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51. Evidence Graphs: Supporting Transparent and FAIR Computation, with Defeasible Reasoning on Data, Methods, and Results

Author

Al Manir, Sadnan, Niestroy, Justin, Levinson, Maxwell Adam, Clark, Timothy, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Woeginger, Gerhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Glavic, Boris, editor, Braganholo, Vanessa, editor, and Koop, David, editor

Published
2021
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53. Managing consequences of climate‐driven species redistribution requires integration of ecology, conservation and social science

Author

Bonebrake, Timothy C, Brown, Christopher J, Bell, Johann D, Blanchard, Julia L, Chauvenet, Alienor, Champion, Curtis, Chen, I‐Ching, Clark, Timothy D, Colwell, Robert K, Danielsen, Finn, Dell, Anthony I, Donelson, Jennifer M, Evengård, Birgitta, Ferrier, Simon, Frusher, Stewart, Garcia, Raquel A, Griffis, Roger B, Hobday, Alistair J, Jarzyna, Marta A, Lee, Emma, Lenoir, Jonathan, Linnetved, Hlif, Martin, Victoria Y, McCormack, Phillipa C, McDonald, Jan, McDonald‐Madden, Eve, Mitchell, Nicola, Mustonen, Tero, Pandolfi, John M, Pettorelli, Nathalie, Possingham, Hugh, Pulsifer, Peter, Reynolds, Mark, Scheffers, Brett R, Sorte, Cascade JB, Strugnell, Jan M, Tuanmu, Mao‐Ning, Twiname, Samantha, Vergés, Adriana, Villanueva, Cecilia, Wapstra, Erik, Wernberg, Thomas, and Pecl, Gretta T

Subjects
Biological Sciences, Ecology, Climate Action, Animals, Climate Change, Conservation of Natural Resources, Humans, Social Sciences, Species Specificity, adaptive conservation, climate change, food security, health, managed relocation, range shift, sustainable development, temperature, Evolutionary Biology, Biological sciences
Abstract

Climate change is driving a pervasive global redistribution of the planet's species. Species redistribution poses new questions for the study of ecosystems, conservation science and human societies that require a coordinated and integrated approach. Here we review recent progress, key gaps and strategic directions in this nascent research area, emphasising emerging themes in species redistribution biology, the importance of understanding underlying drivers and the need to anticipate novel outcomes of changes in species ranges. We highlight that species redistribution has manifest implications across multiple temporal and spatial scales and from genes to ecosystems. Understanding range shifts from ecological, physiological, genetic and biogeographical perspectives is essential for informing changing paradigms in conservation science and for designing conservation strategies that incorporate changing population connectivity and advance adaptation to climate change. Species redistributions present challenges for human well-being, environmental management and sustainable development. By synthesising recent approaches, theories and tools, our review establishes an interdisciplinary foundation for the development of future research on species redistribution. Specifically, we demonstrate how ecological, conservation and social research on species redistribution can best be achieved by working across disciplinary boundaries to develop and implement solutions to climate change challenges. Future studies should therefore integrate existing and complementary scientific frameworks while incorporating social science and human-centred approaches. Finally, we emphasise that the best science will not be useful unless more scientists engage with managers, policy makers and the public to develop responsible and socially acceptable options for the global challenges arising from species redistributions.

