclinical testing of markers and technologies, Infection, Male, Humans, Prospective Studies, Case-Control Studies, Follow-Up Studies, Lipopolysaccharide Receptors, Risk Factors, Bacteria, Immunoglobulin M, Colorectal Neoplasms, Colorectal cancer, Microbial translocation, Gut dysbiosis, Clinical Sciences, Public Health and Health Services, Clinical sciences
Abstract

BackgroundGut microbial dysbiosis contributes to colorectal cancer (CRC) pathogenesis, possibly mediated in part by increased intestinal permeability to endotoxin lipopolysaccharide (LPS), microbial translocation, and subsequent endotoxemia and inflammation. However, epidemiologic evidence linking circulating markers of microbial translocation with CRC risk is limited.MethodsWe conducted a prospective, nested case-control study of 261 incident CRC cases and 261 controls (matched on age and time of blood draw) among 18,159 men with pre-diagnostic blood specimens in the Health Professionals Follow-Up Study (1993-2009). We examined three complementary markers of microbial translocation and host response to bacteria, including LPS-binding protein (LBP), soluble CD14 (sCD14), and endotoxincore antibody (EndoCAb) immunoglobulin M (IgM), with subsequent risk of CRC. Unconditional logistic regressions were used to estimate odds ratios (ORs) and 95% confidence intervals (CIs).FindingsPre-diagnostic circulating levels of sCD14 were associated with a higher risk of incident CRC. Compared to men in the lowest quartile, the multivariable OR was 1.90 (95% CI, 1.13-3.22) for men in the highest quartile (OR per standard deviation [SD] increase, 1.28; 95%CI 1.06-1.53; Ptrend = 0.01). This positive association remained similar after adjusting for C-reactive protein, interleukin-6, and soluble tumor necrosis factor receptor-2, and within strata of putative CRC risk factors. We also observed a suggestive inverse association between EndoCAb IgM and risk of CRC (OR per SD increase, 0.84; 95%CI 0.69-1.02; Ptrend = 0.09).InterpretationMicrobial translocation and host response to bacteria, as reflected by sCD14, is associated with risk of incident CRC in men.FundingUS National Institutes of Health.

Published
2023

18. Author Correction: SLC6A20 transporter: a novel regulator of brain glycine homeostasis and NMDAR function

Author

Bae, Mihyun, Roh, Junyeop Daniel, Kim, Youjoung, Kim, Seong Soon, Han, Hye Min, Yang, Esther, Kang, Hyojin, Lee, Suho, Kim, Jin Yong, Kang, Ryeonghwa, Jung, Hwajin, Yoo, Taesun, Kim, Hyosang, Kim, Doyoun, Oh, Heejeong, Han, Sungwook, Kim, Dayeon, Han, Jinju, Bae, Yong Chul, Kim, Hyun, Ahn, Sunjoo, Chan, Andrew M, Lee, Daeyoup, Kim, Jin Woo, and Kim, Eunjoon

Published
2024
Full Text
View/download PDF

21. Modification of the Association Between Frequent Aspirin Use and Ovarian Cancer Risk: A Meta-Analysis Using Individual-Level Data From Two Ovarian Cancer Consortia

Author

Hurwitz, Lauren M, Townsend, Mary K, Jordan, Susan J, Patel, Alpa V, Teras, Lauren R, Lacey, James V, Doherty, Jennifer A, Harris, Holly R, Goodman, Marc T, Shvetsov, Yurii B, Modugno, Francesmary, Moysich, Kirsten B, Robien, Kim, Prizment, Anna, Schildkraut, Joellen M, Berchuck, Andrew, Fortner, Renée T, Chan, Andrew T, Wentzensen, Nicolas, Hartge, Patricia, Sandler, Dale P, O'Brien, Katie M, Anton-Culver, Hoda, Ziogas, Argyrios, Menon, Usha, Ramus, Susan J, Pearce, Celeste Leigh, Wu, Anna H, White, Emily, Peters, Ulrike, Webb, Penelope M, Tworoger, Shelley S, and Trabert, Britton

Subjects
Biomedical and Clinical Sciences, Oncology and Carcinogenesis, Prevention, Cancer, Patient Safety, Clinical Research, Ovarian Cancer, Rare Diseases, Breast Cancer, 3.3 Nutrition and chemoprevention, Prevention of disease and conditions, and promotion of well-being, Female, Humans, Aspirin, Endometriosis, Ovarian Neoplasms, Case-Control Studies, Risk Factors, Clinical Sciences, Oncology & Carcinogenesis, Oncology and carcinogenesis
Abstract

