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2. The Reactive Synthesis Competition (SYNTCOMP): 2018–2021

Author

Jacobs, Swen, Pérez, Guillermo A., Abraham, Remco, Bruyère, Véronique, Cadilhac, Michaël, Colange, Maximilien, Delfosse, Charly, van Dijk, Tom, Duret-Lutz, Alexandre, Faymonville, Peter, Finkbeiner, Bernd, Khalimov, Ayrat, Klein, Felix, Luttenberger, Michael, Meyer, Klara, Michaud, Thibaud, Pommellet, Adrien, Renkin, Florian, Schlehuber-Caissier, Philipp, Sakr, Mouhammad, Sickert, Salomon, Staquet, Gaëtan, Tamines, Clément, Tentrup, Leander, and Walker, Adam

Published
2024
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5. A transient protein folding response targets aggregation in the early phase of TDP-43-mediated neurodegeneration

Author

San Gil, Rebecca, Pascovici, Dana, Venturato, Juliana, Brown-Wright, Heledd, Mehta, Prachi, Madrid San Martin, Lidia, Wu, Jemma, Luan, Wei, Chui, Yi Kit, Bademosi, Adekunle T., Swaminathan, Shilpa, Naidoo, Serey, Berning, Britt A., Wright, Amanda L., Keating, Sean S., Curtis, Maurice A., Faull, Richard L. M., Lee, John D., Ngo, Shyuan T., Lee, Albert, Morsch, Marco, Chung, Roger S., Scotter, Emma, Lisowski, Leszek, Mirzaei, Mehdi, and Walker, Adam K.

Published
2024
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7. Developmental basis of SHH medulloblastoma heterogeneity

Author

Gold, Maxwell P., Ong, Winnie, Masteller, Andrew M., Ghasemi, David R., Galindo, Julie Anne, Park, Noel R., Huynh, Nhan C., Donde, Aneesh, Pister, Veronika, Saurez, Raul A., Vladoiu, Maria C., Hwang, Grace H., Eisemann, Tanja, Donovan, Laura K., Walker, Adam D., Benetatos, Joseph, Dufour, Christelle, Garzia, Livia, Segal, Rosalind A., Wechsler-Reya, Robert J., Mesirov, Jill P., Korshunov, Andrey, Pajtler, Kristian W., Pomeroy, Scott L., Ayrault, Olivier, Davidson, Shawn M., Cotter, Jennifer A., Taylor, Michael D., and Fraenkel, Ernest

Published
2024
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8. Introducing fluctuation-driven order into density functional theory using the quantum order-by-disorder framework

Author

Walker, Adam H., Pickard, Chris J., and Green, Andrew G.

Subjects
Condensed Matter - Strongly Correlated Electrons, Condensed Matter - Materials Science
Abstract

Density functional theory in the local or semi-local density approximation is a powerful tool for materials simulation, yet it struggles in many cases to describe collective electronic order that is driven by electronic interactions. In this work it is shown how arbitrary, fluctuation-driven electronic order may be introduced into density functional theory using the quantum order-by-disorder framework. This is a method of calculating the free energy correction due to collective spin and charge fluctuations about a state that hosts static order, in a self-consistent manner. In practical terms, the quantum order-by-disorder method is applied to the Kohn-Sham auxiliary system of density functional theory to give an order-dependent correction to the exchange-correlation functional. Calculation of fluctuation propagators within density functional theory renders the result fully first-principles. Two types of order are considered as examples -- fluctuation-driven superconductivity and spin nematic order -- and implementation schemes are presented in each case., Comment: 20 pages, 2 figures; added Section V for context and added clarifying statements in Sections II A and IV A, C and E

