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2. Multiscale topology classifies and quantifies cell types in subcellular spatial transcriptomics

Author

Benjamin, Katherine, Bhandari, Aneesha, Shang, Zhouchun, Xing, Yanan, An, Yanru, Zhang, Nannan, Hou, Yong, Tillmann, Ulrike, Bull, Katherine R., and Harrington, Heather A.

Subjects
Quantitative Biology - Quantitative Methods, Mathematics - Algebraic Topology, Quantitative Biology - Genomics, Statistics - Methodology, 92-08, 55N31, 62R40, 68T09
Abstract

Spatial transcriptomics has the potential to transform our understanding of RNA expression in tissues. Classical array-based technologies produce multiple-cell-scale measurements requiring deconvolution to recover single cell information. However, rapid advances in subcellular measurement of RNA expression at whole-transcriptome depth necessitate a fundamentally different approach. To integrate single-cell RNA-seq data with nanoscale spatial transcriptomics, we present a topological method for automatic cell type identification (TopACT). Unlike popular decomposition approaches to multicellular resolution data, TopACT is able to pinpoint the spatial locations of individual sparsely dispersed cells without prior knowledge of cell boundaries. Pairing TopACT with multiparameter persistent homology landscapes predicts immune cells forming a peripheral ring structure within kidney glomeruli in a murine model of lupus nephritis, which we experimentally validate with immunofluorescent imaging. The proposed topological data analysis unifies multiple biological scales, from subcellular gene expression to multicellular tissue organization., Comment: Main text: 8 pages, 4 figures. Supplement: 12 pages, 5 figures

Published
2022

3. In Their Own Words: Amplifying Critical Literacy and Social Justice Pedagogy through Spoken Word Poetry

Author

Curwood, Jen Scott and Bull, Katherine

Abstract

Drawn from an ethnographic study of spoken word poetry in Australia, this article offers case studies of two youth poets and follows their journeys with spoken word over three years as they performed in community-based slams, engaged with the New South Wales English Extension 2 curriculum, and served as mentor poets in culturally and linguistically diverse schools. Situated in western Sydney, this article considers how spoken word poetry can be integrated into the secondary English curriculum in order to enhance critical literacy and promote social justice pedagogy. As the first study that explores the intersection of spoken word poetry with high-stakes assessment, it offers insight into how social justice shapes young people's creative practices that interrogate and celebrate their intersectional identities.

Published
2023
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4. Structural and non-coding variants increase the diagnostic yield of clinical whole genome sequencing for rare diseases

Author

Pagnamenta, Alistair T., Camps, Carme, Giacopuzzi, Edoardo, Taylor, John M., Hashim, Mona, Calpena, Eduardo, Kaisaki, Pamela J., Hashimoto, Akiko, Yu, Jing, Sanders, Edward, Schwessinger, Ron, Hughes, Jim R., Lunter, Gerton, Dreau, Helene, Ferla, Matteo, Lange, Lukas, Kesim, Yesim, Ragoussis, Vassilis, Vavoulis, Dimitrios V., Allroggen, Holger, Ansorge, Olaf, Babbs, Christian, Banka, Siddharth, Baños-Piñero, Benito, Beeson, David, Ben-Ami, Tal, Bennett, David L., Bento, Celeste, Blair, Edward, Brasch-Andersen, Charlotte, Bull, Katherine R., Cario, Holger, Cilliers, Deirdre, Conti, Valerio, Davies, E. Graham, Dhalla, Fatima, Dacal, Beatriz Diez, Dong, Yin, Dunford, James E., Guerrini, Renzo, Harris, Adrian L., Hartley, Jane, Hollander, Georg, Javaid, Kassim, Kane, Maureen, Kelly, Deirdre, Kelly, Dominic, Knight, Samantha J. L., Kreins, Alexandra Y., Kvikstad, Erika M., Langman, Craig B., Lester, Tracy, Lines, Kate E., Lord, Simon R., Lu, Xin, Mansour, Sahar, Manzur, Adnan, Maroofian, Reza, Marsden, Brian, Mason, Joanne, McGowan, Simon J., Mei, Davide, Mlcochova, Hana, Murakami, Yoshiko, Németh, Andrea H., Okoli, Steven, Ormondroyd, Elizabeth, Ousager, Lilian Bomme, Palace, Jacqueline, Patel, Smita Y., Pentony, Melissa M., Pugh, Chris, Rad, Aboulfazl, Ramesh, Archana, Riva, Simone G., Roberts, Irene, Roy, Noémi, Salminen, Outi, Schilling, Kyleen D., Scott, Caroline, Sen, Arjune, Smith, Conrad, Stevenson, Mark, Thakker, Rajesh V., Twigg, Stephen R. F., Uhlig, Holm H., van Wijk, Richard, Vona, Barbara, Wall, Steven, Wang, Jing, Watkins, Hugh, Zak, Jaroslav, Schuh, Anna H., Kini, Usha, Wilkie, Andrew O. M., Popitsch, Niko, and Taylor, Jenny C.

Published
2023
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5. Exploring the relevance of NUP93 variants in steroid-resistant nephrotic syndrome using next generation sequencing and a fly kidney model

Author

Bierzynska, Agnieszka, Bull, Katherine, Miellet, Sara, Dean, Philip, Neal, Chris, Colby, Elizabeth, McCarthy, Hugh J., Hegde, Shivaram, Sinha, Manish D., Bugarin Diz, Carmen, Stirrups, Kathleen, Megy, Karyn, Mapeta, Rutendo, Penkett, Chris, Marsh, Sarah, Forrester, Natalie, Afzal, Maryam, Stark, Hannah, BioResource, NIHR, Williams, Maggie, Welsh, Gavin I., Koziell, Ania B., Hartley, Paul S., and Saleem, Moin A.

