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1. Additional file 5 of Development and validation of an AI-enabled digital breast cancer assay to predict early-stage breast cancer recurrence within 6 years

Author

Fernandez, Gerardo, Prastawa, Marcel, Madduri, Abishek Sainath, Scott, Richard, Marami, Bahram, Shpalensky, Nina, Cascetta, Krystal, Sawyer, Mary, Chan, Monica, Koll, Giovanni, Shtabsky, Alexander, Feliz, Aaron, Hansen, Thomas, Veremis, Brandon, Cordon-Cardo, Carlos, Zeineh, Jack, and Donovan, Michael J.

Abstract

Additional file 5.. Supplementary Figure 2: Kaplan-Meier Comparison of Histologic Grade vs. AI-grade in Full Train and Validation Cohort.

Published
2023
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2. Additional file 5 of The presence of circulating genetically abnormal cells in blood predicts risk of lung cancer in individuals with indeterminate pulmonary nodules

Author

Tahvilian, Shahram, Kuban, Joshua D., Yankelevitz, David F., Leventon, Daniel, Henschke, Claudia I., Zhu, Jeffrey, Baden, Lara, Yip, Rowena, Hirsch, Fred R., Reed, Rebecca, Brown, Ashley, Muldoon, Allison, Trejo, Michael, Katchman, Benjamin A., Donovan, Michael J., and Pagano, Paul C.

Abstract

Supplementary Material 5

Published
2023
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3. Additional file 4 of The presence of circulating genetically abnormal cells in blood predicts risk of lung cancer in individuals with indeterminate pulmonary nodules

Author

Tahvilian, Shahram, Kuban, Joshua D., Yankelevitz, David F., Leventon, Daniel, Henschke, Claudia I., Zhu, Jeffrey, Baden, Lara, Yip, Rowena, Hirsch, Fred R., Reed, Rebecca, Brown, Ashley, Muldoon, Allison, Trejo, Michael, Katchman, Benjamin A., Donovan, Michael J., and Pagano, Paul C.

Abstract

Supplementary Material 4

Published
2023
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4. Additional file 1 of The presence of circulating genetically abnormal cells in blood predicts risk of lung cancer in individuals with indeterminate pulmonary nodules

Author

Tahvilian, Shahram, Kuban, Joshua D., Yankelevitz, David F., Leventon, Daniel, Henschke, Claudia I., Zhu, Jeffrey, Baden, Lara, Yip, Rowena, Hirsch, Fred R., Reed, Rebecca, Brown, Ashley, Muldoon, Allison, Trejo, Michael, Katchman, Benjamin A., Donovan, Michael J., and Pagano, Paul C.

Abstract

Supplementary Material 1

Published
2023
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5. Additional file 3 of The presence of circulating genetically abnormal cells in blood predicts risk of lung cancer in individuals with indeterminate pulmonary nodules

Author

Tahvilian, Shahram, Kuban, Joshua D., Yankelevitz, David F., Leventon, Daniel, Henschke, Claudia I., Zhu, Jeffrey, Baden, Lara, Yip, Rowena, Hirsch, Fred R., Reed, Rebecca, Brown, Ashley, Muldoon, Allison, Trejo, Michael, Katchman, Benjamin A., Donovan, Michael J., and Pagano, Paul C.

Abstract

Supplementary Material 3

Published
2023
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6. Additional file 6 of The presence of circulating genetically abnormal cells in blood predicts risk of lung cancer in individuals with indeterminate pulmonary nodules

Author

Tahvilian, Shahram, Kuban, Joshua D., Yankelevitz, David F., Leventon, Daniel, Henschke, Claudia I., Zhu, Jeffrey, Baden, Lara, Yip, Rowena, Hirsch, Fred R., Reed, Rebecca, Brown, Ashley, Muldoon, Allison, Trejo, Michael, Katchman, Benjamin A., Donovan, Michael J., and Pagano, Paul C.

Abstract

Supplementary Material 6

Published
2023
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7. Additional file 6 of Development and validation of an AI-enabled digital breast cancer assay to predict early-stage breast cancer recurrence within 6 years

Author

Fernandez, Gerardo, Prastawa, Marcel, Madduri, Abishek Sainath, Scott, Richard, Marami, Bahram, Shpalensky, Nina, Cascetta, Krystal, Sawyer, Mary, Chan, Monica, Koll, Giovanni, Shtabsky, Alexander, Feliz, Aaron, Hansen, Thomas, Veremis, Brandon, Cordon-Cardo, Carlos, Zeineh, Jack, and Donovan, Michael J.

Abstract

Additional file 6. Supplementary Table 3: Demographics of Combined Training and Validation Oncotype Dataset.

Published
2023
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8. Additional file 2 of The presence of circulating genetically abnormal cells in blood predicts risk of lung cancer in individuals with indeterminate pulmonary nodules

Author

Tahvilian, Shahram, Kuban, Joshua D., Yankelevitz, David F., Leventon, Daniel, Henschke, Claudia I., Zhu, Jeffrey, Baden, Lara, Yip, Rowena, Hirsch, Fred R., Reed, Rebecca, Brown, Ashley, Muldoon, Allison, Trejo, Michael, Katchman, Benjamin A., Donovan, Michael J., and Pagano, Paul C.

Abstract

Supplementary Material 2

Published
2023
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9. Additional file 1 of Development and validation of an AI-enabled digital breast cancer assay to predict early-stage breast cancer recurrence within 6 years

Author

Fernandez, Gerardo, Prastawa, Marcel, Madduri, Abishek Sainath, Scott, Richard, Marami, Bahram, Shpalensky, Nina, Cascetta, Krystal, Sawyer, Mary, Chan, Monica, Koll, Giovanni, Shtabsky, Alexander, Feliz, Aaron, Hansen, Thomas, Veremis, Brandon, Cordon-Cardo, Carlos, Zeineh, Jack, and Donovan, Michael J.

Abstract

Additional file 1. Methods.

Published
2023
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10. Additional file 4 of Development and validation of an AI-enabled digital breast cancer assay to predict early-stage breast cancer recurrence within 6 years

Author

Fernandez, Gerardo, Prastawa, Marcel, Madduri, Abishek Sainath, Scott, Richard, Marami, Bahram, Shpalensky, Nina, Cascetta, Krystal, Sawyer, Mary, Chan, Monica, Koll, Giovanni, Shtabsky, Alexander, Feliz, Aaron, Hansen, Thomas, Veremis, Brandon, Cordon-Cardo, Carlos, Zeineh, Jack, and Donovan, Michael J.

Abstract

Additional file 4. Supplementary Figure 1: MindAct Clinical Risk Models vs. PDxBr in training (A) vs validation (B).

Published
2023
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11. Additional file 8 of Development and validation of an AI-enabled digital breast cancer assay to predict early-stage breast cancer recurrence within 6 years

Author

Fernandez, Gerardo, Prastawa, Marcel, Madduri, Abishek Sainath, Scott, Richard, Marami, Bahram, Shpalensky, Nina, Cascetta, Krystal, Sawyer, Mary, Chan, Monica, Koll, Giovanni, Shtabsky, Alexander, Feliz, Aaron, Hansen, Thomas, Veremis, Brandon, Cordon-Cardo, Carlos, Zeineh, Jack, and Donovan, Michael J.

Abstract

Additional file 8. Supplemental Figure 3: AUC/C-index Oncotype Models.

Published
2023
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12. Additional file 7 of Development and validation of an AI-enabled digital breast cancer assay to predict early-stage breast cancer recurrence within 6 years

Author

Fernandez, Gerardo, Prastawa, Marcel, Madduri, Abishek Sainath, Scott, Richard, Marami, Bahram, Shpalensky, Nina, Cascetta, Krystal, Sawyer, Mary, Chan, Monica, Koll, Giovanni, Shtabsky, Alexander, Feliz, Aaron, Hansen, Thomas, Veremis, Brandon, Cordon-Cardo, Carlos, Zeineh, Jack, and Donovan, Michael J.

Abstract

Additional file 7. Supplementary Table 4A-D: Oncotype models.

Published
2023
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13. Additional file 3 of Development and validation of an AI-enabled digital breast cancer assay to predict early-stage breast cancer recurrence within 6 years

Author

Fernandez, Gerardo, Prastawa, Marcel, Madduri, Abishek Sainath, Scott, Richard, Marami, Bahram, Shpalensky, Nina, Cascetta, Krystal, Sawyer, Mary, Chan, Monica, Koll, Giovanni, Shtabsky, Alexander, Feliz, Aaron, Hansen, Thomas, Veremis, Brandon, Cordon-Cardo, Carlos, Zeineh, Jack, and Donovan, Michael J.

Abstract

Additional file 3. Supplementary Table 2: PDxBr Training and Validation: Image Feature Only Model.

Published
2023
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14. Additional file 2 of Development and validation of an AI-enabled digital breast cancer assay to predict early-stage breast cancer recurrence within 6 years

Author

Fernandez, Gerardo, Prastawa, Marcel, Madduri, Abishek Sainath, Scott, Richard, Marami, Bahram, Shpalensky, Nina, Cascetta, Krystal, Sawyer, Mary, Chan, Monica, Koll, Giovanni, Shtabsky, Alexander, Feliz, Aaron, Hansen, Thomas, Veremis, Brandon, Cordon-Cardo, Carlos, Zeineh, Jack, and Donovan, Michael J.