Published
2022

10. The Reactive Synthesis Competition (SYNTCOMP): 2018-2021

Author

Jacobs, Swen, Perez, Guillermo A., Abraham, Remco, Bruyere, Veronique, Cadilhac, Michael, Colange, Maximilien, Delfosse, Charly, van Dijk, Tom, Duret-Lutz, Alexandre, Faymonville, Peter, Finkbeiner, Bernd, Khalimov, Ayrat, Klein, Felix, Luttenberger, Michael, Meyer, Klara, Michaud, Thibaud, Pommellet, Adrien, Renkin, Florian, Schlehuber-Caissier, Philipp, Sakr, Mouhammad, Sickert, Salomon, Staquet, Gaetan, Tamines, Clement, Tentrup, Leander, and Walker, Adam

Subjects
Computer Science - Logic in Computer Science
Abstract

We report on the last four editions of the reactive synthesis competition (SYNTCOMP 2018-2021). We briefly describe the evaluation scheme and the experimental setup of SYNTCOMP. Then, we introduce new benchmark classes that have been added to the SYNTCOMP library and give an overview of the participants of SYNTCOMP. Finally, we present and analyze the results of our experimental evaluations, including a ranking of tools with respect to quantity and quality - that is, the total size in terms of logic and memory elements - of solutions., Comment: accepted for publication in STTT

Published
2022

18. Introducing collective order into Density Functional Theory and modelling the magnetic reorientation transition in Ca₃Ru₂O₇

Author

Walker, Adam Harold

Abstract

This thesis contains two distinct pieces of work. In the first, a framework is presented in which arbitrary electronic order that is driven by collective charge and spin fluctuations is introduced into Density Functional Theory. This is achieved using the Quantum Order-By-Disorder approach, in which a desired collective order is introduced into a system using a variational order parameter, and the free energy of fluctuations about the ordered mean-field state are evaluated self-consistently within perturbation theory. This method is applied to the Kohn-Sham auxiliary system, resulting in a minimal optimisation problem in which the order parameter and the Kohn-Sham quasiparticle states must be solved for in a self-consistent manner. This framework is illustrated with two examples: fluctuation-driven superconductivity and spin nematic order, which are representative of orders in the particle-particle and particle-hole channels. Implementation schemes are considered in both cases. The second piece of work models the spin reorientation transition in the correlated metal Ca3Ru2O7. This is a coupled structural-electronic transition in which the direction of antiferromagnetic ordering reorientates as a function of temperature and applied stress. We identify that the lattice couples to the electronic system via the tilting and rotational of the RuO6 octahedra, which modify the orbital overlaps. This motivates a minimal model for Ca3Ru2O7 in which a phenomenological lattice strain couples to the hopping parameter of an electronic model. This model successfully captures the phenomenology of the spin reorientation transition with varying temperature, including most of its structural and electronic features. It reveals a transition mechanism in which the lattice spontaneously deforms in order to self-consistently lower the electronic energy by modulating the electronic bandwidth, which is validated by temperature-dependent structure measurements. The model also captures the transition with applied stress in a way that is consistent with experimental observations.

Published
2022

20. A Hybrid Transfer Learning and Segmentation Approach for the Detection of Acute Lymphoblastic Leukemia

Author

Hau, Ang Jia, Hameed, Nazia, Walker, Adam, Hasan, Md. Mahmudul, Kacprzyk, Janusz, Series Editor, Gomide, Fernando, Advisory Editor, Kaynak, Okyay, Advisory Editor, Liu, Derong, Advisory Editor, Pedrycz, Witold, Advisory Editor, Polycarpou, Marios M., Advisory Editor, Rudas, Imre J., Advisory Editor, Wang, Jun, Advisory Editor, Mahmud, Mufti, editor, Mendoza-Barrera, Claudia, editor, Kaiser, M. Shamim, editor, Bandyopadhyay, Anirban, editor, Ray, Kanad, editor, and Lugo, Eduardo, editor

Published
2023
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22. Safety of AZD1222 COVID-19 vaccine and low Incidence of SARS-CoV-2 infection in Botswana following ChAdOx1(AZD1222) vaccination: A single-arm open-label interventional study – final study results

