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1,167 results on '"Lo, B."'

5. A real-space Green's function method for the numerical solution of Maxwell's equations

Author

Lo, B, Minden, V, and Colella, P

Subjects
Maxwell's equations, Green's function, high order, Applied Mathematics
Abstract

A new method for solving the transverse part of the free-space Maxwell equations in three dimensions is presented. By taking the Helmholtz decomposition of the electric field and current sources and considering only the divergence-free parts, we obtain an explicit real-space representation for the transverse propagator that explicitly respects finite speed of propagation. Because the propagator involves convolution against a singular distribution, we regularize via convolution with smoothing kernels (B-splines) prior to sampling based on a method due to Beyer and LeVeque (1992). We show that the ultimate discrete convolutional propagator can be constructed to attain an arbitrarily high order of accuracy by using higher-order regularizing kernels and finite difference stencils and that it satisfies von Neumann's stability condition. Furthermore, the propagator is compactly supported and can be applied using Hockney's method (1970) and parallelized using the same observation as made by Vay, Haber, and Godfrey (2013), leading to a method that is computationally efficient.

Published
2016

6. Measurements of Fission Products from the Fukushima Daiichi Incident in San Francisco Bay Area Air Filters, Automobile Filters, Rainwater, and Food

Author

Smith, A. R., Thomas, K. J., Norman, E. B., Hurley, D. L., Lo, B. T., Chan, Y. D., Guillaumon, P. V., and Harvey, B. G.

Subjects
Nuclear Experiment
Abstract

A variety of environmental media were analyzed for fallout radionuclides resulting from the Fukushima nuclear accident by the Low Background Facility (LBF) at the Lawrence Berkeley National Laboratory (LBNL) in Berkeley, CA. Monitoring activities in air and rainwater began soon after the onset of the March 11, 2011 tsunami and are reported here through the end of 2012. Observed fallout isotopes include $^{131}$I, $^{132}$I,$^{132}$Te,$^{134}$Cs, $^{136}$Cs, and $^{137}$Cs. Isotopes were measured on environmental air filters, automobile filters, and in rainwater. An additional analysis of rainwater in search of $^{90}$Sr is also presented. Last, a series of food measurements conducted in September of 2013 are included due to extended media concerns of $^{134, 137}$Cs in fish. Similar measurements of fallout from the Chernobyl disaster at LBNL, previously unpublished publicly, are also presented here as a comparison with the Fukushima incident. All measurements presented also include natural radionuclides found in the environment to provide a basis for comparison., Comment: 11 pages

Published
2013

8. MARCH1-mediated MHCII ubiquitination promotes dendritic cell selection of natural regulatory T cells

Author

Shin, Jeoung-Sook, Oh, J, Wu, N, Baravalle, G, Cohn, B, Ma, J, Lo, B, Mellman, I, Ishido, S, Anderson, M, and Shin, JS

Abstract

Membrane-associated RING-CH1 (MARCH1) is an E3 ubiquitin ligase that mediates ubiquitination of MHCII in dendritic cells (DCs). MARCH1-mediated MHCII ubiquitination in DCs is known to regulate MHCII surface expression, thereby controlling DC-mediated T cel

Published
2013

11. Disease course and treatment outcomes of Crohn's disease patients with early or late surgery:A Danish nationwide cohort study from 1997 to 2015

Author

Sarikaya, M. Z., Zhao, M., Lo, B., Bendtsen, F., Burisch, J., Sarikaya, M. Z., Zhao, M., Lo, B., Bendtsen, F., and Burisch, J.

Abstract

Background: Studies on early surgery among Crohn's disease patients are few and focus on ileocolonic resections. Aim: The aim of this nationwide cohort study was to investigate the disease course in all Crohn's disease patients who underwent early and late major abdominal surgery. Methods: In a Danish nationwide cohort of Crohn's disease patients from 1997 to 2015 we included 493 patients (group 1) resected within 29 days, 472 patients (group 2) resected between 30 and 180 days, and 1,518 patients (group 3) resected after 180 days of diagnosis. Re-operation, hospitalisations and medications were analysed. Results: The cumulative risk of re-operation was lower among patients from group 1 (five-year risk: 16.5% vs. group 2: 18.2% and group 3: 21.2%, p = 0.004). Fewer patients from group 2 and 3 required hospitalisations (269 (56.5%) and 803 (52.8%) vs. group 1: 329 (66.8%) p<0.001). Patients from group 3 had a higher cumulative use of immunomodulators in the first three years after initial surgery (one-year risk: 24.6% vs. group 1: 19.4% and group 2: 17.0%, p<0.001). Conclusion: Crohn's disease patients resected within 29 days of diagnosis had a lower cumulative risk of re-operation and a lower cumulative exposure to immunomodulators in the initial years after surgery.

Published
2023

15. Generalizable movement intention recognition with multiple heterogenous EEG datasets

Author

Gu, X, Han, J, Yang, G-Z, and Lo, B

Abstract

Human movement intention recognition is important for human-robot interaction. Existing work based on motor imagery electroencephalogram (EEG) provides a non-invasive and portable solution for intention detection. However, the data-driven methods may suffer from the limited scale and diversity of the training datasets, which result in poor generalization performance on new test subjects. It is practically difficult to directly aggregate data from multiple datasets for training, since they often employ different channels and collected data suffers from significant domain shifts caused by different devices, experiment setup, etc. On the other hand, the inter-subject heterogeneity is also substantial due to individual differences in EEG representations. In this work, we developed two networks to learn from both the shared and the complete channels across datasets, handling inter-subject and inter-dataset heterogeneity respectively. Based on both networks, we further developed an online knowledge co-distillation framework to collaboratively learn from both networks, achieving coherent performance boosts. Experimental results have shown that our proposed method can effectively aggregate knowledge from multiple datasets, demonstrating better generalization in the context of cross-subject validation.