Published
2022
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6. Demultiplexing of Single-Cell RNA sequencing data using interindividual variation in gene expression

Author

Nassiri, Isar, primary, Kwok, Andrew J, additional, Bhandari, Aneesha, additional, Bull, Katherine R, additional, Garner, Lucy C, additional, Klenerman, Paul, additional, Webber, Caleb, additional, Parkkinen, Laura, additional, Lee, Angela W, additional, Wu, Yanxia, additional, Fairfax, Benjamin, additional, Knight, Julian C, additional, Buck, David, additional, and Piazza, Paolo, additional

Published
2024
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7. An essential role for the Zn2+ transporter ZIP7 in B cell development

Author

Anzilotti, Consuelo, Swan, David J, Boisson, Bertrand, Deobagkar-Lele, Mukta, Oliveira, Catarina, Chabosseau, Pauline, Engelhardt, Karin R, Xu, Xijin, Chen, Rui, Alvarez, Luis, Berlinguer-Palmini, Rolando, Bull, Katherine R, Cawthorne, Eleanor, Cribbs, Adam P, Crockford, Tanya L, Dang, Tarana Singh, Fearn, Amy, Fenech, Emma J, de Jong, Sarah J, Lagerholm, B Christoffer, Ma, Cindy S, Sims, David, van den Berg, Bert, Xu, Yaobo, Cant, Andrew J, Kleiner, Gary, Leahy, T Ronan, de la Morena, M Teresa, Puck, Jennifer M, Shapiro, Ralph S, van der Burg, Mirjam, Chapman, J Ross, Christianson, John C, Davies, Benjamin, McGrath, John A, Przyborski, Stefan, Santibanez Koref, Mauro, Tangye, Stuart G, Werner, Andreas, Rutter, Guy A, Padilla-Parra, Sergi, Casanova, Jean-Laurent, Cornall, Richard J, Conley, Mary Ellen, and Hambleton, Sophie

Subjects
Biochemistry and Cell Biology, Biomedical and Clinical Sciences, Biological Sciences, Prevention, Genetics, Brain Disorders, Underpinning research, Aetiology, 1.1 Normal biological development and functioning, 2.1 Biological and endogenous factors, Agammaglobulinemia, Animals, B-Lymphocytes, Cation Transport Proteins, Child, Preschool, Cytosol, Disease Models, Animal, Endoplasmic Reticulum, Female, Gene Expression Profiling, Humans, Infant, Male, Mice, Inbred C57BL, Mice, Transgenic, Mutation, Pedigree, Zinc, Immunology, Biochemistry and cell biology
Abstract

Despite the known importance of zinc for human immunity, molecular insights into its roles have remained limited. Here we report a novel autosomal recessive disease characterized by absent B cells, agammaglobulinemia and early onset infections in five unrelated families. The immunodeficiency results from hypomorphic mutations of SLC39A7, which encodes the endoplasmic reticulum-to-cytoplasm zinc transporter ZIP7. Using CRISPR-Cas9 mutagenesis we have precisely modeled ZIP7 deficiency in mice. Homozygosity for a null allele caused embryonic death, but hypomorphic alleles reproduced the block in B cell development seen in patients. B cells from mutant mice exhibited a diminished concentration of cytoplasmic free zinc, increased phosphatase activity and decreased phosphorylation of signaling molecules downstream of the pre-B cell and B cell receptors. Our findings highlight a specific role for cytosolic Zn2+ in modulating B cell receptor signal strength and positive selection.

Published
2019

10. B cells require DOCK8 to elicit and integrate T cell help when antigen is limiting.

Author

Deobagkar-Lele, Mukta, Crawford, Greg, Crockford, Tanya L., Back, Jennifer, Hodgson, Rose, Bhandari, Aneesha, Bull, Katherine R., and Cornall, Richard J.

Subjects
GUANINE nucleotide exchange factors, T helper cells, IMMUNOLOGIC memory, HUMORAL immunity, B cells, AGAMMAGLOBULINEMIA
Abstract

Dedicator of cytokinesis 8 (DOCK8) immunodeficiency syndrome is characterized by a failure of the germinal center response, a process involving the proliferation and positive selection of antigen-specific B cells. Here, we describe how DOCK8-deficient B cells are blocked at a light-zone checkpoint in the germinal centers of immunized mice, where they are unable to respond to T cell–dependent survival and selection signals and consequently differentiate into plasma cells or memory B cells. Although DOCK8-deficient B cells can acquire and present antigen to initiate activation of cognate T cells, integrin up-regulation, B cell–T cell conjugate formation, and costimulation are insufficient for sustained B cell and T cell activation when antigen availability is limited. Our findings provide an explanation for the failure of the humoral response in DOCK8 immunodeficiency syndrome and insight into how the level of available antigen modulates B cell–T cell cross-talk to fine-tune humoral immune responses and immunological memory. Editor's summary: In humans, loss-of-function mutations in dedicator of cytokinesis 8 (DOCK8) cause a rare, autosomal recessive primary immunodeficiency characterized, in part, by the failure of B cells to persist in germinal centers (GCs). Deobagkar-Lele et al. used Dock8-null mice to show that B cell–intrinsic DOCK8 bolsters the ability of antigen-specific B cells to receive and integrate survival signals from T follicular helper cells in the GC when the amount of antigen is limiting. This work provides insights into how the selection and affinity maturation of antigen-specific B cells can occur in the context of low antigen levels in the GC. —Seth Thomas Scanlon [ABSTRACT FROM AUTHOR]