Abstract

Additional file 2. Supplementary Table 1: PDxBr Training and Validation: Clinical Feature only model.

Published
2023
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15. Validation of the Attitudes Towards Psychological Online Interventions Questionnaire Among Black Americans: Cross-cultural Confirmatory Factor Analysis (Preprint)

Author

Donovan Michael Ellis and Page Lyn Anderson

Abstract

BACKGROUND Acceptability of digital mental health interventions is a significant predictor of treatment-seeking behavior and engagement. However, acceptability has been conceptualized and operationalized in various ways, which decreases measurement precision and leads to heterogeneous conclusions about acceptability. Standardized self-report measures of acceptability have been developed, which have the potential to ameliorate these problems, but none have demonstrated evidence for validation among Black communities, which limits our understanding of attitudes toward these interventions among racially minoritized groups with well-documented barriers to mental health treatment. OBJECTIVE This study aims to examine the psychometric validity and reliability of one of the first and most widely used measures of acceptability, the Attitudes Towards Psychological Online Interventions Questionnaire, among a Black American sample. METHODS Participants (N=254) were recruited from a large southeastern university and the surrounding metropolitan area and completed the self-report measure via a web-based survey. A confirmatory factor analysis using mean and variance adjusted weighted least squares estimation was conducted to examine the validity of the underlying hierarchical 4-factor structure proposed by the original authors of the scale. An alternative, hierarchical 2-factor structure model and bifactor model were examined for comparative fit. RESULTS The findings indicated that the bifactor model demonstrated a superior fit (comparative fit index=0.96, Tucker-Lewis index=0.94, standardized root mean squared residual=0.03, and root mean square error of approximation=0.09) compared with both 2- and 4-factor hierarchical structure models. CONCLUSIONS The findings suggest that, within a Black American sample, there may be greater utility in interpreting the Attitudes Towards Psychological Online Interventions Questionnaire subscales as attitudinal constructs that are distinct from the global acceptability factor. The theoretical and practical implications for culturally responsive measurements were explored.

Published
2022

16. ASSESSMENT OF MODEL CONVERSION FROM GENESYS TO MAGIC SYSTEM OF SYSTEMS ARCHITECT FOR MODEL-BASED SYSTEMS ENGINEERING INTEROPERABILITY

Author

Donovan, Michael C., Beery, Paul T., Giachetti, Ronald E., and Systems Engineering (SE)

Subjects
MBSE, Vitech, model transformation, modeling, tool interoperability, D/SET, modeling tools, models, SDL, GENESYS, Magic Systems of Systems Architect, Core, model interoperability, ontology, SysML, conversion, Cameo, semantics
Abstract

This thesis investigates whether the information contained in a Vitech Genesys model can retain its informational accuracy after conversion into a Dassault Systemes’ Magic System of Systems Architect (MSOSA) model. The thesis uses a sample system model in Vitech that implements the system definition language (SDL) and converts it to MSOSA, which uses the systems modeling language (SysML). The study reviewed conversion methods available to the user and converted a Genesys model to an MSOSA model using the only available method, Excel. The study then assessed the converted model and outlined any post-migration remediation. The results of this thesis demonstrate that the currently available methods are feasible but inefficient, as only 34% of the entities and 9% of the relationships transferred successfully during the experiment. Genesys can output tabular data that represents system model entities and relationships; however, the MSOSA import function was unable to correctly import entities that had one-to-many relationships with other entities. Consequently, the user must perform manual manipulation during the conversion process. Furthermore, ontological differences between the tools prevented the complete import of behavioral data, since many SDL entities map to more than one SysML entity. Based on the results, this thesis recommends pursuing an extensible markup language–based software solution for Genesys and MSOSA and developing a formal Navy and Marine Corps ontology. Civilian, Department of the Navy Approved for public release. Distribution is unlimited.

Published
2022

17. A laser parameter study on enhancing proton generation from microtube foil targets

Author

Strehlow, Joseph, Kim, Joohwan, Bailly-Grandvaux, Mathieu, Bolaños, Simon, Smith, Herbie, Haid, Alex, Alfonso, Emmanuel L, Aniculaesei, Constantin, Chen, Hui, Ditmire, Todd, Donovan, Michael E, Hansen, Stephanie B, Hegelich, Bjorn M, McLean, Harry S, Quevedo, Hernan J, Spinks, Michael M, and Beg, Farhat N

Subjects
Multidisciplinary
Abstract

The interaction of an intense laser with a solid foil target can drive $$\sim$$ ∼ TV/m electric fields, accelerating ions to MeV energies. In this study, we experimentally observe that structured targets can dramatically enhance proton acceleration in the target normal sheath acceleration regime. At the Texas Petawatt Laser facility, we compared proton acceleration from a $$1\, {\upmu }\hbox {m}$$ 1 μ m flat Ag foil, to a fixed microtube structure 3D printed on the front side of the same foil type. A pulse length (140–450 fs) and intensity ((4–10) $$\times 10^{20}$$ × 10 20 W/cm$$^2$$ 2 ) study found an optimum laser configuration (140 fs, 4 $$\times 10^{20}$$ × 10 20 W/cm$$^2$$ 2 ), in which microtube targets increase the proton cutoff energy by 50% and the yield of highly energetic protons ($$>10$$ > 10 MeV) by a factor of 8$$\times$$ × . When the laser intensity reaches $$10^{21}$$ 10 21 W/cm$$^2$$ 2 , the prepulse shutters the microtubes with an overcritical plasma, damping their performance. 2D particle-in-cell simulations are performed, with and without the preplasma profile imported, to better understand the coupling of laser energy to the microtube targets. The simulations are in qualitative agreement with the experimental results, and show that the prepulse is necessary to account for when the laser intensity is sufficiently high.

Published
2022

18. Validation of the Attitudes Towards Psychological Online Interventions Questionnaire Among Black Americans: Cross-cultural Confirmatory Factor Analysis

Author

Donovan Michael Ellis and Page Lyn Anderson

Subjects
Psychiatry and Mental health
Abstract

Background Acceptability of digital mental health interventions is a significant predictor of treatment-seeking behavior and engagement. However, acceptability has been conceptualized and operationalized in various ways, which decreases measurement precision and leads to heterogeneous conclusions about acceptability. Standardized self-report measures of acceptability have been developed, which have the potential to ameliorate these problems, but none have demonstrated evidence for validation among Black communities, which limits our understanding of attitudes toward these interventions among racially minoritized groups with well-documented barriers to mental health treatment. Objective This study aims to examine the psychometric validity and reliability of one of the first and most widely used measures of acceptability, the Attitudes Towards Psychological Online Interventions Questionnaire, among a Black American sample. Methods Participants (N=254) were recruited from a large southeastern university and the surrounding metropolitan area and completed the self-report measure via a web-based survey. A confirmatory factor analysis using mean and variance adjusted weighted least squares estimation was conducted to examine the validity of the underlying hierarchical 4-factor structure proposed by the original authors of the scale. An alternative, hierarchical 2-factor structure model and bifactor model were examined for comparative fit. Results The findings indicated that the bifactor model demonstrated a superior fit (comparative fit index=0.96, Tucker-Lewis index=0.94, standardized root mean squared residual=0.03, and root mean square error of approximation=0.09) compared with both 2- and 4-factor hierarchical structure models. Conclusions The findings suggest that, within a Black American sample, there may be greater utility in interpreting the Attitudes Towards Psychological Online Interventions Questionnaire subscales as attitudinal constructs that are distinct from the global acceptability factor. The theoretical and practical implications for culturally responsive measurements were explored.

Published
2023

19. High-charge 10 GeV electron acceleration in a 10 cm nanoparticle-assisted hybrid wakefield accelerator

Author

Aniculaesei, Constantin, Ha, Thanh, Yoffe, Samuel, McCary, Edward, Spinks, Michael M, Quevedo, Hernan J., Labun, Lance, Labun, Ou Z., Sain, Ritwik, Hannasch, Andrea, Zgadzaj, Rafal, Pagano, Isabella, Franco-Altamirano, Jose A., Ringuette, Martin L., Gaul, Erhart, Luedtke, Scott V., Tiwari, Ganesh, Ersfeld, Bernhard, Brunetti, Enrico, Ruhl, Hartmut, Ditmire, Todd, Bruce, Sandra, Donovan, Michael E., Jaroszynski, Dino A., Downer, Michael C., and Hegelich, Bjorn Manuel

Subjects
Plasma Physics (physics.plasm-ph), Accelerator Physics (physics.acc-ph), FOS: Physical sciences, Physics - Accelerator Physics, Physics - Plasma Physics
Abstract

In an electron wakefield accelerator, an intense laser pulse or charged particle beam excites plasma waves. Under proper conditions, electrons from the background plasma are trapped in the plasma wave and accelerated to ultra-relativistic velocities. We present recent results from a proof-of-principle wakefield acceleration experiment that reveal a unique synergy between a laser-driven and particle-driven accelerator: a high-charge laser-wakefield accelerated electron bunch can drive its own wakefield while simultaneously drawing energy from the laser pulse via direct laser acceleration. This process continues to accelerate electrons beyond the usual decelerating phase of the wakefield, thus reaching much higher energies. We find that the 10-centimeter-long nanoparticle-assisted wakefield accelerator can generate 340 pC, 10.4+-0.6 GeV electron bunches with 3.4 GeV RMS convolved energy spread and 0.9 mrad RMS divergence. It can also produce bunches with lower energy, a few percent energy spread, and a higher charge. This synergistic mechanism and the simplicity of the experimental setup represent a step closer to compact tabletop particle accelerators suitable for applications requiring high charge at high energies, such as free electron lasers or radiation sources producing muon beams.

