897 results on '"Jensen, Matthew"'
Search Results
2. Microcalcifications in benign breast biopsies: association with lesion type and risk
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Schrup, Sarah, Hardway, Heather, Vierkant, Robert A., Winham, Stacey J., Jensen, Matthew R., McCauley, Bryan, Hoskin, Tanya, Seymour, Lisa, Gehling, Denice, Fischer, Jessica, Vachon, Celine M., Maimone, Santo, Pacheco-Spann, Laura, Radisky, Derek C., Carter, Jodi M., Degnim, Amy C., and Sherman, Mark E.
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- 2024
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3. Single-cell genomics and regulatory networks for 388 human brains.
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Emani, Prashant, Liu, Jason, Clarke, Declan, Jensen, Matthew, Warrell, Jonathan, Gupta, Chirag, Meng, Ran, Lee, Che Yu, Xu, Siwei, Dursun, Cagatay, Lou, Shaoke, Chen, Yuhang, Chu, Zhiyuan, Galeev, Timur, Hwang, Ahyeon, Li, Yunyang, Ni, Pengyu, Zhou, Xiao, Bakken, Trygve, Bendl, Jaroslav, Bicks, Lucy, Chatterjee, Tanima, Cheng, Lijun, Cheng, Yuyan, Dai, Yi, Duan, Ziheng, Flaherty, Mary, Fullard, John, Gancz, Michael, Garrido-Martín, Diego, Gaynor-Gillett, Sophia, Grundman, Jennifer, Hawken, Natalie, Henry, Ella, Hoffman, Gabriel, Huang, Ao, Jiang, Yunzhe, Jin, Ting, Jorstad, Nikolas, Kawaguchi, Riki, Khullar, Saniya, Liu, Jianyin, Liu, Junhao, Liu, Shuang, Ma, Shaojie, Margolis, Michael, Mazariegos, Samantha, Moore, Jill, Moran, Jennifer, Nguyen, Eric, Phalke, Nishigandha, Pjanic, Milos, Pratt, Henry, Quintero, Diana, Rajagopalan, Ananya, Riesenmy, Tiernon, Shedd, Nicole, Shi, Manman, Spector, Megan, Terwilliger, Rosemarie, Travaglini, Kyle, Wamsley, Brie, Wang, Gaoyuan, Xia, Yan, Xiao, Shaohua, Yang, Andrew, Zheng, Suchen, Gandal, Michael, Lee, Donghoon, Lein, Ed, Roussos, Panos, Sestan, Nenad, Weng, Zhiping, White, Kevin, Won, Hyejung, Girgenti, Matthew, Zhang, Jing, Wang, Daifeng, Geschwind, Daniel, and Gerstein, Mark
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Humans ,Aging ,Brain ,Cell Communication ,Chromatin ,Gene Regulatory Networks ,Genomics ,Mental Disorders ,Prefrontal Cortex ,Quantitative Trait Loci ,Single-Cell Analysis - Abstract
Single-cell genomics is a powerful tool for studying heterogeneous tissues such as the brain. Yet little is understood about how genetic variants influence cell-level gene expression. Addressing this, we uniformly processed single-nuclei, multiomics datasets into a resource comprising >2.8 million nuclei from the prefrontal cortex across 388 individuals. For 28 cell types, we assessed population-level variation in expression and chromatin across gene families and drug targets. We identified >550,000 cell type-specific regulatory elements and >1.4 million single-cell expression quantitative trait loci, which we used to build cell-type regulatory and cell-to-cell communication networks. These networks manifest cellular changes in aging and neuropsychiatric disorders. We further constructed an integrative model accurately imputing single-cell expression and simulating perturbations; the model prioritized ~250 disease-risk genes and drug targets with associated cell types.
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- 2024
4. Massively parallel characterization of regulatory elements in the developing human cortex
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Deng, Chengyu, Whalen, Sean, Steyert, Marilyn, Ziffra, Ryan, Przytycki, Pawel F, Inoue, Fumitaka, Pereira, Daniela A, Capauto, Davide, Norton, Scott, Vaccarino, Flora M, Pollen, Alex A, Nowakowski, Tomasz J, Ahituv, Nadav, Pollard, Katherine S, Akbarian, Schahram, Abyzov, Alexej, Arasappan, Dhivya, Almagro Armenteros, Jose Juan, Beliveau, Brian J, Bendl, Jaroslav, Berretta, Sabina, Bharadwaj, Rahul A, Bhattacharya, Arjun, Bicks, Lucy, Brennand, Kristen, Champagne, Frances A, Chatterjee, Tanima, Chatzinakos, Chris, Chen, Yuhang, Chen, H Isaac, Cheng, Yuyan, Cheng, Lijun, Chess, Andrew, Chien, Jo-fan, Chu, Zhiyuan, Clarke, Declan, Clement, Ashley, Collado-Torres, Leonardo, Cooper, Gregory M, Crawford, Gregory E, Dai, Rujia, Daskalakis, Nikolaos P, Davila-Velderrain, Jose, Deep-Soboslay, Amy, DiPietro, Christopher P, Dracheva, Stella, Drusinsky, Shiron, Duan, Ziheng, Duong, Duc, Dursun, Cagatay, Eagles, Nicholas J, Edelstein, Jonathan, Emani, Prashant S, Fullard, John F, Galani, Kiki, Galeev, Timur, Gandal, Michael J, Gaynor, Sophia, Gerstein, Mark, Geschwind, Daniel H, Girdhar, Kiran, Goes, Fernando S, Greenleaf, William, Grundman, Jennifer, Guo, Hanmin, Guo, Qiuyu, Gupta, Chirag, Hadas, Yoav, Hallmayer, Joachim, Han, Xikun, Haroutunian, Vahram, Hawken, Natalie, He, Chuan, Henry, Ella, Hicks, Stephanie C, Ho, Marcus, Ho, Li-Lun, Hoffman, Gabriel E, Huang, Yiling, Huuki-Myers, Louise A, Hwang, Ahyeon, Hyde, Thomas M, Iatrou, Artemis, Jajoo, Aarti, Jensen, Matthew, Jiang, Lihua, Jin, Peng, Jin, Ting, Jops, Connor, Jourdon, Alexandre, Kawaguchi, Riki, Kellis, Manolis, Khullar, Saniya, Kleinman, Joel E, Kleopoulos, Steven P, and Kozlenkov, Alex
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Biological Sciences ,Bioinformatics and Computational Biology ,Biomedical and Clinical Sciences ,Stem Cell Research - Embryonic - Human ,Stem Cell Research ,Human Genome ,Genetics ,Neurosciences ,Underpinning research ,Aetiology ,1.1 Normal biological development and functioning ,2.1 Biological and endogenous factors ,Neurological ,Humans ,Cerebral Cortex ,Chromatin ,Deep Learning ,Enhancer Elements ,Genetic ,Gene Expression Regulation ,Developmental ,Neurogenesis ,Neurons ,Organoids ,Regulatory Sequences ,Nucleic Acid ,Promoter Regions ,Genetic ,Regulatory Elements ,Transcriptional ,PsychENCODE Consortium‡ ,PsychENCODE Consortium ,General Science & Technology - Abstract
Nucleotide changes in gene regulatory elements are important determinants of neuronal development and diseases. Using massively parallel reporter assays in primary human cells from mid-gestation cortex and cerebral organoids, we interrogated the cis-regulatory activity of 102,767 open chromatin regions, including thousands of sequences with cell type-specific accessibility and variants associated with brain gene regulation. In primary cells, we identified 46,802 active enhancer sequences and 164 variants that alter enhancer activity. Activity was comparable in organoids and primary cells, suggesting that organoids provide an adequate model for the developing cortex. Using deep learning we decoded the sequence basis and upstream regulators of enhancer activity. This work establishes a comprehensive catalog of functional gene regulatory elements and variants in human neuronal development.
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- 2024
5. John Is No Exception: Identifying the Subject of εἰμί and Its Implications
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Jensen, Matthew D.
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- 2016
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6. Multivariate testing and effect size measures for batch effect evaluation in radiomic features
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Horng, Hannah, Scott, Christopher, Winham, Stacey, Jensen, Matthew, Pantalone, Lauren, Mankowski, Walter, Kerlikowske, Karla, Vachon, Celine M., Kontos, Despina, and Shinohara, Russell T.
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- 2024
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7. UNITED WE STAND, DIVIDED WE FALL: AN AUTOGENIC PERSPECTIVE ON EMPOWERING CYBERSECURITY IN ORGANIZATIONS.
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Durcikova, Alexandra, Miranda, Shaila M., Jensen, Matthew L., and Wright, Ryan T.
