Bradly Alicea

2015 Contextual Geometric Structures: abstractions of cognition and culture. Society of Postdoctoral Scholars (SOPS) Conference, Beckman Institute, University of Illinois, Urbana-Champaign, IL.

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Alicea, B. Contextual and Structural Representations of Market-mediated Economic Value. arXiv repository, arXiv: 1403.7021 [q-fin.GN] (2014).

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Alicea, B. Modeling Cellular Information Processing Using a Dynamical Approximation of Cellular mRNA. bioRxiv, doi:10.1101/006775 (2014).

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Alicea, B. Carnival of Evolution #70: the game of evolution. April 1, Synthetic Daisies Blog, http://syntheticdaisies.blogspot.com/2014/04/carnival-of-evolution-70-game-of.html doi: 6084/m9.figshare.900957 (2014).

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Alicea, B. Perceptual time and the evolution of informational investment. Published in Machines Like Us. http://machineslikeus.com/news/perceptual-time-and-evolution-informational-investment (2014). in Humanity+. ignorant perspective. Profiled Triangulating Scientific "Truths": an Alicea, B. http://hplusmagazine.com/2012/12/19/triangulating-scientific-truths-an-ignorant-perspective/ (2013).

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Alicea, B., McGrew, S., Gordon, R., Larson, S., Warrington, T., and Watts, M. DevoWorm: differentiation waves and computation in C. elegans embryogenesis. bioRxiv, doi:10.1101/009993 (2014).

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2014 DevoWorm: raising the (Open)Worm . OpenWorm Journal Club, San Diego, CA and Google Hangouts. http://www.youtube.com/channel/UCF76f-eS1QW8OsnkOQFpp1g 2013

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(2014). Special Issue: Patterns of Evolution.

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Alicea, B. Animal-oriented Virtual Environments: illusion, dilation, and discovery. F1000 Research, 3:202. doi: 10.12688/f1000research.3557.1 (2014).

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Alicea, B. with input from S.T. Suhr and J.B. Cibelli Using Polysome Isolation with Mechanism Alteration to Uncover Transcriptional and Translational Dynamics in Key Genes. bioRxiv, doi:10.1101/006213 (2014).

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Alicea, B. Independent features of quantified thermocycling reactions (qRT-PCR). Figshare, doi:10.6084/m9.figshare.649432 (2013).

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2013 Multiscale Integration and Heuristics of Complex Physiological Phenomena . Embryo Physics Course, Silver Bog Research, Second Life.

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Game Theory of Shutting Things Down. October 15, Synthetic Daisies Blog, Alicea, B. http://syntheticdaisies.blogspot.com/2013/10/game-theory-of-shutting-things-down.html doi:10.6084/ m9.figshare.900957 (2013).

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Science to Route New 2013 A http://dx.doi.org/10.6084/m9.figshare.106823 .

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Alicea, B. Collective properties of cellular identity: a computational approach . arXiv repository, arXiv: 1302:0826. [q-bio.GN, q-bio.QM] (2013).

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Alicea, B. and Cibelli, J.B. Comparing indirect-derived ES cells and directly-derived iPS cells. In "Principles of Cloning". Elsevier, Amsterdam (2013).

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Alicea, B. Carnival of Evolution #58: Visions of the Evolutionary Future. April 1, Synthetic Daisies Blog. http://syntheticdaisies.blogspot.com/2013/04/carnival-of-evolution-number-58-vision.html doi:10.6084/ m9. figshare.661698 (2013).

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Alicea, B. A Semi-automated Peer-review System. arXiv repository, arXiv:1311.2504 [cs.DL, cs.HC, cs.SI, physics.soc-ph] (2013).

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Alicea, B. The Emergence of Animal Social Complexity: theoretical and biobehavioral evidence. arXiv repository, arXiv: 1309.7990 [q-bio.PE, q-bio.NC] (2013).

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2013 Discrete Inducible of Modeling Dynamical doi:10.6084/m9.figshare.106824 http://dx.doi.org/10.6084/m9.figshare.106824 .

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2013 Adventures in Quasi-Evolution: evolutionary modulus and evolutionary through the looking glass. BEACON Center, Michigan State University.

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Alicea, B., Murthy, S., Keaton, S.A., Cobbett, P., Cibelli, J.B., and Suhr, S.T. Defining phenotypic respecification diversity using multiple cell lines and reprogramming regimens . Stem Cells and Development, 22(19), 2641-2654 (2013).

