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Article ; Online: spicyR: spatial analysis of in situ cytometry data in R.

Canete, Nicolas P / Iyengar, Sourish S / Ormerod, John T / Baharlou, Heeva / Harman, Andrew N / Patrick, Ellis

2022 Volume 38, Issue 11, Page(s) 3099–3105

Abstract: ... pathology.: Results: We have developed the spicyR R package to perform inference on changes ... pathologies or disease states.: Availability and implementation: R package is freely available at http ...

Abstract	Motivation: High parameter histological techniques have allowed for the identification of a variety of distinct cell types within an image, providing a comprehensive overview of the tissue environment. This allows the complex cellular architecture and environment of diseased tissue to be explored. While spatial analysis techniques have revealed how cell-cell interactions are important within the disease pathology, there remains a gap in exploring changes in these interactions within the disease process. Specifically, there are currently few established methods for performing inference on cell-type co-localization changes across images, hindering an understanding of how cellular environments change with a disease pathology. Results: We have developed the spicyR R package to perform inference on changes in the spatial co-localization of types across groups of images. Application to simulated data demonstrates a high sensitivity and specificity. We the utility of spicyR by applying it to a type 1 diabetes imaging mass cytometry dataset, revealing changes in cellular associations that were relevant to the disease progression. Ultimately, spicyR allows changes in cellular environments to be explored under different pathologies or disease states. Availability and implementation: R package is freely available at http://bioconductor.org/packages/release/bioc/html/spicyR.html and shiny app implementation at http://shiny.maths.usyd.edu.au/spicyR/. Supplementary information: Supplementary data are available at Bioinformatics online.
MeSH term(s)	Software ; Spatial Analysis
Language	English
Publishing date	2022-04-14
Publishing country	England
Document type	Review ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1422668-6
ISSN	1367-4811 ; 1367-4803
ISSN (online)	1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/btac268
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Article ; Online: Synovial fibroblasts assume distinct functional identities and secrete R-spondin 2 in osteoarthritis.

Knights, Alexander J / Farrell, Easton C / Ellis, Olivia M / Lammlin, Lindsey / Junginger, Lucas M / Rzeczycki, Phillip M / Bergman, Rachel F / Pervez, Rida / Cruz, Monique / Knight, Eleanor / Farmer, Dennis / Samani, Alexa A / Wu, Chia-Lung / Hankenson, Kurt D / Maerz, Tristan

Annals of the rheumatic diseases

2022 Volume 82, Issue 2, Page(s) 272–282

Abstract: ... intra-articular injections of the Wnt agonist R-spondin 2 (Rspo2) to assess whether gain of function induced pathologies ...

Abstract	Objectives: Synovium is acutely affected following joint trauma and contributes to post-traumatic osteoarthritis (PTOA) progression. Little is known about discrete cell types and molecular mechanisms in PTOA synovium. We aimed to describe synovial cell populations and their dynamics in PTOA, with a focus on fibroblasts. We also sought to define mechanisms of synovial Wnt/β-catenin signalling, given its emerging importance in arthritis. Methods: We subjected mice to non-invasive anterior cruciate ligament rupture as a model of human joint injury. We performed single-cell RNA-sequencing to assess synovial cell populations, subjected Wnt-GFP reporter mice to joint injury to study Wnt-active cells, and performed intra-articular injections of the Wnt agonist R-spondin 2 (Rspo2) to assess whether gain of function induced pathologies characteristic of PTOA. Lastly, we used cultured fibroblasts, macrophages and chondrocytes to study how Rspo2 orchestrates crosstalk between joint cell types. Results: We uncovered seven distinct functional subsets of synovial fibroblasts in healthy and injured synovium, and defined their temporal dynamics in early and established PTOA. Wnt/β-catenin signalling was overactive in PTOA synovium, and Rspo2 was strongly induced after injury and secreted exclusively by Prg4 Conclusions: Synovial fibroblasts assume distinct functional identities during PTOA in mice, and Prg4
MeSH term(s)	Animals ; Humans ; Mice ; Chondrocytes/metabolism ; Fibroblasts/metabolism ; Osteoarthritis/pathology ; Synovial Membrane/metabolism ; Wnt Signaling Pathway ; Thrombospondins/metabolism
Chemical Substances	RSPO2 protein, mouse ; Thrombospondins
Language	English
Publishing date	2022-09-29
Publishing country	England
Document type	Journal Article
ZDB-ID	7090-7
ISSN	1468-2060 ; 0003-4967
ISSN (online)	1468-2060
ISSN	0003-4967
DOI	10.1136/ard-2022-222773
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Article ; Online: An Interview with Cass R. Sunstein

Cass R. Sunstein / Jason W. Ellis / Sean Scanlan

NANO, Iss

Author of The World According to Star Wars

2017 Volume 12

Abstract: The guest editors of special issue 12, Jason W. Ellis and Sean Scanlan, interview Cass R. Sunstein ...