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Cybersecurity groups navigate complex, challenging environments in their mission to protect their organizations. They experience uncertainty from adaptive threats from external attackers and unpredictable stakeholders. Under such volatility, business groups operate best when they are psychologically empowered. Recognizing the potential for empowerment to reduce organizational risk, we sought to learn how cybersecurity groups come to be (dis)empowered and how this (dis)empowerment is sustained. Instead of the conventional view of the empowerment process as designed, we advance an emergent view of the empowerment process. We abductively surface this process from our case analyses of 15 U.S.organizations. We offer three insights: First, organizations with empowered cybersecurity groups enjoy an enhanced level of protection from breaches. Second, we highlight generative rules through which groups become empowered—via their bridging initiatives that co-opt stakeholders into security behaviors and stakeholder responsiveness to bridging, rather than unilaterally applied buffering initiatives. Third, we highlight reinforcing rules through which empowered states persist—via the group’s ability to safeguard organizational information assets, thereby ensuring cybersecurity group viability, continued bridging, and motivated stakeholder responsiveness. For practitioners, our study underscores the interdependence between cybersecurity groups and their stakeholders in securing an organization and posits processes for empowering cybersecurity groups. [ABSTRACT FROM AUTHOR]
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- 2024
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8. Mammographic Variation Measures, Breast Density, and Breast Cancer Risk.
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Heine, John, Fowler, Erin, Scott, Christopher G, Jensen, Matthew R, Shepherd, John, Hruska, Carrie B, Winham, Stacey J, Brandt, Kathleen R, Wu, Fang F, Norman, Aaron D, Pankratz, Vernon S, Miglioretti, Diana L, Kerlikowske, Karla, and Vachon, Celine M
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Biomedical and Clinical Sciences ,Oncology and Carcinogenesis ,Breast Cancer ,Women's Health ,Cancer ,Prevention ,Biomedical Imaging ,2.1 Biological and endogenous factors ,Adult ,Breast ,Breast Density ,Breast Neoplasms ,Case-Control Studies ,Female ,Humans ,Mammography ,Reproducibility of Results ,breast cancer ,risk prediction ,variation measures ,volumetric breast density ,Clinical Sciences ,Nuclear Medicine & Medical Imaging ,Clinical sciences - Abstract
OBJECTIVE. Our previous work showed that variation measures, which represent breast architecture derived from mammograms, were significantly associated with breast cancer. For replication purposes, we examined the association of three variation measures (variation [V], which is measured in the image domain, and P1 and p1 [a normalized version of P1], which are derived from restricted regions in the Fourier domain) with breast cancer risk in an independent population. We also compared these measures to volumetric density measures (volumetric percent density [VPD] and dense volume [DV]) from a commercial product. MATERIALS AND METHODS. We examined 514 patients with breast cancer and 1377 control patients from a screening practice who were matched for age, date of examination, mammography unit, facility, and state of residence. Spearman rank-order correlation was used to evaluate the monotonic association between measures. Breast cancer associations were estimated using conditional logistic regression, after adjustment for age and body mass index. Odds ratios were calculated per SD increment in mammographic measure. RESULTS. These variation measures were strongly correlated with VPD (correlation, 0.68-0.80) but not with DV (correlation, 0.31-0.48). Similar to previous findings, all variation measures were significantly associated with breast cancer (odds ratio per SD: 1.30 [95% CI, 1.16-1.46] for V, 1.55 [95% CI, 1.35-1.77] for P1, and 1.51 [95% CI, 1.33-1.72] for p1). Associations of volumetric density measures with breast cancer were similar (odds ratio per SD: 1.54 [95% CI, 1.33-1.78] for VPD and 1.34 [95% CI, 1.20-1.50] for DV). When DV was included with each variation measure in the same model, all measures retained significance. CONCLUSION. Variation measures were significantly associated with breast cancer risk (comparable to the volumetric density measures) but were independent of the DV.
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- 2021
9. Assortative mating and parental genetic relatedness contribute to the pathogenicity of variably expressive variants
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Smolen, Corrine, Jensen, Matthew, Dyer, Lisa, Pizzo, Lucilla, Tyryshkina, Anastasia, Banerjee, Deepro, Rohan, Laura, Huber, Emily, El Khattabi, Laila, Prontera, Paolo, Caberg, Jean-Hubert, Van Dijck, Anke, Schwartz, Charles, Faivre, Laurence, Callier, Patrick, Mosca-Boidron, Anne-Laure, Lefebvre, Mathilde, Pope, Kate, Snell, Penny, Lockhart, Paul J., Castiglia, Lucia, Galesi, Ornella, Avola, Emanuela, Mattina, Teresa, Fichera, Marco, Luana Mandarà, Giuseppa Maria, Bruccheri, Maria Grazia, Pichon, Olivier, Le Caignec, Cedric, Stoeva, Radka, Cuinat, Silvestre, Mercier, Sandra, Bénéteau, Claire, Blesson, Sophie, Nordsletten, Ashley, Martin-Coignard, Dominique, Sistermans, Erik, Kooy, R. Frank, Amor, David J., Romano, Corrado, Isidor, Bertrand, Juusola, Jane, and Girirajan, Santhosh
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- 2023
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10. Phishing susceptibility across industries: The differential impact of influence techniques
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Tian, Chuan (Annie), Jensen, Matthew L., and Durcikova, Alexandra
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- 2023
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11. Association of Daily Alcohol Intake, Volumetric Breast Density, and Breast Cancer Risk
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Rustagi, Alison S, Scott, Christopher G, Winham, Stacey J, Brandt, Kathleen R, Norman, Aaron D, Jensen, Matthew R, Shepherd, John A, Hruska, Carrie, Heine, John J, Pankratz, Vernon S, Kerlikowske, Karla, and Vachon, Celine M
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Biomedical and Clinical Sciences ,Oncology and Carcinogenesis ,Women's Health ,Aging ,Substance Misuse ,Prevention ,Cancer ,Breast Cancer ,Biomedical Imaging ,Clinical Research ,Alcoholism ,Alcohol Use and Health ,2.1 Biological and endogenous factors ,Good Health and Well Being ,Age Factors ,Alcohol Drinking ,Body Mass Index ,Breast Density ,Breast Neoplasms ,Case-Control Studies ,Female ,Humans ,Mammography ,Menopause ,Middle Aged ,Odds Ratio ,San Francisco ,Oncology and carcinogenesis - Abstract
High alcohol intake and breast density increase breast cancer (BC) risk, but their interrelationship is unknown. We examined whether volumetric density modifies and/or mediates the alcohol-BC association. BC cases (n = 2233) diagnosed from 2006 to 2013 in the San Francisco Bay area had screening mammograms 6 or more months before diagnosis; controls (n = 4562) were matched on age, mammogram date, race or ethnicity, facility, and mammography machine. Logistic regression was used to estimate alcohol-BC associations adjusted for age, body mass index, and menopause; interaction terms assessed modification. Percent mediation was quantified as the ratio of log (odds ratios [ORs]) from models with and without density measures. Alcohol consumption was associated with increased BC risk (2-sided P trend = .004), as were volumetric percent density (OR = 1.45 per SD, 95% confidence interval [CI] = 1.36 to 1.56) and dense volume (OR = 1.30, 95% CI = 1.24 to 1.37). Breast density did not modify the alcohol-BC association (2-sided P > .10 for all). Dense volume mediated 25.0% (95% CI = 5.5% to 44.4%) of the alcohol-BC association (2-sided P = .01), suggesting alcohol may partially increase BC risk by increasing fibroglandular tissue.
