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18,536 results on '"James, David"'

5. Selecting Differential Splicing Methods: Practical Considerations

Author

Draper, Ben J, Dunning, Mark J, and James, David C

Subjects
Quantitative Biology - Genomics
Abstract

Alternative splicing is crucial in gene regulation, with significant implications in clinical settings and biotechnology. This review article compiles bioinformatics RNA-seq tools for investigating differential splicing; offering a detailed examination of their statistical methods, case applications, and benefits. A total of 22 tools are categorised by their statistical family (parametric, non-parametric, and probabilistic) and level of analysis (transcript, exon, and event). The central challenges in quantifying alternative splicing include correct splice site identification and accurate isoform deconvolution of transcripts. Benchmarking studies show no consensus on tool performance, revealing considerable variability across different scenarios. Tools with high citation frequency and continued developer maintenance, such as DEXSeq and rMATS, are recommended for prospective researchers. To aid in tool selection, a guide schematic is proposed based on variations in data input and the required level of analysis. Additionally, advancements in long-read RNA sequencing are expected to drive the evolution of differential splicing tools, reducing the need for isoform deconvolution and prompting further innovation., Comment: 24 pages, 5 figures and 1 supplementary table included

Published
2024

7. The Gravitational Lensing Imprints of DES Y3 Superstructures on the CMB: A Matched Filtering Approach

Author

Demirbozan, Umut, Nadathur, Seshadri, Ferrero, Ismael, Fosalba, Pablo, Kovacs, Andras, Miquel, Ramon, Davies, Christopher T., Pandey, Shivam, Adamow, Monika, Bechtol, Keith, Drlica-Wagner, Alex, Gruendl, Robert, Hartley, Will, Pieres, Adriano, Ross, Ashley, Rykoff, Eli, Sheldon, Erin, Yanny, Brian, Abbott, Tim, Aguena, Michel, Allam, Sahar, Alves, Otavio, Bacon, David, Bertin, Emmanuel, Bocquet, Sebastian, Brooks, David, Rosell, Aurelio Carnero, Carretero, Jorge, Cawthon, Ross, da Costa, Luiz, Pereira, Maria Elidaiana da Silva, De Vicente, Juan, Desai, Shantanu, Doel, Peter, Everett, Spencer, Flaugher, Brenna, Friedel, Douglas, Frieman, Josh, Gatti, Marco, Gaztanaga, Enrique, Giannini, Giulia, Gutierrez, Gaston, Hinton, Samuel, Hollowood, Devon L., James, David, Jeffrey, Niall, Kuehn, Kyler, Lahav, Ofer, Lee, Sujeong, Marshall, Jennifer, Mena-Fernández, Juan, Mohr, Joe, Myles, Justin, Ogando, Ricardo, Malagón, Andrés Plazas, Roodman, Aaron, Sanchez, Eusebio, Sevilla, Ignacio, Smith, Mathew, Soares-Santos, Marcelle, Suchyta, Eric, Swanson, Molly, Tarle, Gregory, Weaverdyck, Noah, Weller, Jochen, and Wiseman, Philip

Subjects
Astrophysics - Cosmology and Nongalactic Astrophysics
Abstract

$ $Low density cosmic voids gravitationally lens the cosmic microwave background (CMB), leaving a negative imprint on the CMB convergence $\kappa$. This effect provides insight into the distribution of matter within voids, and can also be used to study the growth of structure. We measure this lensing imprint by cross-correlating the Planck CMB lensing convergence map with voids identified in the Dark Energy Survey Year 3 data set, covering approximately 4,200 deg$^2$ of the sky. We use two distinct void-finding algorithms: a 2D void-finder which operates on the projected galaxy density field in thin redshift shells, and a new code, Voxel, which operates on the full 3D map of galaxy positions. We employ an optimal matched filtering method for cross-correlation, using the MICE N-body simulation both to establish the template for the matched filter and to calibrate detection significances. Using the DES Y3 photometric luminous red galaxy sample, we measure $A_\kappa$, the amplitude of the observed lensing signal relative to the simulation template, obtaining $A_\kappa = 1.03 \pm 0.22$ ($4.6\sigma$ significance) for Voxel and $A_\kappa = 1.02 \pm 0.17$ ($5.9\sigma$ significance) for 2D voids, both consistent with $\Lambda$CDM expectations. We additionally invert the 2D void-finding process to identify superclusters in the projected density field, for which we measure $A_\kappa = 0.87 \pm 0.15$ ($5.9\sigma$ significance). The leading source of noise in our measurements is Planck noise, implying that future data from the Atacama Cosmology Telescope (ACT), South Pole Telescope (SPT) and CMB-S4 will increase sensitivity and allow for more precise measurements., Comment: 16 pages, 9 figures. Accepted for publication in MNRAS