Published
2022
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21. Thermodynamics of 5-Bromouracil Tautomerization From First-Principles Molecular Dynamics Simulations

Author

Cyran, Jenée, Donovan, Michael, Vollmer, Doris, Siro Brigiano, Flavio, Pezzotti, Simone, Galimberti, Daria, Bonn, Mischa, Backus, Ellen, Holroyd, Leo, Bühl, Michael, Gaigeot, Marie-Pierre, van Mourik, Tanja, Max Planck Institute for Polymer Research, Max-Planck-Gesellschaft, Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement (LAMBE), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Cergy Pontoise (UCP), Université Paris-Seine-Université Paris-Seine-Université d'Évry-Val-d'Essonne (UEVE)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Saclay (COmUE), EaStCHEM School of Chemistry, University of St Andrews [Scotland], and School of Chemistry

Subjects
Engineering, 010304 chemical physics, business.industry, National service, Library science, 010402 general chemistry, 01 natural sciences, Engineering and Physical Sciences, 0104 chemical sciences, Research council, 0103 physical sciences, European commission, [PHYS.PHYS.PHYS-CHEM-PH]Physics [physics]/Physics [physics]/Chemical Physics [physics.chem-ph], business, ComputingMilieux_MISCELLANEOUS
Abstract

The authors acknowledge support from the Engineering and Physical Sciences Research Council (EPSRC) UK National Service for Computational Chemistry Software (NSCCS); from GENCI (Grand equipement national de calcul intensif); and from CINES (Centre informatique national de l’enseignement superieur). LFH and TvM gratefully acknowledge support from the HPC-EUROPA2 project with the support of the European Commission - Capacities Area - Research Infrastructures. LFH is grateful to the EPSRC for studentship support through the Doctoral Training Account scheme (grant code EP/K503162/1).

Published
2019

22. MOESM1 of Multiple immunofluorescence assay identifies upregulation of Active β-catenin in prostate cancer

Author

Puig, Pere, Nadina Erill, Terricabras, Marta, Subirana, Isaac, González-García, Judit, Adrià Asensi-Puig, Donovan, Michael, Mengual, Lourdes, M. Agulló-Ortuño, Olivan, Mireia, Alcaraz, Antonio, López-Martín, José, Torres, Inés, Rodríguez-Peralto, José, Rodríguez-Antolín, Alfredo, Morote, Juan, and González-Rumayor, Víctor

Abstract

Additional file 1: Figure S1. Subcellular localization of ABC. Magnified images demonstrating subcellular localization of ABC.

Published
2019
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23. SmartCow: a project aimed at improving phenotyping capacity across cattle research infrastructures in Europe

Author

René Baumont, Dewhurst, R. J., Sadjad Danesh Mesragan, Catherine Hurtaud, Abraham Orchard, Bjoern Kuhla, Cécile Martin, Lene Munksgaard, Chris Reynolds, Donovan, Michael O., Bernard Esmein, ProdInra, Archive Ouverte, Unité Mixte de Recherche sur les Herbivores - UMR 1213 (UMRH), Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Scotland's Rural College (SRUC), Leibniz Institute for Farm Animal Biology (FBN), Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Agrimetrics, Aarhus University [Aarhus], University of Reading (UOR), Teagasc Agriculture and Food Development Authority (Teagasc), European Association for Animal Production (EAAP), Unité Mixte de Recherches sur les Herbivores - UMR 1213 (UMRH), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de la Recherche Agronomique (INRA), Scotland's Rural College (SCUR), Leibniz Institute for Farm Animal Biology, AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA), and VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Institut National de la Recherche Agronomique (INRA)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement

Subjects
[SDV] Life Sciences [q-bio], projet européen, bovin, Infrastructure de recherche, [SDV]Life Sciences [q-bio], phénotypage, SmartCow
Abstract

International audience; The future sustainability of cattle production will require improved resource use efficiency, reduced GHG emissions, and improved animal health and welfare. Facing this challenge needs far more complex animal traits than previously and they need to be assessed under a range of conditions. For example, the concepts of feed efficiency, robustness and sensitivity to health disorders are more difficult to include in selection indices than simple productivity traits. It is now time to look for means to investigate complex animal traits using smart technologies and rapid analytical methods in a standardised way applied in many contexts. At the same time, the European Strategy Forum on Research Infrastructures (ESFRI) roadmap clearly identified the need for improved coordination, harmonisation and access to European research infrastructures (RIs) on farm animals. The SmartCow project (www.smartcow.eu) answering the call H2020-INFRAIA2016-2017 was selected by the European Commission for 4 years funding starting from 1st February 2018. Three types of activities are developed to increase the phenotyping capabilities of the cattle European sector. Networking activities will create, thanks to an inventory and an interactive map, a unique portal to key European cattle RIs. The project will ensure that existing guidelines are adopted [e.g., the ICAR Guidelines for Bovine Functional Traits (section 7) are cited in distinct guidelines generated by the Networking activities]. When no international standard exists (e.g. feed efficiency, digestive, behavioural traits…), the project works towards the use of unified measurement methods through common standards and guidelines. The development of the cattle ontology of traits (ATOL and EOL; www.atol-ontology.com) through SmartCow will also be an important step to unify research methodologies and link definition of traits with standardized methods. A cloud-based database platform developed by Agrimetrics using web semantic will ensure integration, sharing and interoperability of data generated by the project leading to an open European database on cattle traits and phenotypes. Joint research activities will generate innovations for the research community on cattle towards the use of less-invasive methods and high-throughput phenotyping. Refining in vivo methods to evaluate feed efficiency and emissions will generate innovations in experimental design and planning for more accuracy. The development of new biomarkers (proxies) that can be easily measured in milk, faeces, urine, or blood through rapid analytical methods (NIRS) will bring new phenotyping capacities. The development of tools to generate new and improved information from animal sensors and other routinely collected data (e.g. prediction of individual cow status in terms of health and welfare) will also enable a more efficient phenotyping and genetic selection of cattle. Finally, the project organizes transnational access to major RIs: INRA in France, Scotland’s Rural College and University of Reading in the UK, Wageningen University and WUR/DLO in the Netherlands, FBN-Leibniz in Germany, Teagasc in Ireland, Aarhus University in Denmark and IRTA in Spain. It provides access to around 2500 dairy and 1000 beef cattle and facilitate up to 30 research projects to be financed by the SmartCow project after selection through specific calls. Eleven projects have already been selected after the first call.

Published
2019

24. Multiple immunofluorescence assay identifies upregulation of Active β-catenin in prostate cancer

Author

Puig Rosell, Pere, Erill, Nadina, Terricabras, Marta, Subirana, Isaac, González-García, Judit, Asensi-Puig, Adrià, Donovan, Michael J., Mengual, Lourdes, Agulló-Ortuño, M. Teresa, Olivan, M., Alcaraz, Antonio, López-Martín, José A., de Torres, Inés, Rodríguez-Peralto, José Luis, Rodríguez-Antolín, Alfredo, Morote Robles, Juan, González-Rumayor, Víctor, Universitat Autònoma de Barcelona, Institut Català de la Salut, [Puig P, Erill N, Terricabras M, Subirana I, González-García J, Asensi-Puig A] R&D Department, Atrys Health, Barcelona, Spain. [Olivan M, De Torres I, Morote J] Grup de Recerca Biomèdica en Urologia, Vall d’Hebron Institut de Recerca, Barcelona, Spain. Universitat Autònoma de Barcelona, Barcelona, Spain., Vall d'Hebron Barcelona Hospital Campus, and Hospital Universitari Vall d'Hebron