Abstract	The guest editors of special issue 12, Jason W. Ellis and Sean Scanlan, interview Cass R. Sunstein, the Robert Walmsley University Professor at Harvard, where he is founder and director of the Program on Behavioral Economics and Public Policy. He is the author of many books, including the bestseller Nudge: Improving Decisions about Health, Wealth, and Happiness (with Richard H. Thaler). His 2016 book The World According to Star Wars attempts to understand the Star Wars universe in ten chapters through the lenses of Sunstein’s academic interests, namely: culture, sociology, psychology, behavioral science, and political science. The book is both personal and theoretical, practical and academic. It takes accurate measure of the genesis of the movies, the movies themselves, and briefly, but trenchantly, it examines concepts such as reputational cascades and speculates on what Star Wars can teach viewers about constitutional disputes.
Keywords	Star Wars ; The Force Awakens ; Cass Sunstein ; The World According to Star Wars ; interview ; History of scholarship and learning. The humanities ; AZ20-999 ; Language and Literature ; P ; Literature (General) ; PN1-6790
Subject code	940
Language	English
Publishing date	2017-12-01T00:00:00Z
Publisher	New York City College of Technology
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: bbeaR: an R package and framework for epitope-specific antibody profiling.

Suprun, Maria / Ellis, Randall J / Sampson, Hugh A / Suárez-Fariñas, Mayte

Bioinformatics (Oxford, England)

2021 Volume 37, Issue 1, Page(s) 131–133

Abstract: ... IgG, IgA and IgD isotypes. bbeaR is an open-source R package, developed for the BBEA, provides ... Availability and implementation: bbeaR is open-source and freely available from GitHub as an R package: https ...

Abstract	Summary: Analysis of epitope-specific antibody repertoires has provided novel insights into the pathogenesis of inflammatory disorders, especially allergies. A novel multiplex immunoassay, termed Bead-Based Epitope Assay (BBEA), was developed to quantify levels of epitope-specific immunoglobulins, including IgE, IgG, IgA and IgD isotypes. bbeaR is an open-source R package, developed for the BBEA, provides a framework to import, process and normalize .csv data files exported from the Luminex reader, evaluate various quality control metrics, analyze differential epitope-binding antibodies with linear modeling, visualize results and map epitopes' amino acid sequences to their respective primary protein structures. bbeaR enables streamlined and reproducible analysis of epitope-specific antibody profiles. Availability and implementation: bbeaR is open-source and freely available from GitHub as an R package: https://github.com/msuprun/bbeaR; vignettes included. Supplementary information: Supplementary data are available at Bioinformatics online.
Language	English
Publishing date	2021-01-18
Publishing country	England
Document type	Journal Article
ZDB-ID	1422668-6
ISSN	1367-4811 ; 1367-4803
ISSN (online)	1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/btaa1064
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Article ; Online: A population-based resource for intergenerational metabolomics analyses in pregnant women and their children: the Generation R Study.

Voerman, Ellis / Jaddoe, Vincent W V / Uhl, Olaf / Shokry, Engy / Horak, Jeannie / Felix, Janine F / Koletzko, Berthold / Gaillard, Romy

Metabolomics : Official journal of the Metabolomic Society

2020 Volume 16, Issue 4, Page(s) 43

Abstract: ... years were low (range between r = - 0.10 and r = 0.35).: Conclusion: Our results suggest that unique ...