Published
2023

18. Author Correction: Somatic mosaicism and common genetic variation contribute to the risk of very-early-onset inflammatory bowel disease (Nature Communications, (2020), 11, 1, (995), 10.1038/s41467-019-14275-y)

Author

Serra E. G., Schwerd T., Moutsianas L., Cavounidis A., Fachal L., Pandey S., Kammermeier J., Croft N. M., Posovszky C., Rodrigues A., Russell R. K., Barakat F., Auth M. K. H., Heuschkel R., Zilbauer M., Fyderek K., Braegger C., Travis S. P., Satsangi J., Parkes M., Thapar N., Ferry H., Matte J. C., Gilmour K. C., Wedrychowicz A., Sullivan P., Moore C., Sambrook J., Ouwehand W., Roberts D., Danesh J., Baeumler T. A., Fulga T. A., Carrami E. M., Ahmed A., Wilson R., Barrett J. C., Elkadri A., Griffiths A. M., Zurek M., Strisciuglio C., Elawad M., Lo B., Arancibia-Carcamo C., Bailey A., Barnes E., Bird-Lieberman E. L., Brain O., Braden B., Collier J., East J., Howarth L., Keshav S., Klenerman P., Leedham S., Palmer R., Powrie F., Simmons A., Walker M., Tolkien Z., Kaptoge S., Allen D., Mehenny S., Mant J., Di Angelantonio E., Thompson S. G., Yilmaz B., Juillerat P., Geuking M., Wiest R., Macpherson A. J., Bravo F. D., Brugger L., Carstens O., Bigler U. G., Heimgartner B., Rusticeanu M., Schmid-Uebelhart S., Strebel B., Tatu A., Tutuian R., Oyas O., Ramon C., Stelling J., Franc Y., Fournier N., Pittet V. E. H., Burnand B., Egger M., Golay D., Marot A., Musso L., Rossel J. -B., Seematter V., Sommer J., Vulliamy R., Michetti P., Maillard M. H., Keller C., Nydegger A., Schoepfe A., Archanioti E., Ezri J., Fraga M., Schoepfer A., Muller C., Rogler G., Biedermann L., Blattmann M., Burk S., Dora B., Fried M., Misselwitz B., Mullhaupt B., Obialo N., Pohl D., Raschle N., Scharl M., Vavricka S., Von Kanel R., Zeitz J., Abdelrahman K., Ademi G., Borovicka J., Brand S., Frei R., Haarer J., Knellwolf-Grieger C., Krieger-Grubel C., Kunzler P., Meyenberger C., Meyer P., Rohrich N., Sawatzki M., Schelling M., Semadeni G. -M., Sulz M., Zimmermann D., Aepli P., Criblez D. H., Hess C., Richterich J. -P., Spalinger J., Staudenmann D., Stulz A., Wohrle S., Thomas A., Anderegg C., Kohler H., Kusche R., Antonino A. -T., Arrigoni E., Bengoa J. M., Cunningham S., de Saussure P., Girard L., de Jong D. B., Basturk P., Brunner S., Degen L., Hruz P., Bakker C. K. -D., Niess J., Balsiger B., Haldemann J., Saner G., Seibold F., Bauerfeind P., Becocci A., Belli D., Binek J., Hengstler P., Boehm S., Boldanov T., Buhr P., Koller R., Rueger V., Senning A., Burri E., Buyse S., Cao D. -T., D'Angelo F., Delarive J., Doerig C., Hessler R., Preissler C., Rentsch R., Risti B., Ritz M. A., Steuerwald M., Vogtlin J., Sagmeister M., Sauter B., Schibli S., Sokollik C., Schlauri H., Schnegg J. -F., Seirafi M., Spangenberger H., Stadler P., Staub P., Stenz V., Tempia-Caliera M., Thorens J., Truninger K., Urfer P., Viani F., Vouillamoz D., Zander S., Wyli T., Jostins L., Kennedy N. A., Ahmad T., Lamb C. A., Edwards C., Hart A., Hawkey C., Mansfield J. C., Mowat C., Newman W. G., Tremelling M., Lee J. C., Prescott N. J., Mathew C. G., Lees C. W., McGovern D. P. B., Targan S. R., Botwin G., Mengesha E., Fleshner P., Landers C., Li D., Rioux J. D., Bitton A., Cote-Daigneault J., Daly M. J., Xavier R., Morris K., Boucher G., Cho J. H., Abraham C., Merad M., Sands B., Peter I., Hao K., Itan Y., Duerr R. H., Konnikova L., Schwartz M. B., Proksell S., Johnston E., Miladinova V., Chen W., Brant S. R., Datta L., Silverberg M. S., Schumm L. P., Birch S., Giri M., Gettler K., Sharma Y., Stevens C., Lazarev M., Haritunians T., Snapper S. B., Shah N., Muise A. M., Wilson D. C., Uhlig H. H., Anderson