Subjects
0301 basic medicine, Male, Active β-catenin, Cell, Fluorescent Antibody Technique, lcsh:Medicine, Other subheadings::/analysis [Other subheadings], Amino Acids, Peptides, and Proteins::Proteins::Armadillo Domain Proteins::beta Catenin [CHEMICALS AND DRUGS], Otros calificadores::Otros calificadores::Otros calificadores::/enzimología [Otros calificadores], Prostate cancer, 0302 clinical medicine, aminoácidos, péptidos y proteínas::proteínas::proteínas del dominio armadillo::beta catenina [COMPUESTOS QUÍMICOS Y DROGAS], Prostate, 030212 general & internal medicine, lcsh:QH301-705.5, beta Catenin, fenómenos químicos::fenómenos bioquímicos::transducción de señales [FENÓMENOS Y PROCESOS], Enzimologia, medicine.diagnostic_test, Otros calificadores::/análisis [Otros calificadores], Biochemical markers, Wnt signaling pathway, General Medicine, Middle Aged, Up-Regulation, Research Note, medicine.anatomical_structure, HLA class1, Marcadors bioquímics, Chemical Phenomena::Biochemical Phenomena::Signal Transduction [PHENOMENA AND PROCESSES], Biomarker (medicine), Adult, Neoplasms::Neoplasms by Site::Urogenital Neoplasms::Genital Neoplasms, Male::Prostatic Neoplasms [DISEASES], Immunofluorescence, General Biochemistry, Genetics and Molecular Biology, Immunofluorescència, 03 medical and health sciences, Downregulation and upregulation, medicine, Biomarkers, Tumor, Humans, Wnt/β-catenin pathway, lcsh:Science (General), Aged, Càncer de pròstata, Pròstata - Càncer, business.industry, lcsh:R, Prostatic Neoplasms, Proteins, medicine.disease, neoplasias::neoplasias por localización::neoplasias urogenitales::neoplasias de los genitales masculinos::neoplasias de la próstata [ENFERMEDADES], 030104 developmental biology, lcsh:Biology (General), Catenin, Cancer research, Systems pathology, business, Proteïnes, Other subheadings::Other subheadings::Other subheadings::/enzymology [Other subheadings], lcsh:Q1-390
Abstract

Prostate cancer; Systems pathology; Wnt/β-catenin pathway Càncer de pròstata; Patologia de sistemes; Via Wnt/β-catenina Cáncer de próstata; Patología de sistemas; Vía Wnt/β-catenina OBJECTIVES: To apply a systems pathology-based approach to the quantification of nuclear Active β-catenin and human leukocyte antigen class I, and assess the biomarker involvement in a cohort of prostate tumor patients. RESULTS: The systems pathology approach applied allows a precise quantification of the marker expression in the different cell compartments as well as the determination of the areas that coexpress two markers. Our data shows that the accumulation of β-catenin in the nuclear compartment is significantly decreased in the adjacent normal areas when compared to tumor of the same patients (p

Published
2019

25. Diverse plant-insect associations from the latest Cretaceous and early Paleocene of Patagonia, Argentina

Author

Donovan, Michael P., Iglesias, Ari, Wilf, Peter, Labandeira, Conrad, and Cúneo, Néstor Rubén

Subjects
herbivory, plant-insects, Paleontología, CIENCIAS NATURALES Y EXACTAS, gondwana, paleobotany, Ciencias de la Tierra y relacionadas con el Medio Ambiente
Abstract

Little is known about the recovery of terrestrial ecosystems after the end-Cretaceous extinction outside of the Western Interiorof North America, relatively close to the 66 Ma bolide impact crater in Chicxulub, Mexico. A previous report showed that in Patagonia, Argentina,insect damage on fossil leaves decreased from the latest Cretaceous to early Paleocene but recovered to pre-extinction levelswithin ca. four million years. Here, we present the first detailed study of these Patagonian plant-insect associations, key componentsof terrestrial food webs, during the latest Cretaceous and three time slices from the early Paleocene recovery. The lithologic units studiedare the uppermost Cretaceous portion of the Lefipán Formation and the Danian Salamanca and Peñas Coloradas formations in Chubut,Argentina. Seven functional feeding groups are present throughout: hole feeding, margin feeding, skeletonization, surface feeding, piercingand sucking, mining, and galling. Fifty damage types (DTs) were present at Maastrichtian localities, and 39?48 were found at Danian localities.Plant-insect associations that apparently went locally extinct at the end of the Cretaceous include several gall, mine, and piercingand-sucking DTs. Based on our preliminary leaf morphotypes, host plants did not provide refuge for specialized insect herbivores across theK/Pg boundary. Despite a decrease in insect damage diversity after the bolide impact, Danian floras hosted a rich array of DTs, including specializeddamage such as mines and galls. Many of these early Paleocene DTs were not found in the terminal Cretaceous, providing evidencefor a rapid recovery of plant-insect associations regionally. Fil: Donovan, Michael P.. State University of Pennsylvania; Estados Unidos Fil: Iglesias, Ari. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. University of Maryland; Estados Unidos Fil: Wilf, Peter. State University of Pennsylvania; Estados Unidos Fil: Labandeira, Conrad. Capital Normal University; China. University of Maryland; Estados Unidos Fil: Cúneo, Néstor Rubén. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Museo Paleontológico Egidio Feruglio; Argentina

Published
2018

27. Additional file 2: of Effects of pathogenic CNVs on physical traits in participants of the UK Biobank

Author

Owen, David, Bracher-Smith, Mathew, Kendall, Kimberley, Rees, Elliott, Einon, Mark, Escott-Price, Valentina, Owen, Michael, O’Donovan, Michael, and Kirov, George

Abstract

Figure S1. Images of the changes in the physical traits (normalised z-score values) associated with each CNV and their 95% confidence intervals (95%CI). (XLSX 335 kb) (DOCX 1040 kb)

Published
2018
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28. Additional file 2: of Expression quantitative trait loci in the developing human brain and their enrichment in neuropsychiatric disorders

Author

O’Brien, Heath, Hannon, Eilis, Hill, Matthew, Toste, Carolina, Robertson, Matthew, Morgan, Joanne, McLaughlin, Gemma, Lewis, Cathryn, Schalkwyk, Leonard, Hall, Lynsey, Pardiñas, Antonio, Owen, Michael, O’Donovan, Michael, Mill, Jonathan, and Bray, Nicholas

Abstract

Figures S1-S8. All supplementary figures. (PDF 1212 kb)

Published
2018
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29. The facebase consortium: A comprehensive resource for craniofacial researchers

Author

Brinkley, James F., Fisher, Shannon, Harris, Matthew P., Holmes, Greg, Hooper, Joan E., Jabs, Ethylin Wang, Jones, Kenneth L., Kesselman, Carl, Klein, Ophir D., Maas, Richard L., Marazita, Mary L., Selleri, Licia, Spritz, Richard A., van Bakel, Harm, Visel, Axel, Williams, Trevor J., Wysocka, Joanna, Chai, Yang, Aho, Robert, Alkuraya, Fowzan, Barozzi, Iros, Chard, Kyle, Cox, Timothy C., Cunningham, Michael L., Detwiler, Landon T., Donovan, Michael J., Feingold, Eleanor, Fitzpatrick, David, Green, Jeremy B A, Grimaldi, Alexandre, Grishina, Irina, Hallgrimsson, Benedikt, Harris, Matthew, Ho, Thach Vu, Hochheiser, Harry, Leslie, Elizabeth J., Li, Hong, Liao, Eric, Mejino, Jose L V, Mio, Washington, Nowak, Catherine B., Parada, Carolina, Park, Peter J., Pennacchio, Len, Potter, S. Steven, Rubin, Edward, Ruffins, Seth, Samuels, Bridget D., Sanchez-Lara, Pedro A., Schuler, Robert, Shapiro, Linda G., Spurrell, Cailyn H., Stoler, Joan, Sunyaev, Shamil, Thomas, Paul, Welsh, Ian, Williams, Cristina, and Fukuda-Yuzawa, Yoko

Subjects
0301 basic medicine, Chromatin Immunoprecipitation, Databases, Factual, Biology, Bioinformatics, 03 medical and health sciences, Mice, Resource (project management), Data visualization, Techniques and Resources, Health care, Profiling (information science), Animals, Humans, Craniofacial, Molecular Biology, FaceBase Consortium, Zebrafish, Modalities, business.industry, Skull, Computational Biology, Genomics, Data science, Research Personnel, 3. Good health, Data resource, 030104 developmental biology, Face, FaceBase, Models, Animal, Faceted search, business, Craniofacial development, Developmental Biology
Abstract

The FaceBase Consortium, funded by the National Institute of Dental and Craniofacial Research, National Institutes of Health, is designed to accelerate understanding of craniofacial developmental biology by generating comprehensive data resources to empower the research community, exploring high-throughput technology, fostering new scientific collaborations among researchers and human/computer interactions, facilitating hypothesis-driven research and translating science into improved health care to benefit patients. The resources generated by the FaceBase projects include a number of dynamic imaging modalities, genome-wide association studies, software tools for analyzing human facial abnormalities, detailed phenotyping, anatomical and molecular atlases, global and specific gene expression patterns, and transcriptional profiling over the course of embryonic and postnatal development in animal models and humans. The integrated data visualization tools, faceted search infrastructure, and curation provided by the FaceBase Hub offer flexible and intuitive ways to interact with these multidisciplinary data. In parallel, the datasets also offer unique opportunities for new collaborations and training for researchers coming into the field of craniofacial studies. Here, we highlight the focus of each spoke project and the integration of datasets contributed by the spokes to facilitate craniofacial research., Summary: The FaceBase Consortium is a dynamic, comprehensive resource of craniofacial development, with hundreds of datasets that are freely available to the research community at the FaceBase Hub website.

