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2. Black Box Probabilistic Numerics

Author

Teymur, Onur, Foley, Christopher N., Breen, Philip G., Karvonen, Toni, and Oates, Chris. J.

Subjects
Mathematics - Numerical Analysis, Statistics - Computation, Statistics - Methodology, Statistics - Machine Learning
Abstract

Probabilistic numerics casts numerical tasks, such the numerical solution of differential equations, as inference problems to be solved. One approach is to model the unknown quantity of interest as a random variable, and to constrain this variable using data generated during the course of a traditional numerical method. However, data may be nonlinearly related to the quantity of interest, rendering the proper conditioning of random variables difficult and limiting the range of numerical tasks that can be addressed. Instead, this paper proposes to construct probabilistic numerical methods based only on the final output from a traditional method. A convergent sequence of approximations to the quantity of interest constitute a dataset, from which the limiting quantity of interest can be extrapolated, in a probabilistic analogue of Richardson's deferred approach to the limit. This black box approach (1) massively expands the range of tasks to which probabilistic numerics can be applied, (2) inherits the features and performance of state-of-the-art numerical methods, and (3) enables provably higher orders of convergence to be achieved. Applications are presented for nonlinear ordinary and partial differential equations, as well as for eigenvalue problems-a setting for which no probabilistic numerical methods have yet been developed.

Published
2021

3. Database Intrusion Detection Systems (DIDs): Insider Threat Detection via Behavioural-based Anomaly Detection Systems -- A Brief Survey of Concepts and Approaches

Author

Khan, Muhammad Imran, Foley, Simon N., and O'Sullivan, Barry

Subjects
Computer Science - Cryptography and Security
Abstract

One of the data security and privacy concerns is of insider threats, where legitimate users of the system abuse the access privileges they hold. The insider threat to data security means that an insider steals or leaks sensitive personal information. Database Intrusion detection systems, specifically behavioural-based database intrusion detection systems, have been shown effective in detecting insider attacks. This paper presents background concepts on database intrusion detection systems in the context of detecting insider threats and examines existing approaches in the literature on detecting malicious accesses by an insider to Database Management Systems (DBMS)., Comment: 24 pages

Published
2020

4. FinnGen provides genetic insights from a well-phenotyped isolated population

Author

Kurki, Mitja I., Karjalainen, Juha, Palta, Priit, Sipilä, Timo P., Kristiansson, Kati, Donner, Kati M., Reeve, Mary P., Laivuori, Hannele, Aavikko, Mervi, Kaunisto, Mari A., Loukola, Anu, Lahtela, Elisa, Mattsson, Hannele, Laiho, Päivi, Della Briotta Parolo, Pietro, Lehisto, Arto A., Kanai, Masahiro, Mars, Nina, Rämö, Joel, Kiiskinen, Tuomo, Heyne, Henrike O., Veerapen, Kumar, Rüeger, Sina, Lemmelä, Susanna, Zhou, Wei, Ruotsalainen, Sanni, Pärn, Kalle, Hiekkalinna, Tero, Koskelainen, Sami, Paajanen, Teemu, Llorens, Vincent, Gracia-Tabuenca, Javier, Siirtola, Harri, Reis, Kadri, Elnahas, Abdelrahman G., Sun, Benjamin, Foley, Christopher N., Aalto-Setälä, Katriina, Alasoo, Kaur, Arvas, Mikko, Auro, Kirsi, Biswas, Shameek, Bizaki-Vallaskangas, Argyro, Carpen, Olli, Chen, Chia-Yen, Dada, Oluwaseun A., Ding, Zhihao, Ehm, Margaret G., Eklund, Kari, Färkkilä, Martti, Finucane, Hilary, Ganna, Andrea, Ghazal, Awaisa, Graham, Robert R., Green, Eric M., Hakanen, Antti, Hautalahti, Marco, Hedman, Åsa K., Hiltunen, Mikko, Hinttala, Reetta, Hovatta, Iiris, Hu, Xinli, Huertas-Vazquez, Adriana, Huilaja, Laura, Hunkapiller, Julie, Jacob, Howard, Jensen, Jan-Nygaard, Joensuu, Heikki, John, Sally, Julkunen, Valtteri, Jung, Marc, Junttila, Juhani, Kaarniranta, Kai, Kähönen, Mika, Kajanne, Risto, Kallio, Lila, Kälviäinen, Reetta, Kaprio, Jaakko, Kerimov, Nurlan, Kettunen, Johannes, Kilpeläinen, Elina, Kilpi, Terhi, Klinger, Katherine, Kosma, Veli-Matti, Kuopio, Teijo, Kurra, Venla, Laisk, Triin, Laukkanen, Jari, Lawless, Nathan, Liu, Aoxing, Longerich, Simonne, Mägi, Reedik, Mäkelä, Johanna, Mäkitie, Antti, Malarstig, Anders, Mannermaa, Arto, Maranville, Joseph, Matakidou, Athena, Meretoja, Tuomo, Mozaffari, Sahar V., Niemi, Mari E. K., Niemi, Marianna, Niiranen, Teemu, O´Donnell, Christopher J., Obeidat, Ma´en, Okafo, George, Ollila, Hanna M., Palomäki, Antti, Palotie, Tuula, Partanen, Jukka, Paul, Dirk S., Pelkonen, Margit, Pendergrass, Rion K., Petrovski, Slavé, Pitkäranta, Anne, Platt, Adam, Pulford, David, Punkka, Eero, Pussinen, Pirkko, Raghavan, Neha, Rahimov, Fedik, Rajpal, Deepak, Renaud, Nicole A., Riley-Gillis, Bridget, Rodosthenous, Rodosthenis, Saarentaus, Elmo, Salminen, Aino, Salminen, Eveliina, Salomaa, Veikko, Schleutker, Johanna, Serpi, Raisa, Shen, Huei-yi, Siegel, Richard, Silander, Kaisa, Siltanen, Sanna, Soini, Sirpa, Soininen, Hilkka, Sul, Jae Hoon, Tachmazidou, Ioanna, Tasanen, Kaisa, Tienari, Pentti, Toppila-Salmi, Sanna, Tukiainen, Taru, Tuomi, Tiinamaija, Turunen, Joni A., Ulirsch, Jacob C., Vaura, Felix, Virolainen, Petri, Waring, Jeffrey, Waterworth, Dawn, Yang, Robert, Nelis, Mari, Reigo, Anu, Metspalu, Andres, Milani, Lili, Esko, Tõnu, Fox, Caroline, Havulinna, Aki S., Perola, Markus, Ripatti, Samuli, Jalanko, Anu, Laitinen, Tarja, Mäkelä, Tomi P., Plenge, Robert, McCarthy, Mark, Runz, Heiko, Daly, Mark J., and Palotie, Aarno

Published
2023
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5. Newton vs the machine: solving the chaotic three-body problem using deep neural networks

Author

Breen, Philip G., Foley, Christopher N., Boekholt, Tjarda, and Zwart, Simon Portegies

Subjects
Astrophysics - Astrophysics of Galaxies, Astrophysics - Solar and Stellar Astrophysics, Computer Science - Machine Learning, Physics - Computational Physics
Abstract

Since its formulation by Sir Isaac Newton, the problem of solving the equations of motion for three bodies under their own gravitational force has remained practically unsolved. Currently, the solution for a given initialization can only be found by performing laborious iterative calculations that have unpredictable and potentially infinite computational cost, due to the system's chaotic nature. We show that an ensemble of solutions obtained using an arbitrarily precise numerical integrator can be used to train a deep artificial neural network (ANN) that, over a bounded time interval, provides accurate solutions at fixed computational cost and up to 100 million times faster than a state-of-the-art solver. Our results provide evidence that, for computationally challenging regions of phase-space, a trained ANN can replace existing numerical solvers, enabling fast and scalable simulations of many-body systems to shed light on outstanding phenomena such as the formation of black-hole binary systems or the origin of the core collapse in dense star clusters., Comment: 6 pages, 6 figures

Published
2019
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6. A Bulirsch-Stoer algorithm using Gaussian processes

Author

Breen, Philip G. and Foley, Christopher N.

