Search

Your search keyword '"Burns, Jessica"' showing total 248 results
Start Over Author "Burns, Jessica"
248 results on '"Burns, Jessica"'

1. Connecting Lyman-$\alpha$ and ionizing photon escape in the Sunburst Arc

Author

Owens, M. Riley, Kim, Keunho J., Bayliss, Matthew B., Rivera-Thorsen, T. Emil, Sharon, Keren, Rigby, Jane R., Navarre, Alexander, Florian, Michael, Gladders, Michael D., Burns, Jessica G., Khullar, Gourav, Chisholm, John, Mahler, Guillaume, Dahle, Hakon, Malhas, Christopher M., Welch, Brian, Hutchison, Taylor A., Gassis, Raven, Choe, Suhyeon, and Adhikari, Prasanna

Subjects
Astrophysics - Astrophysics of Galaxies
Abstract

We investigate the Lyman-$\alpha$ (Ly$\alpha$) and Lyman continuum (LyC) properties of the Sunburst Arc, a $z=2.37$ gravitationally lensed galaxy with a multiply-imaged, compact region leaking LyC and a triple-peaked Ly$\alpha$ profile indicating direct Ly$\alpha$ escape. Non-LyC-leaking regions show a redshifted Ly$\alpha$ peak, a redshifted and central Ly$\alpha$ peak, or a triple-peaked Ly$\alpha$ profile. We measure the properties of the Ly$\alpha$ profile from different regions of the galaxy using $R\sim5000$ Magellan/MagE spectra. We compare the Ly$\alpha$ spectral properties to LyC and narrowband Ly$\alpha$ maps from Hubble Space Telescope (HST) imaging to explore the subgalactic Ly$\alpha-$LyC connection. We find strong correlations (Pearson correlation coefficient $r>0.6$) between the LyC escape fraction ($f_{\rm esc}^{\rm LyC}$) and Ly$\alpha$ (1) peak separation $v_{\rm{sep}}$, (2) ratio of the minimum flux density between the redshifted and blueshifted Ly$\alpha$ peaks to continuum flux density $f_{\rm{min}}/f_{\rm{cont}}$, and (3) equivalent width. We favor a complex \ion{H}{1} geometry to explain the Ly$\alpha$ profiles from non-LyC-leaking regions and suggest two \ion{H}{1} geometries that could diffuse and/or rescatter the central Ly$\alpha$ peak from the LyC-leaking region into our sightline across transverse distances of several hundred parsecs. Our results emphasize the complexity of Ly$\alpha$ radiative transfer and its sensitivity to the anisotropies of \ion{H}{1} gas on subgalactic scales. Large differences in the physical scales on which we observe spatially variable direct escape Ly$\alpha$, blueshifted Ly$\alpha$, and escaping LyC photons in the Sunburst Arc underscore the importance of resolving the physical scales that govern Ly$\alpha$ and LyC escape., Comment: Submitted to The Astrophysical Journal with revisions from the first referee report. Comments welcome

Published
2024

3. Engineering Optomechanically Induced Transparency by coupling a qubit to a spinning resonator

Author

Burns, Jessica, Root, Owen, Jing, Hui, and Mirza, Imran M.

Subjects
Quantum Physics
Abstract

We theoretically study the spectral properties of a pump-probe driven hybrid spinning optomechanical ring resonator optically coupled with a two-level quantum emitter (QE or qubit). Recently we have shown [arXiv:1810.03709] that in the absence of the emitter the coupled cavity version of this setup is not only capable of nonreciprocal light propagation but can also exhibit slow & fast light propagation. In this work, we investigate in what ways the presence of a single QE coupled with the optical whispering gallery modes of the spinning optomechanical resonator can alter the probe light nonreciprocity. Under the weak-excitation assumption and mean-field approximation, we find that the interplay between the rotational/spinning Sagnac-effect and the qubit coupling can lead to the enhancement both in the optomechanically induced transparency (OMIT) peak value and in the width of the transparency window due to the opening of qubit-assisted back reflection channel. However, compared to the no-qubit case, we notice that such an enhancement comes at the cost of degrading the group delay in probe light transmission by a factor of 1/2 for clockwise rotary directions. The target applications of these results can be in the areas of quantum circuitry and in non-reciprocal quantum communication protocols where QEs are a key component., Comment: 9 pages, 6 figures

Published
2022
Full Text
View/download PDF

4. The comprehensive proteomic characterisation of soft tissue sarcoma

Author

Burns, Jessica and Huang, P.