Published
2016

30. The Quantitative Ethology of the Zebra Finch: A Study in Comparitive Psychometrics

Author

Donovan Michael Ross, Lewis Petrinovich, and Aurelio Jose Figuerero

Subjects
Statistics and Probability, Psychometrics, Discriminant validity, Construct validity, Experimental and Cognitive Psychology, General Medicine, Ethology, Developmental psychology, Inter-rater reliability, Ethogram, Arts and Humanities (miscellaneous), Convergent validity, Psychology, Zebra finch
Abstract

A quantitative ethogram was developed for the Zebra finch, using one-zero focal animal sampling on an ethologically comprehensive checklist of 52 behavioral items, and was assessed for both interobserver reliability and construct validity. Interobserver reliabilities were highly acceptable (an eta-squared of, 923 for aggregation periods of 5 minutes). Nine common factors (Singing & Parenting, Social Proximity, Social Contact, Social Submission, Social Aggression, Sex & Violence, Object Handling, Surface Foraging, and General Activity) produced highly acceptable convergent validities (high factor loadings for most behavioral items) and discriminant validities (low factor intercorrelations). Applying the quantitative methods of psychometrics thus permits the verification of ethological theory and the testing of diverse hypotheses with a high degree of sophistication.

Published
2016

31. Additional file 2: of Development and clinical application of an integrative genomic approach to personalized cancer therapy

Author

Uzilov, Andrew, Ding, Wei, Fink, Marc, Antipin, Yevgeniy, Brohl, Andrew, Davis, Claire, Lau, Chun, Chetanya Pandya, Hardik Shah, Kasai, Yumi, Powell, James, Micchelli, Mark, Castellanos, Rafael, Zhongyang Zhang, Linderman, Michael, Kinoshita, Yayoi, Zweig, Micol, Raustad, Katie, Kakit Cheung, Castillo, Diane, Wooten, Melissa, Bourzgui, Imane, Newman, Leah, Deikus, Gintaras, Bino Mathew, Zhu, Jun, Glicksberg, Benjamin, Aye Moe, Liao, Jun, Edelmann, Lisa, Dudley, Joel, Maki, Robert, Kasarskis, Andrew, Holcombe, Randall, Milind Mahajan, Hao, Ke, Reva, Boris, Longtine, Janina, Starcevic, Daniela, Sebra, Robert, Donovan, Michael, Shuyu Li, Schadt, Eric, and Chen, Rong

Abstract

Supplementary Material: Supplementary Results, Supplementary Methods, Supplementary Table legends. (DOCX 67 kb)

Published
2016
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32. Additional file 9: Figure S6. of Development and clinical application of an integrative genomic approach to personalized cancer therapy

Author

Uzilov, Andrew, Ding, Wei, Fink, Marc, Antipin, Yevgeniy, Brohl, Andrew, Davis, Claire, Lau, Chun, Chetanya Pandya, Hardik Shah, Kasai, Yumi, Powell, James, Micchelli, Mark, Castellanos, Rafael, Zhongyang Zhang, Linderman, Michael, Kinoshita, Yayoi, Zweig, Micol, Raustad, Katie, Kakit Cheung, Castillo, Diane, Wooten, Melissa, Bourzgui, Imane, Newman, Leah, Deikus, Gintaras, Bino Mathew, Zhu, Jun, Glicksberg, Benjamin, Aye Moe, Liao, Jun, Edelmann, Lisa, Dudley, Joel, Maki, Robert, Kasarskis, Andrew, Holcombe, Randall, Milind Mahajan, Hao, Ke, Reva, Boris, Longtine, Janina, Starcevic, Daniela, Sebra, Robert, Donovan, Michael, Shuyu Li, Schadt, Eric, and Chen, Rong

Abstract

Comparison of weighed correlations of log2ratio (a, data from Additional file 7: Figure S4) and log2mBAF (b, data from Additional file 8: Figure S5) for assays on FFPE- versus frozen-derived tumor DNA material. D statistic and p-value from 2-sided KS test are shown for FFPE- versus frozen-derived correlation distributions (see "Methods" for details on KS test). (PPTX 76 kb)

Published
2016
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33. Additional file 4: Figure S2. of Development and clinical application of an integrative genomic approach to personalized cancer therapy

Author

Uzilov, Andrew, Ding, Wei, Fink, Marc, Antipin, Yevgeniy, Brohl, Andrew, Davis, Claire, Lau, Chun, Chetanya Pandya, Hardik Shah, Kasai, Yumi, Powell, James, Micchelli, Mark, Castellanos, Rafael, Zhongyang Zhang, Linderman, Michael, Kinoshita, Yayoi, Zweig, Micol, Raustad, Katie, Kakit Cheung, Castillo, Diane, Wooten, Melissa, Bourzgui, Imane, Newman, Leah, Deikus, Gintaras, Bino Mathew, Zhu, Jun, Glicksberg, Benjamin, Aye Moe, Liao, Jun, Edelmann, Lisa, Dudley, Joel, Maki, Robert, Kasarskis, Andrew, Holcombe, Randall, Milind Mahajan, Hao, Ke, Reva, Boris, Longtine, Janina, Starcevic, Daniela, Sebra, Robert, Donovan, Michael, Shuyu Li, Schadt, Eric, and Chen, Rong

Subjects
health care facilities, manpower, and services, health services administration, education, health care economics and organizations
Abstract

Detailed workflow of an integrative genomic approach in personalized cancer therapy. (PPTX 303 kb)

Published
2016
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36. Additional file 8: Figure S5. of Development and clinical application of an integrative genomic approach to personalized cancer therapy

Author

Uzilov, Andrew, Ding, Wei, Fink, Marc, Antipin, Yevgeniy, Brohl, Andrew, Davis, Claire, Lau, Chun, Chetanya Pandya, Hardik Shah, Kasai, Yumi, Powell, James, Micchelli, Mark, Castellanos, Rafael, Zhongyang Zhang, Linderman, Michael, Kinoshita, Yayoi, Zweig, Micol, Raustad, Katie, Kakit Cheung, Castillo, Diane, Wooten, Melissa, Bourzgui, Imane, Newman, Leah, Deikus, Gintaras, Bino Mathew, Zhu, Jun, Glicksberg, Benjamin, Aye Moe, Liao, Jun, Edelmann, Lisa, Dudley, Joel, Maki, Robert, Kasarskis, Andrew, Holcombe, Randall, Milind Mahajan, Hao, Ke, Reva, Boris, Longtine, Janina, Starcevic, Daniela, Sebra, Robert, Donovan, Michael, Shuyu Li, Schadt, Eric, and Chen, Rong

Abstract

Correlation of somatic CNA heterozygosity change (median â log2mBAFâ segment statistic from saasCNV of tumor with respect to normal) between WES and array data. The same partitions are used as in Additional file 7: Figure S4, and weighed correlation in the lower right corner is also computed in the same way. (PPTX 981 kb)

Published
2016
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37. Additional file 10: Figure S7. of Development and clinical application of an integrative genomic approach to personalized cancer therapy

Author

Uzilov, Andrew, Ding, Wei, Fink, Marc, Antipin, Yevgeniy, Brohl, Andrew, Davis, Claire, Lau, Chun, Chetanya Pandya, Hardik Shah, Kasai, Yumi, Powell, James, Micchelli, Mark, Castellanos, Rafael, Zhongyang Zhang, Linderman, Michael, Kinoshita, Yayoi, Zweig, Micol, Raustad, Katie, Kakit Cheung, Castillo, Diane, Wooten, Melissa, Bourzgui, Imane, Newman, Leah, Deikus, Gintaras, Bino Mathew, Zhu, Jun, Glicksberg, Benjamin, Aye Moe, Liao, Jun, Edelmann, Lisa, Dudley, Joel, Maki, Robert, Kasarskis, Andrew, Holcombe, Randall, Milind Mahajan, Hao, Ke, Reva, Boris, Longtine, Janina, Starcevic, Daniela, Sebra, Robert, Donovan, Michael, Shuyu Li, Schadt, Eric, and Chen, Rong

Abstract

Distribution of somatic mutation allelic fractions in patient P0011, by mutation type. (PPTX 191 kb)

Published
2016
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38. Additional file 3: Figure S1. of Development and clinical application of an integrative genomic approach to personalized cancer therapy

Author

Uzilov, Andrew, Ding, Wei, Fink, Marc, Antipin, Yevgeniy, Brohl, Andrew, Davis, Claire, Lau, Chun, Chetanya Pandya, Hardik Shah, Kasai, Yumi, Powell, James, Micchelli, Mark, Castellanos, Rafael, Zhongyang Zhang, Linderman, Michael, Kinoshita, Yayoi, Zweig, Micol, Raustad, Katie, Kakit Cheung, Castillo, Diane, Wooten, Melissa, Bourzgui, Imane, Newman, Leah, Deikus, Gintaras, Bino Mathew, Zhu, Jun, Glicksberg, Benjamin, Aye Moe, Liao, Jun, Edelmann, Lisa, Dudley, Joel, Maki, Robert, Kasarskis, Andrew, Holcombe, Randall, Milind Mahajan, Hao, Ke, Reva, Boris, Longtine, Janina, Starcevic, Daniela, Sebra, Robert, Donovan, Michael, Shuyu Li, Schadt, Eric, and Chen, Rong

Abstract

A decision tree approach to predict drug response based on genetic alterations. (PPTX 96 kb)

Published
2016
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39. Additional file 3: Figure S1. of Development and clinical application of an integrative genomic approach to personalized cancer therapy