Published
2024

8. The DELVE Quadruple Quasar Search I. A Lensed Low Luminosity AGN

Author

Schechter, Paul L., Sluse, Dominique, Zaborowski, Erik A., Drlica-Wagner, Alex, Lemon, Cameron, Courbin, Frederic, Hempel, Angela, Millon, Martin, Treu, Tommaso, Teixeira, Raul, Adamów, Monika, Bom, Clecio R., Carballo-Bello, Julio A., Ferguson, Peter S., Gruendl, Robert A., James, David J., Martinez-Vásquez, Clara E., Massana, Pol, Mau, Sidney, Mutlu-Pakdil, Burçin, Noël, Noëlia E. D., Pace, Andrew B., Sakowska, Joanna D., Stringfellow, Guy S., Tollerud, Erik J., Vivas, Kathy, and Zenteno, Alfredo

Subjects
Astrophysics - Cosmology and Nongalactic Astrophysics
Abstract

A quadruply lensed source, J125856.3-031944, has been discovered using the DELVE survey and WISE W1 - W2 colors. Followup direct imaging carried out with the MPIA 2.2 m and the Baade 6.5 m telescopes is analyzed, as is spectroscopy from the 2.5 m Nordic Optical Telescope. The lensed image configuration is kite-like, with the faintest image 2 magnitudes fainter than the other three. Redward of 6000 AA that image is badly blended with the lensing galaxy, which is elongated along the symmetry axis of the kite. Magellan direct imaging carried out in Sloan g permits better deblending. As the lensed image configuration is nearly circular, simple models give individual magnifications of at least 25 for the 3 brighter images. The source's narrow emission lines and low intrinsic luminosity qualify it as a type 2 AGN., Comment: 8 pages, 5 figures, submitted to AJ, comments welcome

Published
2024

10. $R(K_6-e, K_4) = 30$

Author

James, David, Kahan, Elisha, and Rauer, Erik

Subjects
Mathematics - Combinatorics
Abstract

We settle the Ramsey problem $R(K_6 - e, K_4)$, also known as $R(J_6, K_4)$ and $R(K_6^-, K_4)$. Previously, the best bounds were $30 \leq R(K_6 - e, K4) \leq 32$. We prove that $R(K_6 - e, K_4) = 30$. Our technique is based on the recent approach of Angeltveit and McKay and on older algorithms of McKay and Radziszowski.

Published
2024

16. Thermal and Tidal Evolution of Ice Giants with Growing Frozen Cores: The Case of Neptune

Author

James, David A and Stixrude, Lars

Subjects
Space Sciences, Physical Sciences, Neptune, Neptunian satellites, Giant planet interiors, Planets and satellites, Dynamical evolution, Astronomical and Space Sciences, Astronomy & Astrophysics, Astronomical sciences, Space sciences
Abstract

Abstract: The contrasting internal luminosity of Uranus and Neptune present a challenge to our understanding of the origin and evolution of these bodies, as well as extra-solar ice giants. The thermal evolution of Neptune is known to be nearly consistent with an entirely fluid interior, but this is not a unique solution, and does not account for the tidal dissipation required by the migration of its moons. We examine a model that has been previously shown to explain the thermal and tidal evolution of Uranus: one that features a growing, frozen core. The core traps heat in the interior, affecting the cooling time scale, and provides a source of tidal dissipation. We review the growing, frozen core model, and the computation of thermal and tidal evolution. We then apply this model to Neptune. We find that the growing frozen core model can account for the observed internal luminosity of Neptune and the migration of its moons, in the form of resonances that were either encountered or avoided in the past. We discuss prospects for observational tests of the growing frozen core model and possible implications for understanding the gas giants.