Author

Makhema, Joseph, Shava, Emily, Izu, Alane, Gaolathe, Tendani, Kuate, Lesego, Walker, Adam, Carty, Lucy, Georgiou, Panayiotis, Kgathi, Coulson, Choga, Wonderful T., Sekoto, Tumalano, Seonyatseng, Ngozana, Mogashoa, Tuelo, Maphorisa, Comfort N., Mohammed, Terence, Ntalabgwe, Tshenolo, Frank, Tshepho T., Matlhaku, Boitumelo, Diphoko, Ame, Phindela, Thandie, Kaunda, Agripa, Kgari, Poloko, Kanyakula, Thomas, Palalani, Gape, Phakedi, Isabella, Mmalane, Mompati, Taylor, Sylvia, and Moyo, Sikhulile

Published
2024
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26. Ways of being beyond the perpetuating inequalities of the technosphere : textual artistic intervention as a vital strategy in enabling resistant agency, or, embodying a practice of radical care

Author

Walker, Adam

Subjects
W100 Fine Art, W900 Others in Creative Arts and Design
Abstract

This research project comprises an interwoven, overlapping body of artistic interventions and multiple forms of writing. Drawing on Virno and others, it addresses and theorises the 'technosphere': a would-be totalising, statically reproducing structure of perpetuating inequality, through which contemporary existence occurs. Pivotal within the technosphere are textualised processes of proprietorial individuation and de-humanising abstraction. In response to this, I propose an original concept of 'radical care'. Augmenting the established discourse of 'critical care' introduced by Puig de la Bellacasa and others, radical care is developed as an ethical-methodological framework by which resistance within the immediate, visceral conditions of 'being' is connected with the speculative, forward-flung possibility of holding thinkable foreclosed futures. This is the principal original contribution to knowledge made by this research project. Combining a careful considered-ness and self-reflexivity with the intermittent need to act unknowingly and 'carelessly', radical care holds these facets together as mutually essential to one another, rather than opposing them. Radical care is both manifested and articulated through practice. In a further original contribution, as a method by which it might do so through artistic practice, I propose 'embodied flattened allegorical montage' (a development of Buchloh's concept of 'allegorical montage'). In seeking and then seeking to practice radical care, 'embodied flattened allegorical montage' emphasises a holding together of site, context, affect, situated economies of circulation, process, dissemination and potential encounter with audience as a fragmentary, de-centred, fluid, porous artistic intervention. It does this following Barthes' argument to shift our thinking of the 'artwork' from work to text, and in so doing reopen playfulness and process. These texts are subversively and disruptively intersected into the technosphere's own. Radical care has been refined, conceptualised and made disseminable through the process of these artistic interventions in which it is practiced. In reflection of the inescapability of the technosphere, my 'being' (in its specific positionality, vulnerability and agency) is entangled through the entirety of this project. 'Being', in reflexive parallel with practice and theorising, is acknowledged as a vital co-equal strand of research. The articulation and practicing of 'iterative refracted practice, theorising and being' forms the third thread of this project's enmeshed core contributions. Asserting a value in 'being' contests its technospheric exploitation. Ultimately, through the embodiment of a practice of radical care, this project opens a path whereby more equal ways of being become, momentarily at least, possible.

Published
2021

29. The 5th Reactive Synthesis Competition (SYNTCOMP 2018): Benchmarks, Participants & Results

Author

Jacobs, Swen, Bloem, Roderick, Colange, Maximilien, Faymonville, Peter, Finkbeiner, Bernd, Khalimov, Ayrat, Klein, Felix, Luttenberger, Michael, Meyer, Philipp J., Michaud, Thibaud, Sakr, Mouhammad, Sickert, Salomon, Tentrup, Leander, and Walker, Adam