Subjects
Statistics - Machine Learning, Computer Science - Machine Learning
Abstract

In this paper, we treat the problem of evaluating the asymptotic error in a numerical integration scheme as one with inherent uncertainty. Adding to the growing field of probabilistic numerics, we show that Gaussian process regression (GPR) can be embedded into a numerical integration scheme to allow for (i) robust selection of the adaptive step-size parameter and; (ii) uncertainty quantification in predictions of putatively converged numerical solutions. We present two examples of our approach using Richardson's extrapolation technique and the Bulirsch-Stoer algorithm. In scenarios where the error-surface is smooth and bounded, our proposed approach can match the results of the traditional polynomial (parametric) extrapolation methods. In scenarios where the error surface is not well approximated by a finite-order polynomial, e.g. in the vicinity of a pole or in the assessment of a chaotic system, traditional methods can fail, however, the non-parametric GPR approach demonstrates the potential to continue to furnish reasonable solutions in these situations., Comment: comments welcome

Published
2019

7. Science Hackathons for Cyberphysical System Security Research: Putting CPS testbed platforms to good use

Author

Foley, Simon N., Autrel, Fabien, Bourget, Edwin, Cledel, Thomas, Grunenwald, Stephane, Hernan, Jose Rubio, Kabil, Alexandre, Larsen, Raphael, Rooney, Vivien M., and Vanhulst, Kirsten

Subjects
Computer Science - Cryptography and Security
Abstract

A challenge is to develop cyber-physical system scenarios that reflect the diversity and complexity of real-life cyber-physical systems in the research questions that they address. Time-bounded collaborative events, such as hackathons, jams and sprints, are increasingly used as a means of bringing groups of individuals together, in order to explore challenges and develop solutions. This paper describes our experiences, using a science hackathon to bring individual researchers together, in order to develop a common use-case implemented on a shared CPS testbed platform that embodies the diversity in their own security research questions. A qualitative study of the event was conducted, in order to evaluate the success of the process, with a view to improving future similar events.

Published
2018
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8. An Online Consent Maturity Model: Moving from Acceptable Use towards Ethical Practice

Author

Rooney, Vivien M. and Foley, Simon N.

Subjects
Computer Science - Computers and Society
Abstract

The particular characteristics associated with qualitative longitudinal research in the disciplines of psychology and social science have prompted the development of informed consent. There are analogies between these characteristics and the collection and analysis of data in online settings. How and why informed consent has developed in qualitative longitudinal research, both theoretically and practically, can provide a useful resource for considering what informed consent means in online settings. Building on this analogy, criteria are proposed that can be used to provide an ethical judgement on consent practices in an online data handling activity, and form the basis for a consent maturity model. It is argued that if we are to learn from from the history of informed consent in qualitative longitudinal research, then we should strive for an Ethics of Virtue approach to informed consent online, the highest level of maturity., Comment: 18 pages, 2 tables

Published
2017

11. Author Correction: FinnGen provides genetic insights from a well-phenotyped isolated population

Author

Kurki, Mitja I., Karjalainen, Juha, Palta, Priit, Sipilä, Timo P., Kristiansson, Kati, Donner, Kati M., Reeve, Mary P., Laivuori, Hannele, Aavikko, Mervi, Kaunisto, Mari A., Loukola, Anu, Lahtela, Elisa, Mattsson, Hannele, Laiho, Päivi, Della Briotta Parolo, Pietro, Lehisto, Arto A., Kanai, Masahiro, Mars, Nina, Rämö, Joel, Kiiskinen, Tuomo, Heyne, Henrike O., Veerapen, Kumar, Rüeger, Sina, Lemmelä, Susanna, Zhou, Wei, Ruotsalainen, Sanni, Pärn, Kalle, Hiekkalinna, Tero, Koskelainen, Sami, Paajanen, Teemu, Llorens, Vincent, Gracia-Tabuenca, Javier, Siirtola, Harri, Reis, Kadri, Elnahas, Abdelrahman G., Sun, Benjamin, Foley, Christopher N., Aalto-Setälä, Katriina, Alasoo, Kaur, Arvas, Mikko, Auro, Kirsi, Biswas, Shameek, Bizaki-Vallaskangas, Argyro, Carpen, Olli, Chen, Chia-Yen, Dada, Oluwaseun A., Ding, Zhihao, Ehm, Margaret G., Eklund, Kari, Färkkilä, Martti, Finucane, Hilary, Ganna, Andrea, Ghazal, Awaisa, Graham, Robert R., Green, Eric M., Hakanen, Antti, Hautalahti, Marco, Hedman, Åsa K., Hiltunen, Mikko, Hinttala, Reetta, Hovatta, Iiris, Hu, Xinli, Huertas-Vazquez, Adriana, Huilaja, Laura, Hunkapiller, Julie, Jacob, Howard, Jensen, Jan-Nygaard, Joensuu, Heikki, John, Sally, Julkunen, Valtteri, Jung, Marc, Junttila, Juhani, Kaarniranta, Kai, Kähönen, Mika, Kajanne, Risto, Kallio, Lila, Kälviäinen, Reetta, Kaprio, Jaakko, Kerimov, Nurlan, Kettunen, Johannes, Kilpeläinen, Elina, Kilpi, Terhi, Klinger, Katherine, Kosma, Veli-Matti, Kuopio, Teijo, Kurra, Venla, Laisk, Triin, Laukkanen, Jari, Lawless, Nathan, Liu, Aoxing, Longerich, Simonne, Mägi, Reedik, Mäkelä, Johanna, Mäkitie, Antti, Malarstig, Anders, Mannermaa, Arto, Maranville, Joseph, Matakidou, Athena, Meretoja, Tuomo, Mozaffari, Sahar V., Niemi, Mari E. K., Niemi, Marianna, Niiranen, Teemu, O´Donnell, Christopher J., Obeidat, Ma´en, Okafo, George, Ollila, Hanna M., Palomäki, Antti, Palotie, Tuula, Partanen, Jukka, Paul, Dirk S., Pelkonen, Margit, Pendergrass, Rion K., Petrovski, Slavé, Pitkäranta, Anne, Platt, Adam, Pulford, David, Punkka, Eero, Pussinen, Pirkko, Raghavan, Neha, Rahimov, Fedik, Rajpal, Deepak, Renaud, Nicole A., Riley-Gillis, Bridget, Rodosthenous, Rodosthenis, Saarentaus, Elmo, Salminen, Aino, Salminen, Eveliina, Salomaa, Veikko, Schleutker, Johanna, Serpi, Raisa, Shen, Huei-yi, Siegel, Richard, Silander, Kaisa, Siltanen, Sanna, Soini, Sirpa, Soininen, Hilkka, Sul, Jae Hoon, Tachmazidou, Ioanna, Tasanen, Kaisa, Tienari, Pentti, Toppila-Salmi, Sanna, Tukiainen, Taru, Tuomi, Tiinamaija, Turunen, Joni A., Ulirsch, Jacob C., Vaura, Felix, Virolainen, Petri, Waring, Jeffrey, Waterworth, Dawn, Yang, Robert, Nelis, Mari, Reigo, Anu, Metspalu, Andres, Milani, Lili, Esko, Tõnu, Fox, Caroline, Havulinna, Aki S., Perola, Markus, Ripatti, Samuli, Jalanko, Anu, Laitinen, Tarja, Mäkelä, Tomi P., Plenge, Robert, McCarthy, Mark, Runz, Heiko, Daly, Mark J., and Palotie, Aarno

Published
2023
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24. Comparative mortality of hemodialysis patients at for-profit and not-for-profit dialysis facilities in the United States, 1998 to 2003: A retrospective analysis

Author

Weinhandl Eric D, Gilbertson David T, Liu Jiannong, Fan Qiao, Foley Robert N, Chen Shu-Cheng, and Collins Allan J

Subjects
Diseases of the genitourinary system. Urology, RC870-923
Abstract

Abstract Background Concern lingers that dialysis therapy at for-profit (versus not-for-profit) hemodialysis facilities in the United States may be associated with higher mortality, even though 4 of every 5 contemporary dialysis patients receive therapy in such a setting. Methods Our primary objective was to compare the mortality hazards of patients initiating hemodialysis at for-profit and not-for-profit centers in the United States between 1998 and 2003. For-profit status of dialysis facilities was determined after subjects received 6 months of dialysis therapy, and mean follow-up was 1.7 years. Results Of the study population (N = 205,076), 79.9% were dialyzed in for-profit facilities after 6 months of dialysis therapy. Dialysis at for-profit facilities was associated with higher urea reduction ratios, hemoglobin levels (including levels above 12 and 13 g/dL [120 and 130 g/L]), epoetin doses, and use of intravenous iron, and less use of blood transfusions and lower proportions of patients on the transplant waiting-list (P < 0.05). Patients dialyzed at for-profit and at not-for-profit facilities had similar mortality risks (adjusted hazards ratio 1.02, 95% CI 0.99–1.06, P = 0.143). Conclusion While hemodialysis treatment at for-profit and not-for-profit dialysis facilities is associated with different patterns of clinical benchmark achievement, mortality rates are similar.