Published
2024
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11. The genetics of autoimmune and proteinuric disease

Author

Bull, Katherine Rose and Cornall, Richard

Subjects
616.97
Abstract

The genetics of complex common diseases are not fully understood, but rare variants with large phenotypic effects contribute to heritability. The objective of this thesis is to identify rare variants of relevance to autoimmune and renal disease, by developing ways of analysing whole genome sequencing (WGS) data and exploring the variants identified. Forward genetic experimental approaches are used, both in mutagenised mice, and in humans with extreme trait forms of the steroid resistant nephrotic syndrome (SRNS) and systemic lupus erythematosus (SLE). This work demonstrates that N–ethyl–N–nitrosourea (ENU) mutations can be distinguished within WGS data, including a hypomorphic mutation in Lamb2 in a strain with the nephrotic syndrome, a murine model for the milder spectrum of human Pierson syndrome. In a B–cell deficient ENU strain the causative mutation in Lyn was isolated by sequencing multiple affected mice and applying an implementation of the Lander–Green algorithm to search for identity by descent. This method for the first time overcomes a rate-limiting step in ENU programmes and offers the potential to accelerate gene discovery, eliminating the need for out–crossing and conventional linkage analysis. Knowledge of the ENU genomic intervals allowed calculation of a mutation frequency, 1.5 mutations per mega base, and modelling of an efficient ENU strategy. Short–lists of candidate variants from 14 unrelated patients with steroid resistant nephrotic syndrome or systemic lupus erythematosus provide a substrate for future experiments, for example a candidate in the Wiskott–Aldrich syndrome gene was excluded using DNA from family members. In conclusion, WGS coupled with identity by descent analysis offers a powerful tool to improve the efficiency of ENU programmes. Rare variant discovery in humans without obvious Mendelian inheritance is more challenging and will require strategies to prioritise variants that combine bioinformatic filters and experimental verification in a high throughput way.

Published
2015

12. High-throughput phenotyping reveals expansive genetic and structural underpinnings of immune variation

Author

Abeler-Dörner, Lucie, Laing, Adam G., Lorenc, Anna, Ushakov, Dmitry S., Clare, Simon, Speak, Anneliese O., Duque-Correa, Maria A., White, Jacqueline K., Ramirez-Solis, Ramiro, Saran, Namita, Bull, Katherine R., Morón, Belén, Iwasaki, Jua, Barton, Philippa R., Caetano, Susana, Hng, Keng I., Cambridge, Emma, Forman, Simon, Crockford, Tanya L., Griffiths, Mark, Kane, Leanne, Harcourt, Katherine, Brandt, Cordelia, Notley, George, Babalola, Kolawole O., Warren, Jonathan, Mason, Jeremy C., Meeniga, Amrutha, Karp, Natasha A., Melvin, David, Cawthorne, Eleanor, Weinrick, Brian, Rahim, Albina, Drissler, Sibyl, Meskas, Justin, Yue, Alice, Lux, Markus, Song-Zhao, George X., Chan, Anna, Ballesteros Reviriego, Carmen, Abeler, Johannes, Wilson, Heather, Przemska-Kosicka, Agnieszka, Edmans, Matthew, Strevens, Natasha, Pasztorek, Markus, Meehan, Terrence F., Powrie, Fiona, Brinkman, Ryan, Dougan, Gordon, Jacobs, Jr, William, Lloyd, Clare M., Cornall, Richard J., Maloy, Kevin J., Grencis, Richard K., Griffiths, Gillian M., Adams, David J., and Hayday, Adrian C.

Published
2020
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13. Systemic silencing of Phd2 causes reversible immune regulatory dysfunction

Author

Yamamoto, Atsushi, Hester, Joanna, Macklin, Philip S., Kawai, Kento, Uchiyama, Masateru, Biggs, Daniel, Bishop, Tammie, Bull, Katherine, Cheng, Xiaotong, Cawthorne, Eleanor, Coleman, Mathew L., Crockford, Tanya L., Davies, Ben, Dow, Lukas E., Goldin, Rob, Kranc, Kamil, Kudo, Hiromi, Lawson, Hannah, McAuliffe, James, Milward, Kate, Scudamore, Cheryl L., Soilleux, Elizabeth, Issa, Fadi, Ratcliffe, Peter J., and Pugh, Chris W.

Subjects
Thermo Fisher Scientific Inc., Tetracyclines -- Physiological aspects, B cells -- Physiological aspects, Autoimmunity -- Physiological aspects, Enzymes -- Physiological aspects, RNA -- Physiological aspects, Scientific equipment industry -- Physiological aspects, T cells -- Physiological aspects, RNA interference, Alleles, Animal genetic engineering, Phenotypes, Health care industry, University of Oxford
Abstract