Author

Uzilov, Andrew, Ding, Wei, Fink, Marc, Antipin, Yevgeniy, Brohl, Andrew, Davis, Claire, Lau, Chun, Chetanya Pandya, Hardik Shah, Kasai, Yumi, Powell, James, Micchelli, Mark, Castellanos, Rafael, Zhongyang Zhang, Linderman, Michael, Kinoshita, Yayoi, Zweig, Micol, Raustad, Katie, Kakit Cheung, Castillo, Diane, Wooten, Melissa, Bourzgui, Imane, Newman, Leah, Deikus, Gintaras, Bino Mathew, Zhu, Jun, Glicksberg, Benjamin, Aye Moe, Liao, Jun, Edelmann, Lisa, Dudley, Joel, Maki, Robert, Kasarskis, Andrew, Holcombe, Randall, Milind Mahajan, Hao, Ke, Reva, Boris, Longtine, Janina, Starcevic, Daniela, Sebra, Robert, Donovan, Michael, Shuyu Li, Schadt, Eric, and Chen, Rong

Abstract

A decision tree approach to predict drug response based on genetic alterations. (PPTX 96 kb)

Published
2016
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40. Anastrozole versus tamoxifen for the prevention of locoregional and contralateral breast cancer in postmenopausal women with locally excised ductal carcinoma in situ (IBIS-II DCIS): A double-blind, randomised controlled trial

Author

Forbes, John F, Sestak, Ivana, Howell, Anthony, Bonanni, Bernardo, Bundred, Nigel, Levy, Christelle, von Minckwitz, Gunter, Eiermann, Wolfgang, Neven, Patrick, Stierer, Michael, Holcombe, Chris, Coleman, Robert E, Jones, Louise, Ellis, Ian, Cuzick, Jack, Sainsbury, Richard, Garber, Judy, Warwick, Jane, Buchanan, Mary, Buser, Katharina, Cawthorn, Simon, Coleman, Robert, Dowsett, Mitch, Eastell, Richard, Ejlertsen, Bent, Forbes, John, Kahan, Zsuzsanna, Baclesse, François, Mansel, Robert, Palva, Tiina, Rydén, Lisa, Stuart, Mary, Vaz, Fatima, Marsiglia, Hugo, Benyoucef, Ahmed, Berton-Rigaud, Dominique, Loustalot, Catherine, Serin, Daniel, Kerbrat, Pierre, Eymard, Jean-Christophe, Giard-Lefevre, Sylvia, Bonichon-Lamichhane, Nathalie, Monnier, Alain, Tubiana-Mathieu, Nicole, Piot, Gilles, de Lara, Christine Tunon, Bernard, Olivier, Simon-Swirski, Hélène, Gladieff, Laurence, Regaud, I Claudius, Fouchet-Goudier, Marie-Joseph, Dohollou, Nadine, Aquitaine, Nord, Elgard-Maitre, Anne-Marie, Bergerat, Jean-Pierre, Petit, Thierry, Marti, Adina, Toussaint, Caroline, Del Piano, Francesco, Ibrahim, Mahmoud, Fric, Danièle, Hönig, Arnd, Müller, Volkmar, Marmé, Frederik, Rautenberg, Beate, Schmidt, Marcus, Hanusch, Claus, Paepke, Stefan, Kaltenecker, Gabriele, Lemster, Sabine, Tio, Joke, Reimer, Toralf, Schnappauf, Benjamin, Baumann, Klaus, Schrader, Iris, Mundhenke, Christoph, Liedtke, Cornelia, Meinerz, Wolfgang, Thomssen, Christoph, Christl, Klaus, Hitschold, Thomas, Goerke, Kay, Kast, Karin, Runnebaum, Ingo, Lindner, Christoph, Scheidel, Peter, Herwig, Uwe, Bangemann, Nikola, Sommer, Harald, Göhring, Kornelia, Tulusan, Augustinus, Stauß, Eva, Köhler, Günter, Zahm, Dirk, Augustin, Doris, Hocke, Andrea, Neunhöffer, Tanja, Schmatloch, Sabine, Heinrich, Georg, Groß, Sabine, Breitbach, G P, Scharl, Anton, Klare, Peter, Stefek, Andrea, Hoffmann, Gerald, Martignoni, Franca, Weiss, Erich, Emons, Günter, Tesch, Hans-Christian, Beckmann, Matthias, Schmutzler, Rita, Schütte, Martin, Aktas, Bahriye, Hille-Betz, Ursula, Deryal, Mustafa, Dan Costa, Serban, Blümel, Beate, Göhring, Uwe-Jochen, Kleine-Tebbe, Anke, Schumacher, Claudia, Jasmin, Pourfard, Christoph, Uleer, Kullmer, Uwe, Krabisch, Petra, Gätje, Regine, Schwenzer, Thomas, Hindenburg, Hans-Joachim, Rempen, Andreas, Höffkes, Heinz-Gert, Stickeler, Elmar, Reffert, Christian, Seitz, Stephan, Splitt, Gerd, Böhne, Petra, Gnauert, Karsten, Strittmatter, Hans-Joachim, Baake, Gerold, Rezai, Mahdi, Noesselt, Thomas, Köhne, C-H, Hanf, Volker, Strumberg, Dirk, Dall, Peter, Schleicher, Peter, Schleicher, Bernd, Beldermann, Frank, Berghorn, Michael, Baerens, Dirk-Thoralf, Kolberg, Hans-Christian, Bauer, Lelia, Brucker, Cosima, Steck, Thomas, Boyle, Frances, Chaudhuri, Anupam, Wagga, Wagga, Moylan, Eugene, Donovan, Jenny, Della-Fiorentina, Stephen, Abdi, Ehtesham, Marx, Gavin, Beadle, Geoffrey, Donovan, Michael, Bennett, Ian, Gill, Peter Grantley, Baker, Caroline, Masters, Richard, Blum, Robert, Collins, John, Law, Michael, Hart, Stewart, Kannourakis, George, Snyder, Raymond, Joseph, David, McCrystal, Michael, Campbell, Ian, Jakesz, Raimund, Selim, Ursula, Singer, Christian, Heck, Dietmar, Greil, Richard, Ramoni, Angela, Bjelic-Radisic, Vesna, Reichenauer, Arno, Horvath, Wilfried, Thaler, Josef, Fridrik, Michael, Keckstein, Joerg, Jan, Lamote, L'Hermitte, Marc, Roelstrate, Heidi, Dirix, Luc, Bambust, Inneke, Seret, Monique, Liebens, Fabienne, Maerevoet, Maria, D'Hondt, Lionel, Berliere, Martine, Nogaret, Jean-Marie, Simon, Phillipe, O'Hanlon, Deirdre, Redmond, Henry Paul, Hill, Arnold, Evoy, Denis, Kerin, Michael, Gupta, Rajnish, Martin, Michael J, Fritis, Marcela, Schwartz, Ricardo, Yañez, Maria Loreto, Peralta, Octavio, Graiff, Claudio, Artioli, Fabrizio, Generali, Daniele, Orzalesi, Lorenzo, Visini, Marilena, Michiara, Maria, Pavesi, Lorenzo, Ravaioli, Alberto, Porpiglia, Mauro, Puglisi, Fabio, Pinotti, Graziella, Brincat, Stephen, Buser, Katharina S, Rabaglio, Manuela, Rauch, Daniel, Chappuis, Pierre O, Zaman, Khalil, Bucher, Susanne, Bolliger, Barbara, Pagani, Olivia, Falck, Anna-Karin, Kaij, Jakob, Margolin, Sara, Muslumanoglum, Mahmut, Bertelli, Gianfilippo, Bramley, Maria, Bristol, James, Chandrasekharan, Sankaran, Crellin, Perric, Daoud, Raouf, Dodwell, David, Drew, Philip, Dubey, Sidharth, Evans, Abigail, Ferguson, Douglas, Gendy, Raafat, Hamed, Hisham, Harding-McKean, Claudia, Horgan, Kieran, Iqbal, Shabana, Jibril, Jibril A, Kokan, Jalal, Kneeshaw, Peter, Lansdown, Mark, Lennard, Tom, Linforth, Rick, McIntosh, Stuart, Mitra, Sankha, Neades, Glyn, Ooi, Jane Louise, Patel, Ashraf, Rayter, Zenon, Reichert, Robert, Roberts, Fiona, Roche, Nicola, Rogers, Colin, Royle, Gavin, Shah, Elizabeth, Sibbering, Mark, Skene, Anthony Iain, Smith, Simon, Sparrow, Geoffrey, Thompson, Alastair, Vaidya, Jayant, Wolstenholme, Virginia, Wood, Jeremy, Yiangou, Constantinos, Zammit, Charles, Thornton, Rochelle, Probert, Flonda, Fong, Akiko, Francis, Nicole, Gili, Manuela, Eigenberger, Rosita, Supply, Daisy, Lefever, Inge, Muller, Bettina, Zlatar, Zdenka, Feer, Petra, Gkantiragas, Ioannis, Virkki, Marjo, Everhard, Sibille, Lemonnier, Jerome, Garcia, Sara, Ghanem, Saliha, Cole, Anna, O'Hare, Debra, Cronin, Elaine, Roche, Trudi, Kennedy, Emer, Ballot, Jo, Killilea, Niamh, Jennings, Marian, Lowry, Laura, Maxwell, Moira, Burke, Margaret, Gonzaga, Aliana Guerrieri, Bollani, Giorgia, Bianchetti, Andrea, Scalvini, Anna, Cretella, Elisabetta, Pasqualini, Antonella, Gobbi, Angela, Roselli, Jenny, Lagati, Angelita, Rapacchi, Elena, Lanza, Annalisa, Pini, Emanuela, Picardo, Elisa, Maggiorotto, Furio, Sottile, Roberta, Vallini, Ilaria, Cilia, Nadia, Patel, Mital, Bamford, Linda, Robertshaw, Helen, Inman, Hayle, Hill, Naomi, Dexter, Jane, Peasgood, Emily, Batty, Imogen, Cocks, Shirley, Mistry, Raksha, Sidders, Mary, Foulstone, Emily, Garlicka, Helen, Dawe, Catherine, Elliott, Jackie, Rooke, Kathy, Morris, Christine, Lester, Yvonne, Gibson, Sian, Chittock, Jill, Skelton, Amy, Gallimore, Elizabeth, Downes, Charlotte, Billett, Lynn, Caddy, Simone, Cumming, Helen, Cowell-Smith, Sharon, Turner, Caroline, Fernando, Sunjalee, Goodwin, Sarah, Taylor, Jo-Anne, Baines, Kizzy, Downer, Susan, Pilcher, Alice, Dobson, Tracey, Osborne, Lynn, Kuenzig, Greg, Hancock, Denise, Melia, Deborah, Gullaksen, Elaine, Hartup, Susan, Henson, Amy, Gibb, Jane, Coombs, Sarah, Taylor, Caroline, Kirkby, Amy, Thomas, Issy, Makinson, Karen, Kano, Yukie, Shah, Zoheb, Hardstaff, Lisa, Townley, Barbara, Hill, Philippa, McCurrie, Marilyn, Grassby, Sue, Henderson, Pamela, Talbot, Elizabeth, Bell, Ashley, Kanani, Reshma, Johnson, Joanne, Jones, Richard, Foster, Mel, Troke, Becky, Congdon, Hilary, Pascoe, Julie, Whelan, Sian, Edwards, Jenna, Brinkworth, Elaine, Blizard, Sheila, Clarke, Alison, Stevens, Kim, Harvey, Carol, Stacey, Jill, Mitchell, Sadie, Lowry, Tracey, Buckley, Sarah, Collins, Clare, Green, Liz, Jones, Helen, Conteh, Veronica, Ducket, Tracey, Kotze, Michelle, Strider, Paula, Stouraitis, Marina, Sundberg, Jan, Babiker, Abdel, Collins, Rory, Klijn, Jan, Ralston, Stuart, Tattersall, Martin, Weller, Ian, De Sousa, Andreia, Edwards, Rob, Ferguson, Sheila, Hickman, Jane, Johnson, Damian, Haidar, Nadia, Hammond, Victoria, Heighway, Emma, Ndoutoumou, Amalia, Sahota, Navdip, White, Laura, Aigret, Benoit, Batra, Priyanka, Knox, Jill, Oke, Adedayo, Ostler, Richard, and Sasieni, Peter