Abstract	Introduction: Adverse exposures in early life may predispose children to cardio-metabolic disease in later life. Metabolomics may serve as a valuable tool to disentangle the metabolic adaptations and mechanisms that potentially underlie these associations. Objectives: To describe the acquisition, processing and structure of the metabolomics data available in a population-based prospective cohort from early pregnancy onwards and to examine the relationships between metabolite profiles of pregnant women and their children at birth and in childhood. Methods: In a subset of 994 mothers-child pairs from a prospective population-based cohort study among pregnant women and their children from Rotterdam, the Netherlands, we used LC-MS/MS to determine concentrations of amino acids, non-esterified fatty acids, phospholipids and carnitines in blood serum collected in early pregnancy, at birth (cord blood), and at child's age 10 years. Results: Concentrations of diacyl-phosphatidylcholines, acyl-alkyl-phosphatidylcholines, alkyl-lysophosphatidylcholines and sphingomyelines were the highest in early pregnancy, concentrations of amino acids and non-esterified fatty acids were the highest at birth and concentrations of alkyl-lysophosphatidylcholines, free carnitine and acyl-carnitines were the highest at age 10 years. Correlations of individual metabolites between pregnant women and their children at birth and at the age of 10 years were low (range between r = - 0.10 and r = 0.35). Conclusion: Our results suggest that unique metabolic profiles are present among pregnant women, newborns and school aged children, with limited intergenerational correlations between metabolite profiles. These data will form a valuable resource to address the early metabolic origins of cardio-metabolic disease.
MeSH term(s)	Adult ; Amino Acids/blood ; Amino Acids/metabolism ; Carnitine/blood ; Carnitine/metabolism ; Child ; Chromatography, Liquid ; Cohort Studies ; Fatty Acids/blood ; Fatty Acids/metabolism ; Female ; Humans ; Male ; Metabolomics ; Phospholipids/blood ; Phospholipids/metabolism ; Pregnancy ; Pregnant Women ; Prospective Studies ; Tandem Mass Spectrometry
Chemical Substances	Amino Acids ; Fatty Acids ; Phospholipids ; Carnitine (S7UI8SM58A)
Language	English
Publishing date	2020-03-23
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2250617-2
ISSN	1573-3890 ; 1573-3882
ISSN (online)	1573-3890
ISSN	1573-3882
DOI	10.1007/s11306-020-01667-1
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Article ; Online: Comprehensive Analysis of R-Spondin Fusions and RNF43 Mutations Implicate Novel Therapeutic Options in Colorectal Cancer.

Seeber, Andreas / Battaglin, Francesca / Zimmer, Kai / Kocher, Florian / Baca, Yasmine / Xiu, Joanne / Spizzo, Gilbert / Novotny-Diermayr, Veronica / Rieder, Dietmar / Puccini, Alberto / Swensen, Jeff / Ellis, Michelle / Goldberg, Richard M / Grothey, Axel / Shields, Anthony F / Marshall, John L / Weinberg, Benjamin A / Sackstein, Paul E / Lim, Kiat Hon /

Tan, Gek San / Nabhan, Chadi / Korn, W Michael / Amann, Arno / Trajanoski, Zlatko / Berger, Martin D / Lou, Emil / Wolf, Dominik / Lenz, Heinz-Josef

Clinical cancer research : an official journal of the American Association for Cancer Research

2022 Volume 28, Issue 9, Page(s) 1863–1870

Abstract: Purpose: Gene fusions involving R-spondin (RSPOfp) and RNF43 mutations have been shown to drive ...

Abstract	Purpose: Gene fusions involving R-spondin (RSPOfp) and RNF43 mutations have been shown to drive Wnt-dependent tumor initiation in colorectal cancer. Herein, we aimed to characterize the molecular features of RSPOfp/RNF43 mutated (mut) compared with wild-type (WT) colorectal cancers to gain insights into potential rationales for therapeutic strategies. Experimental design: A discovery cohort was classified for RSPOfp/RNF43 status using DNA/RNA sequencing and IHC. An independent cohort was used to validate our findings. Results: The discovery cohort consisted of 7,245 colorectal cancer samples. RSPOfp and RNF43 mutations were detected in 1.3% (n = 94) and 6.1% (n = 443) of cases. We found 5 RSPO fusion events that had not previously been reported (e.g., IFNGR1-RSPO3). RNF43-mut tumors were associated with right-sided primary tumors. No RSPOfp tumors had RNF43 mutations. In comparison with WT colorectal cancers, RSPOfp tumors were characterized by a higher frequency of BRAF, BMPR1A, and SMAD4 mutations. APC mutations were observed in only a minority of RSPOfp-positive compared with WT cases (4.4% vs. 81.4%). Regarding RNF43 mutations, a higher rate of KMT2D and BRAF mutations were detectable compared with WT samples. Although RNF43 mutations were associated with a microsatellite instability (MSI-H)/mismatch repair deficiency (dMMR) phenotype (64.3%), and a tumor mutation burden ≥10 mt/Mb (65.8%), RSPOfp was not associated with MSI-H/dMMR. The validation cohort replicated our genetic findings. Conclusions: This is the largest series of RSPOfp/RNF43-mut colorectal cancers reported to date. Comprehensive molecular analyses asserted the unique molecular landscape associated with RSPO/RNF43 and suggested potential alternative strategies to overcome the low clinical impact of Wnt-targeted agents and immunotherapy.
MeSH term(s)	Colorectal Neoplasms/drug therapy ; Colorectal Neoplasms/genetics ; Colorectal Neoplasms/pathology ; Humans ; Microsatellite Instability ; Mutation ; Proto-Oncogene Proteins B-raf/genetics ; Ubiquitin-Protein Ligases/genetics
Chemical Substances	RNF43 protein, human (EC 2.3.2.27) ; Ubiquitin-Protein Ligases (EC 2.3.2.27) ; Proto-Oncogene Proteins B-raf (EC 2.7.11.1)
Language	English
Publishing date	2022-03-04
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	1225457-5
ISSN	1557-3265 ; 1078-0432
ISSN (online)	1557-3265
ISSN	1078-0432
DOI	10.1158/1078-0432.CCR-21-3018
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Article ; Online: Correction to: Osborne JA, Botkin R, Colon-Semenza C, et al. Physical Therapist Management of Parkinson Disease: A Clinical Practice Guideline From the American Physical Therapy Association. Phys Ther. 2022;102:pzab302. https://doi.org/10.1093/ptj/pzab302.