Physiological effects of cellular hypoxia are sensed by prolyl hydroxylase (PHD) enzymes, which regulate HIFs. Genetic interventions on HIF/PHD pathways have revealed multiple phenotypes that extend the known biology of hypoxia. Recent studies have unexpectedly implicated HIF in aspects of multiple immune and inflammatory pathways. However, such studies are often limited by systemic lethal effects and/or use tissue- specific recombination systems, which are inherently irreversible, unphysiologically restricted, and difficult to time. To study these processes better, we developed recombinant mice that expressed tetracycline-regulated shRNAs broadly targeting the main components of the HIF/ PHD pathway, permitting timed bidirectional intervention. We show that stabilization of HIF levels in adult mice through PHD2 enzyme silencing by RNA interference or inducible recombination of floxed alleles results in multilineage leukocytosis and features of autoimmunity. This phenotype was rapidly normalized on reestablishment of the hypoxia-sensing machinery when shRNA expression was discontinued. In both situations, these effects were mediated principally through the Hif2[alpha] isoform. Assessment of cells bearing Treg markers from these mice revealed defective function and proinflammatory effects in vivo. We believe our findings reveal a new role for the PHD2/Hif2[alpha] pathway in the reversible regulation of T cell and immune activity., Introduction HIFs are transcription factors composed of 1 of 3 a chains (HIF1[alpha], Hif2[alpha], and HIF3[alpha]) dimerized to a [beta] chain that mediates the transcriptional response to low oxygen tension [...]

Published
2019
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14. Mutation of Fnip1 is associated with B-cell deficiency, cardiomyopathy, and elevated AMPK activity

Author

Siggs, Owen M., Stockenhuber, Alexander, Deobagkar-Lele, Mukta, Bull, Katherine R., Crockford, Tanya L., Kingston, Bethany L., Crawford, Greg, Anzilotti, Consuelo, Steeples, Violetta, Ghaffari, Sahar, Czibik, Gabor, Bellahcene, Mohamed, Watkins, Hugh, Ashrafian, Houman, Davies, Benjamin, Woods, Angela, Carling, David, Yavari, Arash, Beutler, Bruce, and Cornall, Richard J.

Published
2016

15. Prolidase Deficiency Causes Spontaneous T Cell Activation and Lupus-like Autoimmunity

Author

Hodgson, Rose, primary, Crockford, Tanya L., additional, Bhandari, Aneesha, additional, Kepple, Jessica D., additional, Back, Jennifer, additional, Cawthorne, Eleanor, additional, Abeler-Dörner, Lucie, additional, Laing, Adam G., additional, Clare, Simon, additional, Speak, Anneliese, additional, Adams, David J., additional, Dougan, Gordon, additional, Hayday, Adrian C., additional, Deobagkar-Lele, Mukta, additional, Cornall, Richard J., additional, and Bull, Katherine R., additional

Published
2023
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16. Determining the Relationship Between Blood Pressure, Kidney Function, and Chronic Kidney Disease: Insights From Genetic Epidemiology

Author

Staplin, Natalie, primary, Herrington, William G., additional, Murgia, Federico, additional, Ibrahim, Maysson, additional, Bull, Katherine R., additional, Judge, Parminder K., additional, Ng, Sarah Y.A., additional, Turner, Michael, additional, Zhu, Doreen, additional, Emberson, Jonathan, additional, Landray, Martin J., additional, Baigent, Colin, additional, Haynes, Richard, additional, and Hopewell, Jemma C., additional

Published
2022
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17. VEGF regulates local inhibitory complement proteins in the eye and kidney

Author

Keir, Lindsay S., Firth, Rachel, Aponik, Lyndsey, Feitelberg, Daniel, Sakimoto, Susumu, Aguilar, Edith, Welsh, Gavin I., Richards, Anna, Usui, Yoshihiko, Satchell, Simon C., Kuzmuk, Valeryia, Coward, Richard J., Goult, Jonathan, Bull, Katherine R., Sharma, Ruchi, Bharti, Kapil, Westenskow, Peter D., Michael, Iacovos P., Saleem, Moin A., and Friedlander, Martin

Subjects
Neovascularization -- Analysis, Vascular endothelial growth factor -- Analysis, Macular degeneration -- Analysis, Health care industry
Abstract

Outer retinal and renal glomerular functions rely on specialized vasculature maintained by VEGF that is produced by neighboring epithelial cells, the retinal pigment epithelium (RPE) and podocytes, respectively. Dysregulation of RPE- and podocyte-derived VEGF is associated with neovascularization in wet age-related macular degeneration (ARMD), choriocapillaris degeneration, and glomerular thrombotic microangiopathy (TMA). Since complement activation and genetic variants in inhibitory complement factor H (CFH) are also features of both ARMD and TMA, we hypothesized that VEGF and CFH interact. Here, we demonstrated that VEGF inhibition decreases local CFH and other complement regulators in the eye and kidney through reduced VEGFR2/PKC-α/CREB signaling. Patient podocytes and RPE cells carrying disease-associated CFH genetic variants had more alternative complement pathway deposits than controls. These deposits were increased by VEGF antagonism, a common wet ARMD treatment, suggesting that VEGF inhibition could reduce cellular complement regulatory capacity. VEGF antagonism also increased markers of endothelial cell activation, which was partially reduced by genetic complement inhibition. Together, these results suggest that VEGF protects the retinal and glomerular microvasculature, not only through VEGFR2-mediated vasculotrophism, but also through modulation of local complement proteins that could protect against complement-mediated damage. Though further study is warranted, these findings could be relevant for patients receiving VEGF antagonists., Introduction Age-related macular degeneration (ARMD), the leading cause of vision loss in industrialized nations (1), affects 30 to 50 million people worldwide, but this is predicted to rise to 288 [...]