Published
2018

54. Cell Maps for Artificial Intelligence: AI-Ready Maps of Human Cell Architecture from Disease-Relevant Cell Lines

Author

Clark, Timothy, primary, Mohan, Jillian, additional, Schaffer, Leah, additional, Obernier, Kirsten, additional, Al Manir, Sadnan, additional, Churas, Christopher P, additional, Dailamy, Amir, additional, Doctor, Yesh, additional, Forget, Antoine, additional, Hansen, Jan Niklas, additional, Hu, Mengzhou, additional, Lenkiewicz, Joanna, additional, Levinson, Maxwell Adam, additional, Marquez, Charlotte, additional, Nourreddine, Sami, additional, Niestroy, Justin, additional, Pratt, Dexter, additional, Qian, Gege, additional, Thaker, Swathi, additional, Bélisle-Pipon, Jean-Christophe, additional, Brandt, Cynthia, additional, Chen, Jake, additional, Ding, Ying, additional, Fodeh, Samah, additional, Krogan, Nevan, additional, Lundberg, Emma, additional, Mali, Prashant, additional, Payne-Foster, Pamela, additional, Ratcliffe, Sarah, additional, Ravitsky, Vardit, additional, Sali, Andrej, additional, Schulz, Wade, additional, and Ideker, Trey, additional

Published
2024
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57. Nautilus Field Season Overview

Author

Raineault, Nicole A., Gee, Lindsay, Heffron, Erin, Kane, Renato, Peters, Colleen, Gandulla, Stephanie, Waters, Sarah, Schmidt, Val, Marcus, Clint, Ballard, Robert D., Mayer, Larry, Broad, Kenneth, Richmond, Kristof, Shapiro, Beth, Lim, Darlene S.S., Breier, John A., Chan, Eric, Chernov, Josh, Cohen, Tamar, Deans, Matthew, Garcia, Angela, German, Christopher R., Hauer, Michelle, Hu, Sarah, Huber, Julie A., Nawotniak, Shannon Kobs, Lees, David, Lowe, Justin, Lubetkin, Megan, Marsh, Leigh, Milesi, Vincent, Miller, Matthew J., Mirmalek, Zara, Saunders, Miles, Sharif, Khaled, Shields, Ashley, Shock, Everett, Smith, Amy, Sylva, Sean, Auscavitch, Steven, Pockalny, Robert, Konrad, Kevin, Humphreys, Jennifer, Clark, Timothy B., Fundis, Allison, Matthews, Russ, Brennan, Michael L., Schorer, Lonnie, Lickliter-Mundon, Megan, Marx, Deborah, Wishnak, Samantha, Delgado, James P., Trippe, Edward, Hill, John H., Miller, Doug, Jacques, Christopher, Sudek, Mareike, Spathias, Hanae, Coward, Georgia, Que, Nerelle, Roman, Christopher, Petruncio, Emil, Weinnig, Alexis, Coleman, Dwight F., Georgian, Samuel, Richards, Holly, Roletto, Jan, Lipski, Danielle, Graiff, Kaitlin, Williams, Gary, Cochrane, Guy, Stock, Jennifer, Tezak, Sage, King, Chad, Brown, Jennifer, Burton, Erica, Kahn, Amanda, Hartwell, Anne, Wood, Amity, and Hardin, Dane

Published
2020

59. Exploring the social construction of philosophical assumptions : the methodological journeys of doctoral researchers in the social sciences

Author

Clark, Timothy Robin

Subjects
300.72
Abstract

Existing information regarding methodological journeys is predominantly restricted to autobiographical accounts, which may limit understanding, particularly in relation to the development, and significance, of methodological consciousness. This thesis explores the methodological journeys of doctoral social sciences researchers in the UK, in the early stages of their research career. It investigates how they speak of their perceptions of their individual journeys, and the potential relationships between their life histories and educational experiences and the epistemological, ontological and methodological assumptions they hold. The research design consisted of life history interviews with 9 researchers. In addition, 6 of the researchers were then involved in collective biography discussions. Information from these interviews was developed into a series of narrative accounts, which illustrate the complexity of the individual journeys. The analysis of the narrative information also included attempts to approach the information through both an interpretivist and post-structuralist lens, and privileged the value of embracing multiple perspectives. The accounts of the researchers indicated that through their journeys, their philosophical assumptions may be understood as a socially constructed product of their life histories and academic experiences. The journeys were characterised as a series of social experiences which challenged and reinforced individual assumptions. The presentation of these journeys was seen as connected to social context and the nature of the assumptions held by the individual. Experiences of post graduate research training were presented as having the potential to unlock the methodological consciousness required to re-frame these experiences, improve understanding and resolve methodological conflict. This research presents an original contribution to knowledge through its approach to the exploration and illustration of methodological journeys. It has implications for post graduate programmes in the social sciences and makes a case for the need for these to embrace methodological diversity and introduce paradigmatic understandings through teaching and supervision. In addition it asserts that individual researchers may benefit from directly engaging in aspects of reflexivity and contextualisation of their assumptions.