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Alicea, B. Cellular decision-making bias: the missing ingredient in cell functional diversity. arXiv repository, arXiv: 1310:8268 [q-bio.QM] (2013).

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2012 Advancing Dynamic Models of Cellular Processes (and new ways to fund them). Levin Lab, Institute for Developmental Biology and Regenerative Medicine , Tufts University.

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2012 Behavioral Engineering and Brain Science in Virtual Reality. Seminar, Department of Computer Science, Michigan State University.

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Alicea, B. and Grabowski, L. Hard-to-Define-Events (HTDE) 2012. Held in conjunction with Artificial Life 13, East Lansing, MI. Website: http://syntheticdaisies.blogspot.com/p/htde-workshop-2012.html Invited Lectures and Presentations.

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Interview with Sujata Gupta, Virtual windows on brains at work. New Scientist, March 17 (2012).

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Alicea, B. Carnival of Evolution #46: the Tree (Structures) of Life. April 1, Synthetic Daisies Blog. http://syntheticdaisies.blogspot.com/2012/04/carnival-of-evolution-number-46-tree.html doi:10.6084/ m9.figshare.99887 (2012).

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MMG 302: Laboratory Instructor, General Microbiology Laboratory, Department of Microbiology and Molecular Biology, Michigan State University, Spring and Summer 2012.

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2012 Scenes From a Graphical, Parallel Biology. Embryo Physics Course, Silver Bog Research, Second Life.

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Interview with Rachel Nuwer, Why Scientists are fooling animals with virtual reality. Popular Mechanics, April 10 (2012).

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Geodynamics Life Meets Artificial http://hplusmagazine.com/2012/12/07/artificial-life-meets-geodynamics-evogeo/ (2012).

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2012 Simulating the Dynamic Regulation of a Cell: Relevance to Cell Reprogramming. 2nd Midwest Conference of Stem Cell Biology and Therapy, Oakland University, Rochester, MI.

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Proceedings of Artificial Life, 13, 147-154 (2012).

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Alicea, B. Non-uniform Gene Networks. Symposium on Emerging Topics in Control and Modeling: Networked Systems. Coordinated Science Laboratory, University of Illinois, Urbana-Champaign. Poster (2012). npre.2010.5448.1

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Alicea, B. Dynamical Cellular Encodings for Exploring Cellular Reprogramming. Dynamics Days 2012.

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Alicea, B. Relativistic Virtual Worlds: an emerging framework. arXiv repository, arXiv: 1104:4586 [cs.HC, cs.CG, q-bio.NC] (2011).

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Alicea, B. The 'Machinery' of Biocomplexity: understanding non-optimal architectures in biological systems. arXiv repository, arXiv: 1104.3559 [nlin.AO, q-bio.QM, q-bio.PE] (2011).

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Alicea, B. Formal Systems Architectures for Biology. Nature Precedings, npre.2011.6369.1

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Alicea, B. Control in Technological Systems and Physical Intelligence: an emerging theory . Midwest Cognitive Science Conference, Michigan State University, East Lansing, MI. Nature Precedings, npre.2011.5910.1 [http://precedings.nature.com/documents/5910/version/1] . Slideshow (2011).

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Bohil, C., Alicea, B., and Biocca, F. Virtual Reality in Neuroscience Research and Therapy . Nature Reviews Neuroscience, 12, 752-762 (2011). Invited Review.

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2009-2011 Developmental, Stem Cell, and Regenerative Medicine Journal Club presentations, Cellular Reprogramming Laboratory, Michigan State University. Literature reviews and tutorials based on recently 2007 Evolving "Physical" Intelligence: physiology, robotics, and computational biology . Evolving Intelligence Research Group, DevoLab, Department of Computer Science, Michigan State University.

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Alicea, B. Lagrangian Coherent Structures (LCS) may describe evolvable frontiers in natural populations. arXiv repository, arXiv:1101.6071 [nlin.AO, physics.bio-ph, q-bio.PE] (2011).

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2011 Biocomplexity of Inducible Cells . Embryo Physics Course, Silver Bog Research, Second Life.

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Alicea, B. Unmatched muscle power: mapping physiological control to virtual world physics. Symposium on Emerging Topics in Control and Modeling: Biomedical Systems. Beckman Institute, University of Illinois Urbana-Champaign. Poster (2010).

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Alicea, Precedings, Tissues. Nature Biological Nano-enabled [http://precedings.nature.com/documents/5448/version/1] . Slideshow (2010).

