Van Zon Research Articles

Long COVID: which symptoms can be attributed to SARS-CoV-2 infection?

Long COVID: which symptoms can be attributed to SARS-CoV-2 infection?

Characterizing microRNA-mediated modulation of gene expression noise and its effect on synthetic gene circuits.

MicroRNAs (miRNAs) have been shown to modulate gene expression noise, but less is known about how miRNAs with different properties may regulate noise differently. Here, we investigate the role of competing RNAs and the composition of miRNA response elements (MREs) in modulating noise. We find that weak competing RNAs could introduce lower noise than strong competing RNAs. In comparison with a single MRE, both repetitive and composite MREs can reduce the noise at low expression, but repetitive MREs can elevate the noise remarkably at high expression. We further observed the behavior of a synthetic cell-type classifier with miRNAs as inputs and find that miRNAs and MREs that could introduce higher noise tend to enhance cell state transition. These results provide a systematic and quantitative understanding of the function of miRNAs in controlling gene expression noise and the utilization of miRNAs to modulate the behavior of synthetic gene circuits.

Cover Image

Cover Illustration: The cover image is based on the Concise Communication Whole-slide margin control through deep learning in Mohs micrographic surgery for basal cell carcinoma by Mike C.M. van Zon et al., https://doi.org/10.1111/exd.14306.

Explicit Solution of the Generalised Langevin Equation

Generating an initial condition for a Langevin equation with memory is a non trivial issue. We introduce a generalisation of the Laplace transform as a useful tool for solving this problem, in which a limit procedure may send the extension of memory effects to arbitrary times in the past. This method allows us to compute average position, work, their variances and the entropy production rate of a particle dragged in a complex fluid by an harmonic potential, which could represent the effect of moving optical tweezers. For initial conditions in equilibrium we generalise the results by van Zon and Cohen, finding the variance of the work for generic protocols of the trap. In addition, we study a particle dragged for a long time captured in an optical trap with constant velocity in a steady state. Our formulas open the door to thermodynamic uncertainty relations in systems with memory.

Abstract 4261: Development of quantitative multi-platform tests for easy readout of AR, ER, PI3K and MAPK pathway activity to unravel pathophysiology across cancer and tissue types

Abstract Introduction: Currently, the selection of targeted therapy is commonly based on genetic data, such as well-known gene mutations, but these mutations do not provide conclusive evidence for the functional activation of the affected pathway. For this reason, we have developed computational models to assess the molecular phenotype of individual tumors, determining the functional activity of oncogenic signaling pathways based on mRNA expression levels of the direct target genes of the respective pathway transcription factors (Verhaegh et al., Cancer Res 2014; Van Ooijen et al., Am J Pathol 2018; Van de Stolpe et al., Sci Rep 2019). For a broader application of these models, we translated them to RT-qPCR, RNA sequencing and microarray tests, for a quantitative and reproducible assessment of signaling pathway activity. Materials and methods: Focusing on the AR, ER, PI3K-FOXO and MAPK-AP1 pathways, we developed PCR primers and probes to assess mRNA expression levels of the pathways' direct target genes. For model parameter calibration, we performed controlled cell line experiments in which the respective pathways were inactivated and activated, to have calibration samples with known pathway activity status. Per pathway, the same set of calibration samples and the same set of target genes were used to develop RT-qPCR, RNA sequencing and microarray tests, to maximize similarity. The resulting OncoSignal tests can be used for a quantitative assessment of pathway activity on individual samples, giving a score on a 0-100 scale. We verified these tests on independent samples with known pathway status. We ran repeat experiments to assess the reproducibility within each platform, and tested the same samples on all three platforms to assess cross-platform concordance. Results: Using the OncoSignal score, low activity test samples were clearly separated from highly active ones. For example, AR-PCR scores went from 19±3 on androgen-deprived LNCaP cell lines to 70±2 after stimulation with DHT, and went down again to 33±1 and 23±1 when subsequently treated with bicalutamide and enzalutamide, respectively. PI3K-FOXO-microarray scores went from 12±1 on control MCF7 experiments to 50±4 after alpelisib treatment. Measurements on 100+ samples on all three platforms showed Pearson correlations between 0.93 and 0.99 in OncoSignal scores, with absolute differences typically below 10. Conclusion: We developed broadly applicable tests to assess AR, ER, PI3K-FOXO and MAPK-AP1 pathway activity in a quantitative manner on individual samples, with good reproducibility on repeat experiments and good concordance between PCR, RNA sequencing and microarray measurements. These tests can be used to unravel disease pathophysiology in (pre-)clinical samples. The added value of OncoSignal for therapy response prediction is currently being evaluated in different studies. Citation Format: Martijn Akse, Henk van Ooijen, Anke Pierik, Sandra van den Bosch, Hans van Zon, Laurent Holtzer, Anne van Brussel, Márcia Inda, Yvonne Wesseling-Rozendaal, Wim Verhaegh, Eveline den Biezen-Timmermans. Development of quantitative multi-platform tests for easy readout of AR, ER, PI3K and MAPK pathway activity to unravel pathophysiology across cancer and tissue types [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 4261.