Published
2008
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25. Towards Privacy-anomaly Detection: Discovering Correlation between Privacy and Security-anomalies.

Author

Khan, Muhammad Imran, Foley, Simon N., and O'Sullivan, Barry

Subjects
PRIVACY, RELATIONAL databases, DATA privacy, ANOMALY detection (Computer security), INTERNET privacy
Abstract

In this paper a notion of privacy-anomaly detection is presented where normative privacy is modelled using k -anonymity. Based on the model, normative privacy-profiles are constructed, and deviation from normative privacy-profile at runtime is labelled as a privacy-anomaly. Furthermore, the paper investigates whether there is a correlation between security-anomalies and privacy-anomalies, that is, whether the privacy-anomalies labelled by privacy-anomaly detection system are detected by conventional security-anomaly detection system used for detecting malicious accesses to databases by insiders. [ABSTRACT FROM AUTHOR]

Published
2020
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26. Discovery of rare variants associated with blood pressure regulation through meta-analysis of 1.3 million individuals

Author

Surendran, Praveen, Feofanova, Elena V., Lahrouchi, Najim, Ntalla, Ioanna, Karthikeyan, Savita, Cook, James, Chen, Lingyan, Mifsud, Borbala, Yao, Chen, Kraja, Aldi T., Cartwright, James H., Hellwege, Jacklyn N., Giri, Ayush, Tragante, Vinicius, Thorleifsson, Gudmar, Liu, Dajiang J., Prins, Bram P., Stewart, Isobel D., Cabrera, Claudia P., Eales, James M., Akbarov, Artur, Auer, Paul L., Bielak, Lawrence F., Bis, Joshua C., Braithwaite, Vickie S., Brody, Jennifer A., Daw, E. Warwick, Warren, Helen R., Drenos, Fotios, Nielsen, Sune Fallgaard, Faul, Jessica D., Fauman, Eric B., Fava, Cristiano, Ferreira, Teresa, Foley, Christopher N., Franceschini, Nora, Gao, He, Giannakopoulou, Olga, Giulianini, Franco, Gudbjartsson, Daniel F., Guo, Xiuqing, Harris, Sarah E., Havulinna, Aki S., Helgadottir, Anna, Huffman, Jennifer E., Hwang, Shih-Jen, Kanoni, Stavroula, Kontto, Jukka, Larson, Martin G., Li-Gao, Ruifang, Lindström, Jaana, Lotta, Luca A., Lu, Yingchang, Luan, Jian’an, Mahajan, Anubha, Malerba, Giovanni, Masca, Nicholas G. D., Mei, Hao, Menni, Cristina, Mook-Kanamori, Dennis O., Mosen-Ansorena, David, Müller-Nurasyid, Martina, Paré, Guillaume, Paul, Dirk S., Perola, Markus, Poveda, Alaitz, Rauramaa, Rainer, Richard, Melissa, Richardson, Tom G., Sepúlveda, Nuno, Sim, Xueling, Smith, Albert V., Smith, Jennifer A., Staley, James R., Stanáková, Alena, Sulem, Patrick, Thériault, Sébastien, Thorsteinsdottir, Unnur, Trompet, Stella, Varga, Tibor V., Velez Edwards, Digna R., Veronesi, Giovanni, Weiss, Stefan, Willems, Sara M., Yao, Jie, Young, Robin, Yu, Bing, Zhang, Weihua, Zhao, Jing-Hua, Zhao, Wei, Zhao, Wei, Evangelou, Evangelos, Aeschbacher, Stefanie, Asllanaj, Eralda, Blankenberg, Stefan, Bonnycastle, Lori L., Bork-Jensen, Jette, Brandslund, Ivan, Braund, Peter S., Burgess, Stephen, Cho, Kelly, Christensen, Cramer, Connell, John, Mutsert, Renée de, Dominiczak, Anna F., Dörr, Marcus, Eiriksdottir, Gudny, Farmaki, Aliki-Eleni, Gaziano, J. Michael, Grarup, Niels, Grove, Megan L., Hallmans, Göran, Hansen, Torben, Have, Christian T., Heiss, Gerardo, Jørgensen, Marit E., Jousilahti, Pekka, Kajantie, Eero, Kamat, Mihir, Käräjämäki, AnneMari, Karpe, Fredrik, Koistinen, Heikki A., Kovesdy, Csaba P., Kuulasmaa, Kari, Laatikainen, Tiina, Lannfelt, Lars, Lee, I-Te, Lee, Wen-Jane, Linneberg, Allan, Martin, Lisa W., Moitry, Marie, Nadkarni, Girish, Neville, Matt J., Palmer, Colin N. A., Papanicolaou, George J., Pedersen, Oluf, Peters, James, Poulter, Neil, Rasheed, Asif, Rasmussen, Katrine L., Rayner, N. William, Mägi, Reedik, Renström, Frida, Rettig, Rainer, Rossouw, Jacques, Schreiner, Pamela J., Sever, Peter S., Sigurdsson, Emil L., Skaaby, Tea, Sun, Yan V., Sundstrom, Johan, Thorgeirsson, Gudmundur, Esko, Tõnu, Trabetti, Elisabetta, Tsao, Philip S., Tuomi, Tiinamaija, Turner, Stephen T., Tzoulaki, Ioanna, Vaartjes, Ilonca, Vergnaud, Anne-Claire, Willer, Cristen J., Wilson, Peter W. F., Witte, Daniel R., Yonova-Doing, Ekaterina, Zhang, He, Aliya, Naheed, Almgren, Peter, Amouyel, Philippe, Asselbergs, Folkert W., Barnes, Michael R., Blakemore, Alexandra I., Boehnke, Michael, Bots, Michiel L., Bottinger, Erwin P., Buring, Julie E., Chambers, John C., Chen, Yii-Der Ida, Chowdhury, Rajiv, Conen, David, Correa, Adolfo, Davey Smith, George, Boer, Rudolf A. de, Deary, Ian J., Dedoussis, George, Deloukas, Panos, Di Angelantonio, Emanuele, Elliott, Paul, Felix, Stephan B., Ferrières, Jean, Ford, Ian, Fornage, Myriam, Franks, Paul W., Franks, Stephen, Frossard, Philippe, Gambaro, Giovanni, Gaunt, Tom R., Groop, Leif, Gudnason, Vilmundur, Harris, Tamara B., Hayward, Caroline, Hennig, Branwen J., Herzig, Karl-Heinz, Ingelsson, Erik, Tuomilehto, Jaakko, Järvelin, Marjo-Riitta, Jukema, J. Wouter, Kardia, Sharon L. R., Kee, Frank, Kooner, Jaspal S., Kooperberg, Charles, Launer, Lenore J., Lind, Lars, Loos, Ruth J. F., Majumder, Abdulla al Shafi., Laakso, Markku, McCarthy, Mark I., Melander, Olle, Mohlke, Karen L., Murray, Alison D., Nordestgaard, Børge Grønne, Orho-Melander, Marju, Packard, Chris J., Padmanabhan, Sandosh, Palmas, Walter, Polasek, Ozren, Porteous, David J., Prentice, Andrew M., Province, Michael A., Relton, Caroline L., Rice, Kenneth, Ridker, Paul M., Rolandsson, Olov, Rosendaal, Frits R., Rotter, Jerome I., Rudan, Igor, Salomaa, Veikko, Samani, Nilesh J., Sattar, Naveed, Sheu, Wayne H.-H., Smith, Blair H., Soranzo, Nicole, Spector, Timothy D., Starr, John M., Sebert, Sylvain, Taylor, Kent D., Lakka, Timo A., Timpson, Nicholas J., Tobin, Martin D., van der Harst, Pim, van der Meer, Peter, Ramachandran, Vasan S., Verweij, Niek, Virtamo, Jarmo, Völker, Uwe, Weir, David R., Zeggini, Eleftheria, Charchar, Fadi J., Wareham, Nicholas J., Langenberg, Claudia, Tomaszewski, Maciej, Butterworth, Adam S., Caulfield, Mark J., Danesh, John, Edwards, Todd L., Holm, Hilma, Hung, Adriana M., Lindgren, Cecilia M., Liu, Chunyu, Manning, Alisa K., Morris, Andrew P., Morrison, Alanna C., O’Donnell, Christopher J., Psaty, Bruce M., Saleheen, Danish, Stefansson, Kari, Boerwinkle, Eric, Chasman, Daniel I., Levy, Daniel, Newton-Cheh, Christopher, Munroe, Patricia B., and Howson, Joanna M. M.