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Alicea, B. Dynamical approximation of a reprogramming cell culture. Dynamic Days 2010. Evanston, IL.

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QB 828: Module on Evolutionary Systems Biology, Biology for the In terdisciplinary Scientist, Quantitative Biology Program, Michigan State University, Spring 2009 and Spring 2010.

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Alicea, B. Emergent Natural Selection for Engineering Living Systems. Early Career Scientists Symposium (ECSS) 2010: Experimental Evolution, University of Michigan. Poster (2010).

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Alicea, B. Natural Variation and Neuromechanical Systems. ASME International Mechanical Congress and Exposition (IMECE 2009). Lake Buena Vista, FL., Published in Cogprints, http://cogprints.org/6698/ (2009).

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Alicea, B. Range-based techniques for discovering optimality and analyzing scaling relationships in neuromechanical npre.2009.2845.2

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Alicea, B. Stochastic Resonance (SR) can drive adaptive physiological processes. Nature Precedings, npre.2009.3301.1 [http://precedings.nature.com/documents/3301/version/1] (2009).

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Bohil, C., Owen, C.B., Jeong, E.J., Alicea, B., and Biocca, F. Virtual Reality. In "21rst Century Communication: a reference book". Sage Publications, Washington, D.C (2009).

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Alicea, B. Emergent natural selection and the evolution of novel biological surfaces. I2CAM Workshop, Soft Active Materials: from granular rods to flocks, cells, and tissues. Syracuse University . Slideshow (2009).

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Carvallo-Pinto, M.A., Alicea, B., and Rodrigues, J.L.M. Towards a "core" genome: pairwise similarity searches on interspecific genomic data. arXiv repository, arXiv:0807.3353 [q-bio.GN, q-bio.PE] (2008).

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Alicea, B. Hierarchies of Biocomplexity: modeling life's energetic complexity. arXiv repository, arXiv:0810.4547 [q-bio.PE, q-bio.OT] (2008).

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Evolutionary Systems Biology course materials can be found here: Slides: http://syntheticdaisies.blogspot.com/p/evolutionary-systems-biology-course.html CAS 992: Tutorial on physiological measurement techniques, Seminar on Minds and Media, College of Communication Arts and Sciences, Michigan State University, Fall 2008.

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Alicea, B. Fundamental Elements of Muscle-generated Motion: developing a genomic modeling framework. Adaptive Movement and Adaptive Machines (AMAM) 2008, Case Western University, Cleveland, OH. Poster (2008).

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Adaptive Movement and Adaptive Machines (AMAM) 2008, Case Western University, Cleveland, OH.

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Alicea, B. Performance Augmentation in Hybrid Systems: techniques and experiment. arXiv repository, arXiv:0810.4629 [q-bio.NC, q-bio.QM] (2008).

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Alicea, B. The adaptability of physiological systems optimizes performance: new directions in augmentation. arXiv repository, arXiv:0810.4884 [cs.HC, cs.NE] (2008).

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2007 Introduction to Hybrid Bionic Systems . Seminar. Department of Telecommunication, Information Studies, and Media, Michigan State University.

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Society for Automotive Engineering (SAE) Digital Human Modeling , #2007-01-2461 (2007).

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Alicea, B. Real-time representations of whole brain dynamics: towards a computational model for hybrid systems and human performance. Understanding Complex Systems Symposium (2007).

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Dynamic Walking 2006, University of Michigan, Ann Arbor, MI. Poster (2006).

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Alicea, B. Broad-Spectrum Mitigation and the Cognitive Neurobiological Interface: considering biological rhythms in Augmented Cognition. Proceedings of the Human Factors and Ergonomics Society (2006).

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Alicea, B. and Grabowski, L. From Finding Home to Navigational Primitives: using path-integration and tracking technologies to achieve navigational mitigation. Augmented Cognition International, San Francisco, CA. Poster (2006).

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Biocca, F. Alicea, B., Bohil, C., Owen, C.B., and Xiao, F. Targeting and Sensorimotor Behavior in Augmented Reality: from spatial memory to optimal patterns. Proceedings of the International Communication Association (2006).

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Alicea, B. Filling up the tree: considering the self-organization of avian roosting behavior. Understanding Complex Systems Symposium (2006). Also bioRxiv, doi:10.1101/000349.

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Yang, M-J., Alicea, B., Clark, C., and Larose, R. Does E-Trust Matter? A Social Cognitive Theory of Online Shopping Behavior. Proceedings of the International Communication Association (2005).