Abstract

Soft tissue sarcomas (STS) are a group of rare and heterogeneous mesenchymal malignancies. The extensive clinical and biological heterogeneity of STS complicates clinical disease management, and in the advanced setting prognosis is poor. Incomplete biological understanding of STS has long hampered efforts to drive clinical improvements for patients. At present, there is a lack of methods to stratify patients based on risk or their likelihood of treatment response. Additionally, there are limited targeted therapies available for STS patients, and current standard of care is largely a 'one size fits all' approach. Whilst the genomic, epigenomic, and transcriptomic basis of STS has been previously assessed, there is no proteomic understanding of the disease. Herein, my project conducts comprehensive proteomic profiling, by mass spectrometry, of 321 formalin-fixed paraffin-embedded primary tumour specimens from STS patients. This is the largest proteomic characterisation of STS to date and provides an overview of the baseline STS proteome. Specifically, heterogeneity in leiosyosarcoma was investigated, and 3 robust proteomic subtypes were identified. These molecular subtypes showed different functional biology and were associated with different survival outcomes, highlighting potential for risk stratification. Analysis of the immune landscape of undifferentiated pleomorphic sarcoma and dedifferentiated liposarcoma, highlighted a subpopulation of tumours with low lymphocyte infiltration and high complement activity. This revealed this complement cascade as a candidate therapeutic target. Finally, this project defined a protein-centric view of the STS proteome comprised of 'sarcoma proteome modules'. These modules transcended histological subtypes and covered a range of biological activities. Furthermore, modules were found to be associated with clinical outcome, again highlighting the potential for molecular risk stratification in STS. Overall, this project demonstrates the utility of comprehensive proteomic profiling in improving disease understanding, facilitating risk stratification, and identifying candidate therapies. In doing so, it establishes a rich resource for the STS research community.

Published
2023

5. The proteomic landscape of soft tissue sarcomas

Author

Burns, Jessica, Wilding, Christopher P., Krasny, Lukas, Zhu, Xixuan, Chadha, Madhumeeta, Tam, Yuen Bun, PS, Hari, Mahalingam, Aswanth H., Lee, Alexander T. J., Arthur, Amani, Guljar, Nafia, Perkins, Emma, Pankova, Valeriya, Jenks, Andrew, Djabatey, Vanessa, Szecsei, Cornelia, McCarthy, Frank, Ragulan, Chanthirika, Milighetti, Martina, Roumeliotis, Theodoros I., Crosier, Stephen, Finetti, Martina, Choudhary, Jyoti S., Judson, Ian, Fisher, Cyril, Schuster, Eugene F., Sadanandam, Anguraj, Chen, Tom W., Williamson, Daniel, Thway, Khin, Jones, Robin L., Cheang, Maggie C. U., and Huang, Paul H.

Published
2023
Full Text
View/download PDF

6. Use of Metagenomic Next-Generation Sequencing to Identify Pathogens in Pediatric Osteoarticular Infections.

Author

Ramchandar, Nanda, Burns, Jessica, Coufal, Nicole G, Pennock, Andrew, Briggs, Benjamin, Stinnett, Rita, Bradley, John, Arnold, John, Liu, George Y, Pring, Maya, Upasani, Vidyadhar V, Rickert, Kathleen, Dimmock, David, Chiu, Charles, Farnaes, Lauge, and Cannavino, Christopher

Subjects
mNGS, metagenomics, next-generation sequencing, osteomyelitis, septic arthritis, Infectious Diseases, Clinical Research, Rare Diseases, Pediatric, Arthritis, Infection, Inflammatory and immune system
Abstract

BackgroundOsteoarticular infections (OAIs) are frequently encountered in children. Treatment may be guided by isolation of a pathogen; however, operative cultures are often negative. Metagenomic next-generation sequencing (mNGS) allows for broad and sensitive pathogen detection that is culture-independent. We sought to evaluate the diagnostic utility of mNGS in comparison to culture and usual care testing to detect pathogens in acute osteomyelitis and/or septic arthritis in children.MethodsThis was a single-site study to evaluate the use of mNGS in comparison to culture to detect pathogens in acute pediatric osteomyelitis and/or septic arthritis. Subjects admitted to a tertiary children's hospital with suspected OAI were eligible for enrollment. We excluded subjects with bone or joint surgery within 30 days of admission or with chronic osteomyelitis. Operative samples were obtained at the surgeon's discretion per standard care (fluid or tissue) and based on imaging and operative findings. We compared mNGS to culture and usual care testing (culture and polymerase chain reaction [PCR]) from the same site.ResultsWe recruited 42 subjects over the enrollment period. mNGS of the operative samples identified a pathogen in 26 subjects compared to 19 subjects in whom culture identified a pathogen. In 4 subjects, mNGS identified a pathogen where combined usual care testing (culture and PCR) was negative. Positive predictive agreement and negative predictive agreement both were 93.0% for mNGS.ConclusionsIn this single-site prospective study of pediatric OAI, we demonstrated the diagnostic utility of mNGS testing in comparison to culture and usual care (culture and PCR) from operative specimens.