Abstract

Genetic studies of blood pressure (BP) to date have mainly analyzed common variants (minor allele frequency?>?0.05). In a meta-analysis of up to ~1.3 million participants, we discovered 106 new BP-associated genomic regions and 87 rare (minor allele frequency?=?0.01) variant BP associations (P?

Published
2020
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27. A Highly Stereoselective, Efficient, and Scalable Synthesis of the C(1)–C(9) Fragment of the Epothilones

Author

Foley, Corinne N. and Leighton, James L.

Abstract

A second-generation synthesis of the C(1)–C(9) fragment of the epothilones is reported. The key tandem intramolecular silylformylation/crotylsilylation/“aprotic” Tamao oxidation sequence has been redeveloped as a stepwise intermolecular variant, allowing excellent levels of diastereoselectivity in the crotylation step and proceeds in 50% overall yield on gram scale. An improved synthesis of the homopropargyl alcohol starting material is also described, which proceeds in four steps and >99% ee from inexpensive starting materials and is amenable to multigram scales.

Published
2024
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28. Epidemiology and Risk Factors for Early Mortality After Dialysis Initiation.

Author

Foley, Robert N.

Abstract

Confronted with the decision to initiate dialysis, patients and caregivers often seek information about how expected survival chances evolve, both initially and afterward, providing the patient survives beyond arbitrary periods of time. Large registry data, used to examine these issues, may be subject to early ascertainment bias, such as those accruing from nonregistration of with end-stage kidney disease who die shortly after dialysis initiation and inclusion of patients with acute kidney injury with slower than typical recovery rates. Despite these caveats, available studies have suggested that mortality hazards are much higher in the first 3 months of renal replacement therapy. Prominent modifiable associations of early mortality include late referral to nephrology services, initial dialysis with vascular catheters, and, most problematically, higher glomerular filtration rates at initiation of renal replacement therapy. Despite their imperfections, currently available information is relatively user-unfriendly and could be better leveraged to help patients and treatment teams make better decisions. [ABSTRACT FROM AUTHOR]

Published
2017
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29. A grounded theory approach to security policy elicitation

Author

Foley, Simon N. and Rooney, Vivien

Abstract

Purpose: In this paper, the authors consider how qualitative research techniques that are used in applied psychology to understand a person’s feelings and needs provides a means to elicit their security needs. Design/methodology/approach: Recognizing that the codes uncovered during a grounded theory analysis of semi-structured interview data can be interpreted as policy attributes, the paper develops a grounded theory-based methodology that can be extended to elicit attribute-based access control style policies. In this methodology, user-participants are interviewed and machine learning is used to build a Bayesian network-based policy from the subsequent (grounded theory) analysis of the interview data. Findings: Using a running example – based on a social psychology research study centered around photograph sharing – the paper demonstrates that in principle, qualitative research techniques can be used in a systematic manner to elicit security policy requirements. Originality/value: While in principle qualitative research techniques can be used to elicit user requirements, the originality of this paper is a systematic methodology and its mapping into what is actionable, that is, providing a means to generate a machine-interpretable security policy at the end of the elicitation process.

Published
2018
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30. Renal Consequences of Diabetes After Kidney Donation

Author

Ibrahim, H. N., Berglund, D. M., Jackson, S., Vock, D. M., Foley, R. N., and Matas, A. J.

Abstract

Whether diabetes after kidney donation is associated with an accelerated GFRdecay in the remaining kidney has not been studied. We determined the incidence of diabetes in kidney donors, and compared GFRchange over time in diabetic to nondiabetic donors, in addition to the effect of diabetes mellitus (DM)on the development of proteinuria, hypertension, and end‐stage renal disease (ESRD). Of the 4014 donors, 309 (7.7%) developed diabetes at a median age of 56.0 years and after a median of 18 years after donation. The difference in annual estimated GFR(eGFR) change between diabetic and nondiabetic donors in the 7 years before the development of DM was −0.08 mL/min/year; p = 0.51. After DMdevelopment, the difference was −1.10 mL/min/year for diabetic donors with hypertension and proteinuria, p < 0.001; −0.19 for diabetic donors with hypertension but no proteinuria, p = 0.29; −0.75 mL/min/year for diabetic donors with proteinuria but no hypertension, p = 0.19; and −0.09 mL/min/year for diabetic donors without proteinuria or hypertension, p = 0.63. When DMwas considered as a time‐dependent covariate, it was associated with the development of proteinuria (hazard ratio [HR] 2.65, 95% confidence interval [CI]1.89–3.70; p < 0.001) and hypertension (HR2.19, 95% CI1.74–2.75; p < 0.001). It was not, however, associated with ESRD. eGFRdecline after DMdevelopment exceeds that of nondiabetic donors only in diabetic donors with concomitant proteinuria and hypertension. A minority of donors develop diabetes after donation, and their rate of GFR change, prevalence of proteinuria, and hypertension is similar to nondonor patients with diabetes.

Published
2017
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31. Selected abstracts