Published
2017
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19. SARS-CoV-2-Specific T Cell Responses Are Not Associated with Protection against Reinfection in Hemodialysis Patients

Author

Shankar, Sushma, primary, Beckett, Joseph, additional, Tipton, Tom, additional, Ogbe, Ane, additional, Kasanyinga, Mwila, additional, Dold, Christina, additional, Lumley, Sheila, additional, Dengu, Fungai, additional, Rompianesi, Gianluca, additional, Elgilani, Faysal, additional, Longet, Stephanie, additional, Deeks, Alexandra, additional, Payne, Rebecca P., additional, Duncan, Christopher J.A., additional, Richter, Alex, additional, de Silva, Thushan I., additional, Turtle, Lance, additional, Bull, Katherine, additional, Barnardo, Martin, additional, Friend, Peter J., additional, Dunachie, Susanna J., additional, Hester, Joanna, additional, Issa, Fadi, additional, Barnes, Eleanor, additional, Carroll, Miles W., additional, and Klenerman, Paul, additional

Published
2022
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21. Neutralising antibodies after COVID-19 vaccination in UK haemodialysis patients

Author

Adenwalla, Sherna F, Bird, Paul, Holmes, Christopher, Hull, Katherine L, March, Daniel S, Selvaskandan, Haresh, Silva, Jorge J, Tang, Julian W, Hester, Joanna, Issa, Fadi, Barnardo, Martin, Friend, Peter J, Davenport, Andrew, Goodlad, Catriona, Gopalan, Vignesh, Tangwonglert, Theerasak, Stauss, Hans J, Richter, Alex G, Cunningham, Adam F, Perez-Toledo, Marisol, Banham, Gemma D, Wall, Nadya, Clarke, Candice L, Prendecki, Maria, Clayton, Bobbi, Namjou, Sina, Silva, Vanessa, Poulten, Meghan, Bawumia, Philip, Miah, Murad, Sade, Samuel, Miranda, Mauro, Taylor, Tom, D'Angelo, Ilenia, Cabrera Jarana, Mercedes, Rahman, Mahbubur, Abreu, Janet, Sandhar, Sandeep, Bailey, Neil, Caidan, Simon, Caulfield, Marie, Wu, Mary, Harvey, Ruth, Adams, Lorin, Kavanagh, Caitlin, Warchal, Scott, Sawyer, Chelsea, Gavrielides, Mike, Kandasamy, Jag, Ambrose, Karen, Strange, Amy, Abiola, Titilayo, O'Reilly, Nicola, Hobson, Philip, Agau-Doce, Ana, Russell, Emma, Riddell, Andrew, Kjaer, Svend, Borg, Annabel, Roustan, Chloë, Carr, Edward J, Wall, Emma C, Kelly, Gavin, Hussain, Saira, Howell, Michael, Kassiotis, George, Swanton, Charles, Gandhi, Sonia, Bauer, David LV, Billany, Roseanne E, Graham-Brown, Matthew PM, Beckett, Joseph, Bull, Katherine, Shankar, Sushma, Henderson, Scott, Motallebzadeh, Reza, Salama, Alan D, Harper, Lorraine, Mark, Patrick B, McAdoo, Stephen, Willicombe, Michelle, and Beale, Rupert

Published
2021
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22. Neutralising antibodies after COVID-19 vaccination in UK haemodialysis patients

Author

Carr, Edward J, primary, Wu, Mary, additional, Harvey, Ruth, additional, Wall, Emma C, additional, Kelly, Gavin, additional, Hussain, Saira, additional, Howell, Michael, additional, Kassiotis, George, additional, Swanton, Charles, additional, Gandhi, Sonia, additional, Bauer, David LV, additional, Billany, Roseanne E, additional, Graham-Brown, Matthew PM, additional, Beckett, Joseph, additional, Bull, Katherine, additional, Shankar, Sushma, additional, Henderson, Scott, additional, Motallebzadeh, Reza, additional, Salama, Alan D, additional, Harper, Lorraine, additional, Mark, Patrick B, additional, McAdoo, Stephen, additional, Willicombe, Michelle, additional, Beale, Rupert, additional, Adenwalla, Sherna F, additional, Bird, Paul, additional, Holmes, Christopher, additional, Hull, Katherine L, additional, March, Daniel S, additional, Selvaskandan, Haresh, additional, Silva, Jorge J, additional, Tang, Julian W, additional, Hester, Joanna, additional, Issa, Fadi, additional, Barnardo, Martin, additional, Friend, Peter J, additional, Davenport, Andrew, additional, Goodlad, Catriona, additional, Gopalan, Vignesh, additional, Tangwonglert, Theerasak, additional, Stauss, Hans J, additional, Richter, Alex G, additional, Cunningham, Adam F, additional, Perez-Toledo, Marisol, additional, Banham, Gemma D, additional, Wall, Nadya, additional, Clarke, Candice L, additional, Prendecki, Maria, additional, Clayton, Bobbi, additional, Namjou, Sina, additional, Silva, Vanessa, additional, Poulten, Meghan, additional, Bawumia, Philip, additional, Miah, Murad, additional, Sade, Samuel, additional, Miranda, Mauro, additional, Taylor, Tom, additional, D'Angelo, Ilenia, additional, Cabrera Jarana, Mercedes, additional, Rahman, Mahbubur, additional, Abreu, Janet, additional, Sandhar, Sandeep, additional, Bailey, Neil, additional, Caidan, Simon, additional, Caulfield, Marie, additional, Adams, Lorin, additional, Kavanagh, Caitlin, additional, Warchal, Scott, additional, Sawyer, Chelsea, additional, Gavrielides, Mike, additional, Kandasamy, Jag, additional, Ambrose, Karen, additional, Strange, Amy, additional, Abiola, Titilayo, additional, O'Reilly, Nicola, additional, Hobson, Philip, additional, Agau-Doce, Ana, additional, Russell, Emma, additional, Riddell, Andrew, additional, Kjaer, Svend, additional, Borg, Annabel, additional, and Roustan, Chloë, additional

