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273 results on '"Monk, Jonathan"'

8. A $10.7 million compensation deduction miss.

Author

Monk, Jonathan A., Smith, Kristen, Mong, Keith, Martin, Jeff, and Brady, Joshua

Subjects
Vancouver Grizzlies -- Mergers, acquisitions and divestments -- Laws, regulations and rules, Deferred compensation -- Taxation -- Laws, regulations and rules, Vendors and purchasers (Law) -- Contracts -- Taxation -- Laws, regulations and rules, Accrual basis accounting -- Laws, regulations and rules, Partnership -- Taxation -- Laws, regulations and rules, Acquisitions and mergers -- Taxation -- Laws, regulations and rules, Tax deductions -- Laws, regulations and rules, Hoops L.P., In re (77 F.4th 557 (7th Cir. 2023)), Government regulation, Contract agreement, Company acquisition/merger, Internal Revenue Code (I.R.C. 404(a)(5)) (I.R.C. 461)
Abstract

February 1, 2024 The rules governing nonqualified deferred compensation deductions under Secs. 404(a)(5) and 461 are generally straightforward when applied to typical business situations. So why was a partnership disallowed [...]

Published
2024

14. Early access to wages may require new employment tax analyses.

Author

Monk, Jonathan A. and Smith, Kristen

Subjects
Payroll tax -- Laws, regulations and rules, Wages -- Laws, regulations and rules, Government regulation, Salary
Abstract

Employees desiring access to their wages before their payday via early payment programs and arrangements have left employers wondering whether they need to change their employment tax practices. Employers may [...]

Published
2023

15. Cellular responses to reactive oxygen species are predicted from molecular mechanisms

Author

Yang, Laurence, Mih, Nathan, Anand, Amitesh, Park, Joon Ho, Tan, Justin, Yurkovich, James T., Monk, Jonathan M., Lloyd, Colton J., Sandberg, Troy E., Seo, Sang Woo, Kim, Donghyuk, Sastry, Anand V., Phaneuf, Patrick, Gao, Ye, Broddrick, Jared T., Chen, Ke, Heckmann, David, Szubin, Richard, Hefner, Ying, Feist, Adam M., and Palsson, Bernhard O.

Published
2019

21. Walking the Streets of London: Using Zadie Smith's 'NW' to Explore Teenage, Metropolitan Ways of Seeing and Writing

Author

Monk, Jonathan

Abstract

This teaching and learning investigation draws on two adjacent chapters of Zadie Smith's novel (2012). The first chapter delineates one character's journey through north-west London as plotted by the directions feature of Google Maps, while the next chapter focalises this perspective at street level. Ten classes across three year groups conducted a reading and a writing task based on. This task, which linked students' writing to their own walking in London, was influenced by Harold Rosen's writing pedagogy, which privileges environmental experience as being central to developing student writing. The 190 mappings and street-level descriptions of walking through London provide a rich portrait of teenage, metropolitan ways of seeing. The findings indicate an intrinsic link between place and memory for many students, while showing that writing about the metropolis invites literary experimentation influenced by recent changes in technology and communication. The investigation offers insight into a teaching strategy that can develop students' reading and writing skills.

Published
2017
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25. Revealing the Iceberg: Creative Writing, Process & Deliberate Practice

Author

Monk, Jonathan

Abstract

Historical attitudes to literary creativity often focus on it as a genetic or innate characteristic. Ericsson's notion of 'deliberate practice' and Simon & Chase's 'ten-year rule', however, have shown the importance of sustained practice to achieve high-level performance. The iceberg illusion of elite performance leaves observers marvelling at the end product without an appreciation of the hours of work beneath the surface. This case study considers how attitudes to student creative writing may be altered by emphasising creative process. Students engaged in creative writing which literalised the iceberg metaphor, placing greater focused on the 'submerged' planning, drafting and revision alongside the 'visible' end product. Utilising the extended mind hypothesis, student responses demonstrate the importance of planning to order and develop their ideas. The benefits of encouraging an approach to creativity that negates innatist explanations in favour of a growth mindset or deliberate practice approach are evidenced.

