Daniel Rivera | Universidad del Desarrollo (UDD) (original) (raw)

Papers by Daniel Rivera

Research paper thumbnail of Functional Data Analysis for Dynamical System Identification of Behavioral Processes

Psychological Methods

Efficient new technology has made it straightforward for behavioral scientists to collect anywher... more Efficient new technology has made it straightforward for behavioral scientists to collect anywhere from several dozen to several thousand dense, repeated measurements on one or more time-varying variables. These intensive longitudinal data (ILD) are ideal for examining complex change over time but present new challenges that illustrate the need for more advanced analytic methods. For example, in ILD the temporal spacing of observations may be irregular, and individuals may be sampled at different times. Also, it is important to assess both how the outcome changes over time and the variation between participants' time-varying processes to make inferences about a particular intervention's effectiveness within the population of interest. The methods presented in this article integrate 2 innovative ILD analytic techniques: functional data analysis and dynamical systems modeling. An empirical application is presented using data from a smoking cessation clinical trial. Study parti...

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Research paper thumbnail of Application of robustified Model Predictive Control to a production-inventory system

Proceedings of the 48h IEEE Conference on Decision and Control (CDC) held jointly with 2009 28th Chinese Control Conference, 2009

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Research paper thumbnail of Hybrid Discrete Event Simulation with Model Predictive Control for Semiconductor Supply-chain Manufacturing

Proceedings of the Winter Simulation Conference, 2005., 2005

Page 1. Proceedings of the 2005 Winter Simulation Conference ME Kuhl, NM Steiger, BF Armstrong, J... more Page 1. Proceedings of the 2005 Winter Simulation Conference ME Kuhl, NM Steiger, BF Armstrong, JE Joines, eds. ABSTRACT Simulation modeling combined with decision control can offer important benefits for analysis, design ...

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Research paper thumbnail of A methodology for control-relevant nonlinear system identification using restricted complexity models

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Research paper thumbnail of Simulation-based optimization of process control policies for inventory management in supply chains

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Research paper thumbnail of Diversity of Francisella tularensis Schu4 antigens recognized by T lymphocytes after natural infections in humans: Identification of candidate epitopes for inclusion in a rationally designed tularemia vaccine

The T lymphocyte antigens, which may have a role in protection against tularemia, were predicted ... more The T lymphocyte antigens, which may have a role in protection against tularemia, were predicted by immunoinformatics analysis of Francisella tularensis Schu4. Twenty-seven class II putative promiscuous epitopes and 125 putative class I supertype epitopes were chosen for synthesis; peptides were tested in vitro for their ability to bind HLA and to induce immune responses from PBMCs of 23 previously infected subjects. While the immune responses of individual subjects showed heterogeneity, 95% of the subjects responded strongly to a pool of 27 promiscuous peptides; 25%, 33%, and 44% of subjects responded to pools of 25 A2, A24, and B7 peptides, respectively. These data can aid in the development of novel epitope-based and subunit tularemia vaccines.

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Research paper thumbnail of A Model Predictive Control framework for robust management of multi-product, multi-echelon demand networks

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Research paper thumbnail of Immunoinformatics Applied to Modifying and Improving Biological Therapeutics

Immunoinformatics, 2008

Abstract. Protein therapeutics have recently emerged as a viable means of treating chronic diseas... more Abstract. Protein therapeutics have recently emerged as a viable means of treating chronic diseases and are beginning to rival small-molecule drugs in market share. Although their promise of targeted therapy is a major medical advance, repeated administrations in many cases lead to ...