Published
2024

18. A search for pulsars around Sgr A* in the first Event Horizon Telescope dataset

Author

Torne, Pablo, Liu, Kuo, Eatough, Ralph P., Wongphechauxsorn, Jompoj, Cordes, James M., Desvignes, Gregory, De Laurentis, Mariafelicia, Kramer, Michael, Ransom, Scott M., Chatterjee, Shami, Wharton, Robert, Karuppusamy, Ramesh, Blackburn, Lindy, Janssen, Michael, Chan, Chi-kwan, Crew, Geoffrey B., Matthews, Lynn D., Goddi, Ciriaco, Rottmann, Helge, Wagner, Jan, Sanchez, Salvador, Ruiz, Ignacio, Abbate, Federico, Bower, Geoffrey C., Salamanca, Juan J., Gomez-Ruiz, Arturo I., Herrera-Aguilar, Alfredo, Jiang, Wu, Lu, Ru-Sen, Pen, Ue-Li, Raymond, Alexander W., Shao, Lijing, Shen, Zhiqiang, Paubert, Gabriel, Sanchez-Portal, Miguel, Kramer, Carsten, Castillo, Manuel, Navarro, Santiago, John, David, Schuster, Karl-Friedrich, Johnson, Michael D., Rygl, Kazi L. J., Akiyama, Kazunori, Alberdi, Antxon, Alef, Walter, Algaba, Juan Carlos, Anantua, Richard, Asada, Keiichi, Azulay, Rebecca, Bach, Uwe, Baczko, Anne-Kathrin, Ball, David, Balokovic, Mislav, Barrett, John, Bauboeck, Michi, Benson, Bradford A., Bintley, Dan, Blundell, Raymond, Bouman, Katherine L., Boyce, Hope, Bremer, Michael, Brinkerink, Christiaan D., Brissenden, Roger, Britzen, Silke, Broderick, Avery E., Broguiere, Dominique, Bronzwaer, Thomas, Bustamante, Sandra, Byun, Do-Young, Carlstrom, John E., Ceccobello, Chiara, Chael, Andrew, Chang, Dominic O., Chatterjee, Koushik, Chen, Ming-Tang, Chen, Yongjun, Cheng, Xiaopeng, Cho, Ilje, Christian, Pierre, Conroy, Nicholas S., Conway, John E., Crawford, Thomas M., Cruz-Osorio, Alejandro, Cui, Yuzhu, Dahale, Rohan, Davelaar, Jordy, Deane, Roger, Dempsey, Jessica, Dexter, Jason, Dhruv, Vedant, Doeleman, Sheperd S., Dougal, Sean, Dzib, Sergio A., Emami, Razieh, Falcke, Heino, Farah, Joseph, Fish, Vincent L., Fomalont, Ed, Ford, H. Alyson, Foschi, Marianna, Fraga-Encinas, Raquel, Freeman, William T., Friberg, Per, Fromm, Christian M., Fuentes, Antonio, Galison, Peter, Gammie, Charles F., Garcia, Roberto, Gentaz, Olivier, Georgiev, Boris, Gold, Roman, Gomez, Jose L., Gu, Minfeng, Gurwell, Mark, Hada, Kazuhiro, Haggard, Daryl, Haworth, Kari, Hecht, Michael H., Hesper, Ronald, Heumann, Dirk, Ho, Luis C., Ho, Paul, Honma, Mareki, Huang, Chih-Wei L., Huang, Lei, Hughes, David H., Ikeda, Shiro, Impellizzeri, C. M. Violette, Inoue, Makoto, Issaoun, Sara, James, David J., Jannuzi, Buell T., Jeter, Britton, Jimenez-Rosales, Alejandra, Jorstad, Svetlana, Joshi, Abhishek V., Jung, Taehyun, Karami, Mansour, Kawashima, Tomohisa, Keating, Garrett K., Kettenis, Mark, Kim, Dong-Jin, Kim, Jae-Young, Kim, Jongsoo, Kim, Junhan, Kino, Motoki, Koay, Jun Yi, Kocherlakota, Prashant, Kofuji, Yutaro, Koyama, Shoko, Krichbaum, Thomas P., Kuo, Cheng-Yu, La Bella, Noemi, Lauer, Tod R., Lee, Daeyoung, Lee, Sang-Sung, Leung, Po Kin, Levis, Aviad, Li, Zhiyuan, Lico, Rocco, Lindahl, Greg, Lindqvist, Michael, Lisakov, Mikhail, Liu, Jun, Liuzzo, Elisabetta, Lo, Wen-Ping, Lobanov, Andrei P., Loinard, Laurent, Lonsdale, Colin J., MacDonald, Nicholas R., Mao, Jirong, Marchili, Nicola, Markoff, Sera, Marrone, Daniel P., Marscher, Alan P., Marti-Vidal, Ivan, Matsushita, Satoki, Medeiros, Lia, Menten, Karl M., Michalik, Daniel, Mizuno, Izumi, Mizuno, Yosuke, Moran, James M., Moriyama, Kotaro, Moscibrodzka, Monika, Muller, Cornelia, Muller, Hendrik, Mus, Alejandro, Musoke, Gibwa, Myserlis, Ioannis, Nadolski, Andrew, Nagai, Hiroshi, Nagar, Neil M., Nakamura, Masanori, Narayan, Ramesh, Narayanan, Gopal, Natarajan, Iniyan, Nathanail, Antonios, Neilsen, Joey, Neri, Roberto, Ni, Chunchong, Noutsos, Aristeidis, Nowak, Michael A., Oh, Junghwan, Okino, Hiroki, Olivares, Hector, Ortiz-Leon, Gisela N., Oyama, Tomoaki, Ozel, Feryal, Palumbo, Daniel C. M., Paraschos, Georgios Filippos, Park, Jongho, Parsons, Harriet, Patel, Nimesh, Pesce, Dominic W., Pietu, Vincent, Plambeck, Richard, PopStefanija, Aleksandar, Porth, Oliver, Potzl, Felix M., Prather, Ben, Preciado-Lopez, Jorge A., Psaltis, Dimitrios, Pu, Hung-Yi, Ramakrishnan, Venkatessh, Rao, Ramprasad, Rawlings, Mark G., Rezzolla, Luciano, Ricarte, Angelo, Ripperda, Bart, Roelofs, Freek, Rogers, Alan, Ros, Eduardo, Romero-Cañizales, Cristina, Roshanineshat, Arash, Roy, Alan L., Ruszczyk, Chet, Sanchez-Arguelles, David, Sasada, Mahito, Satapathy, Kaushik, Savolainen, Tuomas, Schloerb, F. Peter, Schonfeld, Jonathan, Small, Des, Sohn, Bong Won, SooHoo, Jason, Souccar, Kamal, Sun, He, Tetarenko, Alexandra J., Tiede, Paul, Tilanus, Remo P. J., Titus, Michael, Toscano, Teresa, Traianou, Efthalia, Trent, Tyler, Trippe, Sascha, Turk, Matthew, van Bemmel, Ilse, van Langevelde, Huib Jan, van Rossum, Daniel R., Vos, Jesse, Ward-Thompson, Derek, Wardle, John, Weintroub, Jonathan, Wex, Norbert, Wielgus, Maciek, Wiik, Kaj, Witzel, Gunther, Wondrak, Michael F., Wong, George N., Wu, Qingwen, Yadlapalli, Nitika, Yamaguchi, Paul, Yfantis, Aristomenis, Yoon, Doosoo, Young, Andre, Young, Ken, Younsi, Ziri, Yu, Wei, Yuan, Feng, Yuan, Ye-Fei, Zensus, J. Anton, Zhang, Shuo, Zhao, Guang-Yao, and Zhao, Shan-Shan