Published
2017

61. Biodiversity redistribution under climate change: Impacts on ecosystems and human well-being

Author

Pecl, Gretta T, Araújo, Miguel B, Bell, Johann D, Blanchard, Julia, Bonebrake, Timothy C, Chen, I-Ching, Clark, Timothy D, Colwell, Robert K, Danielsen, Finn, Evengård, Birgitta, Falconi, Lorena, Ferrier, Simon, Frusher, Stewart, Garcia, Raquel A, Griffis, Roger B, Hobday, Alistair J, Janion-Scheepers, Charlene, Jarzyna, Marta A, Jennings, Sarah, Lenoir, Jonathan, Linnetved, Hlif I, Martin, Victoria Y, McCormack, Phillipa C, McDonald, Jan, Mitchell, Nicola J, Mustonen, Tero, Pandolfi, John M, Pettorelli, Nathalie, Popova, Ekaterina, Robinson, Sharon A, Scheffers, Brett R, Shaw, Justine D, Sorte, Cascade JB, Strugnell, Jan M, Sunday, Jennifer M, Tuanmu, Mao-Ning, Vergés, Adriana, Villanueva, Cecilia, Wernberg, Thomas, Wapstra, Erik, and Williams, Stephen E

Subjects
Life on Land, Climate Action, Animals, Biodiversity, Climate Change, Food Supply, Health, Humans, General Science & Technology
Abstract

Distributions of Earth's species are changing at accelerating rates, increasingly driven by human-mediated climate change. Such changes are already altering the composition of ecological communities, but beyond conservation of natural systems, how and why does this matter? We review evidence that climate-driven species redistribution at regional to global scales affects ecosystem functioning, human well-being, and the dynamics of climate change itself. Production of natural resources required for food security, patterns of disease transmission, and processes of carbon sequestration are all altered by changes in species distribution. Consideration of these effects of biodiversity redistribution is critical yet lacking in most mitigation and adaptation strategies, including the United Nation's Sustainable Development Goals.

Published
2017

62. Quiet crisis goes public

Author

Clark, Timothy B. and Wachtel, Marjorie

Subjects
CIVIL SERVICE, MORALE, SURVEYS
Abstract

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Published
1988

64. Spectral Model of Non-Stationary, Inhomogeneous Turbulence

Author

Bragg, Andrew D., Kurien, Susan, and Clark, Timothy T.

Subjects
Physics - Fluid Dynamics
Abstract

We compare results from a spectral model for non-stationary, inhomogeneous turbulence (Besnard et al., Theor. Comp. Fluid. Dyn., vol. 8, pp 1-35, 1996) with Direct Numerical Simulation (DNS) data of a shear-free mixing layer (SFML) (Tordella et al., Phys. Rev. E, vol. 77, 016309, 2008). The SFML is used as a test case in which the efficacy of the model closure for the physical-space transport of the fluid velocity field can be tested in a flow with inhomogeneity, without the additional complexity of mean-flow coupling. The model is able to capture certain features of the SFML quite well for intermediate to long-times, including the evolution of the mixing-layer width and turbulent kinetic energy. At short-times, and for more sensitive statistics such as the generation of the velocity field anisotropy, the model is less accurate. We present arguments, supported by the DNS data, that a significant cause of the discrepancies is the local approximation to the intrinsically non-local pressure-transport in physical-space that was made in the model, the effects of which would be particularly strong at short-times when the inhomogeneity of the SFML is strongest.

Published
2015
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65. Minimal free resolutions of monomial ideals and of toric rings are supported on posets

Author

Clark, Timothy B. P. and Tchernev, Alexandre B.