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Research paper thumbnail of A process control approach to tactical inventory management in production-inventory systems

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Research paper thumbnail of Developing an epitope-driven tuberculosis (TB) vaccine

Vaccine, 2005

Epitope-driven vaccines are created from selected sub-sequences of proteins, or epitopes, derived... more Epitope-driven vaccines are created from selected sub-sequences of proteins, or epitopes, derived by scanning the protein sequences of pathogens for patterns of amino acids that permit binding to human MHC molecules. We developed a prototype tuberculosis (TB) vaccine that contains epitopes derived by (1) EpiMer mapping of previously published secreted proteins derived from Mycobacterium tuberculosis (Mtb), and (2) EpiMatrix mapping

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Research paper thumbnail of Capturing water and sound waves to interact with virtual nature

The Second IEEE and ACM International Symposium on Mixed and Augmented Reality, 2003. Proceedings., 2003

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Research paper thumbnail of HIV vaccine development by computer assisted design: the GAIA vaccine

Vaccine, 2005

The design of epitope-driven vaccines that address the global variability of HIV has been signifi... more The design of epitope-driven vaccines that address the global variability of HIV has been significantly hampered by concerns about conservation of the vaccine epitopes across clades of HIV. We developed two computer-driven methods for improving epitope-driven HIV vaccines: the Epi-Assembler, which derives representative or "immunogenic consensus sequence" (ICS) epitopes from multiple viral variants, and VaccineCAD, which reduces junctional immunogenicity when epitopes are aligned in a string-of-beads format for insertion in a DNA expression vector. In this study, we report on 20 ICS HIV-1 peptides. The core 9-mer contained in these consensus peptides was conserved in 105-2250 individual HIV-1 strains. Nineteen of the 20 ICS epitopes (95%) evaluated in this study were confirmed in ELISpot assays using peripheral blood monocytes obtained from 13 healthy HIV-1 infected subjects. Twenty-five ICS peptides (all 20 of the peptides evaluated in this study and 5 additional ICS epitopes) were then aligned in a pseudoprotein string using "VaccineCAD", an epitope alignment tool that eliminates immunogenicity created by the junctions between the epitopes. Reordering the construct reduced the immunogenicity of the junctions between epitopes as measured by EpiMatrix, an epitope mapping algorithm. The reordered construct was also a more effective immunogen in vivo when tested in HLA-DR transgenic mice. These data confirm the utility of bioinformatics tools to design novel vaccines containing "immunogenic consensus…

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Research paper thumbnail of A Dynamical Systems Model for Understanding Behavioral Interventions for Weight Loss

Lecture Notes in Computer Science, 2010

We propose a dynamical systems model that captures the daily fluctuations of human weight change,... more We propose a dynamical systems model that captures the daily fluctuations of human weight change, incorporating both physiological and psychological factors. The model consists of an energy balance integrated with a mechanistic behavioral model inspired by the Theory ...

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Research paper thumbnail of Diversity of Francisella tularensis Schu4 antigens recognized by T lymphocytes after natural infections in humans: Identification of candidate epitopes for inclusion in a rationally designed tularemia vaccine

Vaccine, 2007

The T lymphocyte antigens, which may have a role in protection against tularemia, were predicted ... more The T lymphocyte antigens, which may have a role in protection against tularemia, were predicted by immunoinformatics analysis of Francisella tularensis Schu4. Twenty-seven class II putative promiscuous epitopes and 125 putative class I supertype epitopes were chosen for synthesis; peptides were tested in vitro for their ability to bind HLA and to induce immune responses from PBMCs of 23 previously infected subjects. While the immune responses of individual subjects showed heterogeneity, 95% of the subjects responded strongly to a pool of 27 promiscuous peptides; 25%, 33%, and 44% of subjects responded to pools of 25 A2, A24, and B7 peptides, respectively. These data can aid in the development of novel epitope-based and subunit tularemia vaccines.

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Research paper thumbnail of Health behavior models in the age of mobile interventions: are our theories up to the task?

Translational behavioral medicine, 2011

Mobile technologies are being used to deliver health behavior interventions. The study aims to de... more Mobile technologies are being used to deliver health behavior interventions. The study aims to determine how health behavior theories are applied to mobile interventions. This is a review of the theoretical basis and interactivity of mobile health behavior interventions. Many of the mobile health behavior interventions reviewed were predominately one way (i.e., mostly data input or informational output), but some have leveraged mobile technologies to provide just-in-time, interactive, and adaptive interventions. Most smoking and weight loss studies reported a theoretical basis for the mobile intervention, but most of the adherence and disease management studies did not. Mobile health behavior intervention development could benefit from greater application of health behavior theories. Current theories, however, appear inadequate to inform mobile intervention development as these interventions become more interactive and adaptive. Dynamic feedback system theories of health behavior ca...