Published
2016
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35. Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing

Author

Lieven, Christian, Beber, Moritz E., Olivier, Brett G., Bergmann, Frank T., Ataman, Meric, Babaei, Parizad, Bartell, Jennifer A., Blank, Lars M., Chauhan, Siddharth, Correia, Kevin, Diener, Christian, Dräger, Andreas, Ebert, Birgitta E., Edirisinghe, Janaka N., Faria, José P., Feist, Adam M., Fengos, Georgios, Fleming, Ronan M. T., García-Jiménez, Beatriz, Hatzimanikatis, Vassily, van Helvoirt, Wout, Henry, Christopher S., Hermjakob, Henning, Herrgård, Markus J., Kaafarani, Ali, Kim, Hyun Uk, King, Zachary, Klamt, Steffen, Klipp, Edda, Koehorst, Jasper J., König, Matthias, Lakshmanan, Meiyappan, Lee, Dong-Yup, Lee, Sang Yup, Lee, Sunjae, Lewis, Nathan E., Liu, Filipe, Ma, Hongwu, Machado, Daniel, Mahadevan, Radhakrishnan, Maia, Paulo, Mardinoglu, Adil, Medlock, Gregory L., Monk, Jonathan M., Nielsen, Jens, Nielsen, Lars Keld, Nogales, Juan, Nookaew, Intawat, Palsson, Bernhard O., Papin, Jason A., Patil, Kiran R., Poolman, Mark, Price, Nathan D., Resendis-Antonio, Osbaldo, Richelle, Anne, Rocha, Isabel, Sánchez, Benjamín J., Schaap, Peter J., Sheriff, Rahuman S. Malik, Shoaie, Saeed, Sonnenschein, Nikolaus, Teusink, Bas, Vilaça, Paulo, Vik, Jon Olav, Wodke, Judith A. H., Xavier, Joana C., Yuan, Qianqian, Zakhartsev, Maksim, and Zhang, Cheng

Published
2020
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43. Transmission of Klebsiella strains and plasmids within and between grey-headed flying fox colonies

Author

Vezina, Ben, Judd, Louise M, McDougall, Fiona K, Boardman, Wayne SJ, Power, Michelle L, Hawkey, Jane, Brisse, Sylvain, Monk, Jonathan M, Holt, Kathryn E, and Wyres, Kelly L

Abstract

The grey-headed flying fox (Pteropus poliocephalus) is an endemic Australian fruit bat, known to carry zoonotic pathogens. We recently showed they harbour bacterial pathogen Klebsiella pneumoniae and closely related species in the K. pneumoniae species complex (KpSC); however, the dynamics of KpSC transmission and gene flow within flying fox colonies are poorly understood. High-resolution genome comparisons of 39 KpSC isolates from grey-headed flying foxes identified five putative strain transmission clusters (four intra- and one inter-colony). The instance of inter-colony strain transmission of K. africana was found between two flying fox populations within flying distance, indicating either direct or indirect transmission through a common food/water source. All 11 plasmids identified within the KpSC isolates showed 73% coverage (mean) and ≥95% identity to human-associated KpSC plasmids, indicating gene flow between human clinical and grey-headed flying fox isolates. Along with strain transmission, inter-species horizontal plasmid transmission between K. pneumoniae and Klebsiella africana was also identified within a flying fox colony. Finally, genome-scale metabolic models were generated to predict and compare substrate usage to previously published KpSC models, from human and environmental sources. These models indicated no distinction on the basis of metabolic capabilities. Instead, metabolic capabilities were consistent with population structure and ST/lineage.

Published
2022

44. Whole-genome sequences from wild-type and laboratory-evolved strains define the alleleome and establish its hallmarks.

Author

Catoiu, Edward Alexander, Phaneuf, Patrick, Monk, Jonathan, and Palsson, Bernhard O.

Subjects
NATURAL selection, SEQUENCE spaces, BACTERIAL diversity, SYNTHETIC biology, ESCHERICHIA coli
Abstract

The genomic diversity across strains of a species forms the genetic basis for differences in their behavior. A large-scale assessment of sequence variation has been made possible by the growing availability of strain-specific whole-genome sequences (WGS) and with the advent of large-scale databases of laboratory-acquired mutations. We define the Escherichia coli "alleleome" through a genome-scale assessment of amino acid (AA) sequence diversity in open reading frames across 2,661 WGS from wild-type strains. We observe a highly conserved alleleome enriched in mutations unlikely to affect protein function. In contrast, 33,000 mutations acquired in laboratory evolution experiments result in more severe AA substitutions that are rarely achieved by natural selection. Large-scale assessment of the alleleome establishes a method for the quantification of bacterial allelic diversity, reveals opportunities for synthetic biology to explore novel sequence space, and offers insights into the constraints governing evolution. [ABSTRACT FROM AUTHOR]