Alignment of Cell Lineage Trees Elucidates Genetic Programs for the Development and Evolution of Cell Types

SummaryA full understanding of the developmental process requires fine-scale characterization of cell divisions and cell types, which are naturally organized as the developmental cell lineage tree (CLT). Technological breakthroughs facilitated determination of more CLTs, but complete comprehension of the data remains difficult without quantitative comparison among CLTs. We hereby quantified phenotypic similarity between CLTs using a novel computational method that exhaustively searches for optimal correspondence between individual cells meanwhile retaining their topological relationships. The revealed CLT similarities allowed us to infer functional similarity at the transcriptome level, identify cell fate transformations, predict functional relationships between mutants, and find evolutionary correspondence between cell types of different species. By allowing quantitative comparison between CLTs, our work is expected to greatly enhance the interpretability of relevant data and help answer the myriad of questions surrounding the developmental process.

The Year's Work in Tolkien Studies 2017

The Year's Work in Tolkien Studies 2017 David Bratman (bio), Kate Neville (bio), Jennifer Rogers (bio), Robin Anne Reid (bio), Jason Fisher (bio), John Wm. Houghton (bio), and John Magoun (bio) Introduction [David Bratman] Several anthologies of note are prominent in the Tolkien literature studied this year. They include the recipients of both the 2018 and 2019 Mythopoeic Scholarship Awards from the Mythopoeic Society. The first of these is The Inklings and King Arthur: J.R.R. Tolkien, Charles Williams, C. S. Lewis, and Owen Barfield on the Matter of Britain, edited by Sørina Higgins (Berkeley, CA: Apocryphile Press, 2017). Its Tolkien-related content, largely but not entirely concerned with The Fall of Arthur, is covered under Source and Comparative Studies. The other award-winner is There Would Always Be a Fairy-tale: More Essays on Tolkien, by Verlyn Flieger (Kent, OH: Kent State UP, 2017), the second not-quite-miscellaneous collection of short essays on Tolkien by this distinguished and prolific author (the first was Green Suns and Faërie, 2012). It is not-quite-miscellaneous because the tracing of recurrent themes in Tolkien's work is a major concern here (and one far from unique to Flieger). It's covered under General Criticism. Two genuinely miscellaneous anthologies in Tolkien studies also feature prominently in this year's consideration. Tolkien Among Scholars, edited by Nathalie Kuijpers, Renée Vink, and Cécile van Zon (Leiden, Netherlands: Tolkien Genootschap Unquendor, 2016), was originally announced as Unquendor's Lembas Extra 2017 issue, which is why it was not covered last year, though when it arrived it turned out to be labeled Lembas Extra 2016 and with that year of publication as well. Binding Them All: Interdisciplinary Perspectives on J.R.R. Tolkien and His Works, edited by Monika Kirner-Ludwig, Stephan Köser, and Sebastian Streitberger (Zurich: Walking Tree, 2017) is volume 37 in the publisher's Cormarë Series of Tolkien-related scholarship. Both contain a large variety of interesting essays whose consideration is spread throughout this survey. There are also two somewhat more focused anthologies this year. Death and Immortality in Middle-earth: Proceedings of The Tolkien Society Seminar 2016, edited by Daniel Helen (Edinburgh: Luna Press, 2017) is volume 17 in the Society's Peter Roe Series, and is largely covered under General Criticism, with a few articles elsewhere. Tolkien and [End Page 253] Alterity, edited by Christopher Vaccaro and Yvette Kisor (Cham, Switzerland: Palgrave Macmillan, 2017), has a broad topic range but a specific thematic focus. Because of the cultural basis of alterity studies, it has been placed in the Gender Studies subsection of General Criticism. Important monographs of the year include J.R.R. Tolkien, Romanticist and Poet by Julian Eilmann, a survey in an area of emerging interest in Tolkien studies (General Criticism); The Great Tower of Elfland: The Mythopoeic Worldview of J.R.R. Tolkien, C. S. Lewis, G. K. Chesterton, and George MacDonald by Zachary A. Rhone, a consideration of some common features and themes among these four authors (Source and Comparative Studies); The Flame Imperishable: Tolkien, St. Thomas, and the Metaphysics of Faërie by Jonathan S. McIntosh, an excursion into deep theology (Religious and Ethical); and Flora of Middle-earth: Plants of J.R.R. Tolkien's Legendarium by Walter S. Judd and Graham A. Judd, a virtuosic encyclopedia that's as much scientific botany as it is Tolkien (Sub-creation). To these could be added the revised and expanded edition of The J.R.R. Tolkien Companion & Guide by Christina Scull and Wayne G. Hammond, an essential scholarly reference work (General Works); and above all what has turned out to be the second in the late Christopher Tolkien's final trilogy of material from his father's papers, his edition of the tale of Beren and Lúthien, one of the Great Tales of the Silmarillion (covered under General Criticism: Other Works). Journals of the year include volume 14 of the present journal, Tolkien Studies: An Annual Scholarly Review; issue 58 of Mallorn: The Journal of The Tolkien Society, dated Winter 2017; two issues of Mythlore: A Journal of J.R.R. Tolkien, C. S. Lewis...