Subjects
Mathematics - Commutative Algebra, Mathematics - Algebraic Geometry, Mathematics - Combinatorics
Abstract

We introduce the notion of a \emph{resolution supported on a poset}. When the poset is a CW-poset, i.e. the face poset of a regular CW-complex, we recover the notion of cellular resolution as introduced by Bayer and Sturmfels. Work of Reiner and Welker, and of Velasco, has shown that there are monomial ideals whose minimal free resolutions are not cellular, hence cannot be supported on any CW-poset. We show that for any monomial ideal there is a \emph{homology CW-poset} that supports a minimal free resolution of the ideal. This allows one to extend to every minimal resolution, essentially verbatim, techniques initially developed to study cellular resolutions. As two demonstrations of this process, we show that minimal resolutions of toric rings are supported on what we call toric hcw-posets, and we give a new combinatorial proof of a fundamental result of Miller on the relationship between Artininizations and Alexander duality of monomial ideals., Comment: The published version of this paper, Trans. Amer. Math. Soc. 371:3995--4027 (2019), claimed incorrectly that Theorem 7.1 is a new result when in fact it is a known consequence of a result of Ezra Miller. In this version we fix this and provide the appropriate references

Published
2015

66. Moments of the inverse participation ratio for the Laplacian on finite regular graphs

Author

Clark, Timothy B. P. and Del Maestro, Adrian

Subjects
Mathematical Physics, Condensed Matter - Disordered Systems and Neural Networks
Abstract

We investigate the first and second moments of the inverse participation ratio (IPR) for all eigenvectors of the Laplacian on finite random regular graphs with $n$ vertices and degree $z$. By exactly diagonalizing a large set of $z$-regular graphs, we find that as $n$ becomes large, the mean of the inverse participation ratio on each graph, when averaged over a large ensemble of graphs, approaches the numerical value $3$. This universal number is understood as the large-$n$ limit of the average of the quartic polynomial corresponding to the IPR over an appropriate $(n-2)$-dimensional hypersphere of $\mathbb{R}^n$. For a large, but not exhaustive ensemble of graphs, the mean variance of the inverse participation ratio for all graph Laplacian eigenvectors deviates from its continuous hypersphere average due to large graph-to-graph fluctuations that arise from the existence of highly localized modes., Comment: 24 pages, 10 figures, fixed typos and included new arguments on graph eigenvector distribution

Published
2015
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78. Rücktitelbild: Intramolekulare Triplett‐Diffusion erleichtert die Triplett‐Dissoziation in einem Pentacen‐Hexamer (Angew. Chem. 8/2024)

Author

Greißel, Phillip M., primary, Thiel, Dominik, additional, Gotfredsen, Henrik, additional, Chen, Lan, additional, Krug, Marcel, additional, Papadopoulos, Ilias, additional, Miskolzie, Mark, additional, Torres, Tomás, additional, Clark, Timothy, additional, Brøndsted Nielsen, Mogens, additional, Tykwinski, Rik R., additional, and Guldi, Dirk M., additional

Published
2024
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79. Back Cover: Intramolecular Triplet Diffusion Facilitates Triplet Dissociation in a Pentacene Hexamer (Angew. Chem. Int. Ed. 8/2024)

Author

Greißel, Phillip M., primary, Thiel, Dominik, additional, Gotfredsen, Henrik, additional, Chen, Lan, additional, Krug, Marcel, additional, Papadopoulos, Ilias, additional, Miskolzie, Mark, additional, Torres, Tomás, additional, Clark, Timothy, additional, Brøndsted Nielsen, Mogens, additional, Tykwinski, Rik R., additional, and Guldi, Dirk M., additional

Published
2024
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80. Intramolekulare Triplett‐Diffusion erleichtert die Triplett‐Dissoziation in einem Pentacen‐Hexamer