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Research paper thumbnail of Novel function of complement C3d as an autologous helper T-cell target

Immunology and Cell Biology, 2008

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Research paper thumbnail of Clinical validation of the “in silico” prediction of immunogenicity of a human recombinant therapeutic protein

Clinical Immunology, 2007

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Research paper thumbnail of Identification of Affine Linear Parameter Varying Models for Adaptive Interventions in Fibromyalgia Treatment

Proceedings of the ... American Control Conference. American Control Conference, Jan 31, 2013

There is good evidence that naltrexone, an opioid antagonist, has a strong neuroprotective role a... more There is good evidence that naltrexone, an opioid antagonist, has a strong neuroprotective role and may be a potential drug for the treatment of fibromyalgia. In previous work, some of the authors used experimental clinical data to identify input-output linear time invariant models that were used to extract useful information about the effect of this drug on fibromyalgia symptoms. Additional factors such as anxiety, stress, mood, and headache, were considered as additive disturbances. However, it seems reasonable to think that these factors do not affect the drug actuation, but only the way in which a participant perceives how the drug actuates on herself. Under this hypothesis the linear time invariant models can be replaced by State-Space Affine Linear Parameter Varying models where the disturbances are seen as a scheduling signal signal only acting at the parameters of the output equation. In this paper a new algorithm for identifying such a model is proposed. This algorithm mini...

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Research paper thumbnail of Su.76. High Throughput Validation of Predicted T-Cell Epitopes in F. Tularensis: the Development of a Novel T-Cell Epitope Based Tularemia Vaccine

Clinical Immunology, 2006

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Research paper thumbnail of Methodologies for optimizing behavioral interventions: introduction to special section

Translational behavioral medicine, 2014

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Research paper thumbnail of Functional Data Analysis for Dynamical System Identification of Behavioral Processes

Psychological Methods

Efficient new technology has made it straightforward for behavioral scientists to collect anywher... more Efficient new technology has made it straightforward for behavioral scientists to collect anywhere from several dozen to several thousand dense, repeated measurements on one or more time-varying variables. These intensive longitudinal data (ILD) are ideal for examining complex change over time but present new challenges that illustrate the need for more advanced analytic methods. For example, in ILD the temporal spacing of observations may be irregular, and individuals may be sampled at different times. Also, it is important to assess both how the outcome changes over time and the variation between participants' time-varying processes to make inferences about a particular intervention's effectiveness within the population of interest. The methods presented in this article integrate 2 innovative ILD analytic techniques: functional data analysis and dynamical systems modeling. An empirical application is presented using data from a smoking cessation clinical trial. Study parti...

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Research paper thumbnail of Application of robustified Model Predictive Control to a production-inventory system

Proceedings of the 48h IEEE Conference on Decision and Control (CDC) held jointly with 2009 28th Chinese Control Conference, 2009

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Hybrid Discrete Event Simulation with Model Predictive Control for Semiconductor Supply-chain Manufacturing

Proceedings of the Winter Simulation Conference, 2005., 2005

Page 1. Proceedings of the 2005 Winter Simulation Conference ME Kuhl, NM Steiger, BF Armstrong, J... more Page 1. Proceedings of the 2005 Winter Simulation Conference ME Kuhl, NM Steiger, BF Armstrong, JE Joines, eds. ABSTRACT Simulation modeling combined with decision control can offer important benefits for analysis, design ...