Subjects
Computer Science - Logic in Computer Science
Abstract

We report on the fifth reactive synthesis competition (SYNTCOMP 2018). We introduce four new benchmark classes that have been added to the SYNTCOMP library, and briefly describe the evaluation scheme and the experimental setup of SYNTCOMP 2018. We give an overview of the participants of SYNTCOMP 2018 and highlight changes compared to previous years. Finally, we present and analyze the results of our experimental evaluation, including a ranking of tools with respect to quantity and quality of solutions., Comment: arXiv admin note: substantial text overlap with arXiv:1711.11439, arXiv:1609.00507

Published
2019

33. Greg Clingham as Teacher and Mentor

Author

Jermey, Dominic, primary, Wood, Elaine, additional, Fassett, Caroline, additional, McNicholas, Joseph, additional, Williams, Margaret, additional, Labbie, Erin, additional, Henry, Patrick Thomas, additional, Walker, Adam, additional, and Tchou, W. K., additional

Published
2022
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39. Self-limiting fall armyworm: a new approach in development for sustainable crop protection and resistance management

Author

Reavey, Catherine E., Walker, Adam S., Joyce, Stephen P., Broom, Lucy, Willse, Alan, Ercit, Kyla, Poletto, Mattia, Barnes, Zoe H., Marubbi, Thea, Troczka, Bartlomiej J., Treanor, David, Beadle, Katherine, Granville, Ben, de Mello, Vanessa, Teal, Joss, Sulston, Edward, Ashton, Anna, Akilan, Luxziyah, Naish, Neil, Stevens, Oliver, Humphreys-Jones, Nerys, Warner, Simon A. J., Spinner, Sian A. M., Rose, Nathan R., Head, Graham, Morrison, Neil I., and Matzen, Kelly J.

Published
2022
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42. Development of a harmonized sociodemographic and clinical questionnaire for mental health research: A Delphi-method-based consensus recommendation.

Author

Lotfaliany, Mojtaba, Agustini, Bruno, Walker, Adam J, Turner, Alyna, Wrobel, Anna L, Williams, Lana J, Dean, Olivia M, Miles, Stephanie, Rossell, Susan L, Berk, Michael, and Mohebbi, Mohammadreza

Subjects
CONSENSUS (Social sciences), PSYCHIATRY, PSYCHIATRIC treatment, QUESTIONNAIRES, EXPERIMENTAL design, RESEARCH methodology, SOCIODEMOGRAPHIC factors
Abstract

Objective: Harmonized tools are essential for reliable data sharing and accurate identification of relevant factors in mental health research. The primary objective of this study was to create a harmonized questionnaire to collect demographic, clinical and behavioral data in diverse clinical trials in adult psychiatry. Methods: We conducted a literature review and examined 24 questionnaires used in previously published randomized controlled trials in psychiatry, identifying a total of 27 domains previously explored. Using a Delphi-method process, a task force team comprising experts in psychiatry, epidemiology and statistics selected 15 essential domains for inclusion in the final questionnaire. Results: The final selection resulted in a concise set of 22 questions. These questions cover factors such as age, sex, gender, ancestry, education, living arrangement, employment status, home location, relationship status, and history of medical and mental illness. Behavioral factors like physical activity, diet, smoking, alcohol and illicit drug use were also included, along with one question addressing family history of mental illness. Income was excluded due to high confounding and redundancy, while language was included as a measure of migration status. Conclusion: The recommendation and adoption of this harmonized tool for the assessment of demographic, clinical and behavioral data in mental health research can enhance data consistency and enable comparability across clinical trials. [ABSTRACT FROM AUTHOR]

Published
2024
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43. Poetry in the Pulpit.