C. A., Serra, E. G., Schwerd, T., Moutsianas, L., Cavounidis, A., Fachal, L., Pandey, S., Kammermeier, J., Croft, N. M., Posovszky, C., Rodrigues, A., Russell, R. K., Barakat, F., Auth, M. K. H., Heuschkel, R., Zilbauer, M., Fyderek, K., Braegger, C., Travis, S. P., Satsangi, J., Parkes, M., Thapar, N., Ferry, H., Matte, J. C., Gilmour, K. C., Wedrychowicz, A., Sullivan, P., Moore, C., Sambrook, J., Ouwehand, W., Roberts, D., Danesh, J., Baeumler, T. A., Fulga, T. A., Carrami, E. M., Ahmed, A., Wilson, R., Barrett, J. C., Elkadri, A., Griffiths, A. M., Zurek, M., Strisciuglio, C., Elawad, M., Lo, B., Arancibia-Carcamo, C., Bailey, A., Barnes, E., Bird-Lieberman, E. L., Brain, O., Braden, B., Collier, J., East, J., Howarth, L., Keshav, S., Klenerman, P., Leedham, S., Palmer, R., Powrie, F., Simmons, A., Walker, M., Tolkien, Z., Kaptoge, S., Allen, D., Mehenny, S., Mant, J., Di Angelantonio, E., Thompson, S. G., Yilmaz, B., Juillerat, P., Geuking, M., Wiest, R., Macpherson, A. J., Bravo, F. D., Brugger, L., Carstens, O., Bigler, U. G., Heimgartner, B., Rusticeanu, M., Schmid-Uebelhart, S., Strebel, B., Tatu, A., Tutuian, R., Oyas, O., Ramon, C., Stelling, J., Franc, Y., Fournier, N., Pittet, V. E. H., Burnand, B., Egger, M., Golay, D., Marot, A., Musso, L., Rossel, J. -B., Seematter, V., Sommer, J., Vulliamy, R., Michetti, P., Maillard, M. H., Keller, C., Nydegger, A., Schoepfe, A., Archanioti, E., Ezri, J., Fraga, M., Schoepfer, A., Muller, C., Rogler, G., Biedermann, L., Blattmann, M., Burk, S., Dora, B., Fried, M., Misselwitz, B., Mullhaupt, B., Obialo, N., Pohl, D., Raschle, N., Scharl, M., Vavricka, S., Von Kanel, R., Zeitz, J., Abdelrahman, K., Ademi, G., Borovicka, J., Brand, S., Frei, R., Haarer, J., Knellwolf-Grieger, C., Krieger-Grubel, C., Kunzler, P., Meyenberger, C., Meyer, P., Rohrich, N., Sawatzki, M., Schelling, M., Semadeni, G. -M., Sulz, M., Zimmermann, D., Aepli, P., Criblez, D. H., Hess, C., Richterich, J. -P., Spalinger, J., Staudenmann, D., Stulz, A., Wohrle, S., Thomas, A., Anderegg, C., Kohler, H., Kusche, R., Antonino, A. -T., Arrigoni, E., Bengoa, J. M., Cunningham, S., de Saussure, P., Girard, L., de Jong, D. B., Basturk, P., Brunner, S., Degen, L., Hruz, P., Bakker, C. K. -D., Niess, J., Balsiger, B., Haldemann, J., Saner, G., Seibold, F., Bauerfeind, P., Becocci, A., Belli, D., Binek, J., Hengstler, P., Boehm, S., Boldanov, T., Buhr, P., Koller, R., Rueger, V., Senning, A., Burri, E., Buyse, S., Cao, D. -T., D'Angelo, F., Delarive, J., Doerig, C., Hessler, R., Preissler, C., Rentsch, R., Risti, B., Ritz, M. A., Steuerwald, M., Vogtlin, J., Sagmeister, M., Sauter, B., Schibli, S., Sokollik, C., Schlauri, H., Schnegg, J. -F., Seirafi, M., Spangenberger, H., Stadler, P., Staub, P., Stenz, V., Tempia-Caliera, M., Thorens, J., Truninger, K., Urfer, P., Viani, F., Vouillamoz, D., Zander, S., Wyli, T., Jostins, L., Kennedy, N. A., Ahmad, T., Lamb, C. A., Edwards, C., Hart, A., Hawkey, C., Mansfield, J. C., Mowat, C., Newman, W. G., Tremelling, M., Lee, J. C., Prescott, N. J., Mathew, C. G., Lees, C. W., Mcgovern, D. P. B., Targan, S. R., Botwin, G., Mengesha, E., Fleshner, P., Landers, C., Li, D., Rioux, J. D., Bitton, A., Cote-Daigneault, J., Daly, M. J., Xavier, R., Morris, K., Boucher, G., Cho, J. H., Abraham, C., Merad, M., Sands, B., Peter, I., Hao, K., Itan, Y., Duerr, R. H., Konnikova, L., Schwartz, M. B., Proksell, S., Johnston, E., Miladinova, V., Chen, W., Brant, S. R., Datta, L., Silverberg, M. S., Schumm, L. P., Birch, S., Giri, M., Gettler, K., Sharma, Y., Stevens, C., Lazarev, M., Haritunians, T., Snapper, S. B., Shah, N., Muise, A. M., Wilson, D. C., Uhlig, H. H., and Anderson, C. A.