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- 2021
12. Impact of Project Updates and Their Social Endorsement in Online Medical Crowdfunding.
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Wu, Yi, Ye, Hua, Jensen, Matthew L., and Liu, Linwei
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CROWD funding ,PANEL analysis ,SOCIAL influence ,INDIVIDUAL needs ,FUNDRAISING ,BOOSTING algorithms ,USER-generated content - Abstract
Online crowdfunding has become an important fundraising channel for medical care. Yet, individuals in need face numerous challenges in meeting their fundraising goals. To improve fundraising, individuals may use project updates to evoke donors' sympathy and secure donations. Informed by the sympathy bias literature, this paper conceptualizes two important but distinct aspects of project updates—positive sentiment and negative sentiment—and hypothesizes their individual and relative impacts on the donation amount of a crowdfunding project. In addition, this paper explores moderating effects of social endorsements on the influence of update sentiment. To test our hypotheses, we conducted two studies. Study 1 examined unique project-day panel data from 1,467 projects on a leading medical crowdfunding platform. Results reveal that both positive and negative update sentiment positively affect the donation amount of a crowdfunding project, but negative updates have a greater effect. Further, endorsements by strong ties and weak ties attenuate the positive effects of update sentiment. Study 2 was a controlled, randomized experiment that corroborated findings from Study 1, established the causality of observed effects, and confirmed the mediating effects of sympathy. The findings of this paper underscore the role of sympathy in enhancing online charitable crowdfunding to individual donors and show project updates with positive or negative sentiment to be potent mechanisms to boost donations. Furthermore, the substitution effect of social endorsement on donation amount also adds nuance to our knowledge suggesting that a proper combination of various information can better help improve crowdfunding performance. Platform operators and fundraisers should prioritize project update sentiment to enhance online charitable crowdfunding success. [ABSTRACT FROM AUTHOR]
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- 2024
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13. Serum hormone levels and normal breast histology among premenopausal women
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Sherman, Mark E., de Bel, Thomas, Heckman, Michael G., White, Launia J., Ogony, Joshua, Stallings-Mann, Melody, Hilton, Tracy, Degnim, Amy C., Vierkant, Robert A., Hoskin, Tanya, Jensen, Matthew R., Pacheco-Spann, Laura, Henry, Jill E., Storniolo, Anna Maria, Carter, Jodi M., Winham, Stacey J., Radisky, Derek C., and van der Laak, Jeroen
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- 2022
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14. Automated volumetric breast density measures: differential change between breasts in women with and without breast cancer
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Brandt, Kathleen R, Scott, Christopher G, Miglioretti, Diana L, Jensen, Matthew R, Mahmoudzadeh, Amir P, Hruska, Carrie, Ma, Lin, Wu, Fang Fang, Cummings, Steven R, Norman, Aaron D, Engmann, Natalie J, Shepherd, John A, Winham, Stacey J, Kerlikowske, Karla, and Vachon, Celine M
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Biomedical and Clinical Sciences ,Oncology and Carcinogenesis ,Women's Health ,Cancer ,Breast Cancer ,Aged ,Automation ,Breast ,Breast Density ,Breast Neoplasms ,Case-Control Studies ,Early Detection of Cancer ,Female ,Humans ,Mammography ,Middle Aged ,Reproducibility of Results ,Sensitivity and Specificity ,Tumor Burden ,Volumetric density ,Breast density ,Breast cancer ,Tissue asymmetry ,Risk ,Oncology & Carcinogenesis ,Oncology and carcinogenesis - Abstract
BackgroundGiven that breast cancer and normal dense fibroglandular tissue have similar radiographic attenuation, we examine whether automated volumetric density measures identify a differential change between breasts in women with cancer and compare to healthy controls.MethodsEligible cases (n = 1160) had unilateral invasive breast cancer and bilateral full-field digital mammograms (FFDMs) at two time points: within 2 months and 1-5 years before diagnosis. Controls (n = 2360) were matched to cases on age and date of FFDMs. Dense volume (DV) and volumetric percent density (VPD) for each breast were assessed using Volpara™. Differences in DV and VPD between mammograms (median 3 years apart) were calculated per breast separately for cases and controls and their difference evaluated by using the Wilcoxon signed-rank test. To simulate clinical practice where cancer laterality is unknown, we examined whether the absolute difference between breasts can discriminate cases from controls using area under the ROC curve (AUC) analysis, adjusting for age, BMI, and time.ResultsAmong cases, the VPD and DV between mammograms of the cancerous breast decreased to a lesser degree (- 0.26% and - 2.10 cm3) than the normal breast (- 0.39% and - 2.74 cm3) for a difference of 0.13% (p value
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- 2019
15. Dissecting the genetic basis of comorbid epilepsy phenotypes in neurodevelopmental disorders
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Chow, Julie, Jensen, Matthew, Amini, Hajar, Hormozdiari, Farhad, Penn, Osnat, Shifman, Sagiv, Girirajan, Santhosh, and Hormozdiari, Fereydoun
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Biological Sciences ,Bioinformatics and Computational Biology ,Genetics ,Neurosciences ,Epilepsy ,Pediatric ,Neurodegenerative ,Intellectual and Developmental Disabilities (IDD) ,Autism ,Human Genome ,Brain Disorders ,Biotechnology ,Mental Health ,2.1 Biological and endogenous factors ,Aetiology ,Neurological ,Mental health ,Comorbidity ,Databases ,Factual ,Gene Regulatory Networks ,Genetic Heterogeneity ,Humans ,Mutation ,Neurodevelopmental Disorders ,Phenotype ,Prognosis ,Intellectual disability ,Developmental disability ,Module discovery ,De novo mutation ,Clinical Sciences - Abstract
BACKGROUND:Neurodevelopmental disorders (NDDs) such as autism spectrum disorder, intellectual disability, developmental disability, and epilepsy are characterized by abnormal brain development that may affect cognition, learning, behavior, and motor skills. High co-occurrence (comorbidity) of NDDs indicates a shared, underlying biological mechanism. The genetic heterogeneity and overlap observed in NDDs make it difficult to identify the genetic causes of specific clinical symptoms, such as seizures. METHODS:We present a computational method, MAGI-S, to discover modules or groups of highly connected genes that together potentially perform a similar biological function. MAGI-S integrates protein-protein interaction and co-expression networks to form modules centered around the selection of a single "seed" gene, yielding modules consisting of genes that are highly co-expressed with the seed gene. We aim to dissect the epilepsy phenotype from a general NDD phenotype by providing MAGI-S with high confidence NDD seed genes with varying degrees of association with epilepsy, and we assess the enrichment of de novo mutation, NDD-associated genes, and relevant biological function of constructed modules. RESULTS:The newly identified modules account for the increased rate of de novo non-synonymous mutations in autism, intellectual disability, developmental disability, and epilepsy, and enrichment of copy number variations (CNVs) in developmental disability. We also observed that modules seeded with genes strongly associated with epilepsy tend to have a higher association with epilepsy phenotypes than modules seeded at other neurodevelopmental disorder genes. Modules seeded with genes strongly associated with epilepsy (e.g., SCN1A, GABRA1, and KCNB1) are significantly associated with synaptic transmission, long-term potentiation, and calcium signaling pathways. On the other hand, modules found with seed genes that are not associated or weakly associated with epilepsy are mostly involved with RNA regulation and chromatin remodeling. CONCLUSIONS:In summary, our method identifies modules enriched with de novo non-synonymous mutations and can capture specific networks that underlie the epilepsy phenotype and display distinct enrichment in relevant biological processes. MAGI-S is available at https://github.com/jchow32/magi-s .
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- 2019
16. Combined effect of volumetric breast density and body mass index on breast cancer risk
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Engmann, Natalie J, Scott, Christopher G, Jensen, Matthew R, Winham, Stacey, Miglioretti, Diana L, Ma, Lin, Brandt, Kathleen, Mahmoudzadeh, Amir, Whaley, Dana H, Hruska, Carrie, Wu, Fang, Norman, Aaron D, Hiatt, Robert A, Heine, John, Shepherd, John, Pankratz, V Shane, Vachon, Celine M, and Kerlikowske, Karla
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Biomedical and Clinical Sciences ,Oncology and Carcinogenesis ,Women's Health ,Cancer ,Clinical Research ,Breast Cancer ,Prevention ,Obesity ,Aging ,Biomedical Imaging ,Estrogen ,Adult ,Aged ,Aged ,80 and over ,Body Mass Index ,Breast Density ,Breast Neoplasms ,Case-Control Studies ,Disease Susceptibility ,Early Detection of Cancer ,Female ,Humans ,Mammography ,Mass Screening ,Menopause ,Middle Aged ,Public Health Surveillance ,Registries ,Risk ,Breast density ,Mammographic density ,Breast cancer ,Body mass index ,Clinical Sciences ,Oncology & Carcinogenesis ,Clinical sciences ,Oncology and carcinogenesis - Abstract
BackgroundBreast density and body mass index (BMI) are used for breast cancer risk stratification. We evaluate whether the positive association between volumetric breast density and breast cancer risk is strengthened with increasing BMI.MethodsThe San Francisco Mammography Registry and Mayo Clinic Rochester identified 781 premenopausal and 1850 postmenopausal women with breast cancer diagnosed between 2007 and 2015 that had a screening digital mammogram at least 6 months prior to diagnosis. Up to three controls (N = 3535) were matched per case on age, race, date, mammography machine, and state. Volumetric percent density (VPD) and dense volume (DV) were measured with Volpara™. Breast cancer risk was assessed with logistic regression stratified by menopause status. Multiplicative interaction tests assessed whether the association of density measures was differential by BMI categories.ResultsThe increased risk of breast cancer associated with VPD was strengthened with higher BMI for both premenopausal (pinteraction = 0.01) and postmenopausal (pinteraction = 0.0003) women. For BMI
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- 2019
17. Longitudinal Changes in Volumetric Breast Density in Healthy Women across the Menopausal Transition
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Engmann, Natalie J, Scott, Christopher, Jensen, Matthew R, Winham, Stacey J, Ma, Lin, Brandt, Kathleen R, Mahmoudzadeh, Amir, Whaley, Dana H, Hruska, Carrie B, Wu, Fang-Fang, Norman, Aaron D, Hiatt, Robert A, Heine, John, Shepherd, John, Pankratz, V Shane, Miglioretti, Diana L, Kerlikowske, Karla, and Vachon, Celine M
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Health Services and Systems ,Biomedical and Clinical Sciences ,Health Sciences ,Oncology and Carcinogenesis ,Estrogen ,Clinical Research ,Contraception/Reproduction ,Biomedical Imaging ,Prevention ,Women's Health ,Cancer ,Aging ,Breast Cancer ,Good Health and Well Being ,Body Mass Index ,Breast ,Breast Density ,Female ,Humans ,Longitudinal Studies ,Mammography ,Middle Aged ,Postmenopause ,Premenopause ,Risk Factors ,Women’s Health ,Medical and Health Sciences ,Epidemiology ,Biomedical and clinical sciences ,Health sciences - Abstract
BackgroundMammographic breast density declines during menopause. We assessed changes in volumetric breast density across the menopausal transition and factors that influence these changes.MethodsWomen without a history of breast cancer, who had full field digital mammograms during both pre- and postmenopausal periods, at least 2 years apart, were sampled from four facilities within the San Francisco Mammography Registry from 2007 to 2013. Dense breast volume (DV) was assessed using Volpara on mammograms across the time period. Annualized change in DV from pre- to postmenopause was estimated using linear mixed models adjusted for covariates and per-woman random effects. Multiplicative interactions were evaluated between premenopausal risk factors and time to determine whether these covariates modified the annualized changes.ResultsAmong the 2,586 eligible women, 1,802 had one premenopausal and one postmenopausal mammogram, 628 had an additional perimenopausal mammogram, and 156 had two perimenopausal mammograms. Women experienced an annualized decrease in DV [-2.2 cm3 (95% confidence interval, -2.7 to -1.7)] over the menopausal transition. Declines were greater among women with a premenopausal DV above the median (54 cm3) versus below (DV, -3.5 cm3 vs. -1.0 cm3; P < 0.0001). Other breast cancer risk factors, including race, body mass index, family history, alcohol, and postmenopausal hormone therapy, had no effect on change in DV over the menopausal transition.ConclusionsHigh premenopausal DV was a strong predictor of greater reductions in DV across the menopausal transition.ImpactWe found that few factors other than premenopausal density influence changes in DV across the menopausal transition, limiting targeted prevention efforts.
