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2. Multi-wavelength spectroscopic analysis of the ULX Holmberg II X-1 and its nebula suggests the presence of a heavy black hole accreting from a B-type donor

Author

Serantes, S. Reyero, Oskinova, L., Hamann, W. -R., Gómez-González, V. M., Todt, H., Pauli, D., Soria, R., Gies, D. R., Torrejón, J. M., Bulik, T., Ramachandran, V., Sander, A. A. C., Bozzo, E., and Poutanen, J.

Subjects
Astrophysics - High Energy Astrophysical Phenomena, Astrophysics - Solar and Stellar Astrophysics
Abstract

Ultra-luminous X-ray sources (ULXs) are high-mass X-ray binaries with an X-ray luminosity above $10^{39}$ erg s$^{-1}$. These ULXs can be powered by black holes that are more massive than $20M_\odot$, accreting in a standard regime, or lighter compact objects accreting supercritically. There are only a few ULXs with known optical or UV counterparts, and their nature is debated. Determining whether optical/UV radiation is produced by the donor star or by the accretion disc is crucial for understanding ULX physics and testing massive binary evolution. We conduct, for the first time, a fully consistent multi-wavelength spectral analysis of a ULX and its circumstellar nebula. We aim to establish the donor star type and test the presence of strong disc winds in the prototypical ULX Holmberg II X-1 (Ho II X-1). We intent to obtain a realistic spectral energy distribution of the ionising source, which is needed for robust nebula analysis. We acquired new UV spectra of Ho II X-1 with the HST and complemented them with archival optical and X-ray data. We explored the spectral energy distribution of the source and analysed the spectra using the stellar atmosphere code PoWR and the photoionisation code Cloudy. Our analysis of the X-ray, UV, and optical spectra of Ho II X-1 and its nebula consistently explains the observations. We do not find traces of disc wind signatures in the UV and the optical, rejecting previous claims of the ULX being a supercritical accretor. The optical/UV counterpart of HoII X-1 is explained by a B-type supergiant donor star. Thus, the observations are fully compatible with Ho II X-1 being a close binary consisting of an $\gtrsim 66\,M_\odot$ black hole accreting matter from an $\simeq 22 M_\odot$ B-supergiant companion. Also, we propose a possible evolution scenario for the system, suggesting that Ho II X-1 is a potential gravitational wave source progenitor., Comment: Accepted in A&A. 14 pages (12 main body + 2 appendix), 6 figures, 6 tables

Published
2024
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3. CACER: Clinical Concept Annotations for Cancer Events and Relations

Author

Fu, Yujuan, Ramachandran, Giridhar Kaushik, Halwani, Ahmad, McInnes, Bridget T., Xia, Fei, Lybarger, Kevin, Yetisgen, Meliha, and Uzuner, Özlem

Subjects
Computer Science - Computation and Language
Abstract

Clinical notes contain unstructured representations of patient histories, including the relationships between medical problems and prescription drugs. To investigate the relationship between cancer drugs and their associated symptom burden, we extract structured, semantic representations of medical problem and drug information from the clinical narratives of oncology notes. We present Clinical Concept Annotations for Cancer Events and Relations (CACER), a novel corpus with fine-grained annotations for over 48,000 medical problems and drug events and 10,000 drug-problem and problem-problem relations. Leveraging CACER, we develop and evaluate transformer-based information extraction (IE) models such as BERT, Flan-T5, Llama3, and GPT-4 using fine-tuning and in-context learning (ICL). In event extraction, the fine-tuned BERT and Llama3 models achieved the highest performance at 88.2-88.0 F1, which is comparable to the inter-annotator agreement (IAA) of 88.4 F1. In relation extraction, the fine-tuned BERT, Flan-T5, and Llama3 achieved the highest performance at 61.8-65.3 F1. GPT-4 with ICL achieved the worst performance across both tasks. The fine-tuned models significantly outperformed GPT-4 in ICL, highlighting the importance of annotated training data and model optimization. Furthermore, the BERT models performed similarly to Llama3. For our task, LLMs offer no performance advantage over the smaller BERT models. The results emphasize the need for annotated training data to optimize models. Multiple fine-tuned transformer models achieved performance comparable to IAA for several extraction tasks., Comment: This is a pre-copy-editing, author-produced PDF of an article accepted for publication in JAMIA following peer review. The definitive publisher-authenticated version is available online at https://academic.oup.com/jamia/advance-article/doi/10.1093/jamia/ocae231/7748302

Published
2024
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4. Binarity at LOw Metallicity (BLOeM): a spectroscopic VLT monitoring survey of massive stars in the SMC