Published
2022

23. Eye-Gaze Driven Surgical Workflow Segmentation

Author

James, A., Vieira, D., Lo, B., Darzi, A., Yang, G. -Z., Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Ayache, Nicholas, editor, Ourselin, Sébastien, editor, and Maeder, Anthony, editor

Published
2007
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24. Revisiting self-supervised constrastive learning for facial expression recognition

Author

Shu, Y, Gu, X, Yang, G-Z, and Lo, B

Abstract

The success of most advanced facial expression recognition works relies heavily on large-scale annotated datasets. However, it poses great challenges in acquiring clean and consistent annotations for facial expression datasets. On the other hand, self-supervised contrastive learning has gained great popularity due to its simple yet effective instance discrimination training strategy, which can potentially circumvent the annotation issue. Nevertheless, there remain inherent disadvantages of instance-level discrimination, which are even more challenging when faced with complicated facial representations. In this paper, we revisit the use of self-supervised contrastive learning and explore three core strategies to enforce expression-specific representations and to minimize the interference from other facial attributes, such as identity and face styling. Experimental results show that our proposed method outperforms the current state-of-the-art self-supervised learning methods, in terms of both categorical and dimensional facial expression recognition tasks. Our project page: https://claudiashu.github.io/SSLFER.

Published
2022

25. Rescue therapy for vasospasm following aneurysmal subarachnoid hemorrhage: a propensity score-matched analysis with machine learning

Author

Martini, M.L., Neifert, S.N., Shuman, W.H., Chapman, E.K., Schüpper, A.J., Oermann, E.K., Mocco, J., Todd, M., Torner, J.C., Molyneux, A., Mayer, S., Roux, P.L., Vergouwen, M.D., Rinkel, G.J., Wong, G.K.C., Kirkpatrick, P., Quinn, A., Hänggi, D., Etminan, N., Bergh, W.M. van den, Jaja, B.N., Cusimano, M., Schweizer, T.A., Suarez, J.I., Fukuda, H., Yamagata, S., Lo, B., Leonardo de Oliveira Manoel, A., Boogaarts, H.D., Macdonald, R.L., Martini, M.L., Neifert, S.N., Shuman, W.H., Chapman, E.K., Schüpper, A.J., Oermann, E.K., Mocco, J., Todd, M., Torner, J.C., Molyneux, A., Mayer, S., Roux, P.L., Vergouwen, M.D., Rinkel, G.J., Wong, G.K.C., Kirkpatrick, P., Quinn, A., Hänggi, D., Etminan, N., Bergh, W.M. van den, Jaja, B.N., Cusimano, M., Schweizer, T.A., Suarez, J.I., Fukuda, H., Yamagata, S., Lo, B., Leonardo de Oliveira Manoel, A., Boogaarts, H.D., and Macdonald, R.L.

Abstract

Item does not contain fulltext, OBJECTIVE: Rescue therapies have been recommended for patients with angiographic vasospasm (aVSP) and delayed cerebral ischemia (DCI) following subarachnoid hemorrhage (SAH). However, there is little evidence from randomized clinical trials that these therapies are safe and effective. The primary aim of this study was to apply game theory-based methods in explainable machine learning (ML) and propensity score matching to determine if rescue therapy was associated with better 3-month outcomes following post-SAH aVSP and DCI. The authors also sought to use these explainable ML methods to identify patient populations that were more likely to receive rescue therapy and factors associated with better outcomes after rescue therapy. METHODS: Data for patients with aVSP or DCI after SAH were obtained from 8 clinical trials and 1 observational study in the Subarachnoid Hemorrhage International Trialists repository. Gradient boosting ML models were constructed for each patient to predict the probability of receiving rescue therapy and the 3-month Glasgow Outcome Scale (GOS) score. Favorable outcome was defined as a 3-month GOS score of 4 or 5. Shapley Additive Explanation (SHAP) values were calculated for each patient-derived model to quantify feature importance and interaction effects. Variables with high SHAP importance in predicting rescue therapy administration were used in a propensity score-matched analysis of rescue therapy and 3-month GOS scores. RESULTS: The authors identified 1532 patients with aVSP or DCI. Predictive, explainable ML models revealed that aneurysm characteristics and neurological complications, but not admission neurological scores, carried the highest relative importance rankings in predicting whether rescue therapy was administered. Younger age and absence of cerebral ischemia/infarction were invariably linked to better rescue outcomes, whereas the other important predictors of outcome varied by rescue type (interventional or noninterventional). In

Published
2022

27. A community effort to create standards for evaluating tumor subclonal reconstruction

Author

Salcedo, A., Tarabichi, M., Espiritu, S.M.G., Deshwar, A.G., David, M., Wilson, N.M., Dentro, S., Wintersinger, J.A., Liu, L.Y., Ko, M., Sivanandan, S., Zhang, H., Zhu, K., Ou Yang, T.-H., Chilton, J.M., Buchanan, A., Lalansingh, C.M., P’ng, C., Anghel, C.V., Umar, I., Lo, B., Zou, W., Jha, A., Huang, T., Yang, T.-P., Peifer, M., Sahinalp, C., Malikic, S., Vázquez-García, I., Mustonen, V., Yang, H.-T., Lee, K.-R., Ji, Y., Sengupta, Subhajit, Rudewicz, J., Nikolski, M., Schaeverbeke, Q., Yuan, K., Markowetz, F., Macintyre, G., Cmero, M., Chaudhary, B., Leshchiner, I., Livitz, D., Getz, G., Loher, P., Yu, K., Wang, W., Zhu, H., Simpson, J.T., Stuart, J.M., Anastassiou, D., Guan, Y., Ewing, A.D., Ellrott, K., Wedge, D.C., Morris, Q., Van Loo, P., Boutros, P.C., Department of Ecology and Evolutionary Biology [University of Toronto] (EEB), University of Toronto, Pennsylvania State University (Penn State), Penn State System, The Wellcome Trust Sanger Institute [Cambridge], Capital Normal University [Beijing], University of Queensland [Brisbane], Nuffield Department of Medicine [Oxford, UK] (Big Data Institute), University of Oxford [Oxford], Department of Computer Science, Helsinki Institute for Information Technology, Bioinformatics, Institute of Biotechnology, and Organismal and Evolutionary Biology Research Programme

Subjects
DNA Copy Number Variations, Tumour heterogeneity, Computer science, 3122 Cancers, Gene Dosage, Biomedical Engineering, Inference, Bioengineering, Computational biology, Polymorphism, Single Nucleotide, Applied Microbiology and Biotechnology, Genome, Tumor heterogeneity, Article, DNA sequencing, 03 medical and health sciences, 0302 clinical medicine, GENOME SIMULATION, Neoplasms, Humans, HETEROGENEITY, Computer Simulation, SOMATIC POINT MUTATIONS, Evolutionary dynamics, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, 318 Medical biotechnology, IDENTIFICATION, Manchester Cancer Research Centre, ResearchInstitutes_Networks_Beacons/mcrc, Reference Standards, CANCER, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], EVOLUTION, Clone Cells, 3. Good health, Cancer evolution, Mutation, Mutation (genetic algorithm), Molecular Medicine, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Algorithms, 030217 neurology & neurosurgery, Biotechnology
Abstract