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- 2019
18. Artificial gravity partially protects space-induced neurological deficits in Drosophila melanogaster
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Mhatre, Siddhita D., Iyer, Janani, Petereit, Juli, Dolling-Boreham, Roberta M., Tyryshkina, Anastasia, Paul, Amber M., Gilbert, Rachel, Jensen, Matthew, Woolsey, Rebekah J., Anand, Sulekha, Sowa, Marianne B., Quilici, David R., Costes, Sylvain V., Girirajan, Santhosh, and Bhattacharya, Sharmila
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- 2022
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19. An Integrated Spiral Model of Trust
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Burgoon, Judee K., Dunbar, Norah E., Jensen, Matthew L., Subrahmanian, V.S., Series Editor, Subrahmanian, V. S., editor, Burgoon, Judee K., editor, and Dunbar, Norah E., editor
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- 2021
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20. Helicopter Emergency Medical Services
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Rodman, Katherine, Jensen, Matthew, Nicholson, Benjamin D., editor, Vitto, Michael J., editor, and Dhindsa, Harinder S., editor
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- 2021
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21. Does mammographic density mediate risk factor associations with breast cancer? An analysis by tumor characteristics
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Rice, Megan S, Tamimi, Rulla M, Bertrand, Kimberly A, Scott, Christopher G, Jensen, Matthew R, Norman, Aaron D, Visscher, Daniel W, Chen, Yunn-Yi, Brandt, Kathleen R, Couch, Fergus J, Shepherd, John A, Fan, Bo, Wu, Fang-Fang, Ma, Lin, Collins, Laura C, Cummings, Steven R, Kerlikowske, Karla, and Vachon, Celine M
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Biomedical and Clinical Sciences ,Oncology and Carcinogenesis ,Prevention ,Women's Health ,Clinical Research ,Cancer ,Breast Cancer ,Aging ,Estrogen ,Adult ,Aged ,Biomarkers ,Tumor ,Breast ,Breast Density ,Breast Neoplasms ,Female ,Humans ,Mammography ,Middle Aged ,Pregnancy ,Receptor ,ErbB-2 ,Receptors ,Estrogen ,Receptors ,Progesterone ,Risk Factors ,Mammographic density ,Breast cancer ,Receptor ,erbB-2 ,Clinical Sciences ,Oncology & Carcinogenesis ,Clinical sciences ,Oncology and carcinogenesis - Abstract
BackgroundThough mammographic density (MD) has been proposed as an intermediate marker of breast cancer risk, few studies have examined whether the associations between breast cancer risk factors and risk are mediated by MD, particularly by tumor characteristics.MethodsOur study population included 3392 cases (1105 premenopausal) and 8882 (3192 premenopausal) controls from four case-control studies. For established risk factors, we estimated the percent of the total risk factor association with breast cancer that was mediated by percent MD (secondarily, by dense area and non-dense area) for invasive breast cancer as well as for subtypes defined by the estrogen receptor (ER+/ER-), progesterone receptor (PR+/PR-), and HER2 (HER2+/HER2-). Analyses were conducted separately in pre- and postmenopausal women.ResultsPositive associations between prior breast biopsy and risk of invasive breast cancer as well as all subtypes were partially mediated by percent MD in pre- and postmenopausal women (percent mediated = 11-27%, p ≤ 0.02). In postmenopausal women, nulliparity and hormone therapy use were positively associated with invasive, ER+ , PR+ , and HER2- breast cancer; percent MD partially mediated these associations (percent mediated ≥ 31%, p ≤ 0.02). Further, among postmenopausal women, percent MD partially mediated the positive association between later age at first birth and invasive as well as ER+ breast cancer (percent mediated = 16%, p ≤ 0.05).ConclusionPercent MD partially mediated the associations between breast biopsy, nulliparity, age at first birth, and hormone therapy with risk of breast cancer, particularly among postmenopausal women, suggesting that these risk factors at least partially influence breast cancer risk through changes in breast tissue composition.
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- 2018
22. Automated and Clinical Breast Imaging Reporting and Data System Density Measures Predict Risk for Screen-Detected and Interval Cancers: A Case-Control Study.
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Kerlikowske, Karla, Scott, Christopher G, Mahmoudzadeh, Amir P, Ma, Lin, Winham, Stacey, Jensen, Matthew R, Wu, Fang Fang, Malkov, Serghei, Pankratz, V Shane, Cummings, Steven R, Shepherd, John A, Brandt, Kathleen R, Miglioretti, Diana L, and Vachon, Celine M
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Biomedical and Clinical Sciences ,Oncology and Carcinogenesis ,Clinical Research ,Cancer ,Women's Health ,Prevention ,Biomedical Imaging ,Breast Cancer ,4.1 Discovery and preclinical testing of markers and technologies ,4.2 Evaluation of markers and technologies ,Aged ,Automation ,Breast Density ,Breast Neoplasms ,Case-Control Studies ,Early Detection of Cancer ,Female ,Humans ,Mammography ,Middle Aged ,Radiographic Image Interpretation ,Computer-Assisted ,Risk Assessment ,San Francisco ,Sensitivity and Specificity ,Time Factors ,Clinical Sciences ,Public Health and Health Services - Abstract
BackgroundIn 30 states, women who have had screening mammography are informed of their breast density on the basis of Breast Imaging Reporting and Data System (BI-RADS) density categories estimated subjectively by radiologists. Variation in these clinical categories across and within radiologists has led to discussion about whether automated BI-RADS density should be reported instead.ObjectiveTo determine whether breast cancer risk and detection are similar for automated and clinical BI-RADS density measures.DesignCase-control.SettingSan Francisco Mammography Registry and Mayo Clinic.Participants1609 women with screen-detected cancer, 351 women with interval invasive cancer, and 4409 matched control participants.MeasurementsAutomated and clinical BI-RADS density assessed on digital mammography at 2 time points from September 2006 to October 2014, interval and screen-detected breast cancer risk, and mammography sensitivity.ResultsOf women whose breast density was categorized by automated BI-RADS more than 6 months to 5 years before diagnosis, those with extremely dense breasts had a 5.65-fold higher interval cancer risk (95% CI, 3.33 to 9.60) and a 1.43-fold higher screen-detected risk (CI, 1.14 to 1.79) than those with scattered fibroglandular densities. Associations of interval and screen-detected cancer with clinical BI-RADS density were similar to those with automated BI-RADS density, regardless of whether density was measured more than 6 months to less than 2 years or 2 to 5 years before diagnosis. Automated and clinical BI-RADS density measures had similar discriminatory accuracy, which was higher for interval than screen-detected cancer (c-statistics: 0.70 vs. 0.62 [P < 0.001] and 0.72 vs. 0.62 [P < 0.001], respectively). Mammography sensitivity was similar for automated and clinical BI-RADS categories: fatty, 93% versus 92%; scattered fibroglandular densities, 90% versus 90%; heterogeneously dense, 82% versus 78%; and extremely dense, 63% versus 64%, respectively.LimitationNeither automated nor clinical BI-RADS density was assessed on tomosynthesis, an emerging breast screening method.ConclusionAutomated and clinical BI-RADS density similarly predict interval and screen-detected cancer risk, suggesting that either measure may be used to inform women of their breast density.Primary funding sourceNational Cancer Institute.