Author

Greißel, Phillip M., primary, Thiel, Dominik, additional, Gotfredsen, Henrik, additional, Chen, Lan, additional, Krug, Marcel, additional, Papadopoulos, Ilias, additional, Miskolzie, Mark, additional, Torres, Tomás, additional, Clark, Timothy, additional, Brøndsted Nielsen, Mogens, additional, Tykwinski, Rik R., additional, and Guldi, Dirk M., additional

Published
2024
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81. Intramolecular Triplet Diffusion Facilitates Triplet Dissociation in a Pentacene Hexamer

Author

Greißel, Phillip M., primary, Thiel, Dominik, additional, Gotfredsen, Henrik, additional, Chen, Lan, additional, Krug, Marcel, additional, Papadopoulos, Ilias, additional, Miskolzie, Mark, additional, Torres, Tomás, additional, Clark, Timothy, additional, Brøndsted Nielsen, Mogens, additional, Tykwinski, Rik R., additional, and Guldi, Dirk M., additional

Published
2024
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82. 11th German Conference on Chemoinformatics (GCC 2015) : Fulda, Germany. 8-10 November 2015.

Author

Fechner, Uli, de Graaf, Chris, Torda, Andrew E, Güssregen, Stefan, Evers, Andreas, Matter, Hans, Hessler, Gerhard, Richmond, Nicola J, Schmidtke, Peter, Segler, Marwin HS, Waller, Mark P, Pleik, Stefanie, Shea, Joan-Emma, Levine, Zachary, Mullen, Ryan, van den Broek, Karina, Epple, Matthias, Kuhn, Hubert, Truszkowski, Andreas, Zielesny, Achim, Fraaije, Johannes Hans, Gracia, Ruben Serral, Kast, Stefan M, Bulusu, Krishna C, Bender, Andreas, Yosipof, Abraham, Nahum, Oren, Senderowitz, Hanoch, Krotzky, Timo, Schulz, Robert, Wolber, Gerhard, Bietz, Stefan, Rarey, Matthias, Zimmermann, Markus O, Lange, Andreas, Ruff, Manuel, Heidrich, Johannes, Onlia, Ionut, Exner, Thomas E, Boeckler, Frank M, Bermudez, Marcel, Firaha, Dzmitry S, Hollóczki, Oldamur, Kirchner, Barbara, Tautermann, Christofer S, Volkamer, Andrea, Eid, Sameh, Turk, Samo, Rippmann, Friedrich, Fulle, Simone, Saleh, Noureldin, Saladino, Giorgio, Gervasio, Francesco L, Haensele, Elke, Banting, Lee, Whitley, David C, Oliveira Santos, Jana Sopkova-de, Bureau, Ronan, Clark, Timothy, Sandmann, Achim, Lanig, Harald, Kibies, Patrick, Heil, Jochen, Hoffgaard, Franziska, Frach, Roland, Engel, Julian, Smith, Steven, Basu, Debjit, Rauh, Daniel, Kohlbacher, Oliver, Essex, Jonathan W, Bodnarchuk, Michael S, Ross, Gregory A, Finkelmann, Arndt R, Göller, Andreas H, Schneider, Gisbert, Husch, Tamara, Schütter, Christoph, Balducci, Andrea, Korth, Martin, Ntie-Kang, Fidele, Günther, Stefan, Sippl, Wolfgang, Mbaze, Luc Meva'a, Simoben, Conrad V, Lifongo, Lydia L, Judson, Philip, Barilla, Jiří, Lokajíček, Miloš V, Pisaková, Hana, Simr, Pavel, Kireeva, Natalia, Petrov, Alexandre, Ostroumov, Denis, Solovev, Vitaly P, Pervov, Vladislav S, and Friedrich, Nils-Ole