284P - Changes in ER pathway activity score during neoadjuvant letrozole to assess therapy response and predict disease free survival (DFS) in ER positive breast cancer patients

BackgroundDespite ER positive IHC staining, some patients do not respond to neoadjuvant endocrine therapy, suggesting that ER staining lacks specificity to predict response. We developed a method to infer a quantitative signal transduction pathway activity score (PAS) from mRNA levels (microarray, qPCR) of pathway-associated transcription factor target genes. Initial studies suggest that ER PAS may have higher specificity than ER IHC in predicting endocrine therapy response. In this study, we correlated pre-treatment ER PAS and changes in ER PAS during neoadjuvant letrozole treatment to therapy response and DFS. MethodsWe collected fresh frozen RNA from tumor samples of 30 ER IHC positive post-menopausal patients with primary localized breast cancer, treated with neoadjuvant letrozole at Edinburgh Western General. In total, 30 pre, 25 mid (median 27 days), and 29 post-treatment (median 136 days) samples were analysed. Clinical outcome was assessed (RECIST, n=29) at circa 3 months treatment by 3D ultrasound, with 1 complete (CR), 21 partial responses (PR), 2 stable (SD), and 5 progressive diseases (PD). Using RT-qPCR, target gene expression was measured for ER, androgen receptor, PI3K, Hedgehog, TGFβ and Wnt pathways. PAS were expressed on a normalized scale (0 to 100). ResultsPre-treatment ER PAS was significantly higher in responders (CR/PR) than non-responders (SD/PD), PAS=45 vs 24, respectively, T-test p=0.01. Pre-treatment ER PAS correlated with decrease in ER PAS during treatment (cor=0.87 and 0.7, mid and-post treatment, respectively). At mid-treatment, ER PAS of responders had decreased to PAS of non-responders (20 vs 19, respectively), remaining low during further treatment. Decrease in ER PAS was significantly higher in responders (-30) than non-responders (-6), p=0.01. Higher ER PAS after treatment correlated to shorter DFS (COX proportional hazards p=0.02). Baseline PAS of other pathways did not correlate with response, but changed significantly during treatment. ConclusionsThis study confirms that ER PAS in ER-positive patients, measured before and after neoadjuvant endocrine therapy, has potential to predict and assess therapy response, and predict DFS. Legal entity responsible for the studyPhilips Electronics Nederland B.V., acting through its HealthWorks Molecular Pathway Dx. FundingHas not received any funding. DisclosureM. A. Inda: Full / Part-time employment: Philips Reseach. A. van de Stolpe: Full / Part-time employment, has Philips stocks: Philips Research. D. Keizer: Full / Part-time employment: Philips. D. Clout: Full / Part-time employment: Philips Reasearch. H. van Zon: Full / Part-time employment: Philips Reasearch. M. Akse: Full / Part-time employment: Philips. All other authors have declared no conflicts of interest.

Abstract B205: Adoptive transfer of autologous T-cells, modified with a MART-1 specific TCR and cultured in IL-7/IL-15, for the treatment of metastatic melanoma patients