Published
2021

10. A microenvironment-inspired synthetic three-dimensional model for pancreatic ductal adenocarcinoma organoids

Author

Below, Christopher R., Kelly, Joanna, Brown, Alexander, Humphries, Jonathan D., Hutton, Colin, Xu, Jingshu, Lee, Brian Y., Cintas, Celia, Zhang, Xiaohong, Hernandez-Gordillo, Victor, Stockdale, Linda, Goldsworthy, Matthew A., Geraghty, Joe, Foster, Lucy, O’Reilly, Derek A., Schedding, Barbara, Askari, Janet, Burns, Jessica, Hodson, Nigel, Smith, Duncan L., Lally, Catherine, Ashton, Garry, Knight, David, Mironov, Aleksandr, Banyard, Antonia, Eble, Johannes A., Morton, Jennifer P., Humphries, Martin J., Griffith, Linda G., and Jørgensen, Claus

Published
2022
Full Text
View/download PDF

11. Clinical implications and molecular features of extracellular matrix networks in soft tissue sarcomas

Author

Pankova, Valeriya, primary, Krasny, Lukas, additional, Kerrison, William, additional, Tam, Yuen Bun, additional, Chadha, Madhumeeta, additional, Burns, Jessica, additional, Wilding, Christopher P., additional, Chen, Liang, additional, Chowdhury, Avirup, additional, Perkins, Emma, additional, Lee, Alexander T.J., additional, Howell, Louise, additional, Guljar, Nafia, additional, Sisley, Karen, additional, Fisher, Cyril, additional, Chudasama, Priya, additional, Thway, Khin, additional, Jones, Robin L., additional, and Huang, Paul H., additional

Published
2024
Full Text
View/download PDF

12. Proteomic profiling improves prognostic risk stratification of the Sarculator nomogram in soft tissue sarcomas of the extremities and trunk wall.

Author

Chadha, Madhumeeta, Iadecola, Sara, Jenks, Andrew, Pankova, Valeriya, Tam, Yuen Bun, Burns, Jessica, Arthur, Amani, Wilding, Christopher P., Chen, Liang, Chudasama, Priya, Callegaro, Dario, Strauss, Dirk C., Thway, Khin, Gronchi, Alessandro, Jones, Robin L., Miceli, Rosalba, Pasquali, Sandro, and Huang, Paul H.

Subjects
CELL cycle proteins, SARCOMA, DNA replication, OVERALL survival, DRUG target
Abstract

Background: High‐risk soft tissue sarcomas of the extremities and trunk wall (eSTS), as defined by the Sarculator nomogram, are more likely to benefit from (neo)adjuvant anthracycline‐based therapy compared to low/intermediate‐risk patients. The biology underpinning these differential treatment outcomes remain unknown. Methods: We analysed proteomic profiles and clinical outcomes of 123 eSTS patients. A Cox model for overall survival including the Sarculator was fitted to individual data to define four risk groups. A DNA replication protein signature‐Sarcoma Proteomic Module 6 (SPM6) was evaluated for association with clinicopathological factors and risk groups. SPM6 was added as a covariate together with Sarculator in a multivariable Cox model to assess improvement in prognostic risk stratification. Results: DNA replication and cell cycle proteins were upregulated in high‐risk versus very low‐risk patients. Evaluation of the functional effects of CRISPR‐Cas9 gene knockdown of proteins enriched in high‐risk patients using the cancer cell line encyclopaedia database identified candidate drug targets. SPM6 was significantly associated with tumour malignancy grade (p = 1.6e‐06), histology (p = 1.4e‐05) and risk groups (p = 2.6e‐06). Cox model analysis showed that SPM6 substantially contributed to a better calibration of the Sarculator nomogram (Index of Prediction Accuracy = 0.109 for Sarculator alone versus 0.165 for Sarculator + SPM6). Conclusions: Risk stratification of patient with STS is defined by distinct biological pathways across a range of cancer hallmarks. Incorporation of SPM6 protein signature improves prognostic risk stratification of the Sarculator nomogram. This study highlights the utility of integrating protein signatures for the development of next‐generation nomograms. [ABSTRACT FROM AUTHOR]