Tumor DNA sequencing data can be interpreted by computational methods that analyse genomic heterogeneity to infer evolutionary dynamics. A growing number of studies have used these approaches to link cancer evolution with clinical progression and response to therapy. Although the inference of tumor phylogenies is rapidly becoming standard practice in cancer genome analyses, standards for evaluating tumor phylogenies are lacking. To address this need, we systematically assess methods for reconstructing tumor sub-clonality. First, we elucidate the main algorithmic problems in subclonal reconstruction and develop quantitative metrics for evaluating them. Then we simulate realistic tumor genomes that harbor all known clonal and subclonal mutation types and processes. We benchmark 580 tumor reconstructions, varying tumor read-depth, tumour type, and somatic variant detection. Our analysis provides a baseline for the establishment of gold-standard methods to analyze tumor heterogeneity., Editors summary Methods for reconstructing tumor evolution are benchmarked in the DREAM Somatic Mutation Calling Tumour Heterogeneity Challenge using novel tools.

Published
2020
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31. P405 Primary non-response and loss-of-response to first-line biological therapies are more common in patients with Ulcerative Colitis than Crohn’s Disease – preliminary results from the Danish IBD Biobank Project

Author

Zhao, M, primary, Larsen, L, additional, Dige, A, additional, Hvas, C L, additional, Poulsen, A, additional, Christiansen, D, additional, Attauabi, M, additional, Lo, B, additional, Wewer, M, additional, Ovesen, P D, additional, Petersen, A M, additional, Bendtsen, F, additional, Seidelin, J B, additional, and Burisch, J, additional

Published
2022
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33. Chronic stroke sensorimotor impairment is related to smaller hippocampal volumes: An ENIGMA analysis

Author

Zavaliangos-Petropulu, A, primary, Lo, B, additional, Donnelly, MR, additional, Schweighofer, N, additional, Lohse, Keith, additional, Jahanshad, Neda, additional, Barisano, G, additional, Banaj, N, additional, Borich, MR, additional, Boyd, LA, additional, Buetefisch, CM, additional, Byblow, WD, additional, Cassidy, JM, additional, Charalambous, CC, additional, Conforto, AB, additional, DiCarlo, JA, additional, Dula, AN, additional, Egorova-Brumley, N, additional, Etherton, MR, additional, Feng, W, additional, Fercho, KA, additional, Geranmayeh, F, additional, Hanlon, CA, additional, Hayward, KS, additional, Hordacre, B, additional, Kautz, SA, additional, Khlif, MS, additional, Kim, H, additional, Kuceyeski, A, additional, Lin, DJ, additional, Lotze, M, additional, Liu, J, additional, MacIntosh, BJ, additional, Margetis, JL, additional, Piras, F, additional, Ramos-Murguialday, A, additional, Revill, KP, additional, Roberts, PS, additional, Robertson, AD, additional, Schambra, HM, additional, Seo, NJ, additional, Shiroishi, MS, additional, Soekadar, SR, additional, Spalletta, G, additional, Taga, M, additional, Tang, WK, additional, Thielman, GT, additional, Vecchio, D, additional, Ward, NS, additional, Westlye, LT, additional, Werden, E, additional, Winstein, C, additional, Wittenberg, GF, additional, Wolf, SL, additional, Wong, KA, additional, Yu, C, additional, Brodtmann, A, additional, Cramer, SC, additional, Thompson, PM, additional, and Liew, S-L, additional

Published
2021
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35. Extending the Common Sense Model to Explore the Impact of the Fear of COVID-19 on Quality of Life in an International Inflammatory Bowel Disease Cohort

Author

Hayes, B, Apputhurai, P, Mikocka-Walus, Antonina, Barreiro-de Acosta, M, Bernstein, CN, Burgell, R, Burisch, J, Bennebroek Evertsz, F, Ferreira, N, Graff, LA, Trindade, IA, Gearry, R, Lo, B, Mokrowiecka, A, Moser, G, Petrik, M, Stengel, A, Knowles, SR, Hayes, B, Apputhurai, P, Mikocka-Walus, Antonina, Barreiro-de Acosta, M, Bernstein, CN, Burgell, R, Burisch, J, Bennebroek Evertsz, F, Ferreira, N, Graff, LA, Trindade, IA, Gearry, R, Lo, B, Mokrowiecka, A, Moser, G, Petrik, M, Stengel, A, and Knowles, SR

Published
2021

36. The impact of the coronavirus (COVID-19) pandemic on individuals with gastrointestinal disorders: A protocol of an international collaborative study

Author

Ferreira, N, Mikocka-Walus, Antonina, van Tilburg, MAL, Graff, LA, Apputhurai, P, Acosta, MBD, Evertsz, FB, Burisch, J, Lo, B, Petrik, M, Trindade, IA, Jedel, S, Moser, G, Mokrowiecka, A, Bernstein, CN, Dumitrascu, D, Ford, AC, Stengel, A, Gearry, R, Knowles, SR, Ferreira, N, Mikocka-Walus, Antonina, van Tilburg, MAL, Graff, LA, Apputhurai, P, Acosta, MBD, Evertsz, FB, Burisch, J, Lo, B, Petrik, M, Trindade, IA, Jedel, S, Moser, G, Mokrowiecka, A, Bernstein, CN, Dumitrascu, D, Ford, AC, Stengel, A, Gearry, R, and Knowles, SR

Published
2021

37. Smaller spared subcortical nuclei are associated with worse post-stroke sensorimotor outcomes in 28 cohorts worldwide