Abstract Currently a TCR gene therapy trial to treat stage IV cutaneous and uveal melanoma patients is being conducted at the NKI. The TCR used for T-cell modification is specific for the HLA-A*0201 restricted MART-126-35 epitope, which is expressed on the majority of melanoma cells. Unique to this trial is the use of the combination of anti-CD3/CD28 beads for T-cell activation plus IL-7/ IL-15 for subsequent culture and expansion, instead of the more commonly used strategy that utilizes the combination of anti-CD3 and IL-2. The aim of this alternative production strategy is to generate a “less differentiated“ T-cell product that may have a better engraftment potential and antitumor activity. Thus far, a total of 12 patients have been treated, of whom 5 were uveal melanoma patients. 1 patient treated with 5x109 cells died 9 days after infusion, among others due to a severe cytokine release syndrome. The other 11 patients were treated in 3 different cell doses: 5x107, 25x107and10x107 transduced CD4 and CD8 T-cells. A prolonged engraftment and higher % of gene modified cells in the blood compartment were observed in patients treated with the highest number of cells infused. Gene modified T-cells could be found back in the circulation for up to two months post infusion, even when as few as 5x107 transduced T-cells were infused. In the highest cell dose, transduced T-cells could be detected up to 10 months following infusion. On-target toxicity against MART-1 expressing melanocytes in the skin (rash and vitiligo) was observed in all patients. Most severe skin toxicity, but also uveitis and inner ear toxicity, were observed in patients treated in the highest dose cohort of 2.5x107 transduced T-cells. These patients also developed a cytokine release syndrome requiring tocilizumab (anti-IL6R) treatment. Unexpected toxicity observed at this highest dose level consisted of development of pancytopenia around 6-8 weeks post T-cell infusion. In one of these patients, T-cell clonality of the infused cell product and of the peripheral blood compartment at the time of pancytopenia was analyzed in order to investigate the mechanism behind this toxicity. The highest clonality was found in the endogenous unmodified CD4 population. TCR diversity and evenness of the CD8 modified and unmodified populations were similar, suggesting that the pancytopenia was not associated with specific expansion of a TCR modified T-cell clone. However, this delayed pancytopenia could be related to 1) the conditioning chemotherapy regimen (fludarabine and cyclophosphamide), 2) cytokine release like IL-6, or 3) expansion of an autoreactive clone derived either from the infused T-cell product or newly generated from the endogenous T-cell pool. Of the 12 patients treated thus far, 8 patients had stable disease (SD) and two showed a partial response (PR) (5.2 and 9.5 month). The type of response or the duration of response was not correlated to the amount of cells infused or the peak and duration of engraftment of the infused T-cells. On the basis of these preliminary data, we conclude that TCR-modified T-cells produced by this method have a high engraftment potential and show in vivo activity at low infused cell doses, thereby suggesting the potential value of this protocol for TCR or CAR gene therapy for the treatment of cancer. Citation Format: Raquel Gomez-Eerland, Maartje Rohaan, Joost van den Berg, Maaike van Zon, Renate de Boer, Noor Bakker, Bastiaan Nuijen, Ton N.M. Schumacher, John B.A.G. Haanen. Adoptive transfer of autologous T-cells, modified with a MART-1 specific TCR and cultured in IL-7/IL-15, for the treatment of metastatic melanoma patients [abstract]. In: Proceedings of the Fourth CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; Sept 30-Oct 3, 2018; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2019;7(2 Suppl):Abstract nr B205.

The Year's Work in Tolkien Studies 2016

The Year's Work in Tolkien Studies 2016 David Bratman (bio), Jason Fisher (bio), John Wm. Houghton (bio), John Magoun (bio), Kate Neville (bio), and Robin Anne Reid (bio) Introduction [David Bratman] An ever-prolific J.R.R. Tolkien published two new books in 2016. The Lay of Aotrou and Itroun: Together with the Corrigan Poems re prints a long Breton-influenced narrative poem, which previously had appeared only in The Welsh Review 4 (Dec. 1945): 254–66, together with drafts, supplementary poetry, and commentary by editor Verlyn Flieger. A Secret Vice: Tolkien on Invented Languages reprints a fuller text of the now-renowned essay on linguistic sub-creation from The Monsters and the Critics and Other Essays (Boston: Houghton Mifflin, 1983), also with supplementary material and commentary by the editors, Dimitra Fimi and Andrew Higgins. The major anthology of the year in Tolkien studies was the two-volume The Return of the Ring: Proceedings of the Tolkien Society Conference 2012, edited by Lynn Forest-Hill (Edinburgh: Luna Press, 2016), a collection of 36 papers on diverse Tolkienian topics, presented at a conference at Loughborough University in August 2012, sponsored by the Tolkien Society and marking the 75th anniversary of the publication of The Hobbit. The year also saw publication of a specialized anthology on the subject of that book, The Hobbit, edited by Stephen W. Potts, in the Critical Insights series (Ipswich, MA: Salem Press, 2016); plus another theme anthology, Laughter in Middle-earth: Humour In and Around the Works of J.R.R. Tolkien, edited by Thomas Honegger and Maureen F. Mann (Zurich: Walking Tree, 2016). Volume 13 of Hither Shore, the yearbook of the Deutsche Tolkien Gesellschaft, formed an anthology on "Tolkien's Philosophy of Language," edited by Thomas Fornet-Ponse, Thomas Honegger, and Julian T. M. Eilmann. Lembas Extra 2016 from the Netherlands group Tolkien Genootschap Unquendor, an anthology titled Tolkien Among Scholars, edited by Nathalie Kuijpers, Renée Vink, and Cécile van Zon, was originally announced as dated 2017 and has been postponed for consideration to next year. The most important monographs of the year were Tolkien, Self and Other:"This Queer Creature"by Jane Chance and Tolkien's Theology of Beauty: Majesty, Splendor, and Transcendence in Middle-earth by Lisa [End Page 179] Coutras, both of which have been finalists for the Mythopoeic Scholarship Award. Beyond the Willing Suspension of Disbelief: Poetic Faith from Coleridge to Tolkien by Michael Tomko and On Eagles' Wings: An Exploration of Eucatastrophe in Tolkien's Fantasy by Anna Thayer were also books of particular note and value. Journals of the year, besides the theme anthologies noted above, included volume 13 of the present journal, Tolkien Studies: An Annual Scholarly Review, and issue 57 of Mallorn: The Journal of the Tolkien Society, dated Winter 2016. The open-access electronic Journal of Tolkien Research, hosted at scholar.valpo.edu, published its third volume over the course of the year, with a special theme issue titled Authorizing Tolkien: Control, Adaptation, and Dissemination of J.R.R. Tolkien's Works, edited by Robin A. Reid and Michael D. Elam, designated as issue 3. The Mythopoeic Society published two print issues of Mythlore: A Journal of J.R.R. Tolkien, C. S. Lewis, Charles Williams, and Mythopoeic Literature, vol. 34.2 (whole number 128, dated Spring–Summer 2016) and vol. 35.1 (whole number 129, dated Fall–Winter 2016); back issues are archived online at dc.swosu.edu/mythlore/. The most active newsletters of the year were the Tolkien Society's bimonthly Amon Hen and the American Mensa Tolkien Special Interest Group's Beyond Bree. Coverage of these is selective for major material. General Works [David Bratman] Bandersnatch: C. S. Lewis, J.R.R. Tolkien, and the Creative Collaboration of the Inklings (Kent, OH: Black Squirrel Press, 2016) is the popular edition of Diana Pavlac Glyer's 2007 scholarly study The Company They Keep: C. S. Lewis and J.R.R. Tolkien as Writers in Community (covered here in Tolkien Studies 7 [2010]: 351–52). About two-thirds the length of the original book, it eliminates its predecessor's massive endnotes (except for source citations...