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- 2018
23. A higher rare CNV burden in the genetic background potentially contributes to intellectual disability phenotypes in 22q11.2 deletion syndrome
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Jensen, Matthew, Kooy, R Frank, Simon, Tony J, Reyniers, Edwin, Girirajan, Santhosh, and Tassone, Flora
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Biological Sciences ,Genetics ,Brain Disorders ,Mental Health ,Pediatric ,Human Genome ,Intellectual and Developmental Disabilities (IDD) ,Clinical Research ,2.1 Biological and endogenous factors ,Aetiology ,Mental health ,DNA Copy Number Variations ,DiGeorge Syndrome ,Humans ,Intellectual Disability ,22q11DS ,Copy number variations ,Intellectual disabilities ,Clinical Sciences ,Genetics & Heredity ,Clinical sciences - Abstract
The 22q11.2 deletion syndrome (22q11DS), the most common survivable human genetic deletion disorder, is caused by a hemizygous deletion of 30-40 contiguous genes on chromosome 22, many of which have not been well characterized. Clinical features seen in patients with this deletion, including intellectual disability, are not completely penetrant and vary in severity between patients, suggesting the involvement of variants elsewhere in the genome in the manifestation of the phenotype. Given that it is a relatively rare disorder (1/2000-6000 in humans), limited research has shed light into the contribution of these second-site variants to the developmental pathogenesis that underlies 22q11DS. As CNVs throughout the genome might constitute such a genetic risk factor for variability in the 22q11DS phenotypes such as intellectual disability, we sought to determine if the overall burden of rare CNVs in the genetic background influenced the phenotypic variability. We analyzed CNV and clinical data from 66 individuals with 22q11DS, and found that 77% (51/66) of individuals with the 22q11DS also carry additional rare CNVs (200 Kb in size) was significantly higher in 22q11DS individuals with intellectual disability than with normal IQ. Our analysis shows that rare CNVs may contribute to intellectual disability 22q11DS, and further analysis on larger 22q11DS cohorts should be performed to confirm this correlation.
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- 2018
24. Towards defining morphologic parameters of normal parous and nulliparous breast tissues by artificial intelligence
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Ogony, Joshua, de Bel, Thomas, Radisky, Derek C., Kachergus, Jennifer, Thompson, E. Aubrey, Degnim, Amy C., Ruddy, Kathryn J., Hilton, Tracy, Stallings-Mann, Melody, Vachon, Celine, Hoskin, Tanya L., Heckman, Michael G., Vierkant, Robert A., White, Launia J., Moore, Raymond M., Carter, Jodi, Jensen, Matthew, Pacheco-Spann, Laura, Henry, Jill E., Storniolo, Anna Maria, Winham, Stacey J., van der Laak, Jeroen, and Sherman, Mark E.
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- 2022
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25. Homomorphic Encryption: An Application to Polygenic Risk Scores
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Knight, Elizabeth, primary, Li, Jiaqi, additional, Jensen, Matthew, additional, Yolou, Israel, additional, Kockan, Can, additional, and Gerstein, Mark, additional
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- 2024
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26. Using a comprehensive atlas and predictive models to reveal the complexity and evolution of brain-active regulatory elements
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Pratt, Henry E., primary, Andrews, Gregory, additional, Shedd, Nicole, additional, Phalke, Nishigandha, additional, Li, Tongxin, additional, Pampari, Anusri, additional, Jensen, Matthew, additional, Wen, Cindy, additional, Consortium, PsychENCODE, additional, Gandal, Michael J., additional, Geschwind, Daniel H., additional, Gerstein, Mark, additional, Moore, Jill, additional, Kundaje, Anshul, additional, Colubri, Andrés, additional, and Weng, Zhiping, additional
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- 2024
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27. Transcriptomic sex differences in postmortem brain samples from patients with psychiatric disorders
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Xia, Yan, primary, Xia, Cuihua, additional, Jiang, Yi, additional, Chen, Yu, additional, Zhou, Jiaqi, additional, Dai, Rujia, additional, Han, Cong, additional, Mao, Zhongzheng, additional, Consortium, PsychENCODE, additional, Liu, Chunyu, additional, Chen, Chao, additional, Akbarian, Schahram, additional, Abyzov, Alexej, additional, Ahituv, Nadav, additional, Arasappan, Dhivya, additional, Almagro Armenteros, Jose Juan, additional, Beliveau, Brian J., additional, Bendl, Jaroslav, additional, Berretta, Sabina, additional, Bharadwaj, Rahul A., additional, Bhattacharya, Arjun, additional, Bicks, Lucy, additional, Brennand, Kristen, additional, Capauto, Davide, additional, Champagne, Frances A., additional, Chatterjee, Tanima, additional, Chatzinakos, Chris, additional, Chen, Yuhang, additional, Chen, H. Isaac, additional, Cheng, Yuyan, additional, Cheng, Lijun, additional, Chess, Andrew, additional, Chien, Jo-fan, additional, Chu, Zhiyuan, additional, Clarke, Declan, additional, Clement, Ashley, additional, Collado-Torres, Leonardo, additional, Cooper, Gregory M., additional, Crawford, Gregory E., additional, Daskalakis, Nikolaos P., additional, Davila-Velderrain, Jose, additional, Deep-Soboslay, Amy, additional, Deng, Chengyu, additional, DiPietro, Christopher P., additional, Dracheva, Stella, additional, Drusinsky, Shiron, additional, Duan, Ziheng, additional, Duong, Duc, additional, Dursun, Cagatay, additional, Eagles, Nicholas J., additional, Edelstein, Jonathan, additional, Emani, Prashant S., additional, Fullard, John F., additional, Galani, Kiki, additional, Galeev, Timur, additional, Gandal, Michael J., additional, Gaynor, Sophia, additional, Gerstein, Mark, additional, Geschwind, Daniel H., additional, Girdhar, Kiran, additional, Goes, Fernando S., additional, Greenleaf, William, additional, Grundman, Jennifer, additional, Guo, Hanmin, additional, Guo, Qiuyu, additional, Gupta, Chirag, additional, Hadas, Yoav, additional, Hallmayer, Joachim, additional, Han, Xikun, additional, Haroutunian, Vahram, additional, Hawken, Natalie, additional, He, Chuan, additional, Henry, Ella, additional, Hicks, Stephanie C., additional, Ho, Marcus, additional, Ho, Li-Lun, additional, Hoffman, Gabriel E., additional, Huang, Yiling, additional, Huuki-Myers, Louise A., additional, Hwang, Ahyeon, additional, Hyde, Thomas M., additional, Iatrou, Artemis, additional, Inoue, Fumitaka, additional, Jajoo, Aarti, additional, Jensen, Matthew, additional, Jiang, Lihua, additional, Jin, Peng, additional, Jin, Ting, additional, Jops, Connor, additional, Jourdon, Alexandre, additional, Kawaguchi, Riki, additional, Kellis, Manolis, additional, Khullar, Saniya, additional, Kleinman, Joel E., additional, Kleopoulos, Steven P., additional, Kozlenkov, Alex, additional, Kriegstein, Arnold, additional, Kundaje, Anshul, additional, Kundu, Soumya, additional, Lee, Cheyu, additional, Lee, Donghoon, additional, Li, Junhao, additional, Li, Mingfeng, additional, Lin, Xiao, additional, Liu, Shuang, additional, Liu, Jason, additional, Liu, Jianyin, additional, Lou, Shaoke, additional, Loupe, Jacob M., additional, Lu, Dan, additional, Ma, Shaojie, additional, Ma, Liang, additional, Margolis, Michael, additional, Mariani, Jessica, additional, Martinowich, Keri, additional, Maynard, Kristen R., additional, Mazariegos, Samantha, additional, Meng, Ran, additional, Myers, Richard M., additional, Micallef, Courtney, additional, Mikhailova, Tatiana, additional, Ming, Guo-li, additional, Mohammadi, Shahin, additional, Monte, Emma, additional, Montgomery, Kelsey S., additional, Moore, Jill E., additional, Moran, Jennifer R., additional, Mukamel, Eran A., additional, Nairn, Angus C., additional, Nemeroff, Charles B., additional, Ni, Pengyu, additional, Norton, Scott, additional, Nowakowski, Tomasz, additional, Omberg, Larsson, additional, Page, Stephanie C., additional, Park, Saejeong, additional, Patowary, Ashok, additional, Pattni, Reenal, additional, Pertea, Geo, additional, Peters, Mette A., additional, Phalke, Nishigandha, additional, Pinto, Dalila, additional, Pjanic, Milos, additional, Pochareddy, Sirisha, additional, Pollard, Katherine S., additional, Pollen, Alex, additional, Pratt, Henry, additional, Przytycki, Pawel F., additional, Purmann, Carolin, additional, Qin, Zhaohui S., additional, Qu, Ping-Ping, additional, Quintero, Diana, additional, Raj, Towfique, additional, Rajagopalan, Ananya S., additional, Reach, Sarah, additional, Reimonn, Thomas, additional, Ressler, Kerry