Author

Liew, S-L, Zavaliangos-Petropulu, A, Schweighofer, N, Jahanshad, N, Lang, CE, Lohse, KR, Banaj, N, Barisano, G, Baugh, LA, Bhattacharya, AK, Bigjahan, B, Borich, MR, Boyd, LA, Brodtmann, A, Buetefisch, CM, Byblow, WD, Cassidy, JM, Charalambous, CC, Ciullo, V, Conforto, AB, Craddock, RC, Dula, AN, Egorova, N, Feng, W, Fercho, KA, Gregory, CM, Hanlon, CA, Hayward, KS, Holguin, JA, Hordacre, B, Hwang, DH, Kautz, SA, Khlif, MS, Kim, B, Kim, H, Kuceyeski, A, Lo, B, Liu, J, Lin, D, Lotze, M, MacIntosh, BJ, Margetis, JL, Mohamed, FB, Nordvik, JE, Petoe, MA, Piras, F, Raju, S, Ramos-Murguialday, A, Revill, KP, Roberts, P, Robertson, AD, Schambra, HM, Seo, NJ, Shiroishi, MS, Soekadar, SR, Spalletta, G, Stinear, CM, Suri, A, Tang, WK, Thielman, GT, Thijs, VN, Vecchio, D, Ward, NS, Westlye, LT, Winstein, CJ, Wittenberg, GF, Wong, KA, Yu, C, Wolf, SL, Cramer, SC, Thompson, PM, Liew, S-L, Zavaliangos-Petropulu, A, Schweighofer, N, Jahanshad, N, Lang, CE, Lohse, KR, Banaj, N, Barisano, G, Baugh, LA, Bhattacharya, AK, Bigjahan, B, Borich, MR, Boyd, LA, Brodtmann, A, Buetefisch, CM, Byblow, WD, Cassidy, JM, Charalambous, CC, Ciullo, V, Conforto, AB, Craddock, RC, Dula, AN, Egorova, N, Feng, W, Fercho, KA, Gregory, CM, Hanlon, CA, Hayward, KS, Holguin, JA, Hordacre, B, Hwang, DH, Kautz, SA, Khlif, MS, Kim, B, Kim, H, Kuceyeski, A, Lo, B, Liu, J, Lin, D, Lotze, M, MacIntosh, BJ, Margetis, JL, Mohamed, FB, Nordvik, JE, Petoe, MA, Piras, F, Raju, S, Ramos-Murguialday, A, Revill, KP, Roberts, P, Robertson, AD, Schambra, HM, Seo, NJ, Shiroishi, MS, Soekadar, SR, Spalletta, G, Stinear, CM, Suri, A, Tang, WK, Thielman, GT, Thijs, VN, Vecchio, D, Ward, NS, Westlye, LT, Winstein, CJ, Wittenberg, GF, Wong, KA, Yu, C, Wolf, SL, Cramer, SC, and Thompson, PM

Abstract

Up to two-thirds of stroke survivors experience persistent sensorimotor impairments. Recovery relies on the integrity of spared brain areas to compensate for damaged tissue. Deep grey matter structures play a critical role in the control and regulation of sensorimotor circuits. The goal of this work is to identify associations between volumes of spared subcortical nuclei and sensorimotor behaviour at different timepoints after stroke. We pooled high-resolution T1-weighted MRI brain scans and behavioural data in 828 individuals with unilateral stroke from 28 cohorts worldwide. Cross-sectional analyses using linear mixed-effects models related post-stroke sensorimotor behaviour to non-lesioned subcortical volumes (Bonferroni-corrected, P < 0.004). We tested subacute (≤90 days) and chronic (≥180 days) stroke subgroups separately, with exploratory analyses in early stroke (≤21 days) and across all time. Sub-analyses in chronic stroke were also performed based on class of sensorimotor deficits (impairment, activity limitations) and side of lesioned hemisphere. Worse sensorimotor behaviour was associated with a smaller ipsilesional thalamic volume in both early (n = 179; d = 0.68) and subacute (n = 274, d = 0.46) stroke. In chronic stroke (n = 404), worse sensorimotor behaviour was associated with smaller ipsilesional putamen (d = 0.52) and nucleus accumbens (d = 0.39) volumes, and a larger ipsilesional lateral ventricle (d = -0.42). Worse chronic sensorimotor impairment specifically (measured by the Fugl-Meyer Assessment; n = 256) was associated with smaller ipsilesional putamen (d = 0.72) and larger lateral ventricle (d = -0.41) volumes, while several measures of activity limitations (n = 116) showed no significant relationships. In the full cohort across all time (n = 828), sensorimotor behaviour was associated with the volumes of the ipsilesional nucleus accumbens (d = 0.23), putamen (d = 0.33), thalamus (d = 0.33) and lateral ventricle (d = -0.23). We demonstrate sig

Published
2021

38. A family harboring an MLKL loss of function variant implicates impaired necroptosis in diabetes

Author

Hildebrand, JM, Lo, B, Tomei, S, Mattei, V, Young, SN, Fitzgibbon, C, Murphy, JM, Fadda, A, Hildebrand, JM, Lo, B, Tomei, S, Mattei, V, Young, SN, Fitzgibbon, C, Murphy, JM, and Fadda, A

Abstract

Maturity-onset diabetes of the young, MODY, is an autosomal dominant disease with incomplete penetrance. In a family with multiple generations of diabetes and several early onset diabetic siblings, we found the previously reported P33T PDX1 damaging mutation. Interestingly, this substitution was also present in a healthy sibling. In contrast, a second very rare heterozygous damaging mutation in the necroptosis terminal effector, MLKL, was found exclusively in the diabetic family members. Aberrant cell death by necroptosis is a cause of inflammatory diseases and has been widely implicated in human pathologies, but has not yet been attributed functions in diabetes. Here, we report that the MLKL substitution observed in diabetic patients, G316D, results in diminished phosphorylation by its upstream activator, the RIPK3 kinase, and no capacity to reconstitute necroptosis in two distinct MLKL-/- human cell lines. This MLKL mutation may act as a modifier to the P33T PDX1 mutation, and points to a potential role of impairment of necroptosis in diabetes. Our findings highlight the importance of family studies in unraveling MODY's incomplete penetrance, and provide further support for the involvement of dysregulated necroptosis in human disease.