Subjects
Macromolecular and Materials Chemistry
Published
2016

85. The Betti poset in monomial resolutions

Author

Clark, Timothy B. P. and Mapes, Sonja

Subjects
Mathematics - Commutative Algebra, Mathematics - Combinatorics
Abstract

Let $P$ be a finite partially ordered set with unique minimal element $\hat{0}$. We study the Betti poset of $P$, created by deleting elements $q\in P$ for which the open interval $(\hat{0}, q)$ is acyclic. Using basic simplicial topology, we demonstrate an isomorphism in homology between open intervals of the form $(\hat{0},p)\subset P$ and corresponding open intervals in the Betti poset. Our motivating application is that the Betti poset of a monomial ideal's lcm-lattice encodes both its $\mathbb{Z}^{d}$-graded Betti numbers and the structure of its minimal free resolution. In the case of rigid monomial ideals, we use the data of the Betti poset to explicitly construct the minimal free resolution. Subsequently, we introduce the notion of rigid deformation, a generalization of Bayer, Peeva, and Sturmfels' generic deformation.

Published
2014

86. Modeling Charge Transport in C60-based Self-assembled Monolayers for Applications in Field-Effect Transistors

Author

Leitherer, Susanne, Jäger, Christof, Halik, Marcus, Clark, Timothy, and Thoss, Michael

Subjects
Condensed Matter - Mesoscale and Nanoscale Physics
Abstract

We have investigated the conductance properties of C60-containing self-assembled monolayers (SAMs), which are used in organic field-effect transistors, employing a combination of molecular-dynamics simulations, semiempirical electronic structure calculations and Landauer transport theory. The results reveal the close relation between the transport characteristics and the structural and electronic properties of the SAM. Furthermore, both local pathways of charge transport in the SAMs and the influence of structural fluctuations are analyzed., Comment: 10 figures

Published
2014
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88. A specific MNDO parameterization for water.

Author

Hennemann, Matthias and Clark, Timothy

Subjects
*PROTONS, *PARAMETERIZATION, *DATABASES, *OLIGOMERS, *OLIGOMERIZATION
Abstract

A modified neglect of differential overlap has been parameterized specifically for water and its oligomers with the addition of polarization functions on both hydrogen and oxygen, Feynman dispersion, and a slight modification of the treatment of the hydrogen nucleus. The results show that it is possible to easily obtain good geometries and energies for hydrogen-bonded water aggregates. Data from the Benchmark Energy and Geometry Database water-cluster database were used to parameterize the new Hamiltonian for water clusters from the dimer to the decamer using MP2/aug-cc-pVDZ optimized geometries and CCSD(T)/CBS oligomerization energies. Seventy five oligomerization and rearrangement energies derived from the parameterization data are reproduced with a root mean-square error (RMSE) of 0.79 kcal mol−1 and the geometries of 38 oligomers with an RMSE of 0.17 Å. Interestingly, the Feynman dispersion term adopts a role different from that intended and tunes the atomic polarizability. The implications of these results in terms of future dedicated neglect of diatomic differential overlap Hamiltonians and those that use force-field-like atom types are discussed. [ABSTRACT FROM AUTHOR]

Published
2023
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90. Ocean acidification does not impair the behaviour of coral reef fishes

Author

Clark, Timothy D., Raby, Graham D., Roche, Dominique G., Binning, Sandra A., Speers-Roesch, Ben, Jutfelt, Fredrik, and Sundin, Josefin

Subjects
Ocean acidification -- Influence, Alarm reaction -- Observations, Coral reef fauna -- Behavior, Marine fishes -- Behavior, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

The partial pressure of CO.sub.2 in the oceans has increased rapidly over the past century, driving ocean acidification and raising concern for the stability of marine ecosystems.sup.1-3. Coral reef fishes are predicted to be especially susceptible to end-of-century ocean acidification on the basis of several high-profile papers.sup.4,5 that have reported profound behavioural and sensory impairments--for example, complete attraction to the chemical cues of predators under conditions of ocean acidification. Here, we comprehensively and transparently show that--in contrast to previous studies--end-of-century ocean acidification levels have negligible effects on important behaviours of coral reef fishes, such as the avoidance of chemical cues from predators, fish activity levels and behavioural lateralization (left-right turning preference). Using data simulations, we additionally show that the large effect sizes and small within-group variances that have been reported in several previous studies are highly improbable. Together, our findings indicate that the reported effects of ocean acidification on the behaviour of coral reef fishes are not reproducible, suggesting that behavioural perturbations will not be a major consequence for coral reef fishes in high CO.sub.2 oceans. In contrast to previous studies, analyses now show that ocean acidification does not perturb important behaviours--such as the avoidance of chemical cues from predators--of coral reef fishes., Author(s): Timothy D. Clark [sup.1] , Graham D. Raby [sup.2] , Dominique G. Roche [sup.3] [sup.4] [sup.5] , Sandra A. Binning [sup.4] [sup.5] , Ben Speers-Roesch [sup.6] , Fredrik Jutfelt [...]