J., additional, Ross, Deanna, additional, Roussos, Panos, additional, Rozowsky, Joel, additional, Ruth, Misir, additional, Ruzicka, W. Brad, additional, Sanders, Stephan J., additional, Schneider, Juliane M., additional, Scuderi, Soraya, additional, Sebra, Robert, additional, Sestan, Nenad, additional, Seyfried, Nicholas, additional, Shao, Zhiping, additional, Shedd, Nicole, additional, Shieh, Annie W., additional, Shin, Joo Heon, additional, Skarica, Mario, additional, Snijders, Clara, additional, Song, Hongjun, additional, State, Matthew W., additional, Stein, Jason, additional, Steyert, Marilyn, additional, Subburaju, Sivan, additional, Sudhof, Thomas, additional, Snyder, Michael, additional, Tao, Ran, additional, Therrien, Karen, additional, Tsai, Li-Huei, additional, Urban, Alexander E., additional, Vaccarino, Flora M., additional, van Bake, Harm, additional, Vo, Daniel, additional, Voloudakis, Georgios, additional, Wamsley, Brie, additional, Wang, Tao, additional, Wang, Sidney H., additional, Wang, Daifeng, additional, Wang, Yifan, additional, Warrell, Jonathan, additional, Wei, Yu, additional, Weimer, Annika K., additional, Weinberger, Daniel R., additional, Wen, Cindy, additional, Weng, Zhiping, additional, Whalen, Sean, additional, White, Kevin P., additional, Willsey, A. Jeremy, additional, Won, Hyejung, additional, Wong, Wing, additional, Wu, Hao, additional, Wu, Feinan, additional, Wuchty, Stefan, additional, Wylie, Dennis, additional, Xu, Siwei, additional, Yap, Chloe X., additional, Zeng, Biao, additional, Zhang, Pan, additional, Zhang, Chunling, additional, Zhang, Bin, additional, Zhang, Jing, additional, Zhang, Yanqiong, additional, Zhou, Xiao, additional, Ziffra, Ryan, additional, Zeier, Zane R., additional, and Zintel, Trisha M., additional
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- 2024
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28. The influence of affective processing on phishing susceptibility
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Tian, Chuan (Annie), primary, Jensen, Matthew L., additional, Bott, Greg, additional, and Luo, Xin (Robert), additional
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- 2024
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29. Transdisciplinary and arts-centred approaches to stewardship and sustainability of urban nature
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Campbell, Lindsay K., primary, Fremantle, Chris, additional, Maddox, David, additional, Svendsen, Erika, additional, Hines, Sarah, additional, Mattingly, Mary, additional, López-Jensen, Matthew, additional, Lindt, Nikki, additional, Paqueo, Liza, additional, and Johnson, Michelle, additional
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- 2024
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30. Combining quantitative and qualitative breast density measures to assess breast cancer risk
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Kerlikowske, Karla, Ma, Lin, Scott, Christopher G, Mahmoudzadeh, Amir P, Jensen, Matthew R, Sprague, Brian L, Henderson, Louise M, Pankratz, V Shane, Cummings, Steven R, Miglioretti, Diana L, Vachon, Celine M, and Shepherd, John A
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Biomedical and Clinical Sciences ,Oncology and Carcinogenesis ,Biomedical Imaging ,Prevention ,Breast Cancer ,Clinical Research ,Women's Health ,Cancer ,4.1 Discovery and preclinical testing of markers and technologies ,Aged ,Breast ,Breast Density ,Breast Neoplasms ,Case-Control Studies ,Early Detection of Cancer ,Female ,Humans ,Middle Aged ,Neoplasm Staging ,Odds Ratio ,Public Health Surveillance ,Risk Assessment ,Risk Factors ,Breast density ,Breast cancer risk ,Dense volume ,Oncology & Carcinogenesis ,Oncology and carcinogenesis - Abstract
BackgroundAccurately identifying women with dense breasts (Breast Imaging Reporting and Data System [BI-RADS] heterogeneously or extremely dense) who are at high breast cancer risk will facilitate discussions of supplemental imaging and primary prevention. We examined the independent contribution of dense breast volume and BI-RADS breast density to predict invasive breast cancer and whether dense breast volume combined with Breast Cancer Surveillance Consortium (BCSC) risk model factors (age, race/ethnicity, family history of breast cancer, history of breast biopsy, and BI-RADS breast density) improves identifying women with dense breasts at high breast cancer risk.MethodsWe conducted a case-control study of 1720 women with invasive cancer and 3686 control subjects. We calculated ORs and 95% CIs for the effect of BI-RADS breast density and Volpara™ automated dense breast volume on invasive cancer risk, adjusting for other BCSC risk model factors plus body mass index (BMI), and we compared C-statistics between models. We calculated BCSC 5-year breast cancer risk, incorporating the adjusted ORs associated with dense breast volume.ResultsCompared with women with BI-RADS scattered fibroglandular densities and second-quartile dense breast volume, women with BI-RADS extremely dense breasts and third- or fourth-quartile dense breast volume (75% of women with extremely dense breasts) had high breast cancer risk (OR 2.87, 95% CI 1.84-4.47, and OR 2.56, 95% CI 1.87-3.52, respectively), whereas women with extremely dense breasts and first- or second-quartile dense breast volume were not at significantly increased breast cancer risk (OR 1.53, 95% CI 0.75-3.09, and OR 1.50, 95% CI 0.82-2.73, respectively). Adding continuous dense breast volume to a model with BCSC risk model factors and BMI increased discriminatory accuracy compared with a model with only BCSC risk model factors (C-statistic 0.639, 95% CI 0.623-0.654, vs. C-statistic 0.614, 95% CI 0.598-0.630, respectively; P
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- 2017
31. Interaction of mammographic breast density with menopausal status and postmenopausal hormone use in relation to the risk of aggressive breast cancer subtypes.
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Chen, Yunn-Yi, Ma, Lin, Beck, Andrew, Cummings, Steven, Kerlikowske, Karla, Vachon, Celine, Yaghjyan, Lusine, Tamimi, Rulla, Bertrand, Kimberly, Scott, Christopher, Jensen, Matthew, Pankratz, V, Brandt, Kathy, Visscher, Daniel, Norman, Aaron, Couch, Fergus, Shepherd, John, and Fan, Bo
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Breast cancer subtypes ,Breast density ,Postmenopausal hormone therapy ,Tumor aggressiveness ,Adult ,Breast ,Breast Density ,Breast Neoplasms ,Case-Control Studies ,Disease Progression ,Estrogen Replacement Therapy ,Female ,Humans ,Menopause ,Middle Aged ,Odds Ratio ,Population Surveillance ,Risk - Abstract
PURPOSE: We examined the associations of mammographic breast density with breast cancer risk by tumor aggressiveness and by menopausal status and current postmenopausal hormone therapy. METHODS: This study included 2596 invasive breast cancer cases and 4059 controls selected from participants of four nested case-control studies within four established cohorts: the Mayo Mammography Health Study, the Nurses Health Study, Nurses Health Study II, and San Francisco Mammography Registry. Percent breast density (PD), absolute dense (DA), and non-dense areas (NDA) were assessed from digitized film-screen mammograms using a computer-assisted threshold technique and standardized across studies. We used polytomous logistic regression to quantify the associations of breast density with breast cancer risk by tumor aggressiveness (defined as presence of at least two of the following tumor characteristics: size ≥2 cm, grade 2/3, ER-negative status, or positive nodes), stratified by menopausal status and current hormone therapy. RESULTS: Overall, the positive association of PD and borderline inverse association of NDA with breast cancer risk was stronger in aggressive vs. non-aggressive tumors (≥51 vs. 11-25% OR 2.50, 95% CI 1.94-3.22 vs. OR 2.03, 95% CI 1.70-2.43, p-heterogeneity = 0.03; NDA 4th vs. 2nd quartile OR 0.54, 95% CI 0.41-0.70 vs. OR 0.71, 95% CI 0.59-0.85, p-heterogeneity = 0.07). However, there were no differences in the association of DA with breast cancer by aggressive status. In the stratified analysis, there was also evidence of a stronger association of PD and NDA with aggressive tumors among postmenopausal women and, in particular, current estrogen+progesterone users (≥51 vs. 11-25% OR 3.24, 95% CI 1.75-6.00 vs. OR 1.93, 95% CI 1.25-2.98, p-heterogeneity = 0.01; NDA 4th vs. 2nd quartile OR 0.43, 95% CI 0.21-0.85 vs. OR 0.56, 95% CI 0.35-0.89, p-heterogeneity = 0.01), even though the interaction was not significant. CONCLUSION: Our findings suggest that associations of mammographic density with breast cancer risk differ by tumor aggressiveness. While there was no strong evidence that these associations differed by menopausal status or hormone therapy, they did appear more prominent among current estrogen+progesterone users.