Author

Corkery, P. P., Leek, B. F., Caulfield, B., Garrett, M., Gormley, J. P., O’Donnell, P. M., Kennedy, N., Sayers, K., Stokes, E., Bresnihan, B., Fitzgerald, O., McGarvey, M. A., Tonra, M., Hooper, A. C. B., Barry, J., Maurer, B., Hussey, J., Gormley, J., Noble, J. G., Alves-Guerreiro, J., Lowe, A. S., Walsh, D. M., NicNiocaill, B., Harte, M., O’Connor, W. T., O’Hara, A. M., Orren, A., Moran, A. P., Hardiman, D. A., Lee, T. C., Croke, D. T., Tolan, R., McBennett, S., Warmington, S., McGuire, M., Bradford, A., O’Hare, T., MacDermott, M., Lynch, F., O’Regan, R. G., McLoughlin, P., Quinn, T., Ryan, J. P., Pickering, M., Campion, D. P., Jones, J. F. X., Ryan, S., McNicholas, W. T., Nolan, P., Doyle, F. J., Rackard, S. M., Beddy, P., Campbell, V. A., Bakhle, Y. S., Bell, C., Usher, C., Chan, L., Keenan, A. K., McQuaid, K. E., Cullen, V. C., Smith, E. M., Kelly, A., Lynch, M. A., Freir, D. B., Holscher, C., Herron, C. E., Pearson, H. A., Curran, B. P., O’Connor, J. J., Quinn, A., McHale, J., Moriarty, D., O’Connor, J., Glennon, J. C., Van Vliet, B. J., Long, S. K., Kruse, C., Gallagher, H. C., Bacon, C. L., Boland, B., Griffin, A. M., Preisler, J., O’Brien, L., Regan, C. M., Hurley, S., Kearney, P. J., Slevin, J., Barry-Kinsella, C., Ryan, C. A., Kllleen, O., Glllan, J., Clarke, T., Matthews, T., Corcoran, D., Dunn, E., Geary, M., O’Herlihy, C., Keane, D., Slattery, M. M., O’Leary, M. J., Morrison, J. J., Ryan, E., Gorman, W. A., Bourke, A., Larkin, J., Mayes, C., Jenkins, J., Ryan, M., Lalchandani, S., Sheil, O., Lynch, N., Costigan, C., Murphy, J. F., Bhatia, R., Foran, A., Donohue, V., McParland, P., LaSjaunais, P., Rodesch, G., McGinn, M., McAloon, J., O’Leary, M., Astbury, K., Harmon, D., Sharkey, A., Gaffney, G., O’Regan, G., McMahon, C., Murray, D., McDermott, C., Woolhead, E., Gillan, J., Cartmill, J. L., Harper, M. A., Al-Shabibi, N., Hanahoe, M., Wingfield, M., Larkin, J. A. M., Bell, A. H., McClure, B. G., Sweeney, L., Martin, D. H., O’Donoghue, P., Davoren, A., Lucas, G. F., McKiernan, J., Gallagher, D. M. T., Dunne, K. P., Fulena, O., Sheridan, M., Griffin, E., White, M., Deasy, P., O’Riordan, M., O’Gorman, C., Mongan, C., McCafferkey, M., Henry, G., McKenna, P., O’Malley, A., Devaney, D., Kelleghan, P., Mooney, E. E., Gillan, J. E., Fitzpatrick, M., McQuillan, K., Heffron, C., Hodnett, P., Curtain, A., O’Connor, T. C. F., Connell, T. G., Waldron, D., Gorman, W., Bolger, T., O’Keefe, M., Murphy, J., Dolan, L. M., Traub, A. I., Slattery, M. M., O’Leary, M. J., Curley, A. E., Halliday, H. L., Tubman, T. R. J., Kileen, O., Riadha, H., Russell, J., Philips, R., Regan, C., Ali, I., Coughlan, A. C. J., Turner, M. J., Smith, A., O’Flanagan, D., Igoe, D., Ryan, F., Forde, D., McArdle, E., Ko, D., Bedford, D., Hegarty, M., Dunlevy, B., Corcoran, R., Holohan, T., Feeney, A., McGee, H., Shannon, W., Condon, M., Hyland, C., Sayers, G., Feely, E., Crowley, D., O’Reilly, D., O’Connell, T., Cronin, M., Johnson, H., Fitzgeraldi, M., Cafferkey, M., Breslin, A., Bonner, C. J., Foley, B., Fitzgerald, M., Wall, P. G., McNamara, E., Costigan, P., Prendergast, T., Foye, K., Cosgrove, C., Keane, A., Murphy, E., O’Donnell, J., Quinlan, A., Thornton, L., Roch, E. A., Lyons, R. A., Maddocks, A., Barnes, P., Price, L., McCabe, M., Nash, P., Midha, A., Doyle, Y., Kilgallen, A., Wright, P., Ryan, T., De La Harpe, D., Harkins, V., Brennan, C., O’Connell, V., Evans, D. S., Ni Mhuircheartaigh, J., O’Donnell, J. M., Rhatigan, A., Shelley, E., Collins, C., Byrne, M., Murphy, A. W., Plunkett, P. K., Murray, A., Bury, G., Lynam, F., McMahon, G., Greally, T., Kane, D., Veale, D., Reece, R., Busteed, S., Bennett, M. W., Stone, M., Molloy, C., O’Connell, J., Molloy, M. G., Shanahan, F., Guerin, J., Casey, E., Feighery, C., Lin, F., Jackson, J., Pendleton, A., Wright, G. D., Hughes, A. E., O’Gradaigh, D., Debham, I., Compston, J., McEvoy, A., Murphy, E. P., Salonen, D., Payne, P., Lax, M., Lapp, V., Inman, R., O’Rourke, K., Brennan, D., Harty, J., McCarthy, C., O’Byrne, J., Eustace, S., Chirayath, H., Liggett, N. W., Morgan, M. P., Fitzgerald, D. J., McCarthy, C. J., McCarthy, G. M., Lee, R. Z., Wai, K., Nevin, D., Leary, A. O., Lee, R., Leary, A. O., Casey, E. B., Leary, A. O., O’Leary, A., Breen, D., Tuite, D., McInerney, D., Sim, R., Frederic, A. L., Smith, O., White, B., Murphy, M., Silke, C., O’Keeffe, E., Fanning, N., Spence, L., Parfrey, N. A., McConnell, J. R., Crockard, A. D., Cairns, A. P., Bell, A. L., Kavanagh, O., Moyes, D. A., Finch, M., Rooney, M., Bell, A., Founas, I., El-Magbri, A., Mooney, S., Kennedy, M., Coughlan, R. J., Ramakrishnan, S. A., Gsel, A., Finnerty, O., Burns, M., Yateman, M., Camaco-Hubner, C., Matthews, C. F., Taggart, A., Fuller, K., Murphy, M. S., Phelan, M., Murphy, T. B., Wynne, F., Quane, K., Daly, M., O’Leary, J., da Silva, I., Bermingham, N., Gogarty, M., Gallagher, L. P., O’Hara, R., Godson, C., Brady, H., Osman, H., El-Rafie, A., Foley-Nolan, D., Kirwan, P., Corcoran, O., Duffy, T., Drummond, F., Madigan, A., Williams, D., Gallagher, P., Hatton, C., Cunningham, S., FitzGerald, O., Minnock, P., Wylie, E., Egan, D., Mc Cormack, J., Shea, M. O., Evans, D., O’Lorcain, P., Comber, H., Evans, A., Jones, J., Garavan, C., Kelleher, K., Boland, M. C., Healy, R., O’Sullivan, M. B., Burke, M., Mc Donald, P., Smithson, R., Glass, J., Mason, C. A., Mullins, N., Nolan, D., McCormick, P., Coughlan, S., Dooley, S., Kelleher, C. C., Hope, A., Murphy, F., Barry, M., Sixsmith, J., MacFarlane, A., MacLeod, C., McElroy, G., O’Loan, D., Kennedy, F., Kerr, R. M., Lim, J., Allwright, S. P. A., Bradley, F. L., Barry, J. M. G., Long, J., Parry, J. V., Creagh, D., Perry, I. J., Collins, A., Neilson, S., Colwell, N., O’Halloran, D., O’Neill, S., McErlain, S., Okasha, M., Gaffney, B., McCarron, P., Hinchion, R., Drew, C., Gavin, A., Fitzpatrick, D., Campbell, R., Wannamethee, S. G., Shaper, A., Friel, S., Kelleher, C., Kee, F., Atterson, C. C., Wilson, E. A., McConnell, J. M., Wheeler, S. M., Watson, J. D., Norashikin Rahman, N., Sheehan, J., Wall, C., Kelleher, B., O’Broin, S. D., Mullan, R. N., McKeveney, P. J., Hodges, V. M., Winter, P. C., Maxwell, P., Simpson, D. A., Lappin, T. R. J., Maxwell, A. P., Eustace, J. A., Coresh, J., Kutchey, C., Te, P. L., Gimenez, L. F., Scheel, P. J., Walser, M., McMahon, R. A., Clarkson, M., Martin, F., Brady, H. R., Blake, C., O’Meara, Y. M., Gupta, S., MacKenzie, H., Doyle, S., Fotheringham, T., Haslam, P., Logan, M. P., Conlon, P., Lee, M., Maderna, P., Cottell, D. C., Mitchell, S., Gulmann, C., Østerby, R., Bangstad, H. J., Rljdberg, S., Dempsey, M., Nathwani, S., Ryan, M. P., McMahon, B., Stenson, C., Murtagh, H., Brown, J. H., Doran, P., McGinty, A., Little, M. A., O’Brien, E., Owens, P., Holian, J., Mee, F., Walshe, J. J., Omer, S. A., Power, D., Diamond, P., Watson, R. W., Shahsafei, A., Jiang, T., Brenner, B. M., Mackenzie, H. S., Neary, J., Dorman, A., Keoghan, M., Campbell, E., Walshe, J., Little, M., Nee, L., O’Ceallaigh, C., McGlynn, H., Bergin, E., Garrett, P. J., Keane, T., Gormley, G., Watson, A., Atta, M. G., Perl, T. M., Song, X., Healy, E., Leonard, M., Lynch, J., Watson, A. J., Lappin, D., Lappin, D. W. P., Hannan, K., Burne, M., Daniels, F., Rabb, H., McBride, B., Kieran, N., Shortt, C., Codd, M., Murray, F., McCormack, A., Brown, C., Wong, C., Dorman, A. M., Keogan, M., Donohue, J., Farrell, J., Donohoe, J., O’Broin, S., Balfe, A., Mellotte, G. J., Abraham, K. A., McGorrian, C., Wood, A. E., Neligan, M., Kelly, B. D., Finnegan, P., Cormican, M., Callaghan, J., Crean, J. K. G., Moffitt, T. A., Devlin, H. L., Garrett, P. J., Soosay, A., O’Neill, D., Counihan, A., Hickey, D., Keogan, M. T., Harvey, K., O’Riordan, E., Waldek, S., Kalra, P. A., O’Donoghue, D. J., Foley, R. N., O’Riordan, A., Kelliher, D., Mellotte, G., Giblin, L., Keogh, J. A. B., O’Connell, M., O’Meara, A., Breatnach, F., Gillick, J., Tazawa, H., Puri, P., Molloy, E., O’Neill, A. J., Sheridan-Pereira, M., Fitzpatrick, J. M., Webb, D. W., Watson, R. W. G., Linnane, B., O’Donnell, C., Clarke, T. A., Martin, C., McKay, M., McBrien, J., Glynn, F., O’Donovan, C., Hall, W. W., Smith, J., Khair, K., Liesner, R., Hann, I. M., Smith, O. P., Gallagher, S., Mahony, M. J., Hilal, A., Cosgrove, J. F., Monaghan, C., Craig, B., Al-Hassan, A., Walsh, K., Duff, D., Slizlok, P. O., Halahakoon, C., MacPherson, C., McMillan, S., Dalzell, E. E., McCaughan, J., Redmond, A. O. B., DeCaluwe, D., Yoneda, A., Akl, U., Dempsey, E., Farrell, M., Webb, D., Elabbas, A., Fox, G., Gormally, S., Grant, B., Corkey, C. W. B., Nicholson, A., Murphy, A., O’Grady, P., Barry, O., Macpherson, C., Stewart, M. C., Alderdice, F., Matthews, T. G., McDonnell, M., McGarvey, C., O’Regan, M., Ní Chróinín, M., Tormey, P., Ennis, S., Green, A. J., Abbas, S., O’Marcaigh, A., Conran, M., Crushell, E., Saidi, A., Curran, P., Donoghue, V., King, M. D., Elnazir, B., Leonard, J., Kavanagh, C., Brown, D., Corrigan, N., McCord, B., Quinn, M., O’Connell, L., Mcdonagh, B., Awan, A., Gill, D., Kakkar, R., Sweet, D. G., Warner, J. A., O’Connor, C., Herzig, M., Twomey, A., White, M. J., Sweeney, B., Surana, R., Hodgson, A., Rafferty, M., Livingstone, W., Peake, D., Wassemer, E., Whitehouse, W., Abdullah, N., Al-Hassan, A., Oslizlok, P., O’Connell, N., Balding, J., Livingstone, W. J., Healy, M., Mynett-Johnson, L., McAllister, I., Dick, A. C., Herron, B., Boston, V. E., Callaghan, C. O., Brien, D. O., Walsh, A., Philip, M., McShane, D., Hoey, M. C. V., Sharif, F., McDermott, M., Dillon, M., Drumm, B., Rowland, M., Imrie, C., Kelleher, S., Bourke, B., Iqbal, M., Ziedan, Y., O’Neill, M., O’Riordan, S., Basheer, S. M. B., O’Callaghan, S., Chong, A., Kelly, M., Nicholson, A. J., Cooke, R., Sreenan, C., Fallon, M., Denham, B., Dowding, V., Cussen, G., McManus, V., Hensey, O., Monaghan, H., Basheer, S. N., Quinn, E., Hoey, H. M. C. V., Mohamed, S., Ramesh, R. R., Mayne, P., Tracy, E., Gormally, S. M., Curtis, E., McCallion, N., Watson, R., O’Mahony, O., Keegan, M., Ward, K., Barton, D., Poulton, J., Treacy, E., Honour, J., deCaluwe, D., Ni Chróinín, M., Cosgrove, J., Chaudhry, T. S., Long, N. M., Lynch, B., Lasjaunais, P., McDonald, D. G. M., McMenamin, J. B., Farrell, M. J., Roche, E. F., Menon, A., Buckley, C., Mackey, A., Ohlandieck, K., Das, A., Reilly, D., Killeen, O., Harper, J., Roche, E., Hoey, H., Caird, J., O’Brien, D., Allcutt, D., Farrington, N., Murphy, J. F. A., Savage, J. M., Sands, A. J., Casey, F. A., Craig, B. G., Dornan, J. C., Johnston, J., Patterson, C., Lynch, C., Mulholland, H. C., Watkins, D. C., Young, I., Cran, G., Boreham, C. A. G., McCallion, W. A., Clements, N. F., Stevenson, M. R., Macpherson, C., O’Donoghue, D., Jenkins, L., Thompson, A. J., Shields, M. D., Taylor, R. T., Kerr, R., Hughes, J. L., Stewart, M., Jackson, P., Fitzpatrick, C., Rasheed, M., Colhoun, E., Bailie, A. G., Gray, S., Brown, S., Curley, A., Sweet, D. G., MacMahon, K. J., O’Connor, C. M., Nichelson, A., Lynch, N. E., Finch, D., Foley, M., Scallan, E., Dillon, B., Lyons, S., O’Loughlin, R., Ward, M., Nally, R., Harkin, A., Kelly, J. P., Leonard, B. E., Nic Niocaill, B., Magee, P., Connor, T. J., Shen, Y., McCullough, G. R., McDonough, S. M., Nic Niocaill, B., Cramp, A. F. L., Hynes, M., Corkery, P., Carey, M., McGarrigle, D., Higgins, S., Murray, H., Moran, C. J., Dennedy, M. C., Brosnan, J., Morris, L., Sheppard, B. L., Black, A., Wilkins, B., Folan-Curran, J., Skelton, K., Owens, M., Nemeroff, C., Houlihan, D., O’Keeffe, C., Nolan, N., McCormick, P. A., Baird, A. W., Raducan, I., Corcoran, P., Brennan, R., Molloy, P., Friel, A., Maher, M., Glennon, M., Smith, T., Nolan, A., Houghton, J. A., Carroll, O., Colleran, S., O’Cuinn, G., Snow, H. M., O’Regan, D., Markos, H. F., Pollock, K., Cannon, D. M., McBean, G., O’Riordan, A., Quinlan, L. R., Kane, M. T., Higglns, B. D., Moriarty, D. M., Fitzgerald, D., Katkada, A., Canny, G., MacMathuna, P., O’Donoghue, D., O’Donovan, M. M., Schuur, A. G., Murphy, K. J., Foley, A. G., ten Bruggencate, S. J. M., and Ireland, L.