Published
2020
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94. Regular CW-complexes and poset resolutions of monomial ideals

Author

Clark, Timothy B. P. and Tchernev, Alexandre

Subjects
Mathematics - Commutative Algebra
Abstract

We use the natural homeomorphism between a regular CW-complex X and its face poset P_X to establish a canonical isomorphism between the cellular chain complex of X and the result of applying the poset construction of arXiv:0806.4532v1 to P_X. For a monomial ideal whose free resolution is supported on a regular CW-complex, this isomorphism allows the free resolution of the ideal to be realized as a CW-poset resolution. Conversely, any CW-poset resolution of a monomial ideal gives rise to a resolution supported on a regular CW-complex.

Published
2013

98. Sociotechnical architecture for biomedical communication on the Web of Argument and Data

Author

Clark, Timothy William and Goble, Carole

Subjects
610.28, Semantic Web, Biomedical Communication, Argumentation, Web of Data, Argumentation Framework, Activity Theory
Abstract

This work undertakes an analysis of problems in the information model by which biomedical research is communicated on the Web, and proposes a semantic model by which these problems can be resolved. It uses and develops Activity Theory and Argumentation Theory as tools in this analysis, and produces a semantic model of biomedical communication on the Web, in OWL2, which it shows can be applied to current research articles and implemented in software. It makes contributions in three areas. This work contributes to Activity Theory, a model used in the Human-Computer Interaction (HCI) and Computer-Supported Collaborative Work (CSCW) domains, by resolving ambiguities and formalizing concepts previously obscure in the theory, and by reformulating it as an Activity Views Model. It contributes to Argumentation Theory, used in AI and Communications Theory, by integrating the work of Toulmin, Dung, and others, and applying it specifically to construct a semantic model of biomedical argumentation, which may be more generally applicable in scientific communications. And it contributes to improving scientific communications on the web, by developing a practical semantic model of biomedical communications, as arguments grounded in reproducible methods, materials and data, in OWL2.Lastly, this work demonstrates that our model can be (a) applied consistently to examples from the biomedical literature, with serialization in RDF; (b) applied independently and successfully, by biomedical research workers not specially trained in informatics; and (c) having published the model as an ontology, that it has been implemented in software, and is capable of further useful application in the biomedical communications ecosystem by others.

Published
2014

100. Rigid monomial ideals

Author

Clark, Timothy B. P. and Mapes, Sonja

Subjects
Mathematics - Commutative Algebra, 13D02
Abstract

In this paper we investigate the class of rigid monomial ideals. We give a characterization of the minimal free resolutions of certain classes of these ideals. Specifically, we show that the ideals in a particular subclass of rigid monomial ideals are lattice-linear and thus their minimal resolution can be constructed as a poset resolution. We then use this result to give a description of the minimal free resolution of a larger class of rigid monomial ideals by using $\mathcal{L}(n)$, the lattice of all lcm-lattices of monomial ideals with $n$ generators. By fixing a stratum in $\mathcal{L}(n)$ where all ideals have the same total Betti numbers we show that rigidity is a property which is upward closed in $\mathcal{L}(n)$. Furthermore, the minimal resolution of all rigid ideals contained in a fixed stratum is shown to be isomorphic to the constructed minimal resolution., Comment: 15 pages, 4 figures

Published
2011

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