6 results
An approach for collaborative development of a federated biomedical knowledge graph-based question-answering system: Question-of-the-Month challenges
- Karamarie Fecho, Chris Bizon, Tursynay Issabekova, Sierra Moxon, Anne E. Thessen, Shervin Abdollahi, Sergio E. Baranzini, Basazin Belhu, William E. Byrd, Lawrence Chung, Andrew Crouse, Marc P. Duby, Stephen Ferguson, Aleksandra Foksinska, Laura Forero, Jennifer Friedman, Vicki Gardner, Gwênlyn Glusman, Jennifer Hadlock, Kristina Hanspers, Eugene Hinderer, Charlotte Hobbs, Gregory Hyde, Sui Huang, David Koslicki, Philip Mease, Sandrine Muller, Christopher J. Mungall, Stephen A. Ramsey, Jared Roach, Irit Rubin, Shepherd H. Schurman, Anath Shalev, Brett Smith, Karthik Soman, Sarah Stemann, Andrew I. Su, Casey Ta, Paul B. Watkins, Mark D. Williams, Chunlei Wu, Colleen H. Xu, The Biomedical Data Translator Consortium
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- Journal:
- Journal of Clinical and Translational Science / Volume 7 / Issue 1 / 2023
- Published online by Cambridge University Press:
- 14 September 2023, e214
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Knowledge graphs have become a common approach for knowledge representation. Yet, the application of graph methodology is elusive due to the sheer number and complexity of knowledge sources. In addition, semantic incompatibilities hinder efforts to harmonize and integrate across these diverse sources. As part of The Biomedical Translator Consortium, we have developed a knowledge graph–based question-answering system designed to augment human reasoning and accelerate translational scientific discovery: the Translator system. We have applied the Translator system to answer biomedical questions in the context of a broad array of diseases and syndromes, including Fanconi anemia, primary ciliary dyskinesia, multiple sclerosis, and others. A variety of collaborative approaches have been used to research and develop the Translator system. One recent approach involved the establishment of a monthly “Question-of-the-Month (QotM) Challenge” series. Herein, we describe the structure of the QotM Challenge; the six challenges that have been conducted to date on drug-induced liver injury, cannabidiol toxicity, coronavirus infection, diabetes, psoriatic arthritis, and ATP1A3-related phenotypes; the scientific insights that have been gleaned during the challenges; and the technical issues that were identified over the course of the challenges and that can now be addressed to foster further development of the prototype Translator system. We close with a discussion on Large Language Models such as ChatGPT and highlight differences between those models and the Translator system.
NTRK2 Fusion Driven Pediatric Glioblastoma: Identification of key molecular drivers by personalized oncology
- Levine, Y Shen, K Mungall, J Serrano, M Snuderl, E Pleasance, SJM Jones, J Laskin, MA Marra, R Rassekh, R Deyell, S Yip, S Cheng, C Dunham
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- Journal:
- Canadian Journal of Neurological Sciences / Volume 46 / Issue s2 / September 2019
- Published online by Cambridge University Press:
- 05 September 2019, p. S64
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We describe the case of an 11-month-old girl with a rare cerebellar glioblastoma driven by a NACC2-NTRK2 (Nucleus Accumbens Associated Protein 2-Neurotrophic Receptor Tyrosine Kinase 2) fusion. Initial workup of our case demonstrated homozygous CDKN2A deletion, but immunohistochemistry for other driver mutations, including IDH1 R132H, BRAF V600E, and H3F3A K27M were negative, and ATRX was retained. Tissue was subsequently submitted for personalized oncogenomic analysis, including whole genome and whole transcriptome sequencing, which demonstrated an activating NTRK2 fusion, as well as high PD-L1 expression, which was subsequently confirmed by immunohistochemistry. Furthermore, H3 and IDH demonstrated wildtype status. These findings suggested the possibility of treatment with either NTRK- or immune checkpoint- inhibitors through active clinical trials. Ultimately, the family pursued standard treatment that involved Head Start III chemotherapy and proton radiotherapy. Notably, at most recent follow upapproximately two years from initial diagnosis, the patient is in disease remission and thriving, suggesting favorable biology despite histologic malignancy. This case illustrates the value of personalized oncogenomics, as the molecular profiling revealed two actionable changes that would not have been apparent through routine diagnostics. NTRK fusions are known oncogenic drivers in a range of cancer types, but this is the first report of a NACC2-NTRK2 fusion in a glioblastoma.