PurposeFrequent aspirin use has been associated with reduced ovarian cancer risk, but no study has comprehensively assessed for effect modification. We leveraged harmonized, individual-level data from 17 studies to examine the association between frequent aspirin use and ovarian cancer risk, overall and across subgroups of women with other ovarian cancer risk factors.MethodsNine cohort studies from the Ovarian Cancer Cohort Consortium (n = 2,600 cases) and eight case-control studies from the Ovarian Cancer Association Consortium (n = 5,726 cases) were included. We used Cox regression and logistic regression to assess study-specific associations between frequent aspirin use (≥ 6 days/week) and ovarian cancer risk and combined study-specific estimates using random-effects meta-analysis. We conducted analyses within subgroups defined by individual ovarian cancer risk factors (endometriosis, obesity, family history of breast/ovarian cancer, nulliparity, oral contraceptive use, and tubal ligation) and by number of risk factors (0, 1, and ≥ 2).ResultsOverall, frequent aspirin use was associated with a 13% reduction in ovarian cancer risk (95% CI, 6 to 20), with no significant heterogeneity by study design (P = .48) or histotype (P = .60). Although no association was observed among women with endometriosis, consistent risk reductions were observed among all other subgroups defined by ovarian cancer risk factors (relative risks ranging from 0.79 to 0.93, all P-heterogeneity > .05), including women with ≥ 2 risk factors (relative risk, 0.81; 95% CI, 0.73 to 0.90).ConclusionThis study, the largest to-date on aspirin use and ovarian cancer, provides evidence that frequent aspirin use is associated with lower ovarian cancer risk regardless of the presence of most other ovarian cancer risk factors. Risk reductions were also observed among women with multiple risk factors, providing proof of principle that chemoprevention programs with frequent aspirin use could target higher-risk subgroups.

Published
2022

22. How people wake up is associated with previous night's sleep together with physical activity and food intake.

Author

Vallat, Raphael, Berry, Sarah E, Tsereteli, Neli, Capdevila, Joan, Khatib, Haya Al, Valdes, Ana M, Delahanty, Linda M, Drew, David A, Chan, Andrew T, Wolf, Jonathan, Franks, Paul W, Spector, Tim D, and Walker, Matthew P

Subjects
Humans, Exercise, Longitudinal Studies, Prospective Studies, Sleep, Eating, Adult, Sleep Research, Behavioral and Social Science, Clinical Research
Abstract

How people wake up and regain alertness in the hours after sleep is related to how they are sleeping, eating, and exercising. Here, in a prospective longitudinal study of 833 twins and genetically unrelated adults, we demonstrate that how effectively an individual awakens in the hours following sleep is not associated with their genetics, but instead, four independent factors: sleep quantity/quality the night before, physical activity the day prior, a breakfast rich in carbohydrate, and a lower blood glucose response following breakfast. Furthermore, an individual's set-point of daily alertness is related to the quality of their sleep, their positive emotional state, and their age. Together, these findings reveal a set of non-genetic (i.e., not fixed) factors associated with daily alertness that are modifiable.

Published
2022

23. 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

24. Is the Centers for Medicare and Medicaid Services Hierarchical Condition Category Risk Adjustment Model Satisfactory for Quantifying Risk After Spine Surgery?

Author

Chan, Andrew K, Shahrestani, Shane, Ballatori, Alexander M, Orrico, Katie O, Manley, Geoffrey T, Tarapore, Phiroz E, Huang, Michael, Dhall, Sanjay S, Chou, Dean, Mummaneni, Praveen V, and DiGiorgio, Anthony M

Subjects
Humans, Length of Stay, Spinal Fusion, Aged, Medicare, Risk Adjustment, United States, Centers for Medicare and Medicaid Services, U.S., Clinical Research, Digestive Diseases, Prevention, Health Services, Rare Diseases, Behavioral and Social Science, Good Health and Well Being, Centers for Medicare and Medicaid, Hierarchical condition category, Risk stratification, Spine surgery, Clinical Sciences, Neurosciences, Neurology & Neurosurgery
Abstract