Published
2024
Full Text
View/download PDF

14. Effects of Voice Pitch on Social Perceptions Vary With Relational Mobility and Homicide Rate

Author

Aung, Toe, primary, Hill, Alexander K., additional, Hlay, Jessica K., additional, Hess, Catherine, additional, Hess, Michael, additional, Johnson, Janie, additional, Doll, Leslie, additional, Carlson, Sara M., additional, Magdinec, Caroline, additional, G-Santoyo, Isaac, additional, Walker, Robert S., additional, Bailey, Drew, additional, Arnocky, Steven, additional, Kamble, Shanmukh, additional, Vardy, Tom, additional, Kyritsis, Thanos, additional, Atkinson, Quentin, additional, Jones, Benedict, additional, Burns, Jessica, additional, Koster, Jeremy, additional, Palomo-Vélez, Gonzalo, additional, Tybur, Joshua M., additional, Muñoz-Reyes, José, additional, Choy, Bryan K. C., additional, Li, Norman P., additional, Klar, Verena, additional, Batres, Carlota, additional, Bascheck, Patricia, additional, Schild, Christoph, additional, Penke, Lars, additional, Pazhoohi, Farid, additional, Kemirembe, Karen, additional, Valentova, Jaroslava Varella, additional, Varella, Marco Antonio Correa, additional, da Silva, Caio Santos Alves, additional, Borras-Guevara, Martha, additional, Hodges-Simeon, Carolyn, additional, Ernst, Moritz, additional, Garr, Collin, additional, Chen, Bin-Bin, additional, and Puts, David, additional

Published
2024
Full Text
View/download PDF

15. SARS-CoV-2 Viral Replication Persists in the Human Lung for Several Weeks after Symptom Onset

Author

Tomasicchio, Michele, primary, Jaumdally, Shameem, additional, Wilson, Lindsay, additional, Kotze, Andrea, additional, Semple, Lynn, additional, Meier, Stuart, additional, Pooran, Anil, additional, Esmail, Aliasgar, additional, Pillay, Komala, additional, Roberts, Riyaadh, additional, Kriel, Raymond, additional, Meldau, Richard, additional, Oelofse, Suzette, additional, Mandviwala, Carley, additional, Burns, Jessica, additional, Londt, Rolanda, additional, Davids, Malika, additional, van der Merwe, Charnay, additional, Roomaney, Aqeedah, additional, Kühn, Louié, additional, Perumal, Tahlia, additional, Scott, Alex J., additional, Hale, Martin J., additional, Baillie, Vicky, additional, Mahtab, Sana, additional, Williamson, Carolyn, additional, Joseph, Rageema, additional, Sigal, Alex, additional, Joubert, Ivan, additional, Piercy, Jenna, additional, Thomson, David, additional, Fredericks, David L., additional, Miller, Malcolm GA, additional, Nunes, Marta C., additional, Madhi, Shabir A., additional, and Dheda, Keertan, additional

Published
2024
Full Text
View/download PDF

23. Abstract 3055: Associations of the mucosal microbiome and circulating bile acids with colorectal adenoma among average-risk women

Author

Gomez, Maria F., primary, Byrd, Doratha A., additional, Hogue, Stephanie R., additional, Burns, Jessica R., additional, Smith, Nathan, additional, Sampson, Joshua, additional, Loftfield, Erikka, additional, Warner, Andrew, additional, Dagnall, Casey, additional, Jones, Kristine, additional, Hicks, Belynda, additional, Wan, Yunhu, additional, Kim, Youngchul, additional, Xu, Jin, additional, Sinha, Rashmi, additional, and Vogtmann, Emily, additional

Published
2023
Full Text
View/download PDF

25. Fetal Alcohol Spectrum Disorder in Northeastern Ontario: A Descriptive examination of Who is Assessed, Who Receives a Diagnosis and Who does Not

Author

Burns, Jessica I., Harding, Kelly D., Watson, Shelley L., Unsworth, Kathy, and Cook, Jocelynn L.

Subjects
Northeastern Ontario, diagnosis, assessment, Fetal Alcohol Spectrum Disorder, prenatal alcohol exposure, mental health
Abstract

As part of a larger project that provides unique insight into the profile of Canadians assessed for Fetal Alcohol Spectrum Disorder (FASD) across various diagnostic clinics, the purpose of the current study was to highlight who presents for FASD assessment in Northeastern Ontario, and the related diagnostic outcomes between those who are diagnosed and those who are not. A total of 326 children and youth were included in the overall sample of individuals assessed at the only diagnostic service in the Northeastern Ontario region in Sudbury, Ontario. Specific comparisons between those diagnosed with FASD and those not diagnosed were further explored. Results indicated that functional difficulties, including both neurodevelopmental and mental health impairments, were evident in all individuals, regardless of an FASD diagnosis. However, for individuals who received a diagnosis of FASD, greater mental health concerns and neurodevelopmental impairment beyond what is necessary to receive a diagnosis were noted. While impairment at the clinical level (i.e., 2 or more standard deviations below the mean, as per Canadian FASD Diagnostic Guideline) was lower in those who did not receive a diagnosis, difficulties pertaining to behaviour and mental health were identified. Overall, the results support a multiservice need among those prenatally exposed to alcohol in the region. The findings are discussed in relation to the existing literature on the common outcomes associated with prenatal alcohol exposure, and FASD more specifically. Limitations and implications are also discussed.

