James Sharpe

Institució Catalana de Recerca i Estudis Avançats

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Jim Swoger

European Molecular Biology Laboratory

Agnes Wong

University of Toronto

Alexandre Robert‐Moreno

Centre for Genomic Regulation

James Cotterell

Centre for Genomic Regulation

Jens V. Stein

University of Fribourg

Neus Martínez‐Abadías

Universitat de Barcelona

Martin J. Steinbach

University of Duisburg-Essen

Michael S. Salman

University of Manitoba

Linda Lillakas

University of Waterloo

Maureen Dennis

Hospital for Sick Children

Cooperative Institutions

Deleted Institution

323

Università Cattolica del Sacro Cuore

207

University of Toronto

184

Centre National pour la Recherche Scientifique et Technique (CNRST)

126

Alberta Bible College

114

Montreal Neurological Institute and Hospital

111

Vancouver Biotech (Canada)

University of Minnesota Rochester

University of Calgary

Harvard University

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Image Processing Assisted Algorithms for Optical Projection Tomography

IEEE Transactions on Medical Imaging (2011)

Abbas Cheddad Christoffer Svensson James Sharpe Fredrik Georgsson Ulf Ahlgren

Since it was first presented in 2002, optical projection tomography (OPT) has emerged as a powerful tool for the study of biomedical specimen on the mm to cm scale. In this paper, we present computational tools to further improve OPT image acquisition and tomographic reconstruction. More specifically, these methods provide: semi-automatic and precise positioning of a sample at the axis of rotation and a fast and robust algorithm for determination of postalignment values throughout the specimen as compared to existing methods. These tools are easily integrated for use with current commercial OPT scanners and should also be possible to implement in "home made" or experimental setups for OPT imaging. They generally contribute to increase acquisition speed and quality of OPT data and thereby significantly simplify and improve a number of three-dimensional and quantitative OPT based assessments.

Tomographic reconstruction

Sample (material)

10.1109/tmi.2011.2161590

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Citations (55)

The Probability Conflation: A Reply

arXiv (Cornell University) (2023)

Nassim Nicholas Taleb Ron Richman Marcos C. Carreira James Sharpe

We respond to Tetlock et al. (2022) showing 1) how expert judgment fails to reflect tail risk, 2) the lack of compatibility between forecasting tournaments and tail risk assessment methods (such as extreme value theory). More importantly, we communicate a new result showing a greater gap between the properties of tail expectation and those of the corresponding probability.

Conflation

10.48550/arxiv.2301.10985

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Containing some Remarks on his Thirteenth Chapter, of the Laws of Nations

Routledge eBooks (2024)

James Sharpe

10.4324/9781003552239-29

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CJN volume 48 issue 3 Cover and Front matter

Canadian Journal of Neurological Sciences / Journal Canadien des Sciences Neurologiques (2021)

Abhishek Lenka Om Shivam Guillaume Mittal Fernando Lamotte Catherine Beyak

An abstract is not available for this content so a preview has been provided. As you have access to this content, a full PDF is available via the ‘Save PDF’ action button.

Front cover

Content (measure theory)

10.1017/cjn.2021.73

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Paresis of contralateral smooth pursuit and normal vestibular smooth eye movements after unilateral brainstem lesions

Annals of Neurology (1992)

Janine L. Johnston James Sharpe Mark J. Morrow

Abstract Pursuit and vestibular smooth eye movements were measured in patients with lesions of the caudal brainstem tegmentum identified by magnetic resonance imaging (MRI) and computed tomography (CT), with neuropathological correlation in 1 patient. Contralateral smooth pursuit gain was significantly lower than ipsilateral gain in each patient. Ipsilateral smooth pursuit gain was also subnormal in patients with unilateral pontine damage that caused slowing of ipsilateral saccades. Horizontal vestibulo‐ocular reflex gain and phase were normal. These quantitative correlations indicate that lesions of the pontine tegmentum that paralyze ipsilateral saccades can spare the vestibulo‐ocular reflex, and that smooth pursuit movement and the vestibulo‐ocular reflex can be impaired independently by pontine or medullary lesions. In contrast to lesions at other sites, unilateral lesions of the pontine or medullary tegmentum impair contralateral smooth pursuit more than ipsilateral pursuit movements. These findings provide evidence that a double decussating pathway mediates smooth pursuit; the first decussation is from the pons to the cerebellum, and the second decussation is from the vestibular nucleus to the contralateral abducens nucleus.

Decussation

Smooth pursuit

Pons

Medial longitudinal fasciculus

Tegmentum

Internuclear ophthalmoplegia

Electronystagmography

Vestibulo–ocular reflex

Hyperreflexia

Abducens nucleus

10.1002/ana.410310506

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Citations (17)

Cell3DPositioning byOptical encoding(C3PO) and its application to spatial transcriptomics

bioRxiv (Cold Spring Harbor Laboratory) (2024)