BackgroundThe Centers for Medicare and Medicaid Services (CMS) hierarchical condition category (HCC) coding is a risk adjustment model that allows for the estimation of risk-and cost-associated with health care provision. Current models may not include key factors that fully delineate the risk associated with spine surgery.ObjectiveTo augment CMS HCC risk adjustment methodology with socioeconomic data to improve its predictive capabilities for spine surgery.MethodsThe National Inpatient Sample was queried for spinal fusion, and the data was merged with county-level coverage and socioeconomic status variables obtained from the Brookings Institute. We predicted outcomes (death, nonroutine discharge, length of stay [LOS], total charges, and perioperative complication) with pairs of hierarchical, mixed effects logistic regression models-one using CMS HCC score alone and another augmenting CMS HCC scores with demographic and socioeconomic status variables. Models were compared using receiver operating characteristic curves. Variable importance was assessed in conjunction with Wald testing for model optimization.ResultsWe analyzed 653 815 patients. Expanded models outperformed models using CMS HCC score alone for mortality, nonroutine discharge, LOS, total charges, and complications. For expanded models, variable importance analyses demonstrated that CMS HCC score was of chief importance for models of mortality, LOS, total charges, and complications. For the model of nonroutine discharge, age was the most important variable. For the model of total charges, unemployment rate was nearly as important as CMS HCC score.ConclusionThe addition of key demographic and socioeconomic characteristics substantially improves the CMS HCC risk-adjustment models when modeling spinal fusion outcomes. This finding may have important implications for payers, hospitals, and policymakers.

Published
2022

27. 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
Full Text
View/download PDF

28. Dysgraphia Phenotypes in Native Chinese Speakers With Primary Progressive Aphasia

Author

Tee, Boon Lead, Lorinda Kwan-Chen, Li Ying, Chen, Ta-Fu, Yan, Connie TY, Tsoh, Joshua, Lung-Tat Chan, Andrew, Wong, Adrian, Lo, Raymond Y, Lu, Chien Long, Wang, Pei-Ning, Lee, YiChen, Yang, Fanpei G, Battistella, Giovanni, Allen, Isabel Elaine, Dronkers, Nina F, Miller, Bruce L, and Gorno-Tempini, Maria Luisa

Subjects
Biomedical and Clinical Sciences, Neurosciences, Clinical Sciences, Rare Diseases, Dementia, Brain Disorders, Acquired Cognitive Impairment, Aging, Neurodegenerative, Aphasia, Frontotemporal Dementia (FTD), Agraphia, Aphasia, Primary Progressive, China, Humans, Language, Phenotype, Primary Progressive Nonfluent Aphasia, Cognitive Sciences, Neurology & Neurosurgery, Clinical sciences
Abstract

Background and objectivesMost primary progressive aphasia (PPA) literature is based on English language users. Linguistic features that vary from English, such as logographic writing systems, are underinvestigated. The current study characterized the dysgraphia phenotypes of patients with PPA who write in Chinese and investigated their diagnostic utility in classifying PPA variants.MethodsThis study recruited 40 participants with PPA and 20 cognitively normal participants from San Francisco, Hong Kong, and Taiwan. We measured dictation accuracy using the Chinese Language Assessment for PPA (CLAP) 60-character orthographic dictation test and examined the occurrence of various writing errors across the study groups. We also performed voxel-based morphometry analysis to identify the gray matter regions correlated with dictation accuracy and prevalence of writing errors.ResultsAll PPA groups produced significantly less accurate writing responses than the control group and no significant differences in dictation accuracy were noted among the PPA variants. With a cut score of 36 out of 60 in the CLAP orthographic dictation task, the test achieved sensitivity and specificity of 90% and 95% in identifying Chinese participants with PPA vs controls. In addition to a character frequency effect, dictation accuracy was affected by homophone density and the number of strokes in semantic variant PPA and logopenic variant PPA groups. Dictation accuracy was correlated with volumetric changes over left ventral temporal cortices, regions known to be critical for orthographic long-term memory. Individuals with semantic variant PPA frequently presented with phonologically plausible errors at lexical level, patients with logopenic variant PPA showed higher preponderance towards visual and stroke errors, and patients with nonfluent/agrammatic variant PPA commonly exhibited compound word and radical errors. The prevalence of phonologically plausible, visual, and compound word errors was negatively correlated with cortical volume over the bilateral temporal regions, left temporo-occipital area, and bilateral orbitofrontal gyri, respectively.DiscussionThe findings demonstrate the potential role of the orthographic dictation task as a screening tool and PPA classification indicator in Chinese language users. Each PPA variant had specific Chinese dysgraphia phenotypes that vary from those previously reported in English-speaking patients with PPA, highlighting the importance of language diversity in PPA.