Published
2021

40. Explaining the emerging Sino-Russian energy partnership

Author

Skalamera, M., Bekkevold, J.I., Lo, B., Bekkevold, J.I., and Lo, B.

Subjects
business.industry, media_common.quotation_subject, Energy (esotericism), International trade, Geopolitics, Negotiation, Politics, Cash, Political science, General partnership, Energy market, business, China, media_common
Abstract

This chapter contends that although geopolitics plays a role in the emerging Sino-Russian energy cooperation, it is important to take into account domestic politics to fully understand this development. Russia’s energy turn to China occurred before the Ukraine crisis, and has in large part been driven by Moscow’s assessment that Asia, and China in particular, would be the primary source of Russia’s future growth. The Sino-Russian gas breakthrough in 2014 was due to the peculiar way in which domestic and international factors combined to produce the outcome at that particular moment. Even though Russia has been able to conclude landmark deals and open the Chinese energy market, China has been able to negotiate favorable deals with a Russia desperate for cash, credit, and new markets.

Published
2019

42. P610 Fear of COVID-19 among persons with Inflammatory Bowel Disease according to employment status, educational background and residential setting, as compared to persons with other gastrointestinal conditions

Author

Lo, B Z S, primary, Mokrowiecka, A, additional, Mikocka-Walus, A, additional, Bernstein, C N, additional, Trindade, I A, additional, Burisch, J, additional, Barreiro-de Acosta, M, additional, Ferreira, N, additional, Gearry, R B, additional, and Knowles, S R, additional

Published
2021
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44. P162 Microscopic inflammation in limited Ulcerative Colitis at diagnosis: can a single histological feature predict prognosis?

Author

Revés, J, primary, Frias Gomes, C, additional, Ellul, P, additional, Callé, C, additional, Almeida, A, additional, Burisch, J, additional, Buhagiar, T, additional, Attard, A, additional, Lo, B, additional, Ungaro, R, additional, Morão, B, additional, Gouveia, C, additional, Branco, J, additional, Rodrigues, J, additional, Teixeira, C, additional, Castro, F, additional, Nunes, G, additional, Brito, M, additional, Antunes, M, additional, Torres, J, additional, and Borralho, P, additional

Published
2021
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48. Human AGR2 Deficiency Causes Mucus Barrier Dysfunction and Infantile Inflammatory Bowel Disease

Author

Al-Shaibi, AA, Abdel-Motal, UM, Hubrack, SZ, Bullock, AN, Al-Marri, AA, Agrebi, N, Al-Subaiey, AA, Ibrahim, NA, Charles, AK, Elawad, M, Uhlig, HH, Lo, B, and group, COLORS in IBD-Qatar study

Subjects
Male, digestive system, TFF3, trefoil factor 3, ER, endoplasmic reticulum, HEK293T, Human Embryonic Kidney 293T, Structure-Activity Relationship, Intestinal Metaplasia, Mucoproteins, BiP, Binding Immunoglobulin Protein, Animals, Humans, Genetic Predisposition to Disease, Amino Acid Sequence, Intestinal Mucosa, Original Research, Mice, Knockout, Oncogene Proteins, Whole Genome Sequencing, CLCA1, Chloride Channel Accessory 1, IBD, inflammatory bowel disease, AGR2, anterior gradient 2, MUC, mucin, Siblings, Mucins, Sequence Analysis, DNA, respiratory system, Endoplasmic Reticulum Stress, Inflammatory Bowel Diseases, WT, wild-type, TBS, Tris-buffered saline, Disease Models, Animal, Mucus, Phenotype, Gastric Mucosa, MUC2, ER Stress, Disease Susceptibility, Goblet Cells, Biomarkers, AGR2, HA, hemagglutinin
Abstract

Background & Aims The gastrointestinal epithelium plays a crucial role in maintaining homeostasis with the gut microbiome. Mucins are essential for intestinal barrier function and serve as a scaffold for antimicrobial factors. Mucin 2 (MUC2) is the major intestinal gel-forming mucin produced predominantly by goblet cells. Goblet cells express anterior gradient 2 (AGR2), a protein disulfide isomerase that is crucial for proper processing of gel-forming mucins. Here, we investigated 2 siblings who presented with severe infantile-onset inflammatory bowel disease. Methods We performed whole-genome sequencing to identify candidate variants. We quantified goblet cell numbers using H&E histology and investigated the expression of gel-forming mucins, stress markers, and goblet cell markers using immunohistochemistry. AGR2-MUC2 binding was evaluated using co-immunoprecipitation. Endoplasmic reticulum (ER) stress regulatory function of mutant AGR2 was examined by expression studies in Human Embryonic Kidney 293T (HEK293T) using tunicamycin to induce ER stress. Results Both affected siblings were homozygous for a missense variant in AGR2. Patient biopsy specimens showed reduced goblet cells; depletion of MUC2, MUC5AC, and MUC6; up-regulation of AGR2; and increased ER stress. The mutant AGR2 showed reduced capacity to bind MUC2 and alleviate tunicamycin-induced ER stress. Conclusions Phenotype–genotype segregation, functional experiments, and the striking similarity of the human phenotype to AGR2-/- mouse models suggest that the AGR2 missense variant is pathogenic. The Mendelian deficiency of AGR2, termed “Enteropathy caused by AGR2 deficiency, Goblet cell Loss, and ER Stress” (EAGLES), results in a mucus barrier defect, the inability to mitigate ER stress, and causes infantile-onset inflammatory bowel disease., Graphical abstract