Published
2021
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25. Poor Antibody Responses to SARS-CoV-2 Infection or Vaccination Are Associated With High Re-Infection Rates in Haemodialysis and Renal Transplant Patients

Author

Beckett, Joseph, primary, Tipton, Tom, additional, Ogbe, Ane, additional, Kasanyinga, Mwila, additional, Dold, Christina, additional, Lumley, Sheila, additional, Dengu, Fungai, additional, Rompianesi, Gianluca, additional, Elgilani, Faysal, additional, Longet, Stephanie, additional, Deeks, Alexandra, additional, Payne, Rebecca P., additional, Duncan, Christopher JA, additional, Richter, Alex G., additional, de Silva, Thushan I., additional, Turtle, Lance, additional, Bull, Katherine, additional, Barnardo, Martin, additional, Friend, Peter, additional, Dunachie, Susanna, additional, Hester, Joanna, additional, Issa, Fadi, additional, Barnes, Eleanor, additional, Carroll, Miles W., additional, and Klenerman, Paul, additional

Published
2021
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26. High-throughput phenotyping reveals expansive genetic and structural underpinnings of immune variation

Author

Abeler-Dörner, Lucie, primary, Laing, Adam G., additional, Lorenc, Anna, additional, Ushakov, Dmitry S., additional, Clare, Simon, additional, Speak, Anneliese O., additional, Duque-Correa, Maria A., additional, White, Jacqueline K., additional, Ramirez-Solis, Ramiro, additional, Saran, Namita, additional, Bull, Katherine R., additional, Morón, Belén, additional, Iwasaki, Jua, additional, Barton, Philippa R., additional, Caetano, Susana, additional, Hng, Keng I., additional, Cambridge, Emma, additional, Forman, Simon, additional, Crockford, Tanya L., additional, Griffiths, Mark, additional, Kane, Leanne, additional, Harcourt, Katherine, additional, Brandt, Cordelia, additional, Notley, George, additional, Babalola, Kolawole O., additional, Warren, Jonathan, additional, Mason, Jeremy C., additional, Meeniga, Amrutha, additional, Karp, Natasha A., additional, Melvin, David, additional, Cawthorne, Eleanor, additional, Weinrick, Brian, additional, Rahim, Albina, additional, Drissler, Sibyl, additional, Meskas, Justin, additional, Yue, Alice, additional, Lux, Markus, additional, Song-Zhao, George X., additional, Chan, Anna, additional, Ballesteros Reviriego, Carmen, additional, Abeler, Johannes, additional, Wilson, Heather, additional, Przemska-Kosicka, Agnieszka, additional, Edmans, Matthew, additional, Strevens, Natasha, additional, Pasztorek, Markus, additional, Meehan, Terrence F., additional, Powrie, Fiona, additional, Brinkman, Ryan, additional, Dougan, Gordon, additional, Jacobs, William, additional, Lloyd, Clare M., additional, Cornall, Richard J., additional, Maloy, Kevin J., additional, Grencis, Richard K., additional, Griffiths, Gillian M., additional, Adams, David J., additional, and Hayday, Adrian C., additional

Published
2019
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27. Slice, dice and analyze

Author

Bull, Katherine

Subjects
Technology overview, Data Warehousing Data Mining, Databases -- Design and construction, Computer software industry -- Product information
Abstract

Does it seem as if you've received a few too many calls from database vendors lately? If so, you're not alone. The phenomenal growth of the data warehousing market has […]

Published
1995

28. Informix: nothing but databases

Author

Bull, Katherine

Subjects
Company business planning, Company analysis, DBMS, Informix Corp. -- Management -- 00321753, Computer software industry -- Management
Abstract

The company's still No. 3, but it's sticking to the basics-and continues to grow by 30% a year If there's one thing Phil White doesn't want, it's for Informix Software […]

Published
1995

29. Where are they now?

Author

Wilder, Clinton, Henry, Amanda Mitchell, Panettieri, Joseph C., Caldwell, Bruce, Bartholomew, Doug, DePompa, Barbara, and Bull, Katherine

Subjects
Achievements and Awards, Chief information officers, United States. Department of Defense, Asia Pacific Consumer Bank -- Officials and employees, Business Technology Consulting Inc. -- Officials and employees, Brady Corp. -- Officials and employees, Electronic Payment Services Inc. -- Officials and employees, Xerox Corp. -- Officials and employees, J.C. Penney Corporation Inc. -- Officials and employees, United States. Department of Defense -- Officials and employees, Chief information officers -- Achievements and awards
Published
1995

30. The ideal file cabinet

Author

Bull, Katherine

Subjects
Industry trend, Relational Database Management System, Information accessibility, DBMS, Database management systems -- Usage
Published
1995

31. Database/system software; Microsoft and Progress finish tied at the top

Author

Bull, Katherine

Subjects
Database industry, DBMS, VAR, Vendor Relations, Microsoft Corp. -- Public relations, Progress Software Corp. -- Public relations, Santa Cruz Operation Inc. -- Public relations, Sybase Inc. -- Public relations, Database industry -- Public relations
Published
1994

32. Top 50 integrators take a vertical market turn

Author

Bull, Katherine

Subjects
Computer Systems Integrator, Marketing Strategy, Vertical Market Software, Business Planning, Strategic Planning, Computer systems integrators -- Marketing
Published
1994

33. Developing with objects

Author

Bull, Katherine

Subjects
Market Entry, Outlook, Object-oriented programming, VAR, Standard, Object Management Group, Object Management Group -- Standards, Value-added resellers -- Marketing, Object-oriented programming -- Standards
Published
1994

34. An ontogenetic switch drives the positive and negative selection of B cells.

Author

Xijin Xu, Deobagkar-Lele, Mukta, Bull, Katherine R., Crockford, Tanya L., Mead, Adam J., Cribbs, Adam P., Sims, David, Anzilotti, Consuelo, and Cornall, Richard J.