Published
2023
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46. Comparative Systems Biology Analysis of Microbial Pathogens

Author

Monk, Jonathan Mayock

Subjects
Chemical engineering, Bioinformatics, Microbiology, core and pan genome, escherichia coli, leptospira, mathematical modelling, staphylococcus aureus, systems biology
Abstract

Genome-scale models of microbial metabolism have become a commonly used tool in the systems biology toolbox. These tools can predict, based solely on an organism’s genome sequence, its metabolic capabilities and unique phenotypes in different conditions and under unique perturbations. Furthermore, an array of in-silico methods have been developed that can be applied to these models to more deeply characterize an organism, re-engineer it and even to design effective ways to interrupt and kill it. This dissertation discusses the creation and analysis of multiple genome-scale models of metabolism for different microbial pathogens. Chapter 1 describes aspects of systems biology that are used throughout this thesis. Topics include the theory and practice of metabolic network reconstruction, genome-scale modelling and flux balance analysis. Chapter 2 focuses on the reconstruction and analysis of multiple genome-scale metabolic reconstructions of diverse Escherichia coli strains. The results highlight strain-specific adaptations to nutritional environments.Chapter 3 details comparative genome-scale modelling of multiple S. aureus strains to identify strain-specific pathogenic characteristics and unique metabolic capabilities that are related to infectious capabilities.Chapter 4 engages in a comparative metabolic network analysis and modelling of four Leptospira species that provide insight into pathogenesis of Leptospirosis.Chapter 5 examines seven industrially relevant strains of E. coli using transcriptomics and genome-scale models to quantifying variation between the strains that will likely have an impact on host strain selection for metabolic engineering applications.Chapter 6 conducts an in-depth analysis of existing metabolic network reconstructions and identifies areas where they may need further development.Chapter 7 details the construction of an updated comprehensive and high-quality genome-scale reconstruction for Escherichia coli K-12 MG1655. The model is experimentally validated with gene-knockout studies. Extension to the model are provided, including an application involving production of reactive oxygen species.Chapter 8 describes the reconstruction of a metabolic network and associated three-dimensional protein structures for Staphlyococcus aureus USA300. The model is used to examine basic S. aureus biochemistry.Chapter 9 examines the current state and predicted future of systems biology applications for studying, examining and comparing microbial pathogens.

Published
2015

48. Genome-scale metabolic network reconstructions of diverse Escherichia strains reveal strain-specific adaptations.

Author

Monk, Jonathan M.

Subjects
*ESCHERICHIA, *CORE competencies, *SYSTEMS biology, *BACTERIAL metabolism, *CELL physiology, *GENE targeting
Abstract

Bottom-up approaches to systems biology rely on constructing a mechanistic basis for the biochemical and genetic processes that underlie cellular functions. Genome-scale network reconstructions of metabolism are built from all known metabolic reactions and metabolic genes in a target organism. A net)work reconstruction can be converted into a mathematical format and thus lend itself to mathematical analysis. Genome-scale models (GEMs) of metab)olism enable a systems approach to characterize the pan and core metabolic capabilities of the Escherichia genus. In this work, GEMs were constructed for 222 representative strains of Escherichia across HC1100 levels spanning the known Escherichia phylogeny. The models were used to study Escherichia metabolic diversity and speciation on a large scale. The results show that unique strain-specific metabolic capabilities correspond to different species and nutrient niches. This work is a first step towards a curated reconstruction of pan-Escherichia metabolism. [ABSTRACT FROM AUTHOR]

Published
2022
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49. Expenses & Deductions.

Author

Monk, Jonathan A., Smith, Kristen, Mong, Keith, Martin, Jeff, and Brady, Joshua

Subjects
TAXATION, DEFERRED compensation, BASKETBALL players, TAX laws
Abstract

The article focuses on the tax implications and disputes surrounding the deduction for nonqualified deferred compensation owed to two basketball players, Mike Conley and Zach Randolph, by Hoops LP, a partnership that sold its assets, including the Memphis Grizzlies NBA franchise, in 2012. It delves into the legal arguments presented by Hoops LP regarding the timing and eligibility of the deduction under relevant tax laws.

Published
2024

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