Subjects
Astrophysics - High Energy Astrophysical Phenomena, Astrophysics - Instrumentation and Methods for Astrophysics
Abstract

The Event Horizon Telescope (EHT) observed in 2017 the supermassive black hole at the center of the Milky Way, Sagittarius A* (Sgr A*), at a frequency of 228.1 GHz ($\lambda$=1.3 mm). The fundamental physics tests that even a single pulsar orbiting Sgr A* would enable motivate searching for pulsars in EHT datasets. The high observing frequency means that pulsars - which typically exhibit steep emission spectra - are expected to be very faint. However, it also negates pulse scattering, an effect that could hinder pulsar detections in the Galactic Center. Additionally, magnetars or a secondary inverse Compton emission could be stronger at millimeter wavelengths than at lower frequencies. We present a search for pulsars close to Sgr A* using the data from the three most-sensitive stations in the EHT 2017 campaign: the Atacama Large Millimeter/submillimeter Array, the Large Millimeter Telescope and the IRAM 30 m Telescope. We apply three detection methods based on Fourier-domain analysis, the Fast-Folding-Algorithm and single pulse search targeting both pulsars and burst-like transient emission; using the simultaneity of the observations to confirm potential candidates. No new pulsars or significant bursts were found. Being the first pulsar search ever carried out at such high radio frequencies, we detail our analysis methods and give a detailed estimation of the sensitivity of the search. We conclude that the EHT 2017 observations are only sensitive to a small fraction ($\lesssim$2.2%) of the pulsars that may exist close to Sgr A*, motivating further searches for fainter pulsars in the region., Comment: 33 pages, 7 figures, 6 Tables. Accepted for publication in ApJ