Subjects
B cells, BONE marrow, TRANSGENE expression, GENE expression, ONTOGENY
Abstract

Developing B cells can be positively or negatively selected by self-antigens, but the mechanisms that determine these outcomes are incompletely understood. Here, we show that a B cell intrinsic switch between positive and negative selection during ontogeny is determined by a change from Lin28b to let-7 gene expression. Ectopic expression of a Lin28b transgene in murine B cells restored the positive selection of autoreactive B-1 B cells by self-antigen in adult bone marrow. Analysis of antigen-specific immature B cells in early and late ontogeny identified Lin28b-dependent genes associated with B-1 B cell development, including Arid3a and Bhleh41, and Lin28b-independent effects are associated with the presence or absence of self-antigen. These findings identify cell intrinsic and extrinsic determinants of B cell fate during ontogeny and reconcile lineage and selection theories of B cell development. They explain how changes in the balance of positive and negative selection may be able to adapt to meet the immunological needs of an individual during its lifetime. [ABSTRACT FROM AUTHOR]

Published
2020
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35. Common Elements in Rare Kidney Diseases: Conclusions from a Kidney Disease: Improving Global Outcomes (KDIGO) Controversies Conference

Author

UCL - SSS/IREC/NEFR - Pôle de Néphrologie, UCL - (SLuc) Service de néphrologie, Aymé, Ségolène, Bockenhauer, Detlef, Day, Simon, Devuyst, Olivier, Guay-Woodford, Lisa M., Ingelfinger, Julie R., Klein, Jon B., Knoers, Nine V.A.M., Perrone, Ronald D., Roberts, Julia, Schaefer, Franz, Torres, Vicente E., Cheung, Michael, Wheeler, David C., Winkelmayer, Wolfgang C., Angelis, Aris, Antignac, Corinne, Bae, Kyongtae, Bergmann, Carsten, Bleyer, Anthony J., Bos, Marjolein, Budde, Klemens, Bull, Katherine, Chauveau, Dominique, Cnaan, Avital, Cornel, Martina, Cosyns, Etienne, de la Fosse, Jane, Ding, Jie, Gear, Susie, Goodship, Timothy H.J., Goodyer, Paul, Gross, Oliver, Harr, Nicole, Harris, Peter C., Harris, Tess, Höfele, Julia, Hogan, Marie C., Hoorn, Ewout, Horie, Shigeo, Kashtan, Clifford E., Kerecuk, Larissa, Kleta, Robert, Konrad, Martin, Langman, Craig B., Mariz, Segundo, McKerracher, Gayle, Nieuwenhoven, Annet, Odland, Dwight, Olinger, Eric, Ortiz, Alberto, Pei, York, Pirson, Yves, Rayner, Brian L., Remuzzi, Giuseppe, Renault, Daniel, Salomon, Rémi, Servais, Aude, Smith, Richard J., Soliman, Neveen A., Stengel, Bénédicte, Storm, Marjolein, Torra, Roser, van't Hoff, William, Vargas-Poussou, Rosa, Vroom, Elizabeth, Wanner, Christoph, Yap, Hui-Kim, UCL - SSS/IREC/NEFR - Pôle de Néphrologie, UCL - (SLuc) Service de néphrologie, Aymé, Ségolène, Bockenhauer, Detlef, Day, Simon, Devuyst, Olivier, Guay-Woodford, Lisa M., Ingelfinger, Julie R., Klein, Jon B., Knoers, Nine V.A.M., Perrone, Ronald D., Roberts, Julia, Schaefer, Franz, Torres, Vicente E., Cheung, Michael, Wheeler, David C., Winkelmayer, Wolfgang C., Angelis, Aris, Antignac, Corinne, Bae, Kyongtae, Bergmann, Carsten, Bleyer, Anthony J., Bos, Marjolein, Budde, Klemens, Bull, Katherine, Chauveau, Dominique, Cnaan, Avital, Cornel, Martina, Cosyns, Etienne, de la Fosse, Jane, Ding, Jie, Gear, Susie, Goodship, Timothy H.J., Goodyer, Paul, Gross, Oliver, Harr, Nicole, Harris, Peter C., Harris, Tess, Höfele, Julia, Hogan, Marie C., Hoorn, Ewout, Horie, Shigeo, Kashtan, Clifford E., Kerecuk, Larissa, Kleta, Robert, Konrad, Martin, Langman, Craig B., Mariz, Segundo, McKerracher, Gayle, Nieuwenhoven, Annet, Odland, Dwight, Olinger, Eric, Ortiz, Alberto, Pei, York, Pirson, Yves, Rayner, Brian L., Remuzzi, Giuseppe, Renault, Daniel, Salomon, Rémi, Servais, Aude, Smith, Richard J., Soliman, Neveen A., Stengel, Bénédicte, Storm, Marjolein, Torra, Roser, van't Hoff, William, Vargas-Poussou, Rosa, Vroom, Elizabeth, Wanner, Christoph, and Yap, Hui-Kim