Author

BAILEY, NOAH and WALKER, ADAM

Subjects
*POETICS, *IMAGINATION, *POETRY (Literary form), *DOCTRINAL theology, *EYE contact, *LOVE of God
Abstract

The article explores the use of poetry in preaching within the English Reformed tradition, emphasizing the value of incorporating poetic language into sermons. It discusses how preachers such as Thomas Adams, Richard Baxter, and John Bunyan used poetry to engage their audience and illuminate Scripture. The text also highlights the belief of Puritan ministers that poetry could effectively convey religious truths and inspire spiritual experiences. It concludes by suggesting that preachers today can learn from the English Reformed practice of combining plain speech with poetic language to effectively communicate the message of the Scriptures. [Extracted from the article]

Published
2024

44. Novel Insights into Changes in Gene Expression within the Hypothalamus in Two Asthma Mouse Models: A Transcriptomic Lung–Brain Axis Study.

Author

Bastawy, Eslam M., Eraslan, Izel M., Voglsanger, Lara, Suphioglu, Cenk, Walker, Adam J., Dean, Olivia M., Read, Justin L., Ziemann, Mark, and Smith, Craig M.

Subjects
LUNGS, GENE expression, HYPOTHALAMUS, ASTHMA, LABORATORY mice, ESCHERICHIA coli, OREXINS
Abstract

Patients with asthma experience elevated rates of mental illness. However, the molecular links underlying such lung–brain crosstalk remain ambiguous. Hypothalamic dysfunction is observed in many psychiatric disorders, particularly those with an inflammatory component due to many hypothalamic regions being unprotected by the blood–brain barrier. To gain a better insight into such neuropsychiatric sequelae, this study investigated gene expression differences in the hypothalamus following lung inflammation (asthma) induction in mice, using RNA transcriptome profiling. BALB/c mice were challenged with either bacterial lipopolysaccharide (LPS, E. coli) or ovalbumin (OVA) allergens or saline control (n = 7 per group), and lung inflammation was confirmed via histological examination of postmortem lung tissue. The majority of the hypothalamus was micro-dissected, and total RNA was extracted for sequencing. Differential expression analysis identified 31 statistically significant single genes (false discovery rate FDR5%) altered in expression following LPS exposure compared to controls; however, none were significantly changed following OVA treatment, suggesting a milder hypothalamic response. When gene sets were examined, 48 were upregulated and 8 were downregulated in both asthma groups relative to controls. REACTOME enrichment analysis suggests these gene sets are involved in signal transduction metabolism, immune response and neuroplasticity. Interestingly, we identified five altered gene sets directly associated with neurotransmitter signaling. Intriguingly, many of these altered gene sets can influence mental health and or/neuroinflammation in humans. These findings help characterize the links between asthma-induced lung inflammation and the brain and may assist in identifying relevant pathways and therapeutic targets for future intervention. [ABSTRACT FROM AUTHOR]

Published
2024
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45. Developing a Practical Reactive Synthesis Tool: Experience and Lessons Learned

Author

Ryzhyk, Leonid and Walker, Adam

Subjects
Computer Science - Software Engineering, Computer Science - Programming Languages
Abstract

We summarise our experience developing and using Termite, the first reactive synthesis tool intended for use by software development practitioners. We identify the main barriers to making reactive synthesis accessible to software developers and describe the key features of Termite designed to overcome these barriers, including an imperative C-like specification language, an interactive source-level debugger, and a user-guided code generator. Based on our experience applying Termite to synthesising real-world reactive software, we identify several caveats of the practical use of the reactive synthesis technology. We hope that these findings will help define the agenda for future research on practical reactive synthesis., Comment: In Proceedings SYNT 2016, arXiv:1611.07178

Published
2016
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48. Immp2l Enhances the Structure and Function of Mitochondrial Gpd2 Dehydrogenase

Author

Clarke, Raymond A., primary, Govindaraju, Hemna, additional, Beretta, Martina, additional, Olzomer, Ellen, additional, Lawther, Adam J., additional, Walker, Adam K., additional, Fang, Zhiming, additional, Eapen, Valsamma, additional, Hyams, Tzipi Cohen, additional, Killingsworth, Murray, additional, Bridge, Wallace, additional, Turner, Nigel, additional, and Siddiqui, Khawar Sohail, additional

Published
2024
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