Published
2023

19. Systems genetics approaches for understanding complex traits with relevance for human disease.

Author

Allayee, Hooman, Farber, Charles, Williams, Evan, James, David, Lusis, Aldons, and Seldin, Marcus

Subjects
complex traits, computational biology, genetics, genomics, human populations, mouse models, omics, systems biology, systems genetics
Abstract

Quantitative traits are often complex because of the contribution of many loci, with further complexity added by environmental factors. In medical research, systems genetics is a powerful approach for the study of complex traits, as it integrates intermediate phenotypes, such as RNA, protein, and metabolite levels, to understand molecular and physiological phenotypes linking discrete DNA sequence variation to complex clinical and physiological traits. The primary purpose of this review is to describe some of the resources and tools of systems genetics in humans and rodent models, so that researchers in many areas of biology and medicine can make use of the data.

Published
2023

20. Service provision for Frailty in European Emergency Departments (FEED): a survey of operational characteristics

Author

Christophe A. Fehlmann, Kara Mc Loughlin, Emma Jane Cosgriff, John Francis Ferrick, James David van Oppen, and European Taskforce for Geriatric Emergency Medicine

Subjects
Emergency care, Frailty, Delirium, Health services, Medical emergencies. Critical care. Intensive care. First aid, RC86-88.9
Abstract

Abstract Background The observational Frailty in European Emergency Departments (FEED) study found 40% of older people attending for care to be living with frailty. Older people with frailty have poorer outcomes from emergency care. Current best practice calls for early identification of frailty and holistic multidisciplinary assessment. This survey of FEED sites explores variations in frailty-attuned service definitions and provision. Methods This cross-sectional survey included study sites across Europe identified through snowball recruitment. Site co-ordinators (healthcare professionals in emergency and geriatric care) were surveyed online using Microsoft Forms. Items covered department and hospital capacity, frailty and delirium identification methods, staffing, and frailty-focused healthcare services in the ED. Descriptive statistics were reported. Results A total of 68 sites from 17 countries participated. Emergency departments had median 30 (IQR 21–53) trolley spaces. Most defined "older people" by age 65+ (64%) or 75+ (25%). Frailty screening was used at 69% of sites and mandated at 38%. Night-time staffing was lower compared to day-time for nursing (10 [IQR 8–14] vs. 14 [IQR 10–18]) and physicians (5 [IQR 3–8] vs. 10 [IQR 7–15]). Most sites had provision for ED frailty specialist services by day, but these services were rarely available at night. Sites mostly had accessible facilities; however, hot meals were rarely available at night (18%). Conclusion This survey demonstrated variability in case definitions, screening practices, and frailty-attuned service provision. There is no unanimous definition for older age, and while the Clinical Frailty Scale was commonly used, this was rarely mandated or captured in electronic records. Frailty services were often unavailable overnight. Appreciation of the variation in frailty service models could inform operational configuration and workforce development.

Published
2024
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22. Glossary

Author

James, David G. and Nunnallee, David

Published
2011

24. Index

Author

James, David G. and Nunnallee, David

Published
2011

25. Acknowledgments

Author

James, David G. and Nunnallee, David

Published
2011

26. Bibliography

Author

James, David G. and Nunnallee, David

Published
2011

30. Fritillaries

Author

James, David G. and Nunnallee, David

Published
2011

32. Satyrs

Author

James, David G. and Nunnallee, David

Published
2011

36. Hairstreaks

Author

James, David G. and Nunnallee, David

Published
2011

37. Coppers

Author

James, David G. and Nunnallee, David

Published
2011

38. Defense

Author

James, David G. and Nunnallee, David

Published
2011

39. Variation

Author

James, David G. and Nunnallee, David

Published
2011

46. Natural Enemies

Author

James, David G. and Nunnallee, David

Published
2011

47. Life Strategies

Author

James, David G. and Nunnallee, David

Published
2011

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