Bibliography (in English) for 2017

Bibliography (in English) for 2017 David Bratman (bio) Primary Sources Tolkien, J.R.R. Beren and Lúthien. Ed. Christopher Tolkien. Boston: Houghton Mifflin Harcourt, 2017. [Compiled from texts extracted from The History of Middle-earth] Books Cholewa-Purgał, Anna. Therapy Through Faërie: Therapeutic Properties of Fantasy Literature by the Inklings and by U. K. Le Guin. Frankfurt; New York: Peter Lang, 2017. Cilli, Oronzo, Arden R. Smith, and Patrick H. Wynne. J.R.R. Tolkien the Esperantist: Before the Arrival of Bilbo Baggins. Barletta, Italy: Cafagna, 2017. [Reprint of 2000 article by Smith and Wynne, "Tolkien and Esperanto," and translation of article by Cilli, "Tolkien and the British Esperantist Movement," with foreword by John Garth and introduction, "1887–1937: 50 Years of Hope and Optimism, with Particular Reference to Great Britain," by Tim Owen.] Clinton, Greg. Reading and Interpreting the Works of J.R.R. Tolkien. New York: Enslow, 2017. Critchley, Peter. Tolkien and the Fellowship of All Living Things: The Politics of Proximity, Person and Place. [UK]: P. Critchley, 2017. Electronic book. http://dx.doi.org/10.17613/M6513TV47 Eilmann, Julian. J.R.R. Tolkien, Romanticist and Poet. Zurich: Walking Tree, 2017. Ellis, James, ed. J.R.R. Tolkien: The Mind of a Genius. (Special Newsweek Edition.) New York: Topix Media Lab, 2017. Flieger, Verlyn. There Would Always Be a Fairy-tale: More Essays on Tolkien. Kent, OH: Kent State UP, 2017. Helen, Daniel, ed. Death and Immortality in Middle-earth: Proceedings of the Tolkien Society Seminar 2016. Edinburgh: Luna Press, 2017. Higgins, Sørina, ed. The Inklings and King Arthur: J.R.R. Tolkien, Charles Williams, C. S. Lewis, and Owen Barfield on the Matter of Britain. Berkeley, CA: Apocryphile Press, 2017. [End Page 255] Jallings, Fiona. A Fan's Guide to Neo-Sindarin: A Textbook for the Elvish of Middle-earth. Lexington, KY: Nemvus, 2017. Judd, Walter S., and Graham A. Judd. Flora of Middle-earth: Plants of J.R.R. Tolkien's Legendarium. New York: Oxford UP, 2017. Kirner-Ludwig, Monika, Stephan Köser, and Sebastian Streitberger, ed. Binding Them All: Interdisciplinary Perspectives on J.R.R. Tolkien and His Works. Zurich: Walking Tree, 2017. Kuijpers, Nathalie, Renée Vink, and Cécile van Zon, ed. Tolkien Among Scholars. (Lembas Extra 2016) [Netherlands]: Tolkien Genootschap Unquendor, 2016. Lee, Stuart D., ed. J.R.R. Tolkien. (Critical Assessments of Major Writers) Abingdon, UK; New York: Routledge, 2017. McAlister, Caroline. John Ronald's Dragons: The Story of J.R.R. Tolkien. New York: Roaring Brook Press, 2017. McIntosh, Jonathan S. The Flame Imperishable: Tolkien, St. Thomas, and the Metaphysics of Faërie. Kettering, OH: Angelico Press, 2017. Morrow, Jeffrey L. Seeking the Lord of Middle Earth: Theological Essays on J.R.R. Tolkien. Eugene, OR: Cascade Books, 2017. Rhone, Zachary A. The Great Tower of Elfland: The Mythopoeic Worldview of J.R.R. Tolkien, G S. Lewis, G. K. Chesterton, and George MacDonald. Kent, OH: Kent State UP, 2017. Ryken, Philip. The Messiah Gomes to Middle-earth: Images of Christ's Threefold Office in The Lord of the Rings. Downers Grove, IL: IVP Academic, 2017. Scull, Christina, and Wayne G. Hammond. The J.R.R. Tolkien Companion & Guide. Rev. and expanded ed. London: HarperCollins, 2017. 3 vols. Vaccaro, Christopher, and Yvette Kisor, ed. Tolkien and Alterity. Cham, Switzerland: Palgrave Macmillan, 2017. Articles and Book Chapters Abaléa, Gaëlle. "Transmission: An Escape from Death in Tolkien's Work?" Helen 135–42. Alberto, Maria. "'It had been his virtue, and therefore also the cause of his fall': Seduction as a Mythopoeic Accounting for Evil in Tolkien's Work." Mythlore 35.2 (Spring–Summer 2017): 63–79. Amendt-Raduege, Amy. "Revising Lobelia." Vaccaro and Kisor 77–93. [End Page 256] Anver, Gazala. "A Deconstructive Reading of Tolkien Criticism with Special Emphasis on The Silmarillion." Kuijpers et al. 237–52. Arul, Melissa Ruth. "Silmarils and Obsession: The Undoing of Fëanor." Vaccaro and Kisor 225–39. Atkins, Jay. "On Tolkien's Presentation of Distributism through the Shire." Mallorn: The Journal of the Tolkien Society 58 (Winter 2017): 23–28. Azevedo, Tânia. "Tolkien and T. S. Eliot: The Waste Land and a Fallen...