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- 2017
32. Longitudinal Changes in Volumetric Breast Density with Tamoxifen and Aromatase Inhibitors
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Engmann, Natalie J, Scott, Christopher G, Jensen, Matthew R, Ma, Lin, Brandt, Kathleen R, Mahmoudzadeh, Amir Pasha, Malkov, Serghei, Whaley, Dana H, Hruska, Carrie B, Wu, Fang Fang, Winham, Stacey J, Miglioretti, Diana L, Norman, Aaron D, Heine, John J, Shepherd, John, Pankratz, V Shane, Vachon, Celine M, and Kerlikowske, Karla
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Health Services and Systems ,Biomedical and Clinical Sciences ,Health Sciences ,Oncology and Carcinogenesis ,Clinical Research ,Cancer ,Breast Cancer ,Biomedical Imaging ,Aging ,Women's Health ,Estrogen ,Adult ,Aromatase Inhibitors ,Breast Density ,Female ,Humans ,Middle Aged ,Tamoxifen ,Medical and Health Sciences ,Epidemiology ,Biomedical and clinical sciences ,Health sciences - Abstract
Background: Reductions in breast density with tamoxifen and aromatase inhibitors may be an intermediate marker of treatment response. We compare changes in volumetric breast density among breast cancer cases using tamoxifen or aromatase inhibitors (AI) to untreated women without breast cancer.Methods: Breast cancer cases with a digital mammogram prior to diagnosis and after initiation of tamoxifen (n = 366) or AI (n = 403) and a sample of controls (n = 2170) were identified from the Mayo Clinic Mammography Practice and San Francisco Mammography Registry. Volumetric percent density (VPD) and dense breast volume (DV) were measured using Volpara (Matakina Technology) and Quantra (Hologic) software. Linear regression estimated the effect of treatment on annualized changes in density.Results: Premenopausal women using tamoxifen experienced annualized declines in VPD of 1.17% to 1.70% compared with 0.30% to 0.56% for controls and declines in DV of 7.43 to 15.13 cm3 compared with 0.28 to 0.63 cm3 in controls, for Volpara and Quantra, respectively. The greatest reductions were observed among women with ≥10% baseline density. Postmenopausal AI users had greater declines in VPD than controls (Volpara P = 0.02; Quantra P = 0.03), and reductions were greatest among women with ≥10% baseline density. Declines in VPD among postmenopausal women using tamoxifen were only statistically greater than controls when measured with Quantra.Conclusions: Automated software can detect volumetric breast density changes among women on tamoxifen and AI.Impact: If declines in volumetric density predict breast cancer outcomes, these measures may be used as interim prognostic indicators. Cancer Epidemiol Biomarkers Prev; 26(6); 930-7. ©2017 AACR.
- Published
- 2017
33. 13. Mitigating Bias and Improving Professional Decision-Making through Persuasive Training Games
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Lee, Yu-Hao, primary, Dunbar, Norah E., additional, Miller, Claude H., additional, Bessarabova, Elena, additional, Jensen, Matthew, additional, Wilson, Scott, additional, Elizondo, Javier, additional, Burgoon, Judee, additional, and Valacich, Joseph, additional
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- 2021
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34. Association of mammographic density measures and breast cancer “intrinsic” molecular subtypes
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Kleinstern, Geffen, Scott, Christopher G., Tamimi, Rulla M., Jensen, Matthew R., Pankratz, V. Shane, Bertrand, Kimberly A., Norman, Aaron D., Visscher, Daniel W., Couch, Fergus J., Brandt, Kathleen, Shepherd, John, Wu, Fang-Fang, Chen, Yunn-Yi, Cummings, Steven R., Winham, Stacey, Kerlikowske, Karla, and Vachon, Celine M.
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- 2021
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35. Leveraging a large language model to predict protein phase transition: A physical, multiscale, and interpretable approach.
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Frank, Mor, Pengyu Ni, Jensen, Matthew, and Gerstein, Mark B.
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LANGUAGE models ,PROTEIN structure prediction ,PHASE transitions ,ALZHEIMER'S disease ,PHASE separation - Abstract
Protein phase transitions (PPTs) from the soluble state to a dense liquid phase (forming droplets via liquid-liquid phase separation) or to solid aggregates (such as amyloids) play key roles in pathological processes associated with age-related diseases such as Alzheimer's disease. Several computational frameworks are capable of separately predicting the formation of droplets or amyloid aggregates based on protein sequences, yet none have tackled the prediction of both within a unified framework. Recently, large language models (LLMs) have exhibited great success in protein structure prediction; however, they have not yet been used for PPTs. Here, we fine-tune a LLM for predicting PPTs and demonstrate its usage in evaluating how sequence variants affect PPTs, an operation useful for protein design. In addition, we show its superior performance compared to suitable classical benchmarks. Due to the "black-box" nature of the LLM, we also employ a classical random forest model along with biophysical features to facilitate interpretation. Finally, focusing on Alzheimer's disease-related proteins, we demonstrate that greater aggregation is associated with reduced gene expression in Alzheimer's disease, suggesting a natural defense mechanism. [ABSTRACT FROM AUTHOR]
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- 2024
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36. Impact of Suction-Assisted Laryngoscopy and Airway Decontamination Technique on Intubation Quality Metrics in a Helicopter Emergency Medical Service: An Educational Intervention
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Jensen, Matthew, Barmaan, Benjamin, Orndahl, Christine M., and Louka, Amir
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- 2020
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37. Benign Breast Disease and Breast Cancer Risk in the Percutaneous Biopsy Era
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Sherman, Mark E., primary, Vierkant, Robert A., additional, Winham, Stacey J., additional, Vachon, Celine M., additional, Carter, Jodi M., additional, Pacheco-Spann, Laura, additional, Jensen, Matthew R., additional, McCauley, Bryan M., additional, Hoskin, Tanya L., additional, Seymour, Lisa, additional, Gehling, Denice, additional, Fischer, Jessica, additional, Ghosh, Karthik, additional, Radisky, Derek C., additional, and Degnim, Amy C., additional
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- 2024
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38. Associations of mammographic breast density with breast stem cell marker-defined breast cancer subtypes
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Yaghjyan, Lusine, Esnakula, Ashwini K., Scott, Christopher G., Wijayabahu, Akemi T., Jensen, Matthew R., and Vachon, Celine M.
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- 2019
39. Ideological group persuasion: A within-person study of how violence, interactivity, and credibility features influence online persuasion
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Taylor, William D, Johnson, Genevieve, Ault, Michael K, Griffith, Jennifer A, Rozzell, Bobby, Connelly, Shane, Jensen, Matthew L, Dunbar, Norah E, and Ness, Alisha M
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Basic Behavioral and Social Science ,Clinical Research ,Behavioral and Social Science ,Violence Research ,Peace ,Justice and Strong Institutions ,Political ideological groups ,Websites ,Credibility ,Interactivity ,Extremism ,Violence ,Information Systems ,Psychology ,Cognitive Sciences ,Education - Abstract
Ideological groups (both non-violent and violent) make extensive use of the Internet for recruiting and other purposes, yet little is known about the effectiveness of the influence of websites of differing ideologies on attitudes and behavior. Furthermore, although credibility and interactivity have been extensively studied in online settings, they have received scant attention with regards to ideological groups. Using a within-subjects design, this study explored how individuals' attitudes, emotional reactions, behaviors and behavioral intentions are affected by two separate websites, with one promoting a liberal ideology and one promoting a conservative ideology. Results indicated that individuals preferred the liberal ideology, that violent websites led to higher negative affect and lowered perceptions of credibility than the non-violent websites, and that violence decreased the likelihood of taking action. Additionally, high interactivity increased the salience of the credibility manipulations with regards to their impact on the likelihood of taking action.