James Cotterell Jim Swoger Alexandre Robert‐Moreno Heura Cardona Marco Musy

Abstract Current state-of-the-art spatial omics approaches suffer from the drawback that they are tissue section-based and thus inherently 2-dimensional. A full understanding of biological processes will only be possible when such data is available in 3-dimensions (3D). Here, we introduce Cell 3D Positioning by Optical encoding (C3PO) - the first technique capable of reconstructing the 3D positions of cells in a tissue, after they have been fully dissociated for single-cell omics analysis. It imposes a Cartesian coordinate system of positions on the tissue and cells of interest, before dissociation. This is created by multiple orthogonal spatial gradients of active fluorophores, carefully shaped by a 3D bleaching method, such that each position in the tissue is encoded by a unique fluorescent address. Upon dissociation of the tissue the fluorescent addresses of the cells can be read via an appropriate device (such as a FACS machine) to computationally reconstruct the tissue in 3D, before omics are performed downstream. Here, we show two proof-of-principle results for C3PO. First, pure C3PO without omics, to reconstruct the 3D geometry of a developing mouse limb bud. Second, an application of C3PO to spatial transcriptomics, revealing the expression patterns of 73 genes with interesting gene expression patterns in the developing limb.. C3PO is a genuinely novel approach to reconstruct the original 3D positions of cells in a tissue after dissociation. Combined with transcriptomics, it can play a significant role in the study of any tissue or organ in which 3D structure and geometry is important, such as developmental biology, cancer biology and neuroscience. It is not an omics technique per se , and in the future could be combined with the growing family of other omics technologies. One sentence summary C3PO is a novel optical technique that can preserve the 3D positional coordinates of cells after tissue dissociation, enabling a radically new approach to spatial transcriptomics.

10.1101/2024.03.12.584578

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Citations (2)

Control of pelvic girdle development by genes of the Pbx family and Emx2

Developmental Dynamics (2011)

Terence D. Capellini Karen Handschuh Laura Quintana Elisabetta Ferretti Giuseppina Di Giacomo

Abstract Genes expressed in the somatopleuric mesoderm, the embryonic domain giving rise to the vertebrate pelvis, appear important for pelvic girdle formation. Among such genes, Pbx family members and Emx2 were found to genetically interact in hindlimb and pectoral girdle formation. Here, we generated compound mutant embryos carrying combinations of mutated alleles for Pbx1 , Pbx2 , and Pbx3 , as well as Pbx1 and Emx2 , to examine potential genetic interactions during pelvic development. Indeed, Pbx genes share overlapping functions and Pbx1 and Emx2 genetically interact in pelvic formation. We show that, in compound Pbx1;Pbx2 and Pbx1;Emx2 mutants, pelvic mesenchymal condensation is markedly perturbed, indicative of an upstream control by these homeoproteins. We establish that expression of Tbx15 , Prrx1 , and Pax1 , among other genes involved in the specification and development of select pelvic structures, is altered in our compound mutants. Lastly, we identify potential Pbx1‐Emx2–regulated enhancers for Tbx15 , Prrx1 , and Pax1 , using bioinformatics analyses. Developmental Dynamics 240:1173–1189, 2011. © 2011 Wiley‐Liss, Inc.

EMX2

10.1002/dvdy.22617

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Citations (36)

Multiview 3D Image Tiling for OPT and SPIM Data

Juergen Mayer Jim Swoger James Sharpe

Imaging mesoscopic samples in OPT (Optical Projection Tomography) and SPIM (Selective Plane Illumination Microscopy) has intrinsic optical limits when trying to acquire high resolution for the entire specimen. To reach high resolution without loosing the global perspective, we want to achieve automated registration and tiling of our multiview 3D datasets. Automation is the key for processing high throughput data. The idea is to embed existing tools and adapt them to our needs, or develop a new approach in case the previous does not work. The tools that we are using right now are: a) Matlab, where we have a variety of programs dealing with the data we acquired, such as general processing and reconstruction. b) FIJI/ imageJ and XuVTools to do the semiautomated stitching and blending of our high resolution 3D image data and c) LabView to control our setup and log approximate positions of the tiles.

Image stitching

Source

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Correction for Jiménez et al., Dynamics of gene circuits shapes evolvability

Proceedings of the National Academy of Sciences (2015)

Alba Jiménez James Cotterell Andreea Munteanu James Sharpe

Evolvability

Dynamics

10.1073/pnas.1515026112

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Citations (1)

N-mycControls Proliferation, Morphogenesis, and Patterning of the Inner Ear

Journal of Neuroscience (2011)

Elena Domínguez‐Frutos Iris López‐Hernández Victor Vendrell Joana Neves Micaela Gallozzi

Myc family members play crucial roles in regulating cell proliferation, size, and differentiation during organogenesis. Both N-myc and c-myc are expressed throughout inner ear development. To address their function in the mouse inner ear, we generated mice with conditional deletions in either N-myc or c-myc . Loss of c-myc in the inner ear causes no apparent defects, whereas inactivation of N-myc results in reduced growth caused by a lack of proliferation. Reciprocally, the misexpression of N-myc in the inner ear increases proliferation. Morphogenesis of the inner ear in N-myc mouse mutants is severely disturbed, including loss of the lateral canal, fusion of the cochlea with the sacculus and utriculus, and stunted outgrowth of the cochlea. Mutant cochleas are characterized by an increased number of cells exiting the cell cycle that express the cyclin-dependent kinase inhibitor p27 Kip1 and lack cyclin D1, both of which control the postmitotic state of hair cells. Analysis of different molecular markers in N-myc mutant ears reveals the development of a rudimentary organ of Corti containing hair cells and the underlying supporting cells. Differentiated cells, however, fail to form the highly ordered structure characteristic for the organ of Corti but appear as rows or clusters with an excess number of hair cells. The Kölliker's organ, a transient structure neighboring the organ of Corti and a potential source of ectopic hair cells, is absent in the mutant ears. Collectively, our data suggest that N-myc regulates growth, morphogenesis, and pattern formation during the development of the inner ear.

10.1523/jneurosci.0785-11.2011

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Citations (47)