Published
2022

29. Non-collinear and strongly asymmetric polar moments at back-gated SrTiO3 interfaces

Author

Lyzwa, Fryderyk, Pashkevich, Yurii G., Marsik, Premysl, Sirenko, Andrei, Chan, Andrew, Mallett, Benjamin P. P., Yazdi-Rizi, Meghdad, Xu, Bing, Vicente-Arche, Luis M., Vaz, Diogo C., Herranz, Gervasi, Cazayous, Maximilien, Hemme, Pierre, Fürsich, Katrin, Minola, Matteo, Keimer, Bernhard, Bibes, Manuel, and Bernhard, Christian

Subjects
Condensed Matter - Materials Science
Abstract

The highly mobile electrons at the interface of SrTiO3 with other oxide insulators, such as LaAlO3 or AlOx, are of great current interest. A vertical gate voltage allows controlling a metal/superconductor-to-insulator transition, as well as electrical modulation of the spin-orbit Rashba coupling for spin-charge conversion. These findings raise important questions about the origin of the confined electrons as well as the mechanisms that govern the interfacial electric field. Here we use infrared ellipsometry and confocal Raman spectroscopy to show that an anomalous polar moment is induced at the interface that is non-collinear, highly asymmetric and hysteretic with respect to the vertical gate electric field. Our data indicate that an important role is played by the electromigration of oxygen vacancies and their clustering at the antiferrodistortive domain boundaries of SrTiO3, which generates local electric and possibly also flexoelectric fields and subsequent polar moments with a large lateral component. Our results open new perspectives for the defect engineering of lateral devices with strongly enhanced and hysteretic local electric fields that can be manipulated with various other parameters, like strain, temperature, or photons.

Published
2021
Full Text
View/download PDF

30. Genome-wide interaction study of dietary intake of fibre, fruits, and vegetables with risk of colorectal cancer

Author

Papadimitriou, Nikos, Kim, Andre, Kawaguchi, Eric S., Morrison, John, Diez-Obrero, Virginia, Albanes, Demetrius, Berndt, Sonja I., Bézieau, Stéphane, Bien, Stephanie A., Bishop, D Timothy, Bouras, Emmanouil, Brenner, Hermann, Buchanan, Daniel D., Campbell, Peter T., Carreras-Torres, Robert, Chan, Andrew T., Chang-Claude, Jenny, Conti, David V., Devall, Matthew A., Dimou, Niki, Drew, David A., Gruber, Stephen B., Harrison, Tabitha A., Hoffmeister, Michael, Huyghe, Jeroen R., Joshi, Amit D., Keku, Temitope O., Kundaje, Anshul, Küry, Sébastien, Le Marchand, Loic, Lewinger, Juan Pablo, Li, Li, Lynch, Brigid M., Moreno, Victor, Newton, Christina C., Obón-Santacana, Mireia, Ose, Jennifer, Pellatt, Andrew J., Peoples, Anita R., Platz, Elizabeth A., Qu, Conghui, Rennert, Gad, Ruiz-Narvaez, Edward, Shcherbina, Anna, Stern, Mariana C., Su, Yu-Ru, Thomas, Duncan C., Thomas, Claire E., Tian, Yu, Tsilidis, Konstantinos K., Ulrich, Cornelia M., Um, Caroline Y., Visvanathan, Kala, Wang, Jun, White, Emily, Woods, Michael O., Schmit, Stephanie L., Macrae, Finlay, Potter, John D., Hopper, John L., Peters, Ulrike, Murphy, Neil, Hsu, Li, Gunter, Marc J., and Gauderman, W. James

Published
2024
Full Text
View/download PDF

35. 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
Full Text
View/download PDF

37. 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
Full Text
View/download PDF

38. Metagenomic assessment of gut microbial communities and risk of severe COVID-19

Author

Nguyen, Long H., Okin, Daniel, Drew, David A., Battista, Vincent M., Jesudasen, Sirus J., Kuntz, Thomas M., Bhosle, Amrisha, Thompson, Kelsey N., Reinicke, Trenton, Lo, Chun-Han, Woo, Jacqueline E., Caraballo, Alexander, Berra, Lorenzo, Vieira, Jacob, Huang, Ching-Ying, Das Adhikari, Upasana, Kim, Minsik, Sui, Hui-Yu, Magicheva-Gupta, Marina, McIver, Lauren, Goldberg, Marcia B., Kwon, Douglas S., Huttenhower, Curtis, Chan, Andrew T., and Lai, Peggy S.