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More information can be found here: MATLAB Code: https://github.com/balicea/neurotech-tutorial/ TC 491: Wearable Computing Module Coordinator, Human -Computer Interaction, Department of Telecommunication, Information Studies, and Media, Michigan State University, Spring 2005.

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Biocca, F. and Alicea, B. Is nanotechnology a communication technology? Proceedings of the International Communication Association (2004).

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ANG 2000: General Anthropology, Department of Anthropology, University of Florida, Guest lectures on Evolution of Sex and Human Evolution, Spring 2001.

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ANG 3141: Development of World Civilizations, Department of Anthropology, University of Florida, Spring 2000.

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ANG 2301: Human Sexuality, Department of Anthropology, University of Florida, Fall 1999 and 2000.

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Alicea, B. From Worst to Most Variable? Only the worst performers may be the most informative .

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Alicea, B. Genomic Signal Processing: one scientist's quest. Figshare, doi:10.6084/m9.figshare.155705

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Alicea, B. Reverse Distributed Computing: doing science experiments in Second Life. Simulation and Second Life Workshop, European Social Simulation Association/Artificial Life Group, Second Life.

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Alicea, B. and Gordon, R. Toy Models for Macroevolutionary Patterns and Trends . Biosystems, 122, 25-37

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Alicea, B. "Virtual" work: the D'Alembert principle and upper-body movement in mixed-reality systems.

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Alicea, B. Naturally Supervised Learning in Motion and Touch-driven Technologies. arXiv repository, arXiv: 1106:1105.

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Teaching History Profile (from most recent)

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The teaching task was to supervise a group of 4 students (from a class of 45-50 students) on a technical research project (the construction of a basic haptic interface for controlling object on a computer screen). Supervision included technical support, in addition to assistance with statistical analysis and mathematical modeling.

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Alicea, B. Environmental switching: characterizing the adaptable range of neuromechanical processes.

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The teaching task was to assist in the instruction of an honors college course (50 -60 students) on cross-cultural perspectives for understanding the rise and fall of "low-visibility" civilizations. Topical focus ranged from paleoanthropology to historical archaeology. Workload involved the grading of written exams along with the development of lectures and exam questions. The degree of student-instructor interaction was moderately high.

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The teaching task was to facilitate discussion and instruction, grade term papers, and develop exam questions for a class of 700 students. Discussion and term paper writing took place in sections of 25-30 students each. In the discussion groups, the degree of student-instructor interaction was moderately high.

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Alicea, B. Hierarchical Evolutionary Dynamics for Understanding Self-Assembly in Nano-Mechanical Systems. IEEE Fall Conference on Nanotechnology, Nanorobots, Nanobusiness, and Nanoeducation.

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Alicea, B. Contextual Geometric Structures: modeling the fundamental components of cultural behavior.

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The teaching task was to introduce and engage quantitative-oriented students (e.g. physicists, engineers) to evolutionary biology. The course was developed as a module of an existing course on Quantitative Biology methods. The module consists of a series of lectures, homework assignments, and exam questions. The course had 10-14 students per year, and the degree of student-instructor interaction was high.

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Weber, R., Alicea, B., and Mathiak, K. The Dynamics of Attention in Interactive Environments: A functional Magnetic Resonance Imaging Study. Submitted to Human Brain Mapping.

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From Switches to Convolution to Tangled Webs: evolving sub-optimal, subtle biological mechanisms. Network Frontiers Workshop, Northwestern University, Evanston, IL.

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The teaching task was to supervise students during a laboratory practicum. Students wro te up reports on their exercises and received feedback from the instructor. The course had 16 -24 students per section, and the degree of student-instructor interaction was high.

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Alicea, B. Towards a theory of human intraspecific variation for ergonomics and human modeling.

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The teaching task was to introduce Engineering, Psychology, and Communications students to physiological recording and psychophysiological techniques for human-computer systems. The course was a single-session tutorial presented as part of an existing course of 15-20 students. The tutorial covered the basic physiology and measurement techniques associated with Biopac hardware and AcqKnowledge software, and MATLAB analysis tools.

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The teaching task was to assist in the instruction of a general education course (100 -120 students) focused on topics ranging from Paleoanthropology to the study of contemporary cultures. My duties included grading written exams, developing two guest lectures, and developing exam questions. The degree of student-instructor interaction was moderate.

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