George Lloyd - Music for Brass, from symphony to test-piece

Name: Pieter Koster Main Subject: Wind band Conducting Research Supervisor: Paul Scheepers Title of Research: George Lloyd – Music for brass, from symphony to test-piece Research Questions: 1. Did George Lloyd change his way of composing from Symphony no. 10 via Royal Parks to Diversions on a Bass Theme? a. In what way does George Lloyd treat the following compositional elements in each piece? i. Structure ii.Harmony iii.Thematic material iv. Musical Tension b. In what way does the treatment of these elements differ in each piece? 2. Did George Lloyd succeed in combining his own views with the demands of the test-piece commissions, to write an appropriate test-piece? Summary of Results: Cornish symphonic and opera composer George Lloyd has written several compositions for brass, starting with a symphony for brass ensemble (Symphony no. 10) and then several test-pieces for brass band. The commission of test-pieces for brass band contests appears to be guided only by implicit criteria for these sort of compositions. Lloyd’s first test-piece, Royal Parks, apparently did not meet the criteria and his second test-piece, Diversions on a Bass Theme, did. This thesis investigates if George Lloyd changed his way of composing to write an appropriate test-piece, by a detailed analysis of Symphony no. 10, Royal Parks and Diversions on a Bass Theme. Besides that the thesis will try to answer the question if Lloyd was able to combine his own musical views with the demands of the test-piece commissions. The main findings are that Lloyd remained within his own musical language when writing the test-pieces, however he made some decisive choices regarding structure, form and thematic material that influenced the compositions significantly. He did partially succeed in combining his own views with the demands of the test-piece commissions. Biography: Pieter Koster (1985) completed his Bachelor’s Degrees at the Royal Conservatory in The Hague as a student of Ad van Zon on the trumpet, and Alex Schillings for conducting. In September 2016 he successfully completed his Master-exam concert with the Bundes Polizeiochester München. Pieter has participated in multiple conducting courses with renowned (professional) orchestras and teachers. Today he is professional conductor of the fanfare orchestras ‘Ons Genoegen’ Hattem, ‘Wilhelmina’ Volendam and the Koninklijke Brassband Utrecht. He is also a brass teacher for numerous students. Since 2014 he is secretary and member of the board of the Dutch Association of Wind band Conductors (Bond van Orkestdirigenten en Instructeurs).