Subjects
Medicine (all), Medizin, skin and connective tissue diseases
Abstract

Third-generation aromatase inhibitors are more effective than tamoxifen for preventing recurrence in postmenopausal women with hormone-receptor-positive invasive breast cancer. However, it is not known whether anastrozole is more effective than tamoxifen for women with hormone-receptor-positive ductal carcinoma in situ (DCIS). Here, we compare the efficacy of anastrozole with that of tamoxifen in postmenopausal women with hormone-receptor-positive DCIS.In a double-blind, multicentre, randomised placebo-controlled trial, we recruited women who had been diagnosed with locally excised, hormone-receptor-positive DCIS. Eligible women were randomly assigned in a 1:1 ratio by central computer allocation to receive 1 mg oral anastrozole or 20 mg oral tamoxifen every day for 5 years. Randomisation was stratified by major centre or hub and was done in blocks (six, eight, or ten). All trial personnel, participants, and clinicians were masked to treatment allocation and only the trial statistician had access to treatment allocation. The primary endpoint was all recurrence, including recurrent DCIS and new contralateral tumours. All analyses were done on a modified intention-to-treat basis (in all women who were randomised and did not revoke consent for their data to be included) and proportional hazard models were used to compute hazard ratios and corresponding confidence intervals. This trial is registered at the ISRCTN registry, number ISRCTN37546358.Between March 3, 2003, and Feb 8, 2012, we enrolled 2980 postmenopausal women from 236 centres in 14 countries and randomly assigned them to receive anastrozole (1449 analysed) or tamoxifen (1489 analysed). Median follow-up was 7·2 years (IQR 5·6-8·9), and 144 breast cancer recurrences were recorded. We noted no statistically significant difference in overall recurrence (67 recurrences for anastrozole vs 77 for tamoxifen; HR 0·89 [95% CI 0·64-1·23]). The non-inferiority of anastrozole was established (upper 95% CI

Published
2016

41. Additional file 14: Figure S10. of Development and clinical application of an integrative genomic approach to personalized cancer therapy

Author

Uzilov, Andrew, Ding, Wei, Fink, Marc, Antipin, Yevgeniy, Brohl, Andrew, Davis, Claire, Lau, Chun, Chetanya Pandya, Hardik Shah, Kasai, Yumi, Powell, James, Micchelli, Mark, Castellanos, Rafael, Zhongyang Zhang, Linderman, Michael, Kinoshita, Yayoi, Zweig, Micol, Raustad, Katie, Kakit Cheung, Castillo, Diane, Wooten, Melissa, Bourzgui, Imane, Newman, Leah, Deikus, Gintaras, Bino Mathew, Zhu, Jun, Glicksberg, Benjamin, Aye Moe, Liao, Jun, Edelmann, Lisa, Dudley, Joel, Maki, Robert, Kasarskis, Andrew, Holcombe, Randall, Milind Mahajan, Hao, Ke, Reva, Boris, Longtine, Janina, Starcevic, Daniela, Sebra, Robert, Donovan, Michael, Shuyu Li, Schadt, Eric, and Chen, Rong

Abstract

Sanger sequencing validation results of novel somatic EGFR mutation p.D587H (chr7:55233009G>C) in patient P0015. Sanger sequencing was carried out on normal and tumor DNA from this patient using forward and reverse primers (Beckman Coulter Genomics, Danvers, Massachusetts). Traces shown are as displayed by 4Peaks visualization software for Mac OS X ( http://nucleobytes.com/4peaks ). Two replicate sequencing reactions were carried out for each primer and sample combination, yielding the same result (second replicate not shown). Base numbering shown is relative to priming site. The allelic fraction of p.D587H in tumor was 19.4 % (387/1998 reads have variant) in targeted panel sequencing, explaining the relatively small size of the Sanger peak for the alternate allele. (PPTX 240 kb)

Published
2016
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42. Additional file 11: Figure S8. of Development and clinical application of an integrative genomic approach to personalized cancer therapy

Author

Uzilov, Andrew, Ding, Wei, Fink, Marc, Antipin, Yevgeniy, Brohl, Andrew, Davis, Claire, Lau, Chun, Chetanya Pandya, Hardik Shah, Kasai, Yumi, Powell, James, Micchelli, Mark, Castellanos, Rafael, Zhongyang Zhang, Linderman, Michael, Kinoshita, Yayoi, Zweig, Micol, Raustad, Katie, Kakit Cheung, Castillo, Diane, Wooten, Melissa, Bourzgui, Imane, Newman, Leah, Deikus, Gintaras, Bino Mathew, Zhu, Jun, Glicksberg, Benjamin, Aye Moe, Liao, Jun, Edelmann, Lisa, Dudley, Joel, Maki, Robert, Kasarskis, Andrew, Holcombe, Randall, Milind Mahajan, Hao, Ke, Reva, Boris, Longtine, Janina, Starcevic, Daniela, Sebra, Robert, Donovan, Michael, Shuyu Li, Schadt, Eric, and Chen, Rong

Subjects
hemic and lymphatic diseases, neoplasms
Abstract

A scatter plot of CCND1 gene expression versus log2 copy number ratio (tumor/normal). Each dot represents a patient tumor sample. Tumor types are color-coded. The two breast cancer patients where we reported CCND1 amplification are P0002 and P0040. (PPTX 112 kb)

Published
2016
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43. Additional file 7: Figure S4. of Development and clinical application of an integrative genomic approach to personalized cancer therapy