LEARNING OBJECTIVESThis presentation will enable the learner to:
1. Explore the current molecular landscape of pediatric high grade gliomas
2. Recognize the value of personalized oncogenomic analysis, particularly in rare and/or aggressive tumors
3. Discuss the current status of NTRK inhibitor clinical trials
Naldrettite, Pd2Sb, a new intermetallic mineral from the Mesamax Northwest deposit, Ungava region, Québec, Canada
- L. J. Cabri, A. M. McDonald, C. J. Stanley, N. S. Rudashevsky, G. Poirier, B. R. Durham, J. E. Mungall, V. N. Rudashevsky
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- Journal:
- Mineralogical Magazine / Volume 69 / Issue 1 / February 2005
- Published online by Cambridge University Press:
- 05 July 2018, pp. 89-97
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Naldrettite, Pd2Sb, is a new intermetallic mineral discovered in the Mesamax Northwest deposit, Cape Smith fold belt, Ungava region, northern Québec. It is associated with monoclinic pyrrhotite, pentlandite, chalcopyrite, galena, sphalerite, cobaltite, clinochlore, magnetite, sudburyite (PdSb), electrum and altaite. Other rarer associated minerals include a second new mineral (ungavaite, Pd4Sb3), sperrylite (PtAs2), michenerite (PdBiTe), petzite (Ag3AuTe4) and hessite (Ag2Te). Naldrettite occurs as anhedral grains, which are commonly attached or moulded to sulphide minerals, and also associated with clinochlore. Grains of naldrettite vary in size (equivalent circle diameter) from ~10 to 239 μm, with an average of 74.4 mm (n = 632). Cleavage was not observed and fracture is irregular. The mineral has a mean micro-indentation hardness of 393 kg/mm2. It is distinctly anisotropic, non-pleochroic, has weak bireflectance, and does not exhibit discernible internal reflections. Some grains display evidence of strain-induced polysynthetic twinning. Naldrettite appears bright creamy white in association with pentlandite, pyrrhotite, clinochlore and chalcopyrite. Reflectance values in air (and in oil) for R1 and R2 are: 49.0, 50.9 (35.9, 37.6) at 470 nm, 53.2, 55.1 (40.3, 42.1) at 546 nm, 55.4, 57.5 (42.5, 44.3) at 589 nm and 58.5, 60.1 (45.4, 47.2) at 650 nm. The average of 69 electron-microprobe analyses on 19 particles gives: Pd 63.49, Fe 0.11, Sb 35.75, As 0.31, and S 0.02, total 99.68 wt.%, corresponding to (Pd1.995Fe0.007)2.002(Sb0.982AS0.014S0.002)0.998. The mineral is orthorhombic, space group Cmc21, a 3.3906(1), b 17.5551(5), c 6.957(2) Å , V 414.097(3) Å3, Z = 8. Dcalc is 10.694(1) g/cm3. The six strongest lines in the X-ray powder-diffraction pattern [d in Å (I)(hkl)] are: 2.2454(100)(132), 2.0567(52)(043), 2.0009(40)(152), 1.2842(42)(115), 1.2122(50)(204) and 0.8584(56)(1.17.4).
Contributors
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- By Eric Adler, Anoushka Afonso, Dean B. Andropoulos, Adel Bassily-Marcus, Yaakov Beilin, Elliott Bennett-Guerrero, Howard H. Bernstein, Marc J. Bloom, David Bronheim, Albert T. Cheung, Samuel DeMaria, Deborah Dubensky, James B. Eisenkraft, Jonathan Elmer, Liza J. Enriquez, Jonathan Epstein, Jeffrey M. Feldman, Gregory W. Fischer, Brigid Flynn, Jennifer A. Frontera, Richard S. Gist, Glenn P. Gravlee, Christina L. Jeng, Ronald A. Kahn, Jenny Kam, Mukul Kapoor, Jung Kim, Roopa Kohli-Seth, Aaron F. Kopman, Tuula S. O. Kurki, Andrew B. Leibowitz, Matthew Levin, Adam I. Levine, Michael S. Lewis, Justin Lipper, Martin London, Michael L. McGarvey, Alexander J. C. Mittnacht, Timothy Mooney, Diana Mungall, Yasuharu Okuda, Peter J. Papadakos, Jayashree Raikhelkar, Lakshmi V. Ramanathan, David L. Reich, Meg A. Rosenblatt, Corey Scurlock, Tamas Seres, Linda Shore-Lesserson, Marc E. Stone, Daniel M. Thys, Judit Tolnai, David Wax, Nathaen Weitzel
- David L. Reich, Mount Sinai School of Medicine, New York
- Edited by Ronald A. Kahn, Mount Sinai School of Medicine, New York, Alexander J. C. Mittnacht, Mount Sinai School of Medicine, New York, Andrew B. Leibowitz, Mount Sinai School of Medicine, New York, Marc E. Stone, Mount Sinai School of Medicine, New York, James B. Eisenkraft, Mount Sinai School of Medicine, New York
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- Book:
- Monitoring in Anesthesia and Perioperative Care
- Published online:
- 05 July 2011
- Print publication:
- 08 August 2011, pp vii-ix
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8 - Combustion
- M. Samimy, Ohio State University, K. S. Breuer, Brown University, Rhode Island, L. G. Leal, University of California, Santa Barbara, P. H. Steen, Cornell University, New York
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- Book:
- A Gallery of Fluid Motion
- Published online:
- 25 January 2010
- Print publication:
- 12 January 2004, pp 81-87
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Summary
Interaction of 2D wake and jet plume
Burner setup. A propane-air turbulent premixed flame is stabilized on a 30 mm Bunsen-type burner by an annular pilot. The equivalence ratio is 0.68. The flame height is about 85 mm. The mean velocity of the unburned mixture is 2.36 m/sec. Turbulence is given to the mixture by a perforated plate. The turbulence rms fluctuations at the burner exit is 0.15 m/sec. The Taylor and the Kolmogorov microscales are 1.81 and 0.22 mm, respectively, and the Reynolds number based on the Taylor microscale is 17.4.