Period Robustness and Entrainability of the Kai System to Changing Nucleotide Concentrations

Circadian clocks must be able to entrain to time-varying signals to keep their oscillations in phase with the day-night rhythm. On the other hand, they must also exhibit input compensation: their period must remain approximately one day in different constant environments. The posttranslational oscillator of the Kai system can be entrained by transient or oscillatory changes in the ATP fraction, yet is insensitive to constant changes in this fraction. We study in three different models of this system how these two seemingly conflicting criteria are met. We find that one of these (our recently published Paijmans model) exhibits the best tradeoff between input compensation and entrainability: on the footing of equal phase-response curves, it exhibits the strongest input compensation. Performing stochastic simulations at the level of individual hexamers allows us to identify a new, to our knowledge, mechanism, which is employed by the Paijmans model to achieve input compensation: at lower ATP fraction, the individual hexamers make a shorter cycle in the phosphorylation state space, which compensates for the slower pace at which they traverse the cycle.

Calculation skills: Otitis media in children

Nurse PrescribingVol. 14, No. 12 Calculation SkillsCalculation skills: Otitis media in childrenDeborah RobertsonDeborah RobertsonSearch for more papers by this authorDeborah RobertsonPublished Online:9 Dec 2016https://doi.org/10.12968/npre.2016.14.12.584AboutSectionsView articleView Full TextPDF/EPUB ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareShare onFacebookTwitterLinked InEmail View article References National Institute for Health and Care Excellence (2015) Clinical Knowledge Summaries. http://cks.nice.org.uk/otitis-media-acute (accessed 10 November 2016) Google ScholarVenekamp RP, Burton MJ, van Dongen TMA, van der Heijden GJ, van Zon A, Schilder AGM (2016) Antibiotics for otitis media with effusion in children. Cochrane Database Syst Rev 6: CD009163. https://doi.org/https://doi.org/10.1002/14651858.CD009163.pub3 Google Scholar FiguresReferencesRelatedDetails 2 December 2016Volume 14Issue 12ISSN (print): 1479-9189ISSN (online): 2052-2924 Metrics History Published online 9 December 2016 Published in print 2 December 2016 Information© MA Healthcare LimitedPDF download

Abstract PL01-03: TIL therapy in the era of immune checkpoint blockade

Abstract Infusion of tumor-infiltrating T-lymphocytes was developed as treatment for metastatic melanoma by Dr. S. Rosenberg (Surgery Branch, NIH, Bethesda, MD, USA) in the late 90's of the past century. This therapy was based on the finding that melanomas oftentimes have infiltrates of CD8 T cells that show recognition of melanoma cells. Many tumor antigens have been characterized for which specific T cells can be found within the tumor or in peripheral blood. As tumors may use mechanisms to induce local T cell unresponsiveness, isolation of TILs and in vitro activation and expansion was shown to overcome this anergic state both in preclinical models and in clinical trials. In order for the TILs to survive, persist, and be cytolytic after infusion, culture time should be as short as possible (to obtain cells with a less terminally differentiated phenotype), patients should receive lymphodepleting treatment (chemotherapy +/- TBI) prior to infusion and interleukin-2 as a survival factor post infusion. Up to date several hundreds of metastatic melanoma patients have been treated with TIL therapy in centers within the US, Europe and Israel. Objective response rates vary between 38 and 72% depending on the phase I/II trial with 10-20% of patients acquiring a CR, which were most often very durable. Many of these oftentimes heavily pretreated patients have benefitted from TIL therapy. As melanomas are heavily mutated cancers, the idea that T cells may react to epitopes derived from mutated proteins could be investigated with new technologies developed at NKI. Using whole exome sequencing, the total mutational burden could be measured for each melanoma. Only those mutations present in expressed genes were used for epitope prediction for every MHC class I molecule of the patient using validated prediction algorithms. Filters were used to select those epitopes with high enough binding affinity for MHC that were subsequently synthesized for production of peptide-MHC multimers that could be used to screen for neo-antigen specific T cells among peripheral blood T- cells or TIL using a multiplex flow cytometric technology. Together with the NCI, using a somewhat different approach, we were able to show that in the vast majority of melanoma TIL, CD8 T cells specific for epitopes resulting from UV light induced DNA damage can be found, sometimes in high frequencies (up to 25-30%), strongly suggesting that neo-antigen-specific T cells play an important role in the success of TIL therapy and possibly other immunotherapies, including checkpoint inhibitors. So far TIL therapy has been mostly used in metastatic melanoma patients pretreated with BRAF inhibitors, anti-CTLA4, high-dose IL-2, and demonstrated activity irrespective of these treatments, although isolation of TIL appeared less successful in patients progressing upon BRAFi. Early results in patients pretreated with PD1 blocking antibodies are promising as well, although the objective response rate is still unknown. Next to metastatic melanoma, TIL can be grown from other cancers as well and promising results have been obtained in patients with cervical cancer and in a patient with cholangiocarcinoma. Trials are planned for patients with epithelial ovarian cancer as well. Citation Format: John B.A.G. Haanen, Joost Van den Berg, Maaike Van Zon, Noor Bakker, Marnix Geukes, Hans Van Thienen, Christian Blank, Pia Kvistborg, Ton Schumacher. TIL therapy in the era of immune checkpoint blockade. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2015 Nov 5-9; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2015;14(12 Suppl 2):Abstract nr PL01-03.