Osborne, Jacqueline A / Botkin, Rachel / Colon-Semenza, Cristina / DeAngelis, Tamara R / Gallardo, Oscar G / Kosakowski, Heidi / Martello, Justin / Pradhan, Sujata / Rafferty, Miriam / Readinger, Janet L / Whitt, Abigail L / Ellis, Terry D

Physical therapy

2022 Volume 102, Issue 8

Language	English
Publishing date	2022-08-27
Publishing country	United States
Document type	Published Erratum
ZDB-ID	415886-6
ISSN	1538-6724 ; 0031-9023
ISSN (online)	1538-6724
ISSN	0031-9023
DOI	10.1093/ptj/pzac098
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Article ; Online: R-loops and regulatory changes in chronologically ageing fission yeast cells drive non-random patterns of genome rearrangements.

Ellis, David A / Reyes-Martín, Félix / Rodríguez-López, María / Cotobal, Cristina / Sun, Xi-Ming / Saintain, Quentin / Jeffares, Daniel C / Marguerat, Samuel / Tallada, Víctor A / Bähler, Jürg

PLoS genetics

2021 Volume 17, Issue 8, Page(s) e1009784

Abstract: ... that accumulated with age were associated with microhomology sequences and R-loops. Global hotspots for age ... associated reduction in an RNA-binding protein triggering R-loops at target loci. This result suggests ...

Abstract	Aberrant repair of DNA double-strand breaks can recombine distant chromosomal breakpoints. Chromosomal rearrangements compromise genome function and are a hallmark of ageing. Rearrangements are challenging to detect in non-dividing cell populations, because they reflect individually rare, heterogeneous events. The genomic distribution of de novo rearrangements in non-dividing cells, and their dynamics during ageing, remain therefore poorly characterized. Studies of genomic instability during ageing have focussed on mitochondrial DNA, small genetic variants, or proliferating cells. To characterize genome rearrangements during cellular ageing in non-dividing cells, we interrogated a single diagnostic measure, DNA breakpoint junctions, using Schizosaccharomyces pombe as a model system. Aberrant DNA junctions that accumulated with age were associated with microhomology sequences and R-loops. Global hotspots for age-associated breakpoint formation were evident near telomeric genes and linked to remote breakpoints elsewhere in the genome, including the mitochondrial chromosome. Formation of breakpoint junctions at global hotspots was inhibited by the Sir2 histone deacetylase and might be triggered by an age-dependent de-repression of chromatin silencing. An unexpected mechanism of genomic instability may cause more local hotspots: age-associated reduction in an RNA-binding protein triggering R-loops at target loci. This result suggests that biological processes other than transcription or replication can drive genome rearrangements. Notably, we detected similar signatures of genome rearrangements that accumulated in old brain cells of humans. These findings provide insights into the unique patterns and possible mechanisms of genome rearrangements in non-dividing cells, which can be promoted by ageing-related changes in gene-regulatory proteins.
MeSH term(s)	Aging/genetics ; Chromosome Aberrations ; Chromosome Breakpoints ; DNA Breaks, Double-Stranded ; Gene Rearrangement/genetics ; Genomic Instability/genetics ; Genomics/methods ; Models, Genetic ; Mutation/genetics ; R-Loop Structures/genetics ; Schizosaccharomyces/genetics ; Schizosaccharomyces/metabolism ; Schizosaccharomyces pombe Proteins/genetics ; Schizosaccharomyces pombe Proteins/metabolism ; Telomere/genetics
Chemical Substances	Schizosaccharomyces pombe Proteins
Language	English
Publishing date	2021-08-31
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2186725-2
ISSN	1553-7404 ; 1553-7390
ISSN (online)	1553-7404
ISSN	1553-7390
DOI	10.1371/journal.pgen.1009784
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Article: burnr: Fire history analysis and graphics in R