Published
2017

37. Common Elements in Rare Kidney Diseases: Conclusions from a Kidney Disease: Improving Global Outcomes (KDIGO) Controversies Conference

Author

Aymé, Ségolène, primary, Bockenhauer, Detlef, additional, Day, Simon, additional, Devuyst, Olivier, additional, Guay-Woodford, Lisa M., additional, Ingelfinger, Julie R., additional, Klein, Jon B., additional, Knoers, Nine V.A.M., additional, Perrone, Ronald D., additional, Roberts, Julia, additional, Schaefer, Franz, additional, Torres, Vicente E., additional, Cheung, Michael, additional, Wheeler, David C., additional, Winkelmayer, Wolfgang C., additional, Angelis, Aris, additional, Antignac, Corinne, additional, Bae, Kyongtae, additional, Bergmann, Carsten, additional, Bleyer, Anthony J., additional, Bos, Marjolein, additional, Budde, Klemens, additional, Bull, Katherine, additional, Chauveau, Dominique, additional, Cnaan, Avital, additional, Cornel, Martina, additional, Cosyns, Etienne, additional, de la Fosse, Jane, additional, Ding, Jie, additional, Gear, Susie, additional, Goodship, Timothy H.J., additional, Goodyer, Paul, additional, Gross, Oliver, additional, Harr, Nicole, additional, Harris, Peter C., additional, Harris, Tess, additional, Höfele, Julia, additional, Hogan, Marie C., additional, Hoorn, Ewout, additional, Horie, Shigeo, additional, Kashtan, Clifford E., additional, Kerecuk, Larissa, additional, Kleta, Robert, additional, Konrad, Martin, additional, Langman, Craig B., additional, Mariz, Segundo, additional, McKerracher, Gayle, additional, Nieuwenhoven, Annet, additional, Odland, Dwight, additional, Olinger, Eric, additional, Ortiz, Alberto, additional, Pei, York, additional, Pirson, Yves, additional, Rayner, Brian L., additional, Remuzzi, Giuseppe, additional, Renault, Daniel, additional, Salomon, Rémi, additional, Servais, Aude, additional, Smith, Richard J., additional, Soliman, Neveen A., additional, Stengel, Bénédicte, additional, Storm, Marjolein, additional, Torra, Roser, additional, van't Hoff, William, additional, Vargas-Poussou, Rosa, additional, Vroom, Elizabeth, additional, Wanner, Christoph, additional, and Yap, Hui-Kim, additional

Published
2017
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39. Themis2 lowers the threshold for B cell activation during positive selection

Author

Cheng, Daian, primary, Deobagkar-Lele, Mukta, additional, Zvezdova, Ekaterina, additional, Choi, Seeyoung, additional, Uehara, Shoji, additional, Baup, Delphine, additional, Bennett, Sophia C, additional, Bull, Katherine R, additional, Crockford, Tanya L, additional, Ferry, Helen, additional, Warzecha, Claude, additional, Marcellin, Marlène, additional, de Peredo, Anne Gonzalez, additional, Lesourne, Renaud, additional, Anzilotti, Consuelo, additional, Love, Paul E, additional, and Cornall, Richard J, additional

Published
2016
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40. VEGF regulates local inhibitory complement proteins in the eye and kidney

Author

Keir, Lindsay S., primary, Firth, Rachel, additional, Aponik, Lyndsey, additional, Feitelberg, Daniel, additional, Sakimoto, Susumu, additional, Aguilar, Edith, additional, Welsh, Gavin I., additional, Richards, Anna, additional, Usui, Yoshihiko, additional, Satchell, Simon C., additional, Kuzmuk, Valeryia, additional, Coward, Richard J., additional, Goult, Jonathan, additional, Bull, Katherine R., additional, Sharma, Ruchi, additional, Bharti, Kapil, additional, Westenskow, Peter D., additional, Michael, Iacovos P., additional, Saleem, Moin A., additional, and Friedlander, Martin, additional

Published
2016
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41. Sell smart, sell more

Author

Bull, Katherine

Subjects
Industry trend, Industry Trend Or Event, MIS, Sears, Roebuck and Co. -- Management -- 00307730, Retail industry -- Surveys, Information technology -- Surveys
Abstract

Old-line merchandisers change IT strategies to not only survive, but to prosper Over the last few years, large U.S. retailers have had to shift the course of their information technology […]

Published
1995

42. TCI goes for gold

Author

Thyfault, Mary E. and Bull, Katherine

Subjects
Telecommunications Industry, Company Operations, Company systems management, AT&T Broadband and Internet Services Inc. -- Product development, Cable television -- Case studies
Abstract

Its reengineering project could result in one of the world's largest customer-service databases For the past several weeks, John Malone, CEO of Tele-Communications Inc., has been in the middle of […]

Published
1995

47. Building a CASE for client/server: CASE tools help developers do more efficient application planning

Author

Bull, Katherine

Subjects
Application Development Software, Program Development Techniques, Programming Management, Strategic Planning, Client/server architecture, Applications programming, Computer-aided software engineering, Program development software -- Usage, Programming management (Computers) -- Planning, Client/server architecture, Applications programming, Computer-aided software engineering -- Usage
Published
1994

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