Author

Shenar, T., Bodensteiner, J., Sana, H., Crowther, P. A., Lennon, D. J., Abdul-Masih, M., Almeida, L. A., Backs, F., Berlanas, S. R., Bernini-Peron, M., Bestenlehner, J. M., Bowman, D. M., Bronner, V. A., Britavskiy, N., de Koter, A., de Mink, S. E., Deshmukh, K., Evans, C. J., Fabry, M., Gieles, M., Gilkis, A., González-Torà, G., Gräfener, G., Götberg, Y., Hawcroft, C., Hénault-Brunet, V., Herrero, A., Holgado, G., Janssens, S., Johnston, C., Josiek, J., Justham, S., Kalari, V. M., Katabi, Z. Z., Keszthelyi, Z., Klencki, J., Kubát, J., Kubátová, B., Langer, N., Lefever, R. R., Ludwig, B., Mackey, J., Mahy, L., Apellániz, J. Maíz, Mandel, I., Maravelias, G., Marchant, P., Menon, A., Najarro, F., Oskinova, L. M., Ovadia, A. J. G. O'Grady R., Patrick, L. R., Pauli, D., Pawlak, M., Ramachandran, V., Renzo, M., Rocha, D. F., Sander, A. A. C., Sayada, T., Schneider, F. R. N., Schootemeijer, A., Schösser, E. C., Schürmann, C., Sen, K., Shahaf, S., Simón-Díaz, S., Stoop, M., van Loon, J. Th., Toonen, S., Tramper, F., Valli, R., van Son, L. A. C., Vigna-Gómez, A., Villaseñor, J. I., Vink, J. S., Wang, C., and Willcox, R.

Subjects
Astrophysics - Solar and Stellar Astrophysics, Astrophysics - Astrophysics of Galaxies
Abstract

Surveys in the Milky Way and Large Magellanic Cloud revealed that the majority of massive stars will interact with companions during their lives. However, knowledge of the binary properties of massive stars at low metallicity, which approaches the conditions of the Early Universe, remains sparse. We present the Binarity at LOw Metallicity (BLOeM) campaign - an ESO large programme designed to obtain 25 epochs of spectroscopy for 929 massive stars in the SMC - the lowest metallicity conditions in which multiplicity is probed to date (Z = 0.2 Zsun). BLOeM will provide (i) the binary fraction, (ii) the orbital configurations of systems with periods P < 3 yr, (iii) dormant OB+BH binaries, and (iv) a legacy database of physical parameters of massive stars at low metallicity. The stars are observed with the LR02 setup of the giraffe instrument of the Very Large Telescope (3960-4570A, resolving power R=6200; typical signal-to-noise ratio S/N=70-100). This paper utilises the first 9 epochs obtained over a three-month time. We describe the survey and data reduction, perform a spectral classification of the stacked spectra, and construct a Hertzsprung-Russell diagram of the sample via spectral-type and photometric calibrations. The sample covers spectral types from O4 to F5, spanning the effective temperature and luminosity ranges 6.5

Published
2024
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9. Genome-wide association study meta-analysis provides insights into the etiology of heart failure and its subtypes