Bookmarks Related papers MentionsView impact

Research paper thumbnail of A methodology for control-relevant nonlinear system identification using restricted complexity models

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Simulation-based optimization of process control policies for inventory management in supply chains

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Diversity of Francisella tularensis Schu4 antigens recognized by T lymphocytes after natural infections in humans: Identification of candidate epitopes for inclusion in a rationally designed tularemia vaccine

The T lymphocyte antigens, which may have a role in protection against tularemia, were predicted ... more The T lymphocyte antigens, which may have a role in protection against tularemia, were predicted by immunoinformatics analysis of Francisella tularensis Schu4. Twenty-seven class II putative promiscuous epitopes and 125 putative class I supertype epitopes were chosen for synthesis; peptides were tested in vitro for their ability to bind HLA and to induce immune responses from PBMCs of 23 previously infected subjects. While the immune responses of individual subjects showed heterogeneity, 95% of the subjects responded strongly to a pool of 27 promiscuous peptides; 25%, 33%, and 44% of subjects responded to pools of 25 A2, A24, and B7 peptides, respectively. These data can aid in the development of novel epitope-based and subunit tularemia vaccines.

Bookmarks Related papers MentionsView impact

Research paper thumbnail of A Model Predictive Control framework for robust management of multi-product, multi-echelon demand networks

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Immunoinformatics Applied to Modifying and Improving Biological Therapeutics

Immunoinformatics, 2008

Abstract. Protein therapeutics have recently emerged as a viable means of treating chronic diseas... more Abstract. Protein therapeutics have recently emerged as a viable means of treating chronic diseases and are beginning to rival small-molecule drugs in market share. Although their promise of targeted therapy is a major medical advance, repeated administrations in many cases lead to ...

Bookmarks Related papers MentionsView impact

Research paper thumbnail of A process control approach to tactical inventory management in production-inventory systems

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Developing an epitope-driven tuberculosis (TB) vaccine

Vaccine, 2005

Epitope-driven vaccines are created from selected sub-sequences of proteins, or epitopes, derived... more Epitope-driven vaccines are created from selected sub-sequences of proteins, or epitopes, derived by scanning the protein sequences of pathogens for patterns of amino acids that permit binding to human MHC molecules. We developed a prototype tuberculosis (TB) vaccine that contains epitopes derived by (1) EpiMer mapping of previously published secreted proteins derived from Mycobacterium tuberculosis (Mtb), and (2) EpiMatrix mapping

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Capturing water and sound waves to interact with virtual nature

The Second IEEE and ACM International Symposium on Mixed and Augmented Reality, 2003. Proceedings., 2003

Bookmarks Related papers MentionsView impact

Research paper thumbnail of HIV vaccine development by computer assisted design: the GAIA vaccine

Vaccine, 2005

The design of epitope-driven vaccines that address the global variability of HIV has been signifi... more The design of epitope-driven vaccines that address the global variability of HIV has been significantly hampered by concerns about conservation of the vaccine epitopes across clades of HIV. We developed two computer-driven methods for improving epitope-driven HIV vaccines: the Epi-Assembler, which derives representative or "immunogenic consensus sequence" (ICS) epitopes from multiple viral variants, and VaccineCAD, which reduces junctional immunogenicity when epitopes are aligned in a string-of-beads format for insertion in a DNA expression vector. In this study, we report on 20 ICS HIV-1 peptides. The core 9-mer contained in these consensus peptides was conserved in 105-2250 individual HIV-1 strains. Nineteen of the 20 ICS epitopes (95%) evaluated in this study were confirmed in ELISpot assays using peripheral blood monocytes obtained from 13 healthy HIV-1 infected subjects. Twenty-five ICS peptides (all 20 of the peptides evaluated in this study and 5 additional ICS epitopes) were then aligned in a pseudoprotein string using "VaccineCAD", an epitope alignment tool that eliminates immunogenicity created by the junctions between the epitopes. Reordering the construct reduced the immunogenicity of the junctions between epitopes as measured by EpiMatrix, an epitope mapping algorithm. The reordered construct was also a more effective immunogen in vivo when tested in HLA-DR transgenic mice. These data confirm the utility of bioinformatics tools to design novel vaccines containing "immunogenic consensus…

Bookmarks Related papers MentionsView impact

Research paper thumbnail of A Dynamical Systems Model for Understanding Behavioral Interventions for Weight Loss

Lecture Notes in Computer Science, 2010

We propose a dynamical systems model that captures the daily fluctuations of human weight change,... more We propose a dynamical systems model that captures the daily fluctuations of human weight change, incorporating both physiological and psychological factors. The model consists of an energy balance integrated with a mechanistic behavioral model inspired by the Theory ...