Photographic setup. This schlieren photograph was taken by a Canon-F1 camera with a 300 mm telephoto lens of f=5.6. Two 200 mm schlieren mirrors with the focal length of 2000 mm were used for the Z-light path arrangement. The vertical knife edge is mounted at the focal point of one mirror. The light source was a xenon stroboscope with a condenser lens and a pinhole. The maximum light power is 8 J (170 1x-sec). The flash duration time is typically 15 μsec. The flash timing was synchronized with the camera shutter. The film used was the Neopan SS (ASA 100) and was developed by Fujidol.
Interpretation. With a moderate or weak turbulence of the unburned mixture, the instantaneous turbulent premixed flame zone consists of a continuous wrinkled laminar flame front. The wrinkle size seems to be irrelevant to the turbulence scale. Along the unburned mixture flow, the amplitude of wrinkles increases from bottom to top. We think that the hydrodynamic instability plays an important role in the flame wrinkling.
1 - Jets and mixing layers
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- By M. M. Koochesfahani, P. E. Dimotakis, M. Gharib, P. Derango, E. Villermaux, H. Rehab, E. J. Hopfinger, D. E. Parekh, W. C. Reynolds, M. G. Mungal, T. Loiseleux, J.-M. Chomaz, T. F. Fric, A. Roshko, S. P. Gogineni, M. M. Whitaker, L. P. Goss, W. M. Roquemore, S. Wernz, H. F. Fasel, S. Gogineni, C. Shih, A. Krothapalli
- M. Samimy, Ohio State University, K. S. Breuer, Brown University, Rhode Island, L. G. Leal, University of California, Santa Barbara, P. H. Steen, Cornell University, New York
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- Book:
- A Gallery of Fluid Motion
- Published online:
- 25 January 2010
- Print publication:
- 12 January 2004, pp 1-10
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Summary
Laser-induced fluorescence (LIF) diagnostics and highspeed, real-time digital image acquisition techniques are combined to map the composition field in a water mixing layer. A fluorescent dye, which is premixed with the lowspeed freestream fluid and dilutes by mixing with the highspeed fluid, is used to monitor the relative concentration of high-speed to low-speed fluid in the layer.
The three digital LIF pictures shown here were obtained by imaging the laser-induced fluorescence originating from a collimated argon ion laser beam, extending across the transverse dimension of the shear layer, onto a 512–element linear photodiode array. Each picture represents 384 contiguous scans, each at 400 points across the layer, for a total of 153 600 point measurements of concentration. The vertical axis maps onto 40 mm of the transverse coordinate of the shear layer, and the horizontal axis is time increasing from right to left for a total flow real time of 307 msec. The pseudocolor assignment is linear in the mixture fraction (ξ) and is arranged as follows: red-unmixed fluid from the low-speed stream (ξ=0); blue-unmixed fluid from the high-speed stream (ξ=1); and the rest of the spectrum corresponds to intermediate compositions.
Figures 1 and 2, a single vortex and pairing vortices, respectively, show the composition field before the mixing transition. The Reynolds number based on the local visual thickness of the layer and the velocity difference across the layer is Re=1750 with U2/U1=0.46 and U1=13 cm/sec. Note the large excess of high-speed stream fluid in the cores of the structures.