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34. A Logic for Analysing Subterfuge in Delegation Chains.

Author

Dimitrakos, Theo, Martinelli, Fabio, Ryan, Peter Y. A., Schneider, Steve, Zhou, Hongbin, and Foley, Simon N.

Abstract

Trust Management is an approach to construct and interpret the trust relationships among public-keys that are used to mediate security-critical actions. Cryptographic credentials are used to specify delegation of authorisation among public keys. Existing trust management schemes are operational in nature, defining security in terms of specific controls such as delegation chains, threshold schemes, and so forth. However, they tend not to consider whether a particular authorisation policy is well designed in the sense that a principle cannot somehow bypass the intent of a complex series of authorisation delegations via some unexpected circuitous route. In this paper we consider the problem of authorisation subterfuge, whereby, in a poorly designed system, delegation chains that are used by principals to prove authorisation may not actually reflect the original intention of all of the participants in the chain. A logic is proposed that provides a systematic way of determining whether a particular delegation scheme using particular authorisation is sufficiently robust to be able to withstand attempts at subterfuge. This logic provides a new characterisation of certificate reduction that, we argue, is more appropriate to open systems. [ABSTRACT FROM AUTHOR]

Published
2006
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36. Trading Off Security in a Service Oriented Architecture.

Author

Jajodia, Sushil, Wijesekera, Duminda, Swart, G., Aziz, Benjamin, Foley, Simon N., and Herbert, John

Abstract

Service oriented architectures provide a simple yet flexible model of a computing system as a graph of services making requests and providing results to each other. In this paper we define a formal model of a service oriented architecture and using it, we define metrics for performance, for availability, and for various security properties. These metrics serve as the basis for expressing the business requirements. To make trade-offs possible we also define a set of cost metrics, denominated in a uniform currency, to measure the cost of not meeting a requirement. The model, the property metrics, and the cost metrics are then used to generate a Constraint Satisfaction Problem where the objective function is set to minimize the aggregate system cost. We have written these constraints and defined realistic requirements in OPL and we have used them to generate system configurations that minimize the overall cost by optimally trading off the business requirements. [ABSTRACT FROM AUTHOR]

Published
2005
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37. Towards a Framework for Autonomic Security Protocols.

Author

Christianson, Bruce, Crispo, Bruno, Malcolm, James A., Roe, Michael, and Foley, Simon N.

Abstract

We've been looking at what we call the security protocol negotiation problem. People who use security protocols to authenticate, do key exchange, or whatever, are typically stuck with using whatever protocol is available. If the participants can't agree on a suitable protocol, then they don't get to use each other's services. We are interested in self-configuring security protocols where the participants have to say what their requirements are and synthesise or con.gure their own suitable protocol that would meet their respective goals. If we have this idea of self-configuring security protocols then, as a consequence, we also have selfhealing security protocols. If the requirements change, or if the assumptions about our principals and keys change, then we have this ability to recon.gure and produce a security protocol that will meet those new goals, based on those assumptions. [ABSTRACT FROM AUTHOR]

Published
2005
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38. The Brain in Kidney Disease (BRINK) Cohort Study: Design and Baseline Cognitive Function

Author

Murray, Anne M., Bell, Elizabeth J., Tupper, David E., Davey, Cynthia S., Pederson, Sarah L., Amiot, Elizabeth M., Miley, Kathleen M., McPherson, Lauren, Heubner, Brooke M., Gilbertson, David T., Foley, Robert N., Drawz, Paul E., Slinin, Yelena, Rossom, Rebecca C., Lakshminarayan, Kamakshi, Vemuri, Prashanthi, Jack, Clifford R., and Knopman, David S.