Author

Henry, Albert, Mo, Xiaodong, Finan, Chris, Chaffin, Mark D., Speed, Doug, Issa, Hanane, Denaxas, Spiros, Ware, James S., Zheng, Sean L., Malarstig, Anders, Gratton, Jasmine, Bond, Isabelle, Roselli, Carolina, Miller, David, Chopade, Sandesh, Schmidt, A. Floriaan, Abner, Erik, Adams, Lance, Andersson, Charlotte, Aragam, Krishna G., Ärnlöv, Johan, Asselin, Geraldine, Raja, Anna Axelsson, Backman, Joshua D., Bartz, Traci M., Biddinger, Kiran J., Biggs, Mary L., Bloom, Heather L., Boersma, Eric, Brandimarto, Jeffrey, Brown, Michael R., Brunak, Søren, Bruun, Mie Topholm, Buckbinder, Leonard, Bundgaard, Henning, Carey, David J., Chasman, Daniel I., Chen, Xing, Cook, James P., Czuba, Tomasz, de Denus, Simon, Dehghan, Abbas, Delgado, Graciela E., Doney, Alexander S., Dörr, Marcus, Dowsett, Joseph, Dudley, Samuel C., Engström, Gunnar, Erikstrup, Christian, Esko, Tõnu, Farber-Eger, Eric H., Felix, Stephan B., Finer, Sarah, Ford, Ian, Ghanbari, Mohsen, Ghasemi, Sahar, Ghouse, Jonas, Giedraitis, Vilmantas, Giulianini, Franco, Gottdiener, John S., Gross, Stefan, Guðbjartsson, Daníel F., Gui, Hongsheng, Gutmann, Rebecca, Hägg, Sara, Haggerty, Christopher M., Hedman, Åsa K., Helgadottir, Anna, Hemingway, Harry, Hillege, Hans, Hyde, Craig L., Aagaard Jensen, Bitten, Jukema, J. Wouter, Kardys, Isabella, Karra, Ravi, Kavousi, Maryam, Kizer, Jorge R., Kleber, Marcus E., Køber, Lars, Koekemoer, Andrea, Kuchenbaecker, Karoline, Lai, Yi-Pin, Lanfear, David, Langenberg, Claudia, Lin, Honghuang, Lind, Lars, Lindgren, Cecilia M., Liu, Peter P., London, Barry, Lowery, Brandon D., Luan, Jian’an, Lubitz, Steven A., Magnusson, Patrik, Margulies, Kenneth B., Marston, Nicholas A., Martin, Hilary, März, Winfried, Melander, Olle, Mordi, Ify R., Morley, Michael P., Morris, Andrew P., Morrison, Alanna C., Morton, Lori, Nagle, Michael W., Nelson, Christopher P., Niessner, Alexander, Niiranen, Teemu, Noordam, Raymond, Nowak, Christoph, O’Donoghue, Michelle L., Ostrowski, Sisse Rye, Owens, Anjali T., Palmer, Colin N. A., Paré, Guillaume, Pedersen, Ole Birger, Perola, Markus, Pigeyre, Marie, Psaty, Bruce M., Rice, Kenneth M., Ridker, Paul M., Romaine, Simon P. R., Rotter, Jerome I., Ruff, Christian T., Sabatine, Marc S., Sallah, Neneh, Salomaa, Veikko, Sattar, Naveed, Shalaby, Alaa A., Shekhar, Akshay, Smelser, Diane T., Smith, Nicholas L., Sørensen, Erik, Srinivasan, Sundararajan, Stefansson, Kari, Sveinbjörnsson, Garðar, Svensson, Per, Tammesoo, Mari-Liis, Tardif, Jean-Claude, Teder-Laving, Maris, Teumer, Alexander, Thorgeirsson, Guðmundur, Thorsteinsdottir, Unnur, Torp-Pedersen, Christian, Tragante, Vinicius, Trompet, Stella, Uitterlinden, Andre G., Ullum, Henrik, van der Harst, Pim, van Heel, David, van Setten, Jessica, van Vugt, Marion, Veluchamy, Abirami, Verschuuren, Monique, Verweij, Niek, Vissing, Christoffer Rasmus, Völker, Uwe, Voors, Adriaan A., Wallentin, Lars, Wang, Yunzhang, Weeke, Peter E., Wiggins, Kerri L., Williams, L. Keoki, Yang, Yifan, Yu, Bing, Zannad, Faiez, Zheng, Chaoqun, Asselbergs, Folkert W., Cappola, Thomas P., Dubé, Marie-Pierre, Dunn, Michael E., Lang, Chim C., Samani, Nilesh J., Shah, Svati, Vasan, Ramachandran S., Smith, J. Gustav, Holm, Hilma, Shah, Sonia, Ellinor, Patrick T., Hingorani, Aroon D., Wells, Quinn, and Lumbers, R. Thomas

Published
2025
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12. Production of bacterial nanocellulose as green adsorbent matrix using distillery wastes for dye removal: a combined approach for waste management and pollution mitigation

Author

Walling, Bendangtula, Borah, Alimpia, Hazarika, Swapnali, Bharali, Pranjal, Ramachandran, D., Kanagasabai, Viswanathan, Dutta, Nipu, Maadurshni, Gobichettipalayam Balasubramaniam, Manivannan, Jeganathan, Mudoi, Pronab, Kaman, Pranjal Kumar, Sorhie, Viphrezolie, Gogoi, Bhagyudoy, Alemtoshi, Acharjee, Shiva Aley, Vishwakarma, Vinita, and Nath, Palash Deb

Published
2025
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18. ISSLS Prize in Clinical Science 2025: Cartilage End Plate Defects Precede and Initiate Bony End Plate Defects and Disc Degeneration– An ‘Integrated Total End Plate Score’ Identify Preclinical Discs at Risk for Degeneration

Author

Rajasekaran, Shanmuganathan, Thippeswamy, Pushpa Bhari, Gurusamy, Gnanaprakash, Ramachandran, Karthik, Yirdaw, Tewodros Asegie, Basu, Suprotik, Kamodia, Jinal Sanjiv, Abdelwahed, Ayman Mohamed, K. S., Sri Vijay Anand, Shetty, Ajoy Prasad, and Kanna, Rishi Mugesh

Published
2025
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21. A statistical framework for multi-trait rare variant analysis in large-scale whole-genome sequencing studies