Response to Heller and Bolz

Response to Heller and Bolz

Editorial: Special Issue on Stochastic Modelling of Reaction–Diffusion Processes in Biology

Editorial: Special Issue on Stochastic Modelling of Reaction–Diffusion Processes in Biology

The Joubert Syndrome-associated Missense Mutation (V443D) in the Abelson-helper Integration Site 1 (AHI1) Protein Alters Its Localization and Protein-Protein Interactions

Missense mutations in AHI1 result in the neurodevelopmental ciliopathy called Joubert syndrome. Mutations in AHI1 decrease cilia formation, alter its localization and stability, and change its binding to HAP1 and NPHP1. Mutations in AHI1 affect ciliogenesis, AHI1 protein localization, and AHI1-protein interactions. This study begins to describe how missense mutations in AHI1 can cause Joubert syndrome. Mutations in AHI1 cause Joubert syndrome (JBTS), a neurodevelopmental ciliopathy, characterized by midbrain-hindbrain malformations and motor/cognitive deficits. Here, we show that primary cilia (PC) formation is decreased in fibroblasts from individuals with JBTS and AHI1 mutations. Most missense mutations in AHI1, causing JBTS, occur in known protein domains, however, a common V443D mutation in AHI1 is found in a region with no known protein motifs. We show that cells transfected with AHI1-V443D, or a new JBTS-causing mutation, AHI1-R351L, have aberrant localization of AHI1 at the basal bodies of PC and at cell-cell junctions, likely through decreased binding of mutant AHI1 to NPHP1 (another JBTS-causing protein). The AHI1-V443D mutation causes decreased AHI1 stability because there is a 50% reduction in AHI1-V443D protein levels compared with wild type AHI1. Huntingtin-associated protein-1 (Hap1) is a regulatory protein that binds Ahi1, and Hap1 knock-out mice have been reported to have JBTS-like phenotypes, suggesting a role for Hap1 in ciliogenesis. Fibroblasts and neurons with Hap1 deficiency form PC with normal growth factor-induced ciliary signaling, indicating that the Hap1 JBTS phenotype is likely not through effects at PC. These results also suggest that the binding of Ahi1 and Hap1 may not be critical for ciliary function. However, we show that HAP1 has decreased binding to AHI1-V443D indicating that this altered binding could be responsible for the JBTS-like phenotype through an unknown pathway. Thus, these JBTS-associated missense mutations alter their subcellular distribution and protein interactions, compromising functions of AHI1 in cell polarity and cilium-mediated signaling, thereby contributing to JBTS.

Balancing of Histone H3K4 Methylation States by the Kdm5c/SMCX Histone Demethylase Modulates Promoter and Enhancer Function

The functional organization of eukaryotic genomes correlates with specific patterns of histone methylations. Regulatory regions in genomes such as enhancers and promoters differ in their extent of methylation of histone H3 at lysine-4 (H3K4), but it is largely unknown how the different methylation states are specified and controlled. Here, we show that the Kdm5c/Jarid1c/SMCX member of the Kdm5 family of H3K4 demethylases can be recruited to both enhancer and promoter elements in mouse embryonic stem cells and in neuronal progenitor cells. Knockdown of Kdm5c deregulates transcription via local increases in H3K4me3. Our data indicate that by restricting H3K4me3 modification at core promoters, Kdm5c dampens transcription, but at enhancers Kdm5c stimulates their activity. Remarkably, an impaired enhancer function activates the intrinsic promoter activity of Kdm5c-bound distal elements. Our results demonstrate that the Kdm5c demethylase plays a crucial and dynamic role in the functional discrimination between enhancers and core promoters.

A Design Principle for a Posttranslational Biochemical Oscillator

Multisite phosphorylation plays an important role in biological oscillators such as the circadian clock. Its general role, however, has been elusive. In this theoretical study, we show that a simple substrate with two modification sites acted upon by two opposing enzymes (e.g., a kinase and a phosphatase) can show oscillations in its modification state. An unbiased computational analysis of this oscillator reveals two common characteristics: a unidirectional modification cycle and sequestering of an enzyme by a specific modification state. These two motifs cause a substrate to act as a coupled system in whicha unidirectional cycle generates single-molecule oscillators, whereas sequestration synchronizes the population by limiting the available enzyme under conditions in which substrate is in excess. We also demonstrate the conditions under which the oscillation period is temperature compensated, an important feature of the circadian clock. This theoretical model will provide a framework for analyzing and synthesizing posttranslational oscillators.