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Diversity of Francisella tularensis Schu4 antigens recognized by T lymphocytes after natural infections in humans: Identification of candidate epitopes for inclusion in a rationally designed tularemia vaccine

Vaccine, 2007

The T lymphocyte antigens, which may have a role in protection against tularemia, were predicted ... more The T lymphocyte antigens, which may have a role in protection against tularemia, were predicted by immunoinformatics analysis of Francisella tularensis Schu4. Twenty-seven class II putative promiscuous epitopes and 125 putative class I supertype epitopes were chosen for synthesis; peptides were tested in vitro for their ability to bind HLA and to induce immune responses from PBMCs of 23 previously infected subjects. While the immune responses of individual subjects showed heterogeneity, 95% of the subjects responded strongly to a pool of 27 promiscuous peptides; 25%, 33%, and 44% of subjects responded to pools of 25 A2, A24, and B7 peptides, respectively. These data can aid in the development of novel epitope-based and subunit tularemia vaccines.

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Health behavior models in the age of mobile interventions: are our theories up to the task?

Translational behavioral medicine, 2011

Mobile technologies are being used to deliver health behavior interventions. The study aims to de... more Mobile technologies are being used to deliver health behavior interventions. The study aims to determine how health behavior theories are applied to mobile interventions. This is a review of the theoretical basis and interactivity of mobile health behavior interventions. Many of the mobile health behavior interventions reviewed were predominately one way (i.e., mostly data input or informational output), but some have leveraged mobile technologies to provide just-in-time, interactive, and adaptive interventions. Most smoking and weight loss studies reported a theoretical basis for the mobile intervention, but most of the adherence and disease management studies did not. Mobile health behavior intervention development could benefit from greater application of health behavior theories. Current theories, however, appear inadequate to inform mobile intervention development as these interventions become more interactive and adaptive. Dynamic feedback system theories of health behavior ca...

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Novel function of complement C3d as an autologous helper T-cell target

Immunology and Cell Biology, 2008

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Clinical validation of the “in silico” prediction of immunogenicity of a human recombinant therapeutic protein

Clinical Immunology, 2007

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Identification of Affine Linear Parameter Varying Models for Adaptive Interventions in Fibromyalgia Treatment

Proceedings of the ... American Control Conference. American Control Conference, Jan 31, 2013

There is good evidence that naltrexone, an opioid antagonist, has a strong neuroprotective role a... more There is good evidence that naltrexone, an opioid antagonist, has a strong neuroprotective role and may be a potential drug for the treatment of fibromyalgia. In previous work, some of the authors used experimental clinical data to identify input-output linear time invariant models that were used to extract useful information about the effect of this drug on fibromyalgia symptoms. Additional factors such as anxiety, stress, mood, and headache, were considered as additive disturbances. However, it seems reasonable to think that these factors do not affect the drug actuation, but only the way in which a participant perceives how the drug actuates on herself. Under this hypothesis the linear time invariant models can be replaced by State-Space Affine Linear Parameter Varying models where the disturbances are seen as a scheduling signal signal only acting at the parameters of the output equation. In this paper a new algorithm for identifying such a model is proposed. This algorithm mini...

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Research paper thumbnail of Su.76. High Throughput Validation of Predicted T-Cell Epitopes in F. Tularensis: the Development of a Novel T-Cell Epitope Based Tularemia Vaccine

Clinical Immunology, 2006

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Methodologies for optimizing behavioral interventions: introduction to special section

Translational behavioral medicine, 2014

Bookmarks Related papers MentionsView impact