Author

Li, Xihao, Chen, Han, Selvaraj, Margaret Sunitha, Van Buren, Eric, Zhou, Hufeng, Wang, Yuxuan, Sun, Ryan, McCaw, Zachary R., Yu, Zhi, Jiang, Min-Zhi, DiCorpo, Daniel, Gaynor, Sheila M., Dey, Rounak, Arnett, Donna K., Benjamin, Emelia J., Bis, Joshua C., Blangero, John, Boerwinkle, Eric, Bowden, Donald W., Brody, Jennifer A., Cade, Brian E., Carson, April P., Carlson, Jenna C., Chami, Nathalie, Chen, Yii-Der Ida, Curran, Joanne E., de Vries, Paul S., Fornage, Myriam, Franceschini, Nora, Freedman, Barry I., Gu, Charles, Heard-Costa, Nancy L., He, Jiang, Hou, Lifang, Hung, Yi-Jen, Irvin, Marguerite R., Kaplan, Robert C., Kardia, Sharon L. R., Kelly, Tanika N., Konigsberg, Iain, Kooperberg, Charles, Kral, Brian G., Li, Changwei, Li, Yun, Lin, Honghuang, Liu, Ching-Ti, Loos, Ruth J. F., Mahaney, Michael C., Martin, Lisa W., Mathias, Rasika A., Mitchell, Braxton D., Montasser, May E., Morrison, Alanna C., Naseri, Take, North, Kari E., Palmer, Nicholette D., Peyser, Patricia A., Psaty, Bruce M., Redline, Susan, Reiner, Alexander P., Rich, Stephen S., Sitlani, Colleen M., Smith, Jennifer A., Taylor, Kent D., Tiwari, Hemant K., Vasan, Ramachandran S., Viali, Satupa’itea, Wang, Zhe, Wessel, Jennifer, Yanek, Lisa R., Yu, Bing, Dupuis, Josée, Meigs, James B., Auer, Paul L., Raffield, Laura M., Manning, Alisa K., Rice, Kenneth M., Rotter, Jerome I., Peloso, Gina M., Natarajan, Pradeep, Li, Zilin, Liu, Zhonghua, and Lin, Xihong

Published
2025
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48. Genome-wide association analysis provides insights into the molecular etiology of dilated cardiomyopathy

Author

Zheng, Sean L., Henry, Albert, Cannie, Douglas, Lee, Michael, Miller, David, McGurk, Kathryn A., Bond, Isabelle, Xu, Xiao, Issa, Hanane, Francis, Catherine, De Marvao, Antonio, Theotokis, Pantazis I., Buchan, Rachel J., Speed, Doug, Abner, Erik, Adams, Lance, Aragam, Krishna G., Ärnlöv, Johan, Raja, Anna Axelsson, Backman, Joshua D., Baksi, John, Barton, Paul J. R., Biddinger, Kiran J., Boersma, Eric, Brandimarto, Jeffrey, Brunak, Søren, Bundgaard, Henning, Carey, David J., Charron, Philippe, Cook, James P., Cook, Stuart A., Denaxas, Spiros, Deleuze, Jean-François, Doney, Alexander S., Elliott, Perry, Erikstrup, Christian, Esko, Tõnu, Farber-Eger, Eric H., Finan, Chris, Garnier, Sophie, Ghouse, Jonas, Giedraitis, Vilmantas, Guðbjartsson, Daniel F., Haggerty, Christopher M., Halliday, Brian P., Helgadottir, Anna, Hemingway, Harry, Hillege, Hans L., Kardys, Isabella, Lind, Lars, Lindgren, Cecilia M., Lowery, Brandon D., Manisty, Charlotte, Margulies, Kenneth B., Moon, James C., Mordi, Ify R., Morley, Michael P., Morris, Andrew D., Morris, Andrew P., Morton, Lori, Noursadeghi, Mahdad, Ostrowski, Sisse R., Owens, Anjali T., Palmer, Colin N. A., Pantazis, Antonis, Pedersen, Ole B. V., Prasad, Sanjay K., Shekhar, Akshay, Smelser, Diane T., Srinivasan, Sundararajan, Stefansson, Kari, Sveinbjörnsson, Garðar, Syrris, Petros, Tammesoo, Mari-Liis, Tayal, Upasana, Teder-Laving, Maris, Thorgeirsson, Guðmundur, Thorsteinsdottir, Unnur, Tragante, Vinicius, Trégouët, David-Alexandre, Treibel, Thomas A., Ullum, Henrik, Valdes, Ana M., van Setten, Jessica, van Vugt, Marion, Veluchamy, Abirami, Verschuren, W. M. Monique, Villard, Eric, Yang, Yifan, Asselbergs, Folkert W., Cappola, Thomas P., Dube, Marie-Pierre, Dunn, Michael E., Ellinor, Patrick T., Hingorani, Aroon D., Lang, Chim C., Samani, Nilesh J., Shah, Svati H., Smith, J. Gustav, Vasan, Ramachandran S., O’Regan, Declan P., Holm, Hilma, Noseda, Michela, Wells, Quinn, Ware, James S., and Lumbers, R. Thomas

Published
2024
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