Abstract

The Brain in Kidney Disease (BRINK) Study aims to identify mechanisms that contribute to increased risk for cognitive impairment in patients with chronic kidney disease (CKD). We describe the rationale, design, and methods of the study and report baseline recruitment and cognitive function results.

Published
2016
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40. Couples Therapy: Treating Selected Personality-disordered Couples Within a Dynamic Therapy Framework.

Author

LANDUCCI, JENNIFER and FOLEY, GRETCHEN N.

Subjects
PERSONALITY disorder treatment, CASE studies, FAMILY conflict, NARCISSISTIC personality disorder, COUPLES therapy, HISTRIONIC personality disorder
Abstract

Personality disordered couples present unique challenges for couples therapy. Novice therapists may feel daunted when taking on such a case, especially given the limited literature available to guide them in this specific area of therapy. Much of what is written on couples therapy is embedded in the larger body of literature on family therapy. While family therapy techniques may apply to couples therapy, this jump requires a level of understanding the novice therapist may not yet have. Additionally, the treatment focus within the body of literature on couples therapy tends to be situation-based (how to treat couples dealing with divorce, an affair, illness), neglecting how to treat couples whose dysfunction is not the product of a crisis, but rather a longstanding pattern escalated to the level of crisis. This is exactly the issue in therapy with personality disordered couples, and it is an important topic, as couples with personality pathology often do present for treatment. This article strives to present practical techniques, modeled in case vignettes, that can be applied directly to couples therapy--specifically therapy with personality disordered couples. [ABSTRACT FROM AUTHOR]

Published
2014

42. United States Renal Data System public health surveillance of chronic kidney disease and end-stage renal disease

Author

Collins, Allan J., Foley, Robert N., Gilbertson, David T., and Chen, Shu-Cheng

Abstract

The United States Renal Data System (USRDS) began in 1989 through US Congressional authorization under National Institutes of Health competitive contracting. Its history includes five contract periods, two of 5 years, two of 7.5 years, and the fifth, awarded in February 2014, of 5 years. Over these 25 years, USRDS reporting transitioned from basic incidence and prevalence of end-stage renal disease (ESRD), modalities, and overall survival, as well as focused special studies on dialysis, in the first two contract periods to a comprehensive assessment of aspects of care that affect morbidity and mortality in the second two periods. Beginning in 1999, the Minneapolis Medical Research Foundation investigative team transformed the USRDS into a total care reporting system including disease severity, hospitalizations, pediatric populations, prescription drug use, and chronic kidney disease and the transition to ESRD. Areas of focus included issues related to death rates in the first 4 months of treatment, sudden cardiac death, ischemic and valvular heart disease, congestive heart failure, atrial fibrillation, and infectious complications (particularly related to dialysis catheters) in hemodialysis and peritoneal dialysis patients; the burden of congestive heart failure and infectious complications in pediatric dialysis and transplant populations; and morbidity and access to care. The team documented a plateau and decline in incidence rates, a 28% decline in death rates since 2001, and changes under the 2011 Prospective Payment System with expanded bundled payments for each dialysis treatment. The team reported on Bayesian methods to calculate mortality ratios, which reduce the challenges of traditional methods, and introduced objectives under the Health People 2010 and 2020 national health care goals for kidney disease.

Published
2015
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43. A kernelized architecture for multilevel secure application policies.

Author

Goos, Gerhard, Hartmanis, Juris, Leeuwen, Jan, Quisquater, Jean-Jacques, Deswarte, Yves, Meadows, Catherine, Gollmann, Dieter, and Foley, Simon N.

Abstract

Mandatory label-based policies may be used to support a wide-range of application security requirements. Labels encode the security state of system entities and the security policy specifies how these labels may change. Building on previous results, this paper develops a model for a kernelized framework for supporting these policies. The framework provides the basis for, what is essentially, an interpreter of multilevel programs: programs that manipulate multilevel label data-structures. This enables application functionality and security concerns to be developed separately, bringing with it the advantages of a separation of concerns paradigm. [ABSTRACT FROM AUTHOR]

Published
1998
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44. Organ and Metabolic Complications: Cardiac.

Author

Jacobs, C., Kjellstrand, C. M., Koch, K. M., Winchester, J. F., Parfrey, Patrick S., Foley, R. N., and Harnett, J. D.

Abstract

The burden of illness due to cardiac disease in chronic uremia is high. Cardiac disease is the major cause of death in dialysis patients, accounting for about 40% of deaths in dialysis patients (1). When compared to a nonrenal cohort aged 45-64 years the death rate in a dialysis cohort of similar age was 3.5 times higher (2). Indices of morbidity are also high. The prevalence of clinical manifestations of cardiac disease on initiation of ESRD therapy is high (3) (Table 1). The probability of having a myocardial infarction or angina requiring hospitalization in hemodialysis patents is 10%/year (4). There is a similar probability of developing pulmonary edema requiring hospitalization or additional ultrafiltration (4). The prevalence of persistent or recurrent congestive heart failure in patients established on dialysis is 10% (5), Ischemic heart disease 17-34% (6), and complex premature ventricular complexes 18% (7). [ABSTRACT FROM AUTHOR]

Published
1996
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45. Factors Associated With Kidney Disease Progression and Mortality in a Referred CKD Population.

Author

Hoefield, Richard A., Kalra, Philip A., Baker, Patricia, Lane, Beverley, New, John P., O'Donoghue, Donal J., Foley, Robert N., and Middleton, Rachel J.

Abstract

Background: Knowing how kidney disease progresses is important for decision making in patients with chronic kidney disease (CKD) and for designing clinical services. Study Design: Prospective cohort study. Setting & Participants: We examined renal function trajectories in CRISIS (Chronic Renal Insufficiency Standards Implementation Study), in which 1,325 patients with CKD stages 3-5 and mean age of 65.1 years were followed up prospectively for a median of 26 months after referral to a regional nephrology center in the United Kingdom. By protocol, estimated glomerular filtration rate was determined every 12 months. Predictors: CKD stage defined as estimated glomerular filtration rate ≤45 (stage 3a), 30-44 (3b), 15-29 (4), and <15 (5) mL/min/1.73 m². Outcomes: Onset of renal replacement therapy (RRT), death, the composite end point of RRT or death, or decreasing CKD stage. Results: During a median follow-up of 26 months, 13% reached the end point of RRT (5.1 events/100 patient-years), 20% died (9.6 deaths/100 patient-years), and 33% reached the combined end point of RRT or death (14.7 events/100 patient-years). For stage 3a, baseline prevalence and annual probabilities of decreasing CKD stage, RRT, and death were 18.0%, 0.41, 0.01, and 0.02, respectively. Corresponding values for stage 3b were 32.5%, 0.22, <0.01, and 0.06; for stage 4, 36.5%, 0.17, 0.03, and 0.10; and for stage 5, 13.2%, zero (by definition), 0.31, and 0.08, respectively. Markov model projections suggested a steady decrease for proportions with stages 3a, 3b, and 4; a steady increase for death and RRT; and a biphasic pattern for (non-RRT) stage 5, with a plateau in the first 2 years followed by a steady decrease. Limitations: Single-center observational study. Conclusion: This study suggests that death and RRT are the dominant outcomes in patients referred for management of CKD and that most patients spend comparatively little time in late stages without RRT. [ABSTRACT FROM AUTHOR]

Published
2010
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46. NONVERBAL COMMUNICATION IN PSYCHOTHERAPY.

Author

Foley, Gretchen N. and Gentile, Julie P.