Malevich, Steven B / Christopher H. Guiterman / Ellis Q. Margolis

Elsevier GmbH Dendrochronologia. 2018 June, v. 49

2018

Abstract: We developed a new software package, burnr, for fire history analysis and plotting in the R ... with the thousands of packages available in R. In this paper, we describe the basic functionality of burnr and ... introduce users to fire history analyses in R. ...

Abstract	We developed a new software package, burnr, for fire history analysis and plotting in the R statistical programming environment. It was developed for tree-ring fire-scar analysis, but is broadly applicable to other event analyses (e.g., avalanches, frost rings, or culturally modified trees). Our new package can read, write, and manipulate standard tree-ring fire history FHX files, produce fire—demography charts, calculate fire frequency and seasonality statistics, and run superposed epoch analysis (SEA). A key benefit of burnr is that it enables automation of analyses and plotting, especially for large data sets. The package also facilitates creative plotting, mapping, and analyses when combined with the thousands of packages available in R. In this paper, we describe the basic functionality of burnr and introduce users to fire history analyses in R.
Keywords	automation ; avalanches ; computer software ; data collection ; fire frequency ; fire history ; frost ; growth rings ; statistics ; trees
Language	English
Dates of publication	2018-06
Size	p. 9-15.
Publishing place	Elsevier GmbH
Document type	Article
ZDB-ID	2088117-4
ISSN	1612-0051 ; 1125-7865
ISSN (online)	1612-0051
ISSN	1125-7865
DOI	10.1016/j.dendro.2018.02.005
Database	NAL-Catalogue (AGRICOLA)

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Book ; Online ; E-Book: Capitalist agriculture and the global bee crisis

Ellis, Rebeca

2023

Abstract: Capitalist agriculture relies heavily on the pollination work of bees, but this system harms bees in innumerable ways. Indeed, human agriculture is one of the main culprits for the declining populations of wild bees and the declining health of honeybees. ...

Author's details	Rebecca Ellis
Abstract	Capitalist agriculture relies heavily on the pollination work of bees, but this system harms bees in innumerable ways. Indeed, human agriculture is one of the main culprits for the declining populations of wild bees and the declining health of honeybees. This book presents a political ecology of pollination that critically examines how managed honey bees and wild bees are harmed by capitalist agriculture. The book focuses on the three most urgent problems: the standardization and simplification of landscapes through monocultures; the use of pesticides including neonicotinoids, other insecticides, herbicides, and fungicides; and the embeddedness of commercial, migratory beekeeping in the capitalist agriculture system which, among other things, has the potential to spread pests and pathogens across continents. At the heart of this crisis is the power and influence that a small group of agrochemical corporations have over national and international agricultural policy. The book argues for an interspecies alliance of small-scale farmers, bee advocates, beekeepers, environmentalists, and bees themselves, along with a vision for an agricultural system that nurtures multispecies flourishing. This book will be of significant interest to readers of political ecology, animal geography, environmental anthropology, food system studies, and critical animal studies.
Keywords	Agriculture/Economic aspects ; Bee culture ; Political ecology
Subject code	638/.1
Language	English
Dates of publication	2023-2022
Size	1 online resource (vii, 171 pages)
Publisher	Routledge
Publishing place	London
Document type	Book ; Online ; E-Book
Remark	Zugriff für angemeldete ZB MED-Nutzerinnen und -Nutzer
ISBN	1-00-314229-X ; 1-003-14229-X ; 1-000-64590-8 ; 1-000-64587-8 ; 9780367695613 ; 978-1-00-314229-4 ; 978-1-003-14229-4 ; 978-1-000-64590-3 ; 978-1-000-64587-3 ; 0367695618
Database	ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

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