Published
2023
Full Text
View/download PDF

30. Survey of healthcare professionals’ knowledge, attitudes and practices regarding spontaneous intracranial hypotension

Author

Cheema, Sanjay, primary, Anderson, Jane, additional, Duncan, Callum, additional, Davagnanam, Indran, additional, Armstrong, Paul, additional, Redfern, Nancy, additional, Ordman, Anthony, additional, D’Antona, Linda, additional, Nissen, Justin, additional, Sayal, Parag, additional, Vaughan-Huxley, Eyston, additional, Lagrata, Susie, additional, Iodice, Valeria, additional, Snape-Burns, Jessica, additional, Joy, Clare, additional, and Matharu, Manjit, additional

Published
2022
Full Text
View/download PDF

34. Pancreatic ductal adenocarcinoma cells employ integrin α6β4 to form hemidesmosomes and regulate cell proliferation

Author

Humphries, Jonathan D., primary, Zha, Junzhe, additional, Burns, Jessica, additional, Askari, Janet A., additional, Below, Christopher R., additional, Chastney, Megan R., additional, Jones, Matthew C., additional, Mironov, Aleksandr, additional, Knight, David, additional, O'Reilly, Derek A., additional, Dunne, Mark J., additional, Garrod, David R., additional, Jorgensen, Claus, additional, and Humphries, Martin J., additional

Published
2022
Full Text
View/download PDF

40. Fixation using Alternative Implants for the Treatment of Hip Fractures (FAITH-2): The Exploratory Health-Related Quality of Life and Patient-Reported Functional Outcomes of a Multi-Centre 2 × 2 Factorial Randomized Controlled Pilot Trial in Young Femoral Neck Fracture Patients