Abstract

The mental status examination is the objective portion of any comprehensive psychiatric assessment and has key diagnostic and treatment implications. This includes elements such as a patient's baseline general appearance and behavior, affect, eye contact, and psychomotor functioning. Changes in these parameters from session to session allow the psychiatrist to gather important information about the patient. In psychiatry, much emphasis is placed on not only listening to what patients communicate verbally but also observing their interactions with the environment and the psychiatrist. In a complimentary fashion, psychiatrists must be aware of their own nonverbal behaviors and communication, as these can serve to either facilitate or hinder the patient-physician interaction. In this article, clinical vignettes will be used to illustrate various aspects of nonverbal communication that may occur within the setting of psychotherapy. Being aware of these unspoken subtleties can offer a psychiatrist valuable information that a patient may be unwilling or unable to put into words. [ABSTRACT FROM AUTHOR]

Published
2010

47. Network Access Control Configuration Management using Semantic Web Techniques.

Author

Fitzgerald, William M., Foley, Simon N., and Foghlú, Micheál Ó

Subjects
CONFIGURATION management, ACCESS control of computer networks, COMPUTER network security, SEMANTIC Web, ONTOLOGIES (Information retrieval)
Abstract

Network Access Control requirements are typically implemented in practice as a series of heterogeneous security-mechanism-centric policies that span system services and application domains. For example, a Network Access Control policy might be configured in terms of firewall, proxy, intrusion prevention and user-access policies. While defined separately, these security policies may interoperate in the sense that the access requirements of one may conflict and/or be redundant with respect to the access requirements of another. Thus, managing a large number of distinct policies becomes a major challenge in terms of deploying and maintaining a meaningful and consistent configuration. It is argued that employing techniques of the Semantic Web--an architecture that supports the formal representation, reasoning and sharing of heterogeneous domain knowledge--provides a natural approach to solving this challenge. A risk-based approach to configuring interoperable Network Access Control policies is described. Each Network Access Control mechanism has an ontology that is used to represent its configuration. This knowledge is unified with higher-level business (risk) rules, providing a single (extensible) ontology that supports reasoning across the different Network Access Control policy configurations. [ABSTRACT FROM AUTHOR]

Published
2009

48. Prevalence of CKD in the United States: a sensitivity analysis using the National Health and Nutrition Examination Survey (NHANES) 1999-2004.

Author

Snyder JJ, Foley RN, Collins AJ, Snyder, Jon J, Foley, Robert N, and Collins, Allan J

Abstract

Background: Estimates of chronic kidney disease (CKD) in the United States using the continuous National Health and Nutrition Examination Survey (NHANES) data set 1999-2004 indicate that 13.1% of the population (26.3 million people based on the 2000 census) has CKD stages 1 to 4.Study Design: We performed sensitivity analyses to highlight assumptions underlying these estimates and illustrate their robustness to varying assumptions.Setting& Participants: NHANES 1999-2004 was a nationally representative cross-sectional continuous survey of the civilian noninstitutionalized US population. Our sample included participants 20 years and older.Reference Test: Estimated glomerular filtration rate (GFR) less than 60 mL/min/1.73 m(2) defined from the 4-variable Modification of Diet in Renal Disease (MDRD) Study equation; albuminuria defined as persistence of urinary albumin-creatinine ratio greater than 30 mg/g.Index Tests: We compared prevalence estimates using the MDRD Study equation with 2 other GFR estimating equations (equation 5 by Rule et al from the Mayo Clinic Donors study; Cockcroft-Gault equation adjusted for body surface area and corrected for the bias in the MDRD Study sample), and sex-specific cutoff values to define albuminuria.Results: We found CKD stages 1 to 4 prevalence estimates ranging from 11.7% to 24.9%, a more than 2-fold difference resulting in population estimates of 25.8 million to 54.0 million people using 2006 population estimates. Considering only stages 3 and 4, which are not affected by the choice of cutoff values to define albuminuria, prevalence estimates ranged from 6.3% to 18.6%, resulting in population estimates of 13.7 million to 40.3 million people, a nearly 3-fold difference.Limitations: NHANES 1999-2004 is a cross-sectional survey and allows for GFR and albumin-creatinine ratio estimates at 1 point in time. NHANES does not account for seniors in long-term care facilities.Conclusions: Although CKD prevalence is high regardless of varying modeling assumptions, different assumptions yield large differences in prevalence estimates. [ABSTRACT FROM AUTHOR]

Published
2009
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49. Calcium-phosphate levels and cardiovascular disease in community-dwelling adults: The Atherosclerosis Risk in Communities (ARIC) Study.

Author

Foley, Robert N., Collins, Allan J., Ishani, Areef, and Kalra, Philip A.

Subjects
CARDIOVASCULAR diseases, CALCIUM phosphate, DISEASES in adults, ATHEROSCLEROSIS risk factors, KIDNEY diseases, HEART disease risk factors
Abstract

Background: Calcium-phosphate levels, linked to vascular dysfunction in chronic kidney disease, may represent novel risk factors for coronary heart disease, stroke, and death in community-dwelling adults. Methods: We tested this hypothesis over 12.6 years of follow-up in the prospective, community-based Atherosclerosis Risk in Communities Study (n = 15,732). Results: At baseline, mean (SD) values were 9.8 (0.4) mg/dL for serum calcium, 3.4 (0.5) mg/dL for serum phosphate, 33.6 (5.3) mg2/dL2 for calcium-phosphate product, 54.2 (5.7) years for age, and 93.1 (21.5) mL/min per 1.73 m2 for glomerular filtration rate (GFR). Shared associations of calcium, phosphate, and calcium-phosphate product included older age, female sex, African American race, cigarette-years, current cigarette smoking, low body mass index, low-density lipoprotein cholesterol, high-density lipoprotein cholesterol, triglycerides, low serum albumin, low GFR, low caloric intake, and phosphorus intake. With adjustment for age, demographic characteristics, comorbid conditions, albumin, and GFR, calcium-associated hazards ratios for coronary heart disease, stroke, and death were, respectively, 1.01 (95% confidence interval 0.96-1.06), 1.16 (1.07-1.26, P = .0005), and 1.03 (0.98-1.08); phosphate-associated hazards ratios were 1.03 (0.98-1.08), 1.11 (1.02-1.21, P = .0219), and 1.14 (1.09-1.20, P < .0001); calcium-phosphate product-associated hazards ratios were 1.03 (0.98-1.08), 1.15 (1.05-1.26, P = .0017), and 1.15 (1.09-1.20, P < .0001). Conclusions: Although calcium, phosphate, and calcium-phosphate product levels exhibit complex associations with traditional cardiovascular risk factors and outcomes, they may be potentially modifiable risk factors for stroke and death in community-dwelling adults. [Copyright &y& Elsevier]

Published
2008
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50. Mosquito host-feeding patterns and implications for Japanese encephalitis virus transmission in northern Australia and Papua New Guinea.

Author

Van Den Hurk, A. F., Johansen, C. A., Zborowski, P., Paru, R., Foley, P. N., Beebe, N. W., Mackenzie, J. S., and Ritchie, A.

Subjects
JAPANESE B encephalitis, MOSQUITO vectors, VIRUS disease transmission
Abstract

Japanese encephalitis (JE) virus spread to northern Australia during the 1990s, transmitted by Culex annulirostris Skuse and other mosquitoes (Diptera: Culicidae). To determine the relative importance of various hosts for potential vectors of JE virus, we investigated the host-feeding patterns of mosquitoes in northern Australia and Western Province of Papua New Guinea, with particular attention to pigs, Sus scrofa L. – the main amplifying host of JE virus in South-east Asia. Mosquitoes were collected by CDC light traps baited with dry ice and 1-octen-3-ol, run 16.00–08.00 hours, mostly set away from human habitations, if possible in places frequented by feral pigs. Bloodmeals of 2569 mosquitoes, representing 15 species, were identified by gel diffusion assay. All species had fed mostly on mammals: only <10% of bloodmeals were from birds. The predominant species was Cx. annulirostris (88%), with relatively few (4.4%) bloodmeals obtained from humans. From all 12 locations sampled, the mean proportion of Cx. annulirostris fed on pigs (9.1%) was considerably lower than fed on other animals (90.9%). Highest rates of pig-fed mosquitoes (>30%) were trapped where domestic pigs were kept close to human habitation. From seven of eight locations on the Australian mainland, the majority of Cx. annulirostris had obtained their bloodmeals from marsupials, probably the Agile wallaby Macropus agilis (Gould). Overall proportions of mosquito bloodmeals identified as marsupial were 60% from the Gulf Plains region of Australia, 78% from the Cape York Peninsula and 64% from the Daru area of Papua New Guinea. Thus, despite the abundance of feral pigs in northern Australia, our findings suggest that marsupials divert host-seeking Cx. annulirostris away from pigs. As marsupials are poor JE virus hosts, the prevalence of marsupials may impede the establishment of JE virus in Australia. [ABSTRACT FROM AUTHOR]

Published
2003
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