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- 2015
40. Dense and Nondense Mammographic Area and Risk of Breast Cancer by Age and Tumor Characteristics
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Bertrand, Kimberly A, Scott, Christopher G, Tamimi, Rulla M, Jensen, Matthew R, Pankratz, V Shane, Norman, Aaron D, Visscher, Daniel W, Couch, Fergus J, Shepherd, John, Chen, Yunn-Yi, Fan, Bo, Wu, Fang-Fang, Ma, Lin, Beck, Andrew H, Cummings, Steven R, Kerlikowske, Karla, and Vachon, Celine M
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Health Services and Systems ,Biomedical and Clinical Sciences ,Health Sciences ,Oncology and Carcinogenesis ,Cancer ,Women's Health ,Aging ,Breast Cancer ,Prevention ,Adult ,Age Factors ,Breast Density ,Breast Neoplasms ,Female ,Humans ,Mammary Glands ,Human ,Middle Aged ,Radiography ,Receptor ,ErbB-2 ,Receptors ,Estrogen ,Risk Factors ,Young Adult ,Receptor ,erbB-2 ,Medical and Health Sciences ,Epidemiology ,Biomedical and clinical sciences ,Health sciences - Abstract
BackgroundMammographic density (MD) is a strong breast cancer risk factor. We previously reported associations of percent mammographic density (PMD) with larger and node-positive tumors across all ages, and estrogen receptor (ER)-negative status among women ages
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- 2015
41. The Contributions of Breast Density and Common Genetic Variation to Breast Cancer Risk
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Vachon, Celine M, Pankratz, V Shane, Scott, Christopher G, Haeberle, Lothar, Ziv, Elad, Jensen, Matthew R, Brandt, Kathleen R, Whaley, Dana H, Olson, Janet E, Heusinger, Katharina, Hack, Carolin C, Jud, Sebastian M, Beckmann, Matthias W, Schulz-Wendtland, Ruediger, Tice, Jeffrey A, Norman, Aaron D, Cunningham, Julie M, Purrington, Kristen S, Easton, Douglas F, Sellers, Thomas A, Kerlikowske, Karla, Fasching, Peter A, and Couch, Fergus J
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Biomedical and Clinical Sciences ,Oncology and Carcinogenesis ,Breast Cancer ,Prevention ,Cancer ,Clinical Research ,Women's Health ,4.1 Discovery and preclinical testing of markers and technologies ,Adult ,Aged ,Area Under Curve ,Breast ,Breast Density ,Breast Neoplasms ,Case-Control Studies ,Female ,Genetic Predisposition to Disease ,Genetic Variation ,Germany ,Humans ,Logistic Models ,Mammary Glands ,Human ,Middle Aged ,Odds Ratio ,Polymorphism ,Single Nucleotide ,Radiography ,Risk Assessment ,Risk Factors ,United States ,Oncology & Carcinogenesis ,Oncology and carcinogenesis - Abstract
We evaluated whether a 76-locus polygenic risk score (PRS) and Breast Imaging Reporting and Data System (BI-RADS) breast density were independent risk factors within three studies (1643 case patients, 2397 control patients) using logistic regression models. We incorporated the PRS odds ratio (OR) into the Breast Cancer Surveillance Consortium (BCSC) risk-prediction model while accounting for its attributable risk and compared five-year absolute risk predictions between models using area under the curve (AUC) statistics. All statistical tests were two-sided. BI-RADS density and PRS were independent risk factors across all three studies (P interaction = .23). Relative to those with scattered fibroglandular densities and average PRS (2(nd) quartile), women with extreme density and highest quartile PRS had 2.7-fold (95% confidence interval [CI] = 1.74 to 4.12) increased risk, while those with low density and PRS had reduced risk (OR = 0.30, 95% CI = 0.18 to 0.51). PRS added independent information (P < .001) to the BCSC model and improved discriminatory accuracy from AUC = 0.66 to AUC = 0.69. Although the BCSC-PRS model was well calibrated in case-control data, independent cohort data are needed to test calibration in the general population.
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- 2015
42. Conformational rearrangements enable iterative backbone N-methylation in RiPP biosynthesis
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Miller, Fredarla S., Crone, Kathryn K., Jensen, Matthew R., Shaw, Sudipta, Harcombe, William R., Elias, Mikael H., and Freeman, Michael F.
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- 2021
- Full Text
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43. Combinatorial patterns of gene expression changes contribute to variable expressivity of the developmental delay-associated 16p12.1 deletion
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Jensen, Matthew, Tyryshkina, Anastasia, Pizzo, Lucilla, Smolen, Corrine, Das, Maitreya, Huber, Emily, Krishnan, Arjun, and Girirajan, Santhosh
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- 2021
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44. Mitigating Bias and Improving Professional Decision-Making through Persuasive Training Games
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Lee, Yu-Hao, primary, Dunbar, Norah E., additional, Miller, Claude H., additional, Bessarabova, Elena, additional, Jensen, Matthew, additional, Wilson, Scott, additional, Elizondo, Javier, additional, Burgoon, Judee, additional, and Valacich, Joseph, additional
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- 2021
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45. Rare variants in the genetic background modulate cognitive and developmental phenotypes in individuals carrying disease-associated variants
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Pizzo, Lucilla, Jensen, Matthew, Polyak, Andrew, Rosenfeld, Jill A., Mannik, Katrin, Krishnan, Arjun, McCready, Elizabeth, Pichon, Olivier, Le Caignec, Cedric, Van Dijck, Anke, Pope, Kate, Voorhoeve, Els, Yoon, Jieun, Stankiewicz, Paweł, Cheung, Sau Wai, Pazuchanics, Damian, Huber, Emily, Kumar, Vijay, Kember, Rachel L., Mari, Francesca, Curró, Aurora, Castiglia, Lucia, Galesi, Ornella, Avola, Emanuela, Mattina, Teresa, Fichera, Marco, Mandarà, Luana, Vincent, Marie, Nizon, Mathilde, Mercier, Sandra, Bénéteau, Claire, Blesson, Sophie, Martin-Coignard, Dominique, Mosca-Boidron, Anne-Laure, Caberg, Jean-Hubert, Bucan, Maja, Zeesman, Susan, Nowaczyk, Małgorzata J.M., Lefebvre, Mathilde, Faivre, Laurence, Callier, Patrick, Skinner, Cindy, Keren, Boris, Perrine, Charles, Prontera, Paolo, Marle, Nathalie, Renieri, Alessandra, Reymond, Alexandre, Kooy, R. Frank, Isidor, Bertrand, Schwartz, Charles, Romano, Corrado, Sistermans, Erik, Amor, David J., Andrieux, Joris, and Girirajan, Santhosh
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- 2019
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46. Implicit and explicit training in the mitigation of cognitive bias through the use of a serious game
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Dunbar, Norah E, Miller, Claude H, Adame, Bradley J, Elizondo, Javier, Wilson, Scott N, Lane, Brianna L, Kauffman, Abigail Allums, Bessarabova, Elena, Jensen, Matthew L, Straub, Sara K, Lee, Yu-Hao, Burgoon, Judee K, Valacich, Joseph J, Jenkins, Jeffrey, and Zhang, Jun
- Subjects
Video games ,Cognitive biases ,Training ,Bias mitigation ,Instructional testing ,Information Systems ,Psychology ,Cognitive Sciences ,Education - Abstract
Heuristics can interfere with information processing and hinder decision-making when more systematic processes that might lead to better decisions are ignored. Based on the heuristic-systematic model (HSM) of information processing, a serious training game (called MACBETH) was designed to address and mitigate cognitive biases that interfere with the analysis of evidence and the generation of hypotheses. Two biases are the focus of this paper - fundamental attribution error and confirmation bias. The efficacy of the serious game on knowledge and mitigation of biases was examined using an experiment in which participants (N = 703) either played the MACBETH game or watched an instructional video about the biases. Results demonstrate the game to be more effective than the video at mitigating cognitive biases when explicit training methods are combined with repetitive play. Moreover, explicit instruction within the game provided greater familiarity and knowledge of the biases relative to implicit instruction. Suggestions for game development for purposes of enhancing cognitive processing and bias mitigation based on the MACBETH game design are discussed. © 2014 Elsevier Ltd. All rights reserved.
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- 2014
47. Leveraging a large language model to predict protein phase transition: a physical, multiscale and interpretable approach
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Frank, Mor, primary, Ni, Pengyu, additional, Jensen, Matthew, additional, and Gerstein, Mark B, additional
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- 2023
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48. Online Information Filtering: The Role of Contextual Cues in Electronic Networks of Practice
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Fadel, Kelly J., primary, Jensen, Matthew L., additional, and Meservy, Thomas O., additional
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- 2023
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49. Book Review
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Jensen, Matthew D.
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- 2018
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50. Structure and Biosynthesis of Proteusin RiPP Natural Products
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Jensen, Matthew R., primary and Freeman, Michael F., additional
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- 2020
- Full Text
- View/download PDF
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