Author

Slobogean, Gerard P., primary, Sprague, Sheila, additional, Bzovsky, Sofia, additional, Scott, Taryn, additional, Thabane, Lehana, additional, Heels-Ansdell, Diane, additional, O'Toole, Robert V., additional, Howe, Andrea, additional, Gaski, Greg E., additional, Hill, Lauren C., additional, Brown, Krista M., additional, Viskontas, Darius, additional, Zomar, Mauri, additional, Della Rocca, Gregory J., additional, O'Hara, Nathan N., additional, Bhandari, Mohit, additional, Malekzadeh, A. Stephen, additional, Nauth, Aaron, additional, Perdue, Aaron, additional, Mamun, Abdullah, additional, Wasim, Abeer, additional, Klein, Adam, additional, Brandon, Adrienne, additional, Theriault, Aimee, additional, Garibaldi, Alisha, additional, Liew, Allan, additional, Atrey, Amit, additional, Lialios-Ramfos, Anastasia, additional, Spiguel, André, additional, Howe, Andrea L., additional, Furey, Andrew, additional, Marcantonio, Andrew J., additional, Pollak, Andrew N., additional, Schmidt, Andrew, additional, Dowbenka, Ann, additional, Mak, Anne, additional, Sorkin, Anthony T., additional, Sivananthan, Araby, additional, Buck, Ashley, additional, Okocha, Benita, additional, Frye, Benjamin, additional, Perey, Bertrand, additional, Mohan, Bindu, additional, Eyberg, Blake, additional, Sumner, Bonnie, additional, Fan, Brenda Chen, additional, Lindsey, Brock, additional, Schoonover, Carrie, additional, Schwartzbach, Cary C., additional, Lieder, Charles, additional, Koenig, Chris, additional, Boulton, Christina, additional, LeBrun, Christopher, additional, Jones, Clifford B., additional, Barber, Collin, additional, Donahue, Craig, additional, Ventry, Cyndi, additional, Carter, Cynthia, additional, Williams, Dale, additional, Richardson, Damien, additional, Connelly, Daniel, additional, Mascarenhas, Daniel, additional, Squire, Daniel, additional, Whelan, Daniel, additional, Dias, Danyella, additional, Roffey, Darren M., additional, Hubbard, David, additional, Stephen, David J.G., additional, Shearer, David, additional, Teague, David, additional, Templeman, David, additional, Walmsley, David, additional, Malish, Dean, additional, Sietsema, Debra L., additional, Nam, Diane, additional, Marinos, Dimitrius, additional, Boyer, Dory, additional, McDonough, E. Barry, additional, Bogoch, Earl, additional, Westrick, Edward, additional, Pullenayegum, Eleanor M., additional, Berhaneselase, Eleni, additional, Agustin, Elizabeth, additional, Schemitsch, Emil H., additional, Meinberg, Eric, additional, Baker, Erin, additional, Moola, Farhad, additional, Adamsahib, Fathima, additional, Howells, Fiona, additional, Wells, Garrett, additional, Bal, George K., additional, Reahl, George, additional, Slobogean, Gerard P., additional, Ramonas, Gitana, additional, Guyatt, Gordon, additional, Rocca, Gregory J. Della, additional, Mueller, Gudrun Mirick, additional, Lemke, H. Michael, additional, Kreder, Hans J., additional, Grant, Heather, additional, Ahn, Henry, additional, Broekhuyse, Henry, additional, Leung, Irene, additional, Goulet, James, additional, Waddell, James, additional, Lowe, Jason, additional, Nascone, Jason W., additional, Schulman, Jeff E., additional, Potter, Jeffrey, additional, Hagen, Jennifer, additional, Hidy, Jennifer T., additional, Westberg, Jerald R., additional, Hall, Jeremy A., additional, Burns, Jessica, additional, Peattie, Jessica, additional, Goodwin, Jill, additional, Gagnier, Joel J., additional, France, John, additional, Iazzetta, John, additional, Lubicky, John P., additional, Garfi, John S., additional, Kwong, Johnathan, additional, Walker, Joseph, additional, Hustedt, Joshua, additional, Rudnicki, Joshua, additional, Foxall, Julia, additional, Robbins, Julie, additional, Sadasivan, Kalia, additional, Ryan, Karen, additional, Walsh, Karen, additional, Moon, Karyn, additional, Polihronidis, Katerina, additional, Ordonio, Katherine, additional, Hatzifilalithis, Katrina, additional, Milner, Katrine, additional, Au, Keegan, additional, Apostle, Kelly, additional, Lefaivre, Kelly, additional, Madden, Kim, additional, Swasey, Krystal, additional, Jeray, Kyle, additional, Deeter, Lakye, additional, Fine, Landon, additional, Parsons, Laura, additional, Kempton, Laurence B., additional, Buckingham, Lisa, additional, Sutton, Lisa Giblin, additional, Ramsey, Lolita, additional, Swiontkowski, Marc, additional, Sciadini, Marcus F., additional, Hake, Mark, additional, Richardson, Mark, additional, Nousiainen, Markku, additional, Bernaus, Martí, additional, Heetveld, Martin J., additional, Dietz, Matthew, additional, Menon, Matthew, additional, Patrick, Matthew, additional, MacNevin, Melanie, additional, Johnson, Melissa, additional, Fuerst, Merryjessica, additional, McKee, Michael D., additional, Duran, Michael, additional, Holzman, Michael, additional, Lucero, Michael, additional, Kain, Michael S.H., additional, Bramer, Michelle A., additional, Vogt, Michelle, additional, Vicente, Milena R., additional, Kunz, Monica, additional, Pekmezci, Murat, additional, Harris, Nicole, additional, Simunovic, Nicole, additional, Sultana, Nigar, additional, Dehghan, Niloofar, additional, Clovis, Nina, additional, Chutkan, Norman, additional, Suthar, Paril, additional, Henry, Patrick, additional, Knaus, Paul, additional, Muccino, Paul, additional, Toogood, Paul, additional, Berger, Peter, additional, O'Brien, Peter, additional, Rockwood, Peter, additional, Johnson, Pierce, additional, Guy, Pierre, additional, Blachut, Piotr, additional, Devereaux, PJ, additional, Pritchard (Moon), Raely, additional, Johal, Raman, additional, Tuazon, Ravianne, additional, Pensy, Raymond, additional, Zaidi, Raza, additional, Jenkinson, Richard J., additional, Hymes, Robert A., additional, McCormack, Robert, additional, O'Toole, RobertV., additional, Walker, Robert, additional, Natoli, Roman, additional, Meldrum, Russell, additional, Bicknell, Ryan, additional, DiGiovanni, Ryan, additional, Montalvo, Ryan, additional, Shelhamer, Ryan, additional, Morshed, Saam, additional, McFarland, Sara, additional, Anthony, Sarah, additional, Ward, Sarah, additional, Ahmed, Sarim, additional, Daffner, Scott, additional, Karr, Sean, additional, Mitchell, Sean, additional, Haaser, Sharon, additional, Rye, Sheila, additional, Davis, Sherri, additional, Weir, Sherry, additional, Brisbane, Sonya, additional, Papp, Steven, additional, Beltz, Susan, additional, Liew, Susan, additional, Mauro, Susan, additional, Murphy, T. Ryan, additional, Moore, Tara, additional, Dykes, Taylor, additional, Manson, Theodore, additional, DiPasquale, Thomas, additional, Belaye, Tigist, additional, Daniels, Timothy, additional, Carter, Tina, additional, Oliver, Todd M., additional, McKinley, Todd O., additional, Salopek, Traci, additional, Stone, Trevor, additional, Caron, Troy, additional, Tufescu, Tudor V., additional, Leviton, Tzivia, additional, Keough, Valisha, additional, Jones, Vicki, additional, Eglseder Jr., W. Andrew, additional, Gofton, Wade, additional, Virkus, Walter W., additional, Ghent, Wesley, additional, Degani, Yasmin, additional, Hannaford, Zeta, additional, and Murdoch, Zoe, additional