Author

Uzilov, Andrew, Ding, Wei, Fink, Marc, Antipin, Yevgeniy, Brohl, Andrew, Davis, Claire, Lau, Chun, Chetanya Pandya, Hardik Shah, Kasai, Yumi, Powell, James, Micchelli, Mark, Castellanos, Rafael, Zhongyang Zhang, Linderman, Michael, Kinoshita, Yayoi, Zweig, Micol, Raustad, Katie, Kakit Cheung, Castillo, Diane, Wooten, Melissa, Bourzgui, Imane, Newman, Leah, Deikus, Gintaras, Bino Mathew, Zhu, Jun, Glicksberg, Benjamin, Aye Moe, Liao, Jun, Edelmann, Lisa, Dudley, Joel, Maki, Robert, Kasarskis, Andrew, Holcombe, Randall, Milind Mahajan, Hao, Ke, Reva, Boris, Longtine, Janina, Starcevic, Daniela, Sebra, Robert, Donovan, Michael, Shuyu Li, Schadt, Eric, and Chen, Rong

Abstract

Correlation of somatic CNA fold-change (median “log2ratio” segment statistic from saasCNV of tumor with respect to normal) between WES and array data. The genome was split into non-overlapping partitions such that each partition begins and ends on a CNA segment break from either assay, but no CNA segment breaks occur inside any partition (“partition” feature of “bedops” software tool v2.4.14, https://github.com/bedops/bedops ). Thus, each partition overlaps exactly one segment from WES data and exactly one segment from array data. Each point is a partition, with plotted values taken from the pair of segments that overlap it. Lower right corner shows the weighed (by partition length) Pearson correlation between WES- and array-derived log2ratio values for partitions, computed using the “corr” function from R (v3.2.1) package “boot” (v1.3-17). “FFPE” and “frozen” in all plots refers to tissue source of tumor DNA. (PPTX 1114 kb)

Published
2016
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44. Additional file 9: Figure S6. of Development and clinical application of an integrative genomic approach to personalized cancer therapy

Author

Uzilov, Andrew, Ding, Wei, Fink, Marc, Antipin, Yevgeniy, Brohl, Andrew, Davis, Claire, Lau, Chun, Chetanya Pandya, Hardik Shah, Kasai, Yumi, Powell, James, Micchelli, Mark, Castellanos, Rafael, Zhongyang Zhang, Linderman, Michael, Kinoshita, Yayoi, Zweig, Micol, Raustad, Katie, Kakit Cheung, Castillo, Diane, Wooten, Melissa, Bourzgui, Imane, Newman, Leah, Deikus, Gintaras, Bino Mathew, Zhu, Jun, Glicksberg, Benjamin, Aye Moe, Liao, Jun, Edelmann, Lisa, Dudley, Joel, Maki, Robert, Kasarskis, Andrew, Holcombe, Randall, Milind Mahajan, Hao, Ke, Reva, Boris, Longtine, Janina, Starcevic, Daniela, Sebra, Robert, Donovan, Michael, Shuyu Li, Schadt, Eric, and Chen, Rong

Abstract

Comparison of weighed correlations of log2ratio (a, data from Additional file 7: Figure S4) and log2mBAF (b, data from Additional file 8: Figure S5) for assays on FFPE- versus frozen-derived tumor DNA material. D statistic and p-value from 2-sided KS test are shown for FFPE- versus frozen-derived correlation distributions (see "Methods" for details on KS test). (PPTX 76 kb)

Published
2016
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47. Additional file 7: Figure S4. of Development and clinical application of an integrative genomic approach to personalized cancer therapy

Author

Uzilov, Andrew, Ding, Wei, Fink, Marc, Antipin, Yevgeniy, Brohl, Andrew, Davis, Claire, Lau, Chun, Chetanya Pandya, Hardik Shah, Kasai, Yumi, Powell, James, Micchelli, Mark, Castellanos, Rafael, Zhongyang Zhang, Linderman, Michael, Kinoshita, Yayoi, Zweig, Micol, Raustad, Katie, Kakit Cheung, Castillo, Diane, Wooten, Melissa, Bourzgui, Imane, Newman, Leah, Deikus, Gintaras, Bino Mathew, Zhu, Jun, Glicksberg, Benjamin, Aye Moe, Liao, Jun, Edelmann, Lisa, Dudley, Joel, Maki, Robert, Kasarskis, Andrew, Holcombe, Randall, Milind Mahajan, Hao, Ke, Reva, Boris, Longtine, Janina, Starcevic, Daniela, Sebra, Robert, Donovan, Michael, Shuyu Li, Schadt, Eric, and Chen, Rong

Abstract

Correlation of somatic CNA fold-change (median “log2ratio” segment statistic from saasCNV of tumor with respect to normal) between WES and array data. The genome was split into non-overlapping partitions such that each partition begins and ends on a CNA segment break from either assay, but no CNA segment breaks occur inside any partition (“partition” feature of “bedops” software tool v2.4.14, https://github.com/bedops/bedops ). Thus, each partition overlaps exactly one segment from WES data and exactly one segment from array data. Each point is a partition, with plotted values taken from the pair of segments that overlap it. Lower right corner shows the weighed (by partition length) Pearson correlation between WES- and array-derived log2ratio values for partitions, computed using the “corr” function from R (v3.2.1) package “boot” (v1.3-17). “FFPE” and “frozen” in all plots refers to tissue source of tumor DNA. (PPTX 1114 kb)

Published
2016
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48. Additional file 8: Figure S5. of Development and clinical application of an integrative genomic approach to personalized cancer therapy

Author

Uzilov, Andrew, Ding, Wei, Fink, Marc, Antipin, Yevgeniy, Brohl, Andrew, Davis, Claire, Lau, Chun, Chetanya Pandya, Hardik Shah, Kasai, Yumi, Powell, James, Micchelli, Mark, Castellanos, Rafael, Zhongyang Zhang, Linderman, Michael, Kinoshita, Yayoi, Zweig, Micol, Raustad, Katie, Kakit Cheung, Castillo, Diane, Wooten, Melissa, Bourzgui, Imane, Newman, Leah, Deikus, Gintaras, Bino Mathew, Zhu, Jun, Glicksberg, Benjamin, Aye Moe, Liao, Jun, Edelmann, Lisa, Dudley, Joel, Maki, Robert, Kasarskis, Andrew, Holcombe, Randall, Milind Mahajan, Hao, Ke, Reva, Boris, Longtine, Janina, Starcevic, Daniela, Sebra, Robert, Donovan, Michael, Shuyu Li, Schadt, Eric, and Chen, Rong

Abstract

Correlation of somatic CNA heterozygosity change (median â log2mBAFâ segment statistic from saasCNV of tumor with respect to normal) between WES and array data. The same partitions are used as in Additional file 7: Figure S4, and weighed correlation in the lower right corner is also computed in the same way. (PPTX 981 kb)

Published
2016
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49. Additional file 5: of Development and clinical application of an integrative genomic approach to personalized cancer therapy

Author

Uzilov, Andrew, Ding, Wei, Fink, Marc, Antipin, Yevgeniy, Brohl, Andrew, Davis, Claire, Lau, Chun, Chetanya Pandya, Hardik Shah, Kasai, Yumi, Powell, James, Micchelli, Mark, Castellanos, Rafael, Zhongyang Zhang, Linderman, Michael, Kinoshita, Yayoi, Zweig, Micol, Raustad, Katie, Kakit Cheung, Castillo, Diane, Wooten, Melissa, Bourzgui, Imane, Newman, Leah, Deikus, Gintaras, Bino Mathew, Zhu, Jun, Glicksberg, Benjamin, Aye Moe, Liao, Jun, Edelmann, Lisa, Dudley, Joel, Maki, Robert, Kasarskis, Andrew, Holcombe, Randall, Milind Mahajan, Hao, Ke, Reva, Boris, Longtine, Janina, Starcevic, Daniela, Sebra, Robert, Donovan, Michael, Shuyu Li, Schadt, Eric, and Chen, Rong

Subjects
body regions, nervous system, fungi
Abstract

Example PDF document of genomic findings returned to patients and their treating physicians in this study. Each section of this document was taken from an actual returned document, but to protect patient privacy, different sections were taken from different patient documents and information identifying the patient and specimens was removed. (PDF 367 kb)

Published
2016
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50. Additional file 4: Figure S2. of Development and clinical application of an integrative genomic approach to personalized cancer therapy

Author

Uzilov, Andrew, Ding, Wei, Fink, Marc, Antipin, Yevgeniy, Brohl, Andrew, Davis, Claire, Lau, Chun, Chetanya Pandya, Hardik Shah, Kasai, Yumi, Powell, James, Micchelli, Mark, Castellanos, Rafael, Zhongyang Zhang, Linderman, Michael, Kinoshita, Yayoi, Zweig, Micol, Raustad, Katie, Kakit Cheung, Castillo, Diane, Wooten, Melissa, Bourzgui, Imane, Newman, Leah, Deikus, Gintaras, Bino Mathew, Zhu, Jun, Glicksberg, Benjamin, Aye Moe, Liao, Jun, Edelmann, Lisa, Dudley, Joel, Maki, Robert, Kasarskis, Andrew, Holcombe, Randall, Milind Mahajan, Hao, Ke, Reva, Boris, Longtine, Janina, Starcevic, Daniela, Sebra, Robert, Donovan, Michael, Shuyu Li, Schadt, Eric, and Chen, Rong

Subjects
health care facilities, manpower, and services, health services administration, education, health care economics and organizations
Abstract

Detailed workflow of an integrative genomic approach in personalized cancer therapy. (PPTX 303 kb)

Published
2016
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