Published
2020

49. Between-center and between-country differences in outcome after aneurysmal subarachnoid hemorrhage in the subarachnoid hemorrhage international trialists (SAHIT) repository

Author

Dijkland, S.A. (Simone), Jaja, B.N.R. (Blessing), Jagt, M. (Mathieu) van der, Roozenbeek, B. (Bob), Vergouwen, M.D.I. (Mervyn D.I.), Suarez, J.I. (Jose I.), Torner, J.C. (James C.), Todd, M.M. (Michael M.), Van Den Bergh, H. (Huub), Saposnik, G. (Gustavo), Zumofen, D.W. (Daniel W.), Cusimano, M.D. (Michael D.), Mayer, S. (Stephan), Lo, B. (Benjamin), Steyerberg, E.W. (Ewout), Dippel, D.W.J. (Diederik), Schweizer, T.A. (Tom), Loch Macdonald, R. (R.), Lingsma, H.F. (Hester), Dijkland, S.A. (Simone), Jaja, B.N.R. (Blessing), Jagt, M. (Mathieu) van der, Roozenbeek, B. (Bob), Vergouwen, M.D.I. (Mervyn D.I.), Suarez, J.I. (Jose I.), Torner, J.C. (James C.), Todd, M.M. (Michael M.), Van Den Bergh, H. (Huub), Saposnik, G. (Gustavo), Zumofen, D.W. (Daniel W.), Cusimano, M.D. (Michael D.), Mayer, S. (Stephan), Lo, B. (Benjamin), Steyerberg, E.W. (Ewout), Dippel, D.W.J. (Diederik), Schweizer, T.A. (Tom), Loch Macdonald, R. (R.), and Lingsma, H.F. (Hester)

Abstract

OBJECTIVE Differences in clinical outcomes between centers and countries may reflect variation in patient characteristics, diagnostic and therapeutic policies, or quality of care. The purpose of this study was to investigate the presence and magnitude of between-center and between-country differences in outcome after aneurysmal subarachnoid hemorrhage (aSAH). METHODS The authors analyzed data from 5972 aSAH patients enrolled in randomized clinical trials of 3 different treatments from the Subarachnoid Hemorrhage International Trialists (SAHIT) repository, including data from 179 centers and 20 countries. They used random effects logistic regression adjusted for patient characteristics and timing of aneurysm treatment to estimate between

Published
2020
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50. A community effort to create standards for evaluating tumor subclonal reconstruction

Author

Salcedo, A, Tarabichi, M, Espiritu, SMG, Deshwar, AG, David, M, Wilson, NM, Dentro, S, Wintersinger, JA, Liu, LY, Ko, M, Sivanandan, S, Zhang, H, Zhu, K, Ou Yang, T-H, Chilton, JM, Buchanan, A, Lalansingh, CM, P'ng, C, Anghel, CV, Umar, I, Lo, B, Zou, W, Simpson, JT, Stuart, JM, Anastassiou, D, Guan, Y, Ewing, AD, Ellrott, K, Wedge, DC, Morris, Q, Van Loo, P, Boutros, PC, Jha, A, Huang, T, Yang, T-P, Peifer, M, Sahinalp, C, Malikic, S, Vazquez-Garcia, I, Mustonen, V, Yang, H-T, Lee, K-R, Ji, Y, Sengupta, S, Rudewicz, J, Nikolski, M, Schaeverbeke, Q, Yuan, K, Markowetz, F, Macintyre, G, Cmero, M, Chaudhary, B, Leshchiner, I, Livitz, D, Getz, G, Loher, P, Yu, K, Wang, W, Zhu, H, Salcedo, A, Tarabichi, M, Espiritu, SMG, Deshwar, AG, David, M, Wilson, NM, Dentro, S, Wintersinger, JA, Liu, LY, Ko, M, Sivanandan, S, Zhang, H, Zhu, K, Ou Yang, T-H, Chilton, JM, Buchanan, A, Lalansingh, CM, P'ng, C, Anghel, CV, Umar, I, Lo, B, Zou, W, Simpson, JT, Stuart, JM, Anastassiou, D, Guan, Y, Ewing, AD, Ellrott, K, Wedge, DC, Morris, Q, Van Loo, P, Boutros, PC, Jha, A, Huang, T, Yang, T-P, Peifer, M, Sahinalp, C, Malikic, S, Vazquez-Garcia, I, Mustonen, V, Yang, H-T, Lee, K-R, Ji, Y, Sengupta, S, Rudewicz, J, Nikolski, M, Schaeverbeke, Q, Yuan, K, Markowetz, F, Macintyre, G, Cmero, M, Chaudhary, B, Leshchiner, I, Livitz, D, Getz, G, Loher, P, Yu, K, Wang, W, and Zhu, H

Abstract

Tumor DNA sequencing data can be interpreted by computational methods that analyze genomic heterogeneity to infer evolutionary dynamics. A growing number of studies have used these approaches to link cancer evolution with clinical progression and response to therapy. Although the inference of tumor phylogenies is rapidly becoming standard practice in cancer genome analyses, standards for evaluating them are lacking. To address this need, we systematically assess methods for reconstructing tumor subclonality. First, we elucidate the main algorithmic problems in subclonal reconstruction and develop quantitative metrics for evaluating them. Then we simulate realistic tumor genomes that harbor all known clonal and subclonal mutation types and processes. Finally, we benchmark 580 tumor reconstructions, varying tumor read depth, tumor type and somatic variant detection. Our analysis provides a baseline for the establishment of gold-standard methods to analyze tumor heterogeneity.

Published
2020

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