Published
2021
Full Text
View/download PDF

41. A microenvironment-inspired synthetic three-dimensional model for pancreatic ductal adenocarcinoma organoids

Author

Below, Christopher R., primary, Kelly, Joanna, additional, Brown, Alexander, additional, Humphries, Jonathan D., additional, Hutton, Colin, additional, Xu, Jingshu, additional, Lee, Brian Y., additional, Cintas, Celia, additional, Zhang, Xiaohong, additional, Hernandez-Gordillo, Victor, additional, Stockdale, Linda, additional, Goldsworthy, Matthew A., additional, Geraghty, Joe, additional, Foster, Lucy, additional, O’Reilly, Derek A., additional, Schedding, Barbara, additional, Askari, Janet, additional, Burns, Jessica, additional, Hodson, Nigel, additional, Smith, Duncan L., additional, Lally, Catherine, additional, Ashton, Garry, additional, Knight, David, additional, Mironov, Aleksandr, additional, Banyard, Antonia, additional, Eble, Johannes A., additional, Morton, Jennifer P., additional, Humphries, Martin J., additional, Griffith, Linda G., additional, and Jørgensen, Claus, additional

Published
2021
Full Text
View/download PDF

42. Pancreatic ductal adenocarcinoma cells employ integrin α6β4 to form hemidesmosomes and regulate cell proliferation

Author

Humphries, Jonathan D., primary, Zha, Junzhe, additional, Burns, Jessica, additional, Askari, Janet A., additional, Below, Christopher R., additional, Chastney, Megan R., additional, Jones, Matthew C., additional, Mironov, Aleksandr, additional, Knight, David, additional, O’Reilly, Derek A., additional, Dunne, Mark J., additional, Garrod, David R., additional, Jorgensen, Claus, additional, and Humphries, Martin J., additional

Published
2021
Full Text
View/download PDF

43. A mouse SWATH-mass spectrometry reference spectral library enables deconvolution of species-specific proteomic alterations in human tumour xenografts

Author

Krasny, Lukas, Bland, Philip, Burns, Jessica, Lima, Nadia Carvalho, Harrison, Peter T., Pacini, Laura, Elms, Mark L., Ning, Jian, Martinez, Victor Garcia, Yu, Yi-Ru, Acton, Sophie E., Ho, Ping-Chih, Calvo, Fernando, Swain, Amanda, Howard, Beatrice A., Natrajan, Rachael C., Huang, Paul H., The Institute of Cancer Research (UK), Breast Cancer Research Foundation, Medical Research Council (UK), Ministerio de Economía y Competitividad (España), Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), and European Research Council

Subjects
Male, Proteomics, Proteome, Mouse, DCIS, lcsh:Medicine, Mice, Nude, Mouse Models, Breast Neoplasms, Cell Communication, Mice, SCID, Mice, Breast cancer, Species Specificity, Tandem Mass Spectrometry, Cell Line, Tumor, lcsh:Pathology, Tumor Microenvironment, Animals, Humans, Resource Article, Databases, Protein, Xenografts, Breast Neoplasms/metabolism, Breast Neoplasms/pathology, Carcinoma, Intraductal, Noninfiltrating/metabolism, Carcinoma, Intraductal, Noninfiltrating/pathology, Chromatography, Liquid, Female, Heterografts, Mice, Inbred C57BL, NIH 3T3 Cells, Neoplasm Proteins/metabolism, Neoplasm Transplantation, Stromal Cells/metabolism, Stromal Cells/pathology, Mass spectrometry, SWATH-MS, lcsh:R, Neoplasm Proteins, Carcinoma, Intraductal, Noninfiltrating, Stromal Cells, lcsh:RB1-214
Abstract