Published
2023
Full Text
View/download PDF

40. Bayesian risk prediction model for colorectal cancer mortality through integration of clinicopathologic and genomic data

Author

Zhao, Melissa, Lau, Mai Chan, Haruki, Koichiro, Väyrynen, Juha P., Gurjao, Carino, Väyrynen, Sara A., Dias Costa, Andressa, Borowsky, Jennifer, Fujiyoshi, Kenji, Arima, Kota, Hamada, Tsuyoshi, Lennerz, Jochen K., Fuchs, Charles S., Nishihara, Reiko, Chan, Andrew T., Ng, Kimmie, Zhang, Xuehong, Meyerhardt, Jeffrey A., Song, Mingyang, Wang, Molin, Giannakis, Marios, Nowak, Jonathan A., Yu, Kun-Hsing, Ugai, Tomotaka, and Ogino, Shuji

Published
2023
Full Text
View/download PDF

42. 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
Full Text
View/download PDF

44. Histopathology images predict multi-omics aberrations and prognoses in colorectal cancer patients

Author

Tsai, Pei-Chen, Lee, Tsung-Hua, Kuo, Kun-Chi, Su, Fang-Yi, Lee, Tsung-Lu Michael, Marostica, Eliana, Ugai, Tomotaka, Zhao, Melissa, Lau, Mai Chan, Väyrynen, Juha P., Giannakis, Marios, Takashima, Yasutoshi, Kahaki, Seyed Mousavi, Wu, Kana, Song, Mingyang, Meyerhardt, Jeffrey A., Chan, Andrew T., Chiang, Jung-Hsien, Nowak, Jonathan, Ogino, Shuji, and Yu, Kun-Hsing

Published
2023
Full Text
View/download PDF

45. 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

46. DEWPython: A Python Implementation of the Deep Earth Water Model and Application to Ocean Worlds

Author

Chan, Andrew, Daswani, Mohit Melwani, and Vance, Steven

Subjects
Physics - Geophysics
Abstract

There are two main methods of calculating the thermodynamic properties of water and solutes: mass action (including the Helgeson-Kirkham-Flowers (HKF) equations of state and model) and Gibbs free energy minimization (e.g. Leal et al., 2016). However, in certain regions of pressure and temperature the HKF model inaccurately predicts the speciation and concentration of solutes (e.g. Miron et al., 2019). The Deep Earth Water (DEW) model uses a series of HKF-type equations to calculate the properties of water and solute concentrations at high temperatures (373 - 1473 K) and pressures (0.1 - 6 GPa) (e.g. Huang and Sverjensky, 2019; Pan et al., 2013; Sverjensky et al., 2014). The DEW model is synthesized in an Excel spreadsheet and calculates Gibbs energies of formation, equilibrium constants, and standard volume changes for reactions. Here we present an object-oriented Python implementation of the DEW model, called DEWPython. Our model expands on DEW by increasing model efficiency, streamlining the input process, and incorporating SUPCRT in-line. Additionally, our model builds in minerals and aqueous species from the thermodynamic database slop16.dat (Boyer, 2019) which would normally be calculated separately. We also present a set of reactions relevant to icy ocean world interiors calculated with the DEWPython. The favorability of these reactions indicates likely formation of certain organic species under extreme pressures relevant to ocean worlds., Comment: 18 pages, 5 figures, 1 table

Published
2021

50. Accessible Data Curation and Analytics for International-Scale Citizen Science Datasets

Author

Murray, Benjamin, Kerfoot, Eric, Graham, Mark S., Sudre, Carole H., Molteni, Erika, Canas, Liane S., Antonelli, Michela, Klaser, Kerstin, Visconti, Alessia, Chan, Andrew T., Franks, Paul W., Davies, Richard, Wolf, Jonathan, Spector, Tim, Steves, Claire J., Modat, Marc, and Ourselin, Sebastien

Subjects
Computer Science - Databases, Computer Science - Information Retrieval, D.m, E.2, H.3.3, I.7
Abstract

The Covid Symptom Study, a smartphone-based surveillance study on COVID-19 symptoms in the population, is an exemplar of big data citizen science. Over 4.7 million participants and 189 million unique assessments have been logged since its introduction in March 2020. The success of the Covid Symptom Study creates technical challenges around effective data curation for two reasons. Firstly, the scale of the dataset means that it can no longer be easily processed using standard software on commodity hardware. Secondly, the size of the research group means that replicability and consistency of key analytics used across multiple publications becomes an issue. We present ExeTera, an open source data curation software designed to address scalability challenges and to enable reproducible research across an international research group for datasets such as the Covid Symptom Study dataset.

Published
2020

Catalog

Books, media, physical & digital resources
See catalog results