© 2020. Published by The Company of Biologists Ltd., SWATH-mass spectrometry (MS) enables accurate and reproducible proteomic profiling in multiple model organisms including the mouse. Here, we present a comprehensive mouse reference spectral library (MouseRefSWATH) that permits quantification of up to 10,597 proteins (62.2% of the mouse proteome) by SWATH-MS. We exploit MouseRefSWATH to develop an analytical pipeline for species-specific deconvolution of proteomic alterations in human tumour xenografts (XenoSWATH). This method overcomes the challenge of high sequence similarity between mouse and human proteins, facilitating the study of host microenvironment-tumour interactions from ‘bulk tumour’ measurements. We apply the XenoSWATH pipeline to characterize an intraductal xenograft model of breast ductal carcinoma in situ and uncover complex regulation consistent with stromal reprogramming, where the modulation of cell migration pathways is not restricted to tumour cells but also operates in the mouse stroma upon progression to invasive disease. MouseRefSWATH and XenoSWATH open new opportunities for in-depth and reproducible proteomic assessment to address wide-ranging biological questions involving this important model organism., P.H.H. is supported by grants from the Institute of Cancer Research, Breast Cancer Now (2013NovPhD185 and 2014NovPR360) and Cancer Research UK (C36478/ A19281). B.A.H. and R.C.N. are supported by Breast Cancer Now programmatic funding. S.E.A. is supported by grants from Cancer Research UK (CRUK/A19763) and the Medical Research Council (MC_U12266B). F.C. is supported by grants from the Institute of Cancer Research, the Ramon y Cajal Research Programme (RYC2016-20352) and Ministerio de Ciencia, Innovación y Universidades/Agencia Estatal de Investigación/European Regional Development Fund (RTI2018-096778- A-I00). P.-C.H. is supported in part by a Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung project grant (31003A_182470) and a European Research Council Starting Grant (802773-MitoGuide).

Published
2020

44. A mouse SWATH-mass spectrometry reference spectral library enables deconvolution of species-specific proteomic alterations in human tumour xenografts

Author

The Institute of Cancer Research (UK), Breast Cancer Research Foundation, Medical Research Council (UK), Ministerio de Economía y Competitividad (España), Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), European Research Council, Krasny, Lukas, Bland, Philip, Burns, Jessica, Carvalho Lima, Nadia, Harrison, Peter T., Pacini, Laura, Elms, Mark L., Ning, Jian, Garcia Martinez, Victor, Yu, Yi-Ru, Acton, Sophie E., Ho, Ping-Chih, Calvo, Fernando, Swain, Amanda, Howard, Beatrice A., Natrajan, Rachael C., Huang, Paul H., The Institute of Cancer Research (UK), Breast Cancer Research Foundation, Medical Research Council (UK), Ministerio de Economía y Competitividad (España), Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), European Research Council, Krasny, Lukas, Bland, Philip, Burns, Jessica, Carvalho Lima, Nadia, Harrison, Peter T., Pacini, Laura, Elms, Mark L., Ning, Jian, Garcia Martinez, Victor, Yu, Yi-Ru, Acton, Sophie E., Ho, Ping-Chih, Calvo, Fernando, Swain, Amanda, Howard, Beatrice A., Natrajan, Rachael C., and Huang, Paul H.

Abstract

SWATH-mass spectrometry (MS) enables accurate and reproducible proteomic profiling in multiple model organisms including the mouse. Here, we present a comprehensive mouse reference spectral library (MouseRefSWATH) that permits quantification of up to 10,597 proteins (62.2% of the mouse proteome) by SWATH-MS. We exploit MouseRefSWATH to develop an analytical pipeline for species-specific deconvolution of proteomic alterations in human tumour xenografts (XenoSWATH). This method overcomes the challenge of high sequence similarity between mouse and human proteins, facilitating the study of host microenvironment-tumour interactions from ‘bulk tumour’ measurements. We apply the XenoSWATH pipeline to characterize an intraductal xenograft model of breast ductal carcinoma in situ and uncover complex regulation consistent with stromal reprogramming, where the modulation of cell migration pathways is not restricted to tumour cells but also operates in the mouse stroma upon progression to invasive disease. MouseRefSWATH and XenoSWATH open new opportunities for in-depth and reproducible proteomic assessment to address wide-ranging biological questions involving this important model organism.

Published
2020

Catalog

